diff --git a/pymolfile/libpymolfile-old/AUTHORS b/pymolfile/libpymolfile-old/AUTHORS
deleted file mode 100644
index fadaded083b607c3f29dbb0fa4feebaa5565f9ee..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/AUTHORS
+++ /dev/null
@@ -1,42 +0,0 @@
-libvmdmolfile
-======================================
-
-All the modified files mentioned below are part of libvmdmolfile and are published under
-the GNU GENERAL PUBLIC LICENSE Version 2 (or higher):
-
- * vmdmolfile.c
- * vmdmolfile.h
- * libvmdmolfile.i
- * libvmdmolfile_wrap.c
- * libvmdmolfile.py
-
-
-numpy SWIG interface
-====================
-
-Bill Spotz wrote
-
- * numpy.i
-
-which was obtained from the trunk of the numpy distribution,
-2010-03-25. As it appears in numpy it is presumably licensed under the
-`BSD Licence <http://opensource.org/licenses/bsd-license.php>`_.
-
-
-Berk Onat wrote
-
- * libvmdmolfile.i
-
-``libvmdmolfile_wrap.c`` and ``libvmdmolfile.py`` are
-generated from ``libvmdmolfile.i`` with:
-
- swig -python -outdir . libxdrfile.i
-
-Up to and including MDAnalysis version 0.7.7 the files
-
- * libvmdmolfile.i
- * libvmdmolfile_wrap.c
- * libvmdmolfile.py
-
-are published under the GNU GENERAL PUBLIC LICENSE Version 3 (or higher).
-
diff --git a/pymolfile/libpymolfile-old/COPYING b/pymolfile/libpymolfile-old/COPYING
deleted file mode 100644
index d159169d1050894d3ea3b98e1c965c4058208fe1..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/COPYING
+++ /dev/null
@@ -1,339 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
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diff --git a/pymolfile/libpymolfile-old/README b/pymolfile/libpymolfile-old/README
deleted file mode 100644
index 4b7658f9f08062a3d80721d8efd12b7b58ed1de9..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/README
+++ /dev/null
@@ -1,49 +0,0 @@
-libxdrfile2
-=============
-
-This library allows to read GROMACS trr and xtc files and also to
-convert from one format to another. libxdrfile2 is a derivative of the
-`libxdrfile library`_ written by the Gromacs developers. For MDAnalysis we
-added Python bindings (generated with SWIG_). For libxdrfile2 we added
-new indexing and seeking capabilities to the library.
-
-.. _`libxdr library`:
- http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
-.. _SWIG:
- http://www.swig.org/
-
-
-Licensing
-=========
-
-libxdrfile is provided by the Gromacs developers under the GNU Lesser
-General Public License version 3.
-While under development together with the MDAnalysis code, the library
-was enhanced to provide xtc/trr frame indexing and seeking. This derivative
-version of the library, named libxdrfile2, is now provided under the GNU
-General Public License version 2. Read the AUTHORS and COPYING files
-for details.
-
-
-Python bindings
-===============
-
-Although the whole ``xdrfile`` package is distributed together with
-`MDAnalysis <http://mdanalysis.googlecode.com>` it is also possible to
-use it as a stand-alone library. Build the library from the src
-directory::
-
- mv xdrfile/setup_py setup.py
- mv xdrfile/__init___py xdrfile/__init__.py
- swig -python xdrfile/libxdrfile2.i # or copy libxdrfile2.py to xdrfile/
- python setup.py build --build-lib=.
-
-(This does an in-place build but you can also do a normal ``python
-setup.py install``.)
-
-Note that in order to import the module you will have to do:
-
- from xdrfile import libxdrfile2
-
-
-
diff --git a/pymolfile/libpymolfile-old/__init__.py b/pymolfile/libpymolfile-old/__init__.py
deleted file mode 100644
index 584c3db77a365e537797219d8d866cef43fdd84e..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-
-# Stand-alone python bindings for libvmdmolfile
-# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
-# Published under the GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-"""Stand-alone vmdmolfile library.
-
-"""
diff --git a/pymolfile/libpymolfile-old/libvmdmolfile.i b/pymolfile/libpymolfile-old/libvmdmolfile.i
deleted file mode 100644
index 5bc26bba13286284a3c168a6d2394d526c215668..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/libvmdmolfile.i
+++ /dev/null
@@ -1,665 +0,0 @@
-/* -*- C -*- (not really, but good for syntax highlighting) */
-/* SWIG interface for libvmdmolfile of VMD molfile_plugins
- Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
- Published under the GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
- swig -python -outdir MDAnalysis/coordinates/xdrfile src/xdrfile/libxdrfile2.i
-*/
-%define DOCSTRING
-"
-:Author: Berk Onat <b.onat@warwick.ac.uk>
-:Year: 2017
-:Licence: GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
-
-The Gromacs XTC/TRR library :mod:`libxdrfile2`
-==============================================
-
-:mod:`libxdrfile2`, a derivative of the Gromacs_ `libxdrfile library`_, provides an
-interface to some high-level functions for XTC/TRR trajectory handling.
-Only functions required for reading and processing whole trajectories are exposed at
-the moment; low-level routines to read individual numbers are not provided. In
-addition, :mod:`libxdrfile2` exposes functions to allow fast frame indexing and XDR
-file seeking.
-
-The functions querying the numbers of atoms in a trajectory frame
-(:func:`read_xtc_natoms` and :func:`read_trr_natoms`) open a file themselves and
-only require the file name.
-
-All other functions operate on a *XDRFILE* object, which is a special file
-handle for xdr files. Any xdr-based trajectory file (XTC or TRR format) always
-has to be opened with :func:`xdrfile_open`. When done, close the trajectory
-with :func:`xdrfile_close`.
-
-The functions fill or read existing arrays of coordinates; they never allocate
-these arrays themselves. Hence they need to be setup outside libxdrfile2 as
-numpy arrays. The exception to these are the indexing ones functions that take
-care of array allocation and transference to a garbage-collectable memory object.
-
-
-.. _Gromacs: http://www.gromacs.org
-.. _libxdrfile library: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
-
-.. versionchanged:: 0.8.0
- :mod:`libxdrfile2` is now used instead of :mod:`libxdrfile`. :mod:`libxdrfile2` is
- based on :mod:`libxdrfile` but has xdr seeking and indexing capabilities.
- Unlike :mod:`libxdrfile` before it, :mod:`libxdrfile2` is distributed under the GNU
- GENERAL PUBLIC LICENSE, version 2 (or higher).
-
-
-Example: Reading from a XTC
----------------------------
-
-In the example we read coordinate frames from an existing XTC trajectory::
-
- import numpy as np
- from libxdrfile2 import xdrfile_open, xdrfile_close, read_xtc_natoms, read_xtc, DIM, exdrOK
- xtc = 'md.xtc'
-
- # get number of atoms
- natoms = read_xtc_natoms(xtc)
-
- # allocate coordinate array of the right size and type
- # (the type float32 is crucial to match the underlying C-code!!)
- x = np.zeros((natoms, DIM), dtype=np.float32)
- # allocate unit cell box
- box = np.zeros((DIM, DIM), dtype=np.float32)
-
- # open file
- XTC = xdrfile_open(xtc, 'r')
-
- # loop through file until return status signifies end or a problem
- # (it should become exdrENDOFFILE on the last iteration)
- status = exdrOK
- while status == exdrOK:
- status,step,time,prec = read_xtc(XTC, box, x)
- # do something with x
- centre = x.mean(axis=0)
- print 'Centre of geometry at %(time)g ps: %(centre)r' % vars()
-
- # finally close file
- xdrfile_close(XTC)
-
-Note that only the *contents* of the coordinate and unitcell arrays *x* and
-*box* change.
-
-
-Functions and constants
------------------------
-
-The module defines a number of constants such as :data:`DIM` or the
-`Status symbols`_.
-
-.. data:: DIM
-
- The number of cartesian dimensions for which the underlying C-code
- was compiled; this is most certainly 3.
-
-
-Status symbols
-~~~~~~~~~~~~~~
-
-A number of symbols are exported; they all start with the letters
-``exdr``. Important ones are:
-
-.. data:: exdrOK
-
- Success of xdr file read/write operation.
-
-.. data:: exdrCLOSE
-
- xdr file is closed
-
-.. data:: exdrENDOFFILE
-
- end of file was reached (response of :func:`read_xtc` and
- :func:`read_trr` after the last read frame)
-
-.. data:: exdrFILENOTFOUND
-
- :func:`xdrfile_open` cannot find the requested file
-
-Other symbols that are used internally are:
-
-.. data:: exdrHEADER
-
- header
-
-.. data:: exdrSTRING
-
- string
-
-.. data:: exdrDOUBLE
-
- double precision floating point number
-
-.. data:: exdrINT
-
- integer
-
-.. data:: exdrFLOAT
-
- floating point number
-
-.. data:: exdrUINT
-
- unsigned integer
-
-.. data:: exdr3DX
-
- compressed 3D coordinates
-
-.. data:: exdrMAGIC
-
- magic number
-
-.. data:: exdrNOMEM
-
- not enough memory to allocate space for a XDR data structure.
-
-Opening and closing of XDR files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Two low-level functions are used to obtain a *XDRFILE* object (a file handle)
-to access xdr files such as XTC or TRR trajectories.
-
-.. function:: xdrfile_open(path, mode) -> XDRFILE
-
- Open *path* and returns a *XDRFILE* handle that is required by other
- functions.
-
- :Arguments:
- *path*
- file name
- *mode*
- 'r' for reading and 'w' for writing
- :Returns: *XDRFILE* handle
-
-.. function:: xdrfile_close(XDRFILE) -> status
-
- Close the xdrfile pointed to by *XDRFILE*.
-
- .. Warning:: Closing an already closed file will lead to a
- crash with a double-free pointer error.
-
-XTC functions
-~~~~~~~~~~~~~
-
-The XTC trajectory format is a lossy compression format that only stores
-coordinates. Compression level is determined by the *precision* argument to the
-:func:`write_xtc` function. Coordinates (Gromacs_ uses nm natively) are
-multiplied by *precision* and truncated to the integer part. A typical value is
-1000.0, which gives an accuracy of 1/100 of an Angstroem.
-
-The advantage of XTC over TRR is its significantly reduced size.
-
-
-.. function:: read_xtc_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a xtc file *fn*.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc(XDRFILE, box, x) -> (status, step, time, precision)
-
- Read the next frame from the opened xtc trajectory into *x*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=numpy.float32)``
- which is updated with the coordinates from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see `Status symbols`_ for other
- values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
-.. function:: write_xtc(XDRFILE, step, time, box, x, prec) -> status
-
- Write the next frame *x* to the opened xtc trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the coordinates from the frame
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-TRR functions
-~~~~~~~~~~~~~
-
-TRR is the Gromacs_ native full-feature trajectory storage format. It can contain position
-coordinates, velocities and forces, and the lambda value for free energy perturbation
-calculations. Velocities and forces are optional in the sense that they can be all zero.
-
-.. function:: read_trr_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a trr file *fn*.
-
- :Arguments:
- *fn*
- file name of a trr file
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR
- or if it is not readable.
-
-.. function:: read_trr_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR or if it is not readable.
-
-.. function:: read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)
-
- Read the next frame from the opened trr trajectory into *x*, *v*, and *f*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **coordinates** from the frame
- *v*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **velocities** from the frame
- *f*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **forces** from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see the ``libxdrfile2.exdr*`` constants
- under `Status symbols`_ for other values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *lambda*
- current lambda value (only interesting for free energy perturbation)
- *has_x*
- boolean indicating whether coordinates were read from the TRR
- *has_v*
- boolean indicating whether velocities were read from the TRR
- *has_f*
- boolean indicating whether forces were read from the TRR
-
-.. function:: write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status
-
- Write the next frame to the opened trr trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *lambda*
- free energy lambda value (typically 0.0)
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **coordinates** from the frame
- *v*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **velocities** from the frame
- *f*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **forces** from the frame
-
- .. versionchanged:: 0.8.0
- either one of *x*, *v*, or *f* can now be set as a natom,0-DIM
- numpy ``array((natom, 0),dtype=nump.float32)``. This will cause the
- corresponding property to be skipped when writing to file.
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-"
-%enddef
-
-%module(docstring=DOCSTRING) libvmdmolfile
-
-
-%{
-/* Python SWIG interface to molfile_plugin of VMD version 1.9.3
- Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
- Published under the GNU LESSER GENERAL PUBLIC LICENSE Version 3 (or higher)
- */
-#define SWIG_FILE_WITH_INIT
-#include <stdio.h>
-#include "molfile_plugin.h"
-%}
-
-%include "numpy.i"
-
-%init %{
-import_array();
-%}
-
-
-/*
-
- I am only wrapping 'high level' functions and modify call
- signatures so that one does not need anything like pointers from
- python.
-*/
-
-
-/* status codes */
-enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
- exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
- exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
-
-/* These com from stdio.h, for file seeking. Gives all the flexibility to _fseek(). */
-enum { SEEK_SET, SEEK_CUR, SEEK_END };
-
-/* open/close xdr files */
-%feature("autodoc", "0") xdrfile_open;
-extern XDRFILE* xdrfile_open(const char *path, const char *mode);
-
-%feature("autodoc", "0") xdrfile_close;
-extern int xdrfile_close(XDRFILE *fp);
-
-
-/* from xdrfile_xtc.c */
-/* This function returns the number of atoms in the xtc file in *natoms
- extern int read_xtc_natoms(char *fn,int *natoms);
- ... but the wrapped function returns natoms as the python return value
-*/
-%feature("autodoc", "0") my_read_xtc_natoms;
-%rename (read_xtc_natoms) my_read_xtc_natoms;
-%exception my_read_xtc_natoms {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
- int my_read_xtc_natoms(char *fn) {
- int natoms;
- int status;
- status = read_xtc_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from xtc '%s'", status, fn);
- return 0;
- }
- return natoms;
- }
-%}
-
-%feature("autodoc", "0") my_read_xtc_numframes;
-%rename (read_xtc_numframes) my_read_xtc_numframes;
-%exception my_read_xtc_numframes {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
-PyObject * my_read_xtc_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_xtc_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through xtc '%s'", status, fn);
- return 0;
- }
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
- }
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
- }
-%}
-
-
-/* This function returns the number of atoms in the trr file in *natoms
- extern int read_trr_natoms(char *fn,int *natoms);
- ... but the wrapped function returns natoms as the python return value
-*/
-%feature("autodoc", "0") my_read_trr_natoms;
-%rename (read_trr_natoms) my_read_trr_natoms;
-%exception my_read_trr_natoms {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
- int my_read_trr_natoms(char *fn) {
- int natoms;
- int status;
- status = read_trr_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from trr '%s'", status, fn);
- return 0;
- }
- return natoms;
- }
-%}
-
-
-%feature("autodoc", "0") my_read_trr_numframes;
-%rename (read_trr_numframes) my_read_trr_numframes;
-%exception my_read_trr_numframes {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
-PyObject * my_read_trr_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_trr_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through trr '%s'", status, fn);
- return 0;
- }
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
- }
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
- }
-%}
-
-
-
-#define DIM 3
-typedef float matrix[DIM][DIM];
-typedef float rvec[DIM];
-
-
-/* Reading from xdr files */
-
-%apply (float INPLACE_ARRAY2[ANY][ANY]) {(matrix box)}
-%apply (int DIM1, int DIM2, float* INPLACE_ARRAY2) {(int natoms, int _DIM, float *x),
- (int vnatoms, int v_DIM, float *v),
- (int fnatoms, int f_DIM, float *f)}
-
-/* Read one frame of an open xtc file */
-/*
-extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
- matrix box,rvec *x,float *prec);
-*/
-%feature("autodoc", "read_xtc(XDRFILE, box, x) -> (status, step, time, precision)") my_read_xtc;
-%rename (read_xtc) my_read_xtc;
-%inline %{
-PyObject * my_read_xtc(XDRFILE *xd, matrix box, int natoms, int _DIM, float *x) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step;
- float time, prec;
- PyObject *tuple = PyTuple_New(4);
- status = read_xtc(xd, natoms, &step, &time, box, (rvec *)x, &prec);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)prec));
- return tuple; // return (status, step, time, prec)
-}
-%}
-
-%feature("autodoc", "read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)") my_read_trr;
-%rename (read_trr) my_read_trr;
-%inline %{
-PyObject * my_read_trr(XDRFILE *xd, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step, has_prop=0;
- float time, lmbda;
- PyObject *tuple = PyTuple_New(7);
- status = read_trr(xd, natoms, &step, &time, &lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f, &has_prop);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)lmbda));
- PyTuple_SET_ITEM(tuple, 4, PyBool_FromLong((long)(has_prop & HASX)));
- PyTuple_SET_ITEM(tuple, 5, PyBool_FromLong((long)(has_prop & HASV)));
- PyTuple_SET_ITEM(tuple, 6, PyBool_FromLong((long)(has_prop & HASF)));
- return tuple; // return (status, step, time, lmbda, has_x, has_v, has_f)
-}
-%}
-
-%clear (matrix box);
-%clear (int natoms, int _DIM, float *x);
-%clear (int vnatoms, int v_DIM, float *v);
-%clear (int fnatoms, int f_DIM, float *f);
-
-
-/* Writing of xdr files */
-
-%apply (float IN_ARRAY2[ANY][ANY]) {(matrix box)}
-%apply (int DIM1, int DIM2, float* IN_ARRAY2) {(int natoms, int _DIM, float *x),
- (int vnatoms, int v_DIM, float *v),
- (int fnatoms, int f_DIM, float *f)}
-
-/* Write a frame to xtc file */
-/*
-extern int write_xtc(XDRFILE *xd, int natoms,int step,float time,
- matrix box,rvec *x,float prec);
-*/
-%feature("autodoc", "write_xtc(XDRFILE, step, time, box, x, prec) -> status") my_write_xtc;
-%rename (write_xtc) my_write_xtc;
-%inline %{
-int my_write_xtc(XDRFILE *xd, int step, float time,
- matrix box, int natoms, int _DIM, float *x, float prec) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- return write_xtc(xd, natoms, step, time, box, (rvec *)x, prec);
-}
-%}
-
-%feature("autodoc", "write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status") my_write_trr;
-%rename (write_trr) my_write_trr;
-%inline %{
-int my_write_trr(XDRFILE *xd, int step, float time, float lmbda, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* Preparing for the case of empty arrays - NULL pointers tell the library to skip this property. */
- if (_DIM == 0) x = NULL;
- if (v_DIM == 0) v = NULL;
- if (f_DIM == 0) f = NULL;
- return write_trr(xd, natoms, step, time, lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f);
-}
-%}
-
-%feature("autodoc", "0") xdr_seek;
-extern int xdr_seek(XDRFILE *xd, long long pos, int whence);
-
-%feature("autodoc", "0") xdr_tell;
-extern long long xdr_tell(XDRFILE *xd);
-
-%clear (matrix box);
-%clear (int natoms, int _DIM, float *x);
-%clear (int vnatoms, int v_DIM, float *v);
-%clear (int fnatoms, int f_DIM, float *f);
-
-
diff --git a/pymolfile/libpymolfile-old/libvmdmolfile.py b/pymolfile/libpymolfile-old/libvmdmolfile.py
deleted file mode 100644
index 87a2c6692427936a46427739df076f2582fc4fef..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/libvmdmolfile.py
+++ /dev/null
@@ -1,487 +0,0 @@
-# This file was automatically generated by SWIG (http://www.swig.org).
-# Version 2.0.11
-#
-# Do not make changes to this file unless you know what you are doing--modify
-# the SWIG interface file instead.
-
-
-
-
-"""
-
-:Author: Oliver Beckstein <orbeckst@gmail.com>
-:Author: Manuel Melo <manuel.nuno.melo@gmail.com>
-:Year: 2014
-:Licence: GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
-
-The Gromacs XTC/TRR library :mod:`libxdrfile2`
-==============================================
-
-:mod:`libxdrfile2`, a derivative of the Gromacs_ `libxdrfile library`_, provides an
-interface to some high-level functions for XTC/TRR trajectory handling.
-Only functions required for reading and processing whole trajectories are exposed at
-the moment; low-level routines to read individual numbers are not provided. In
-addition, :mod:`libxdrfile2` exposes functions to allow fast frame indexing and XDR
-file seeking.
-
-The functions querying the numbers of atoms in a trajectory frame
-(:func:`read_xtc_natoms` and :func:`read_trr_natoms`) open a file themselves and
-only require the file name.
-
-All other functions operate on a *XDRFILE* object, which is a special file
-handle for xdr files. Any xdr-based trajectory file (XTC or TRR format) always
-has to be opened with :func:`xdrfile_open`. When done, close the trajectory
-with :func:`xdrfile_close`.
-
-The functions fill or read existing arrays of coordinates; they never allocate
-these arrays themselves. Hence they need to be setup outside libxdrfile2 as
-numpy arrays. The exception to these are the indexing ones functions that take
-care of array allocation and transference to a garbage-collectable memory object.
-
-
-.. _Gromacs: http://www.gromacs.org
-.. _libxdrfile library: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
-
-.. versionchanged:: 0.8.0
- :mod:`libxdrfile2` is now used instead of :mod:`libxdrfile`. :mod:`libxdrfile2` is
- based on :mod:`libxdrfile` but has xdr seeking and indexing capabilities.
- Unlike :mod:`libxdrfile` before it, :mod:`libxdrfile2` is distributed under the GNU
- GENERAL PUBLIC LICENSE, version 2 (or higher).
-
-
-Example: Reading from a XTC
----------------------------
-
-In the example we read coordinate frames from an existing XTC trajectory::
-
- import numpy as np
- from libxdrfile2 import xdrfile_open, xdrfile_close, read_xtc_natoms, read_xtc, DIM, exdrOK
- xtc = 'md.xtc'
-
- # get number of atoms
- natoms = read_xtc_natoms(xtc)
-
- # allocate coordinate array of the right size and type
- # (the type float32 is crucial to match the underlying C-code!!)
- x = np.zeros((natoms, DIM), dtype=np.float32)
- # allocate unit cell box
- box = np.zeros((DIM, DIM), dtype=np.float32)
-
- # open file
- XTC = xdrfile_open(xtc, 'r')
-
- # loop through file until return status signifies end or a problem
- # (it should become exdrENDOFFILE on the last iteration)
- status = exdrOK
- while status == exdrOK:
- status,step,time,prec = read_xtc(XTC, box, x)
- # do something with x
- centre = x.mean(axis=0)
- print 'Centre of geometry at %(time)g ps: %(centre)r' % vars()
-
- # finally close file
- xdrfile_close(XTC)
-
-Note that only the *contents* of the coordinate and unitcell arrays *x* and
-*box* change.
-
-
-Functions and constants
------------------------
-
-The module defines a number of constants such as :data:`DIM` or the
-`Status symbols`_.
-
-.. data:: DIM
-
- The number of cartesian dimensions for which the underlying C-code
- was compiled; this is most certainly 3.
-
-
-Status symbols
-~~~~~~~~~~~~~~
-
-A number of symbols are exported; they all start with the letters
-``exdr``. Important ones are listed here:
-
-.. data:: exdrOK
-
- Success of xdr file read/write operation.
-
-.. data:: exdrCLOSE
-
- xdr file is closed
-
-.. data:: exdrENDOFFILE
-
- end of file was reached (response of :func:`read_xtc` and
- :func:`read_trr` after the last read frame)
-
-.. data:: exdrFILENOTFOUND
-
- :func:`xdrfile_open` cannot find the requested file
-
-
-Opening and closing of XDR files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Two low-level functions are used to obtain a *XDRFILE* object (a file handle)
-to access xdr files such as XTC or TRR trajectories.
-
-.. function:: xdrfile_open(path, mode) -> XDRFILE
-
- Open *path* and returns a *XDRFILE* handle that is required by other
- functions.
-
- :Arguments:
- *path*
- file name
- *mode*
- 'r' for reading and 'w' for writing
- :Returns: *XDRFILE* handle
-
-.. function:: xdrfile_close(XDRFILE) -> status
-
- Close the xdrfile pointed to by *XDRFILE*.
-
- .. Warning:: Closing an already closed file will lead to a
- crash with a double-free pointer error.
-
-XTC functions
-~~~~~~~~~~~~~
-
-The XTC trajectory format is a lossy compression format that only stores
-coordinates. Compression level is determined by the *precision* argument to the
-:func:`write_xtc` function. Coordinates (Gromacs_ uses nm natively) are
-multiplied by *precision* and truncated to the integer part. A typical value is
-1000.0, which gives an accuracy of 1/100 of an Angstroem.
-
-The advantage of XTC over TRR is its significantly reduced size.
-
-
-.. function:: read_xtc_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a xtc file *fn*.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc(XDRFILE, box, x) -> (status, step, time, precision)
-
- Read the next frame from the opened xtc trajectory into *x*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=numpy.float32)``
- which is updated with the coordinates from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see `Status symbols`_ for other
- values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
-.. function:: write_xtc(XDRFILE, step, time, box, x, prec) -> status
-
- Write the next frame *x* to the opened xtc trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the coordinates from the frame
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-TRR functions
-~~~~~~~~~~~~~
-
-TRR is the Gromacs_ native full-feature trajectory storage format. It can contain position
-coordinates, velocities and forces, and the lambda value for free energy perturbation
-calculations. Velocities and forces are optional in the sense that they can be all zero.
-
-.. function:: read_trr_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a trr file *fn*.
-
- :Arguments:
- *fn*
- file name of a trr file
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR
- or if it is not readable.
-
-.. function:: read_trr_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR or if it is not readable.
-
-.. function:: read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)
-
- Read the next frame from the opened trr trajectory into *x*, *v*, and *f*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **coordinates** from the frame
- *v*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **velocities** from the frame
- *f*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **forces** from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see the ``libxdrfile2.exdr*`` constants
- under `Status symbols`_ for other values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *lambda*
- current lambda value (only interesting for free energy perturbation)
- *has_x*
- boolean indicating whether coordinates were read from the TRR
- *has_v*
- boolean indicating whether velocities were read from the TRR
- *has_f*
- boolean indicating whether forces were read from the TRR
-
-.. function:: write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status
-
- Write the next frame to the opened trr trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *lambda*
- free energy lambda value (typically 0.0)
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **coordinates** from the frame
- *v*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **velocities** from the frame
- *f*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **forces** from the frame
-
- .. versionchanged:: 0.8.0
- either one of *x*, *v*, or *f* can now be set as a natom,0-DIM
- numpy ``array((natom, 0),dtype=nump.float32)``. This will cause the
- corresponding property to be skipped when writing to file.
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-
-"""
-
-
-from sys import version_info
-if version_info >= (2,6,0):
- def swig_import_helper():
- from os.path import dirname
- import imp
- fp = None
- try:
- fp, pathname, description = imp.find_module('_libxdrfile2', [dirname(__file__)])
- except ImportError:
- import _libxdrfile2
- return _libxdrfile2
- if fp is not None:
- try:
- _mod = imp.load_module('_libxdrfile2', fp, pathname, description)
- finally:
- fp.close()
- return _mod
- _libxdrfile2 = swig_import_helper()
- del swig_import_helper
-else:
- import _libxdrfile2
-del version_info
-try:
- _swig_property = property
-except NameError:
- pass # Python < 2.2 doesn't have 'property'.
-def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
- if (name == "thisown"): return self.this.own(value)
- if (name == "this"):
- if type(value).__name__ == 'SwigPyObject':
- self.__dict__[name] = value
- return
- method = class_type.__swig_setmethods__.get(name,None)
- if method: return method(self,value)
- if (not static):
- self.__dict__[name] = value
- else:
- raise AttributeError("You cannot add attributes to %s" % self)
-
-def _swig_setattr(self,class_type,name,value):
- return _swig_setattr_nondynamic(self,class_type,name,value,0)
-
-def _swig_getattr(self,class_type,name):
- if (name == "thisown"): return self.this.own()
- method = class_type.__swig_getmethods__.get(name,None)
- if method: return method(self)
- raise AttributeError(name)
-
-def _swig_repr(self):
- try: strthis = "proxy of " + self.this.__repr__()
- except: strthis = ""
- return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
-
-try:
- _object = object
- _newclass = 1
-except AttributeError:
- class _object : pass
- _newclass = 0
-
-
-exdrOK = _libxdrfile2.exdrOK
-exdrHEADER = _libxdrfile2.exdrHEADER
-exdrSTRING = _libxdrfile2.exdrSTRING
-exdrDOUBLE = _libxdrfile2.exdrDOUBLE
-exdrINT = _libxdrfile2.exdrINT
-exdrFLOAT = _libxdrfile2.exdrFLOAT
-exdrUINT = _libxdrfile2.exdrUINT
-exdr3DX = _libxdrfile2.exdr3DX
-exdrCLOSE = _libxdrfile2.exdrCLOSE
-exdrMAGIC = _libxdrfile2.exdrMAGIC
-exdrNOMEM = _libxdrfile2.exdrNOMEM
-exdrENDOFFILE = _libxdrfile2.exdrENDOFFILE
-exdrFILENOTFOUND = _libxdrfile2.exdrFILENOTFOUND
-exdrNR = _libxdrfile2.exdrNR
-SEEK_SET = _libxdrfile2.SEEK_SET
-SEEK_CUR = _libxdrfile2.SEEK_CUR
-SEEK_END = _libxdrfile2.SEEK_END
-
-def xdrfile_open(*args):
- """xdrfile_open(path, mode) -> XDRFILE *"""
- return _libxdrfile2.xdrfile_open(*args)
-
-def xdrfile_close(*args):
- """xdrfile_close(fp) -> int"""
- return _libxdrfile2.xdrfile_close(*args)
-
-def read_xtc_natoms(*args):
- """read_xtc_natoms(fn) -> int"""
- return _libxdrfile2.read_xtc_natoms(*args)
-
-def read_xtc_numframes(*args):
- """read_xtc_numframes(fn) -> PyObject *"""
- return _libxdrfile2.read_xtc_numframes(*args)
-
-def read_trr_natoms(*args):
- """read_trr_natoms(fn) -> int"""
- return _libxdrfile2.read_trr_natoms(*args)
-
-def read_trr_numframes(*args):
- """read_trr_numframes(fn) -> PyObject *"""
- return _libxdrfile2.read_trr_numframes(*args)
-DIM = _libxdrfile2.DIM
-
-def read_xtc(*args):
- """read_xtc(XDRFILE, box, x) -> (status, step, time, precision)"""
- return _libxdrfile2.read_xtc(*args)
-
-def read_trr(*args):
- """read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)"""
- return _libxdrfile2.read_trr(*args)
-
-def write_xtc(*args):
- """write_xtc(XDRFILE, step, time, box, x, prec) -> status"""
- return _libxdrfile2.write_xtc(*args)
-
-def write_trr(*args):
- """write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status"""
- return _libxdrfile2.write_trr(*args)
-
-def xdr_seek(*args):
- """xdr_seek(xd, pos, whence) -> int"""
- return _libxdrfile2.xdr_seek(*args)
-
-def xdr_tell(*args):
- """xdr_tell(xd) -> long long"""
- return _libxdrfile2.xdr_tell(*args)
-# This file is compatible with both classic and new-style classes.
-
-
diff --git a/pymolfile/libpymolfile-old/numpy.i b/pymolfile/libpymolfile-old/numpy.i
deleted file mode 100644
index ec649b942fac2682d78bf8a99edcccbb698c7d17..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/numpy.i
+++ /dev/null
@@ -1,1638 +0,0 @@
-/* -*- C -*- (not really, but good for syntax highlighting) */
-#ifdef SWIGPYTHON
-
-%{
-#ifndef SWIG_FILE_WITH_INIT
-# define NO_IMPORT_ARRAY
-#endif
-#include "stdio.h"
-#include <numpy/arrayobject.h>
-%}
-
-/**********************************************************************/
-
-%fragment("NumPy_Backward_Compatibility", "header")
-{
-/* Support older NumPy data type names
-*/
-%#if NDARRAY_VERSION < 0x01000000
-%#define NPY_BOOL PyArray_BOOL
-%#define NPY_BYTE PyArray_BYTE
-%#define NPY_UBYTE PyArray_UBYTE
-%#define NPY_SHORT PyArray_SHORT
-%#define NPY_USHORT PyArray_USHORT
-%#define NPY_INT PyArray_INT
-%#define NPY_UINT PyArray_UINT
-%#define NPY_LONG PyArray_LONG
-%#define NPY_ULONG PyArray_ULONG
-%#define NPY_LONGLONG PyArray_LONGLONG
-%#define NPY_ULONGLONG PyArray_ULONGLONG
-%#define NPY_FLOAT PyArray_FLOAT
-%#define NPY_DOUBLE PyArray_DOUBLE
-%#define NPY_LONGDOUBLE PyArray_LONGDOUBLE
-%#define NPY_CFLOAT PyArray_CFLOAT
-%#define NPY_CDOUBLE PyArray_CDOUBLE
-%#define NPY_CLONGDOUBLE PyArray_CLONGDOUBLE
-%#define NPY_OBJECT PyArray_OBJECT
-%#define NPY_STRING PyArray_STRING
-%#define NPY_UNICODE PyArray_UNICODE
-%#define NPY_VOID PyArray_VOID
-%#define NPY_NTYPES PyArray_NTYPES
-%#define NPY_NOTYPE PyArray_NOTYPE
-%#define NPY_CHAR PyArray_CHAR
-%#define NPY_USERDEF PyArray_USERDEF
-%#define npy_intp intp
-
-%#define NPY_MAX_BYTE MAX_BYTE
-%#define NPY_MIN_BYTE MIN_BYTE
-%#define NPY_MAX_UBYTE MAX_UBYTE
-%#define NPY_MAX_SHORT MAX_SHORT
-%#define NPY_MIN_SHORT MIN_SHORT
-%#define NPY_MAX_USHORT MAX_USHORT
-%#define NPY_MAX_INT MAX_INT
-%#define NPY_MIN_INT MIN_INT
-%#define NPY_MAX_UINT MAX_UINT
-%#define NPY_MAX_LONG MAX_LONG
-%#define NPY_MIN_LONG MIN_LONG
-%#define NPY_MAX_ULONG MAX_ULONG
-%#define NPY_MAX_LONGLONG MAX_LONGLONG
-%#define NPY_MIN_LONGLONG MIN_LONGLONG
-%#define NPY_MAX_ULONGLONG MAX_ULONGLONG
-%#define NPY_MAX_INTP MAX_INTP
-%#define NPY_MIN_INTP MIN_INTP
-
-%#define NPY_FARRAY FARRAY
-%#define NPY_F_CONTIGUOUS F_CONTIGUOUS
-%#endif
-}
-
-/**********************************************************************/
-
-/* The following code originally appeared in
- * enthought/kiva/agg/src/numeric.i written by Eric Jones. It was
- * translated from C++ to C by John Hunter. Bill Spotz has modified
- * it to fix some minor bugs, upgrade from Numeric to numpy (all
- * versions), add some comments and functionality, and convert from
- * direct code insertion to SWIG fragments.
- */
-
-%fragment("NumPy_Macros", "header")
-{
-/* Macros to extract array attributes.
- */
-%#define is_array(a) ((a) && PyArray_Check((PyArrayObject *)a))
-%#define array_type(a) (int)(PyArray_TYPE(a))
-%#define array_numdims(a) (((PyArrayObject *)a)->nd)
-%#define array_dimensions(a) (((PyArrayObject *)a)->dimensions)
-%#define array_size(a,i) (((PyArrayObject *)a)->dimensions[i])
-%#define array_data(a) (((PyArrayObject *)a)->data)
-%#define array_is_contiguous(a) (PyArray_ISCONTIGUOUS(a))
-%#define array_is_native(a) (PyArray_ISNOTSWAPPED(a))
-%#define array_is_fortran(a) (PyArray_ISFORTRAN(a))
-}
-
-/**********************************************************************/
-
-%fragment("NumPy_Utilities", "header")
-{
- /* Given a PyObject, return a string describing its type.
- */
- const char* pytype_string(PyObject* py_obj) {
- if (py_obj == NULL ) return "C NULL value";
- if (py_obj == Py_None ) return "Python None" ;
- if (PyCallable_Check(py_obj)) return "callable" ;
- if (PyString_Check( py_obj)) return "string" ;
- if (PyInt_Check( py_obj)) return "int" ;
- if (PyFloat_Check( py_obj)) return "float" ;
- if (PyDict_Check( py_obj)) return "dict" ;
- if (PyList_Check( py_obj)) return "list" ;
- if (PyTuple_Check( py_obj)) return "tuple" ;
- #if PY_MAJOR_VERSION < 3
- if (PyFile_Check( py_obj)) return "file" ;
- #endif
- if (PyModule_Check( py_obj)) return "module" ;
- #if PY_MAJOR_VERSION < 3
- if (PyInstance_Check(py_obj)) return "instance" ;
- #endif
-
- return "unkown type";
- }
-
- /* Given a NumPy typecode, return a string describing the type.
- */
- const char* typecode_string(int typecode) {
- static const char* type_names[25] = {"bool", "byte", "unsigned byte",
- "short", "unsigned short", "int",
- "unsigned int", "long", "unsigned long",
- "long long", "unsigned long long",
- "float", "double", "long double",
- "complex float", "complex double",
- "complex long double", "object",
- "string", "unicode", "void", "ntypes",
- "notype", "char", "unknown"};
- return typecode < 24 ? type_names[typecode] : type_names[24];
- }
-
- /* Make sure input has correct numpy type. Allow character and byte
- * to match. Also allow int and long to match. This is deprecated.
- * You should use PyArray_EquivTypenums() instead.
- */
- int type_match(int actual_type, int desired_type) {
- return PyArray_EquivTypenums(actual_type, desired_type);
- }
-}
-
-/**********************************************************************/
-
-%fragment("NumPy_Object_to_Array", "header",
- fragment="NumPy_Backward_Compatibility",
- fragment="NumPy_Macros",
- fragment="NumPy_Utilities")
-{
- /* Given a PyObject pointer, cast it to a PyArrayObject pointer if
- * legal. If not, set the python error string appropriately and
- * return NULL.
- */
- PyArrayObject* obj_to_array_no_conversion(PyObject* input, int typecode)
- {
- PyArrayObject* ary = NULL;
- if (is_array(input) && (typecode == NPY_NOTYPE ||
- PyArray_EquivTypenums(array_type(input), typecode)))
- {
- ary = (PyArrayObject*) input;
- }
- else if is_array(input)
- {
- const char* desired_type = typecode_string(typecode);
- const char* actual_type = typecode_string(array_type(input));
- PyErr_Format(PyExc_TypeError,
- "Array of type '%s' required. Array of type '%s' given",
- desired_type, actual_type);
- ary = NULL;
- }
- else
- {
- const char * desired_type = typecode_string(typecode);
- const char * actual_type = pytype_string(input);
- PyErr_Format(PyExc_TypeError,
- "Array of type '%s' required. A '%s' was given",
- desired_type, actual_type);
- ary = NULL;
- }
- return ary;
- }
-
- /* Convert the given PyObject to a NumPy array with the given
- * typecode. On success, return a valid PyArrayObject* with the
- * correct type. On failure, the python error string will be set and
- * the routine returns NULL.
- */
- PyArrayObject* obj_to_array_allow_conversion(PyObject* input, int typecode,
- int* is_new_object)
- {
- PyArrayObject* ary = NULL;
- PyObject* py_obj;
- if (is_array(input) && (typecode == NPY_NOTYPE ||
- PyArray_EquivTypenums(array_type(input),typecode)))
- {
- ary = (PyArrayObject*) input;
- *is_new_object = 0;
- }
- else
- {
- py_obj = PyArray_FROMANY(input, typecode, 0, 0, NPY_DEFAULT);
- /* If NULL, PyArray_FromObject will have set python error value.*/
- ary = (PyArrayObject*) py_obj;
- *is_new_object = 1;
- }
- return ary;
- }
-
- /* Given a PyArrayObject, check to see if it is contiguous. If so,
- * return the input pointer and flag it as not a new object. If it is
- * not contiguous, create a new PyArrayObject using the original data,
- * flag it as a new object and return the pointer.
- */
- PyArrayObject* make_contiguous(PyArrayObject* ary, int* is_new_object,
- int min_dims, int max_dims)
- {
- PyArrayObject* result;
- if (array_is_contiguous(ary))
- {
- result = ary;
- *is_new_object = 0;
- }
- else
- {
- result = (PyArrayObject*) PyArray_ContiguousFromObject((PyObject*)ary,
- array_type(ary),
- min_dims,
- max_dims);
- *is_new_object = 1;
- }
- return result;
- }
-
- /* Given a PyArrayObject, check to see if it is Fortran-contiguous.
- * If so, return the input pointer, but do not flag it as not a new
- * object. If it is not Fortran-contiguous, create a new
- * PyArrayObject using the original data, flag it as a new object
- * and return the pointer.
- */
- PyArrayObject* make_fortran(PyArrayObject* ary, int* is_new_object,
- int min_dims, int max_dims)
- {
- PyArrayObject* result;
- if (array_is_fortran(ary))
- {
- result = ary;
- *is_new_object = 0;
- }
- else
- {
- Py_INCREF(ary->descr);
- result = (PyArrayObject*) PyArray_FromArray(ary, ary->descr, NPY_FORTRAN);
- *is_new_object = 1;
- }
- return result;
- }
-
- /* Convert a given PyObject to a contiguous PyArrayObject of the
- * specified type. If the input object is not a contiguous
- * PyArrayObject, a new one will be created and the new object flag
- * will be set.
- */
- PyArrayObject* obj_to_array_contiguous_allow_conversion(PyObject* input,
- int typecode,
- int* is_new_object)
- {
- int is_new1 = 0;
- int is_new2 = 0;
- PyArrayObject* ary2;
- PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode,
- &is_new1);
- if (ary1)
- {
- ary2 = make_contiguous(ary1, &is_new2, 0, 0);
- if ( is_new1 && is_new2)
- {
- Py_DECREF(ary1);
- }
- ary1 = ary2;
- }
- *is_new_object = is_new1 || is_new2;
- return ary1;
- }
-
- /* Convert a given PyObject to a Fortran-ordered PyArrayObject of the
- * specified type. If the input object is not a Fortran-ordered
- * PyArrayObject, a new one will be created and the new object flag
- * will be set.
- */
- PyArrayObject* obj_to_array_fortran_allow_conversion(PyObject* input,
- int typecode,
- int* is_new_object)
- {
- int is_new1 = 0;
- int is_new2 = 0;
- PyArrayObject* ary2;
- PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode,
- &is_new1);
- if (ary1)
- {
- ary2 = make_fortran(ary1, &is_new2, 0, 0);
- if (is_new1 && is_new2)
- {
- Py_DECREF(ary1);
- }
- ary1 = ary2;
- }
- *is_new_object = is_new1 || is_new2;
- return ary1;
- }
-
-} /* end fragment */
-
-
-/**********************************************************************/
-
-%fragment("NumPy_Array_Requirements", "header",
- fragment="NumPy_Backward_Compatibility",
- fragment="NumPy_Macros")
-{
- /* Test whether a python object is contiguous. If array is
- * contiguous, return 1. Otherwise, set the python error string and
- * return 0.
- */
- int require_contiguous(PyArrayObject* ary)
- {
- int contiguous = 1;
- if (!array_is_contiguous(ary))
- {
- PyErr_SetString(PyExc_TypeError,
- "Array must be contiguous. A non-contiguous array was given");
- contiguous = 0;
- }
- return contiguous;
- }
-
- /* Require that a numpy array is not byte-swapped. If the array is
- * not byte-swapped, return 1. Otherwise, set the python error string
- * and return 0.
- */
- int require_native(PyArrayObject* ary)
- {
- int native = 1;
- if (!array_is_native(ary))
- {
- PyErr_SetString(PyExc_TypeError,
- "Array must have native byteorder. "
- "A byte-swapped array was given");
- native = 0;
- }
- return native;
- }
-
- /* Require the given PyArrayObject to have a specified number of
- * dimensions. If the array has the specified number of dimensions,
- * return 1. Otherwise, set the python error string and return 0.
- */
- int require_dimensions(PyArrayObject* ary, int exact_dimensions)
- {
- int success = 1;
- if (array_numdims(ary) != exact_dimensions)
- {
- PyErr_Format(PyExc_TypeError,
- "Array must have %d dimensions. Given array has %d dimensions",
- exact_dimensions, array_numdims(ary));
- success = 0;
- }
- return success;
- }
-
- /* Require the given PyArrayObject to have one of a list of specified
- * number of dimensions. If the array has one of the specified number
- * of dimensions, return 1. Otherwise, set the python error string
- * and return 0.
- */
- int require_dimensions_n(PyArrayObject* ary, int* exact_dimensions, int n)
- {
- int success = 0;
- int i;
- char dims_str[255] = "";
- char s[255];
- for (i = 0; i < n && !success; i++)
- {
- if (array_numdims(ary) == exact_dimensions[i])
- {
- success = 1;
- }
- }
- if (!success)
- {
- for (i = 0; i < n-1; i++)
- {
- sprintf(s, "%d, ", exact_dimensions[i]);
- strcat(dims_str,s);
- }
- sprintf(s, " or %d", exact_dimensions[n-1]);
- strcat(dims_str,s);
- PyErr_Format(PyExc_TypeError,
- "Array must have %s dimensions. Given array has %d dimensions",
- dims_str, array_numdims(ary));
- }
- return success;
- }
-
- /* Require the given PyArrayObject to have a specified shape. If the
- * array has the specified shape, return 1. Otherwise, set the python
- * error string and return 0.
- */
- int require_size(PyArrayObject* ary, npy_intp* size, int n)
- {
- int i;
- int success = 1;
- int len;
- char desired_dims[255] = "[";
- char s[255];
- char actual_dims[255] = "[";
- for(i=0; i < n;i++)
- {
- if (size[i] != -1 && size[i] != array_size(ary,i))
- {
- success = 0;
- }
- }
- if (!success)
- {
- for (i = 0; i < n; i++)
- {
- if (size[i] == -1)
- {
- sprintf(s, "*,");
- }
- else
- {
- sprintf(s, "%ld,", (long int)size[i]);
- }
- strcat(desired_dims,s);
- }
- len = strlen(desired_dims);
- desired_dims[len-1] = ']';
- for (i = 0; i < n; i++)
- {
- sprintf(s, "%ld,", (long int)array_size(ary,i));
- strcat(actual_dims,s);
- }
- len = strlen(actual_dims);
- actual_dims[len-1] = ']';
- PyErr_Format(PyExc_TypeError,
- "Array must have shape of %s. Given array has shape of %s",
- desired_dims, actual_dims);
- }
- return success;
- }
-
- /* Require the given PyArrayObject to to be FORTRAN ordered. If the
- * the PyArrayObject is already FORTRAN ordered, do nothing. Else,
- * set the FORTRAN ordering flag and recompute the strides.
- */
- int require_fortran(PyArrayObject* ary)
- {
- int success = 1;
- int nd = array_numdims(ary);
- int i;
- if (array_is_fortran(ary)) return success;
- /* Set the FORTRAN ordered flag */
- ary->flags = NPY_FARRAY;
- /* Recompute the strides */
- ary->strides[0] = ary->strides[nd-1];
- for (i=1; i < nd; ++i)
- ary->strides[i] = ary->strides[i-1] * array_size(ary,i-1);
- return success;
- }
-}
-
-/* Combine all NumPy fragments into one for convenience */
-%fragment("NumPy_Fragments", "header",
- fragment="NumPy_Backward_Compatibility",
- fragment="NumPy_Macros",
- fragment="NumPy_Utilities",
- fragment="NumPy_Object_to_Array",
- fragment="NumPy_Array_Requirements") { }
-
-/* End John Hunter translation (with modifications by Bill Spotz)
- */
-
-/* %numpy_typemaps() macro
- *
- * This macro defines a family of 41 typemaps that allow C arguments
- * of the form
- *
- * (DATA_TYPE IN_ARRAY1[ANY])
- * (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
- * (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
- *
- * (DATA_TYPE IN_ARRAY2[ANY][ANY])
- * (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
- * (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
- *
- * (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
- * (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
- * (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
- *
- * (DATA_TYPE INPLACE_ARRAY1[ANY])
- * (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
- * (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
- *
- * (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
- * (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
- * (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
- *
- * (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
- * (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
- * (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- * (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
- *
- * (DATA_TYPE ARGOUT_ARRAY1[ANY])
- * (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
- * (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
- *
- * (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
- *
- * (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
- *
- * (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
- * (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
- *
- * (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
- * (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
- * (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
- * (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
- *
- * (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
- * (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
- * (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
- * (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_FARRAY3)
- *
- * where "DATA_TYPE" is any type supported by the NumPy module, and
- * "DIM_TYPE" is any int-like type suitable for specifying dimensions.
- * The difference between "ARRAY" typemaps and "FARRAY" typemaps is
- * that the "FARRAY" typemaps expect FORTRAN ordering of
- * multidimensional arrays. In python, the dimensions will not need
- * to be specified (except for the "DATA_TYPE* ARGOUT_ARRAY1"
- * typemaps). The IN_ARRAYs can be a numpy array or any sequence that
- * can be converted to a numpy array of the specified type. The
- * INPLACE_ARRAYs must be numpy arrays of the appropriate type. The
- * ARGOUT_ARRAYs will be returned as new numpy arrays of the
- * appropriate type.
- *
- * These typemaps can be applied to existing functions using the
- * %apply directive. For example:
- *
- * %apply (double* IN_ARRAY1, int DIM1) {(double* series, int length)};
- * double prod(double* series, int length);
- *
- * %apply (int DIM1, int DIM2, double* INPLACE_ARRAY2)
- * {(int rows, int cols, double* matrix )};
- * void floor(int rows, int cols, double* matrix, double f);
- *
- * %apply (double IN_ARRAY3[ANY][ANY][ANY])
- * {(double tensor[2][2][2] )};
- * %apply (double ARGOUT_ARRAY3[ANY][ANY][ANY])
- * {(double low[2][2][2] )};
- * %apply (double ARGOUT_ARRAY3[ANY][ANY][ANY])
- * {(double upp[2][2][2] )};
- * void luSplit(double tensor[2][2][2],
- * double low[2][2][2],
- * double upp[2][2][2] );
- *
- * or directly with
- *
- * double prod(double* IN_ARRAY1, int DIM1);
- *
- * void floor(int DIM1, int DIM2, double* INPLACE_ARRAY2, double f);
- *
- * void luSplit(double IN_ARRAY3[ANY][ANY][ANY],
- * double ARGOUT_ARRAY3[ANY][ANY][ANY],
- * double ARGOUT_ARRAY3[ANY][ANY][ANY]);
- */
-
-%define %numpy_typemaps(DATA_TYPE, DATA_TYPECODE, DIM_TYPE)
-
-/************************/
-/* Input Array Typemaps */
-/************************/
-
-/* Typemap suite for (DATA_TYPE IN_ARRAY1[ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE IN_ARRAY1[ANY])
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE IN_ARRAY1[ANY])
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[1] = { $1_dim0 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 1) ||
- !require_size(array, size, 1)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(freearg)
- (DATA_TYPE IN_ARRAY1[ANY])
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[1] = { -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 1) ||
- !require_size(array, size, 1)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
-}
-%typemap(freearg)
- (DATA_TYPE* IN_ARRAY1, DIM_TYPE DIM1)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[1] = {-1};
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 1) ||
- !require_size(array, size, 1)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DATA_TYPE*) array_data(array);
-}
-%typemap(freearg)
- (DIM_TYPE DIM1, DATA_TYPE* IN_ARRAY1)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE IN_ARRAY2[ANY][ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE IN_ARRAY2[ANY][ANY])
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE IN_ARRAY2[ANY][ANY])
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[2] = { $1_dim0, $1_dim1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 2) ||
- !require_size(array, size, 2)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(freearg)
- (DATA_TYPE IN_ARRAY2[ANY][ANY])
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[2] = { -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 2) ||
- !require_size(array, size, 2)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
-}
-%typemap(freearg)
- (DATA_TYPE* IN_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[2] = { -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 2) ||
- !require_size(array, size, 2)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DATA_TYPE*) array_data(array);
-}
-%typemap(freearg)
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_ARRAY2)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[2] = { -1, -1 };
- array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 2) ||
- !require_size(array, size, 2) || !require_fortran(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
-}
-%typemap(freearg)
- (DATA_TYPE* IN_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[2] = { -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 2) ||
- !require_size(array, size, 2) || !require_fortran(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DATA_TYPE*) array_data(array);
-}
-%typemap(freearg)
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* IN_FARRAY2)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[3] = { $1_dim0, $1_dim1, $1_dim2 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 3) ||
- !require_size(array, size, 3)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(freearg)
- (DATA_TYPE IN_ARRAY3[ANY][ANY][ANY])
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
- * DIM_TYPE DIM3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[3] = { -1, -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 3) ||
- !require_size(array, size, 3)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
- $4 = (DIM_TYPE) array_size(array,2);
-}
-%typemap(freearg)
- (DATA_TYPE* IN_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
- * DATA_TYPE* IN_ARRAY3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[3] = { -1, -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 3) ||
- !require_size(array, size, 3)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DIM_TYPE) array_size(array,2);
- $4 = (DATA_TYPE*) array_data(array);
-}
-%typemap(freearg)
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_ARRAY3)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
- * DIM_TYPE DIM3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[3] = { -1, -1, -1 };
- array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 3) ||
- !require_size(array, size, 3) | !require_fortran(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
- $4 = (DIM_TYPE) array_size(array,2);
-}
-%typemap(freearg)
- (DATA_TYPE* IN_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
- * DATA_TYPE* IN_FARRAY3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
-{
- $1 = is_array($input) || PySequence_Check($input);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
- (PyArrayObject* array=NULL, int is_new_object=0)
-{
- npy_intp size[3] = { -1, -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
- &is_new_object);
- if (!array || !require_dimensions(array, 3) ||
- !require_size(array, size, 3) || !require_fortran(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DIM_TYPE) array_size(array,2);
- $4 = (DATA_TYPE*) array_data(array);
-}
-%typemap(freearg)
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* IN_FARRAY3)
-{
- if (is_new_object$argnum && array$argnum)
- { Py_DECREF(array$argnum); }
-}
-
-/***************************/
-/* In-Place Array Typemaps */
-/***************************/
-
-/* Typemap suite for (DATA_TYPE INPLACE_ARRAY1[ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE INPLACE_ARRAY1[ANY])
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE INPLACE_ARRAY1[ANY])
- (PyArrayObject* array=NULL)
-{
- npy_intp size[1] = { $1_dim0 };
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,1) || !require_size(array, size, 1) ||
- !require_contiguous(array) || !require_native(array)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* INPLACE_ARRAY1, DIM_TYPE DIM1)
- (PyArrayObject* array=NULL, int i=1)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,1) || !require_contiguous(array)
- || !require_native(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = 1;
- for (i=0; i < array_numdims(array); ++i) $2 *= array_size(array,i);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DATA_TYPE* INPLACE_ARRAY1)
- (PyArrayObject* array=NULL, int i=0)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,1) || !require_contiguous(array)
- || !require_native(array)) SWIG_fail;
- $1 = 1;
- for (i=0; i < array_numdims(array); ++i) $1 *= array_size(array,i);
- $2 = (DATA_TYPE*) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE INPLACE_ARRAY2[ANY][ANY])
- (PyArrayObject* array=NULL)
-{
- npy_intp size[2] = { $1_dim0, $1_dim1 };
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,2) || !require_size(array, size, 2) ||
- !require_contiguous(array) || !require_native(array)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* INPLACE_ARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,2) || !require_contiguous(array)
- || !require_native(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_ARRAY2)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,2) || !require_contiguous(array) ||
- !require_native(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DATA_TYPE*) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* INPLACE_FARRAY2, DIM_TYPE DIM1, DIM_TYPE DIM2)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,2) || !require_contiguous(array)
- || !require_native(array) || !require_fortran(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DATA_TYPE* INPLACE_FARRAY2)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,2) || !require_contiguous(array) ||
- !require_native(array) || !require_fortran(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DATA_TYPE*) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE INPLACE_ARRAY3[ANY][ANY][ANY])
- (PyArrayObject* array=NULL)
-{
- npy_intp size[3] = { $1_dim0, $1_dim1, $1_dim2 };
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,3) || !require_size(array, size, 3) ||
- !require_contiguous(array) || !require_native(array)) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
- * DIM_TYPE DIM3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* INPLACE_ARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,3) || !require_contiguous(array) ||
- !require_native(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
- $4 = (DIM_TYPE) array_size(array,2);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
- * DATA_TYPE* INPLACE_ARRAY3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_ARRAY3)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,3) || !require_contiguous(array)
- || !require_native(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DIM_TYPE) array_size(array,2);
- $4 = (DATA_TYPE*) array_data(array);
-}
-
-/* Typemap suite for (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2,
- * DIM_TYPE DIM3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DATA_TYPE* INPLACE_FARRAY3, DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,3) || !require_contiguous(array) ||
- !require_native(array) || !require_fortran(array)) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
- $2 = (DIM_TYPE) array_size(array,0);
- $3 = (DIM_TYPE) array_size(array,1);
- $4 = (DIM_TYPE) array_size(array,2);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3,
- * DATA_TYPE* INPLACE_FARRAY3)
- */
-%typecheck(SWIG_TYPECHECK_DOUBLE_ARRAY,
- fragment="NumPy_Macros")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
-{
- $1 = is_array($input) && PyArray_EquivTypenums(array_type($input),
- DATA_TYPECODE);
-}
-%typemap(in,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DIM_TYPE DIM2, DIM_TYPE DIM3, DATA_TYPE* INPLACE_FARRAY3)
- (PyArrayObject* array=NULL)
-{
- array = obj_to_array_no_conversion($input, DATA_TYPECODE);
- if (!array || !require_dimensions(array,3) || !require_contiguous(array)
- || !require_native(array) || !require_fortran(array)) SWIG_fail;
- $1 = (DIM_TYPE) array_size(array,0);
- $2 = (DIM_TYPE) array_size(array,1);
- $3 = (DIM_TYPE) array_size(array,2);
- $4 = (DATA_TYPE*) array_data(array);
-}
-
-/*************************/
-/* Argout Array Typemaps */
-/*************************/
-
-/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY1[ANY])
- */
-%typemap(in,numinputs=0,
- fragment="NumPy_Backward_Compatibility,NumPy_Macros")
- (DATA_TYPE ARGOUT_ARRAY1[ANY])
- (PyObject * array = NULL)
-{
- npy_intp dims[1] = { $1_dim0 };
- array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
- if (!array) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(argout)
- (DATA_TYPE ARGOUT_ARRAY1[ANY])
-{
- $result = SWIG_Python_AppendOutput($result,array$argnum);
-}
-
-/* Typemap suite for (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
- */
-%typemap(in,numinputs=1,
- fragment="NumPy_Fragments")
- (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
- (PyObject * array = NULL)
-{
- npy_intp dims[1];
- if (!PyInt_Check($input))
- {
- const char* typestring = pytype_string($input);
- PyErr_Format(PyExc_TypeError,
- "Int dimension expected. '%s' given.",
- typestring);
- SWIG_fail;
- }
- $2 = (DIM_TYPE) PyInt_AsLong($input);
- dims[0] = (npy_intp) $2;
- array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
- if (!array) SWIG_fail;
- $1 = (DATA_TYPE*) array_data(array);
-}
-%typemap(argout)
- (DATA_TYPE* ARGOUT_ARRAY1, DIM_TYPE DIM1)
-{
- $result = SWIG_Python_AppendOutput($result,array$argnum);
-}
-
-/* Typemap suite for (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
- */
-%typemap(in,numinputs=1,
- fragment="NumPy_Fragments")
- (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
- (PyObject * array = NULL)
-{
- npy_intp dims[1];
- if (!PyInt_Check($input))
- {
- const char* typestring = pytype_string($input);
- PyErr_Format(PyExc_TypeError,
- "Int dimension expected. '%s' given.",
- typestring);
- SWIG_fail;
- }
- $1 = (DIM_TYPE) PyInt_AsLong($input);
- dims[0] = (npy_intp) $1;
- array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
- if (!array) SWIG_fail;
- $2 = (DATA_TYPE*) array_data(array);
-}
-%typemap(argout)
- (DIM_TYPE DIM1, DATA_TYPE* ARGOUT_ARRAY1)
-{
- $result = SWIG_Python_AppendOutput($result,array$argnum);
-}
-
-/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
- */
-%typemap(in,numinputs=0,
- fragment="NumPy_Backward_Compatibility,NumPy_Macros")
- (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
- (PyObject * array = NULL)
-{
- npy_intp dims[2] = { $1_dim0, $1_dim1 };
- array = PyArray_SimpleNew(2, dims, DATA_TYPECODE);
- if (!array) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(argout)
- (DATA_TYPE ARGOUT_ARRAY2[ANY][ANY])
-{
- $result = SWIG_Python_AppendOutput($result,array$argnum);
-}
-
-/* Typemap suite for (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
- */
-%typemap(in,numinputs=0,
- fragment="NumPy_Backward_Compatibility,NumPy_Macros")
- (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
- (PyObject * array = NULL)
-{
- npy_intp dims[3] = { $1_dim0, $1_dim1, $1_dim2 };
- array = PyArray_SimpleNew(3, dims, DATA_TYPECODE);
- if (!array) SWIG_fail;
- $1 = ($1_ltype) array_data(array);
-}
-%typemap(argout)
- (DATA_TYPE ARGOUT_ARRAY3[ANY][ANY][ANY])
-{
- $result = SWIG_Python_AppendOutput($result,array$argnum);
-}
-
-/*****************************/
-/* Argoutview Array Typemaps */
-/*****************************/
-
-/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
- */
-%typemap(in,numinputs=0)
- (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1 )
- (DATA_TYPE* data_temp , DIM_TYPE dim_temp)
-{
- $1 = &data_temp;
- $2 = &dim_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DATA_TYPE** ARGOUTVIEW_ARRAY1, DIM_TYPE* DIM1)
-{
- npy_intp dims[1] = { *$2 };
- PyObject * array = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$1));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
- */
-%typemap(in,numinputs=0)
- (DIM_TYPE* DIM1 , DATA_TYPE** ARGOUTVIEW_ARRAY1)
- (DIM_TYPE dim_temp, DATA_TYPE* data_temp )
-{
- $1 = &dim_temp;
- $2 = &data_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DIM_TYPE* DIM1, DATA_TYPE** ARGOUTVIEW_ARRAY1)
-{
- npy_intp dims[1] = { *$1 };
- PyObject * array = PyArray_SimpleNewFromData(1, dims, DATA_TYPECODE, (void*)(*$2));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
- */
-%typemap(in,numinputs=0)
- (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
- (DATA_TYPE* data_temp , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
-{
- $1 = &data_temp;
- $2 = &dim1_temp;
- $3 = &dim2_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DATA_TYPE** ARGOUTVIEW_ARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
-{
- npy_intp dims[2] = { *$2, *$3 };
- PyObject * array = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
- */
-%typemap(in,numinputs=0)
- (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEW_ARRAY2)
- (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp )
-{
- $1 = &dim1_temp;
- $2 = &dim2_temp;
- $3 = &data_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_ARRAY2)
-{
- npy_intp dims[2] = { *$1, *$2 };
- PyObject * array = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
- */
-%typemap(in,numinputs=0)
- (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1 , DIM_TYPE* DIM2 )
- (DATA_TYPE* data_temp , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp)
-{
- $1 = &data_temp;
- $2 = &dim1_temp;
- $3 = &dim2_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
- (DATA_TYPE** ARGOUTVIEW_FARRAY2, DIM_TYPE* DIM1, DIM_TYPE* DIM2)
-{
- npy_intp dims[2] = { *$2, *$3 };
- PyObject * obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$1));
- PyArrayObject * array = (PyArrayObject*) obj;
- if (!array || !require_fortran(array)) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,obj);
-}
-
-/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
- */
-%typemap(in,numinputs=0)
- (DIM_TYPE* DIM1 , DIM_TYPE* DIM2 , DATA_TYPE** ARGOUTVIEW_FARRAY2)
- (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DATA_TYPE* data_temp )
-{
- $1 = &dim1_temp;
- $2 = &dim2_temp;
- $3 = &data_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DATA_TYPE** ARGOUTVIEW_FARRAY2)
-{
- npy_intp dims[2] = { *$1, *$2 };
- PyObject * obj = PyArray_SimpleNewFromData(2, dims, DATA_TYPECODE, (void*)(*$3));
- PyArrayObject * array = (PyArrayObject*) obj;
- if (!array || !require_fortran(array)) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,obj);
-}
-
-/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
- DIM_TYPE* DIM3)
- */
-%typemap(in,numinputs=0)
- (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
- (DATA_TYPE* data_temp, DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
-{
- $1 = &data_temp;
- $2 = &dim1_temp;
- $3 = &dim2_temp;
- $4 = &dim3_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DATA_TYPE** ARGOUTVIEW_ARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
-{
- npy_intp dims[3] = { *$2, *$3, *$4 };
- PyObject * array = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
- DATA_TYPE** ARGOUTVIEW_ARRAY3)
- */
-%typemap(in,numinputs=0)
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
- (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp)
-{
- $1 = &dim1_temp;
- $2 = &dim2_temp;
- $3 = &dim3_temp;
- $4 = &data_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility")
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_ARRAY3)
-{
- npy_intp dims[3] = { *$1, *$2, *$3 };
- PyObject * array = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$3));
- if (!array) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,array);
-}
-
-/* Typemap suite for (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
- DIM_TYPE* DIM3)
- */
-%typemap(in,numinputs=0)
- (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
- (DATA_TYPE* data_temp, DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp)
-{
- $1 = &data_temp;
- $2 = &dim1_temp;
- $3 = &dim2_temp;
- $4 = &dim3_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
- (DATA_TYPE** ARGOUTVIEW_FARRAY3, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
-{
- npy_intp dims[3] = { *$2, *$3, *$4 };
- PyObject * obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$1));
- PyArrayObject * array = (PyArrayObject*) obj;
- if (!array || require_fortran(array)) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,obj);
-}
-
-/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3,
- DATA_TYPE** ARGOUTVIEW_FARRAY3)
- */
-%typemap(in,numinputs=0)
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_FARRAY3)
- (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DATA_TYPE* data_temp)
-{
- $1 = &dim1_temp;
- $2 = &dim2_temp;
- $3 = &dim3_temp;
- $4 = &data_temp;
-}
-%typemap(argout,
- fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements")
- (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DATA_TYPE** ARGOUTVIEW_FARRAY3)
-{
- npy_intp dims[3] = { *$1, *$2, *$3 };
- PyObject * obj = PyArray_SimpleNewFromData(3, dims, DATA_TYPECODE, (void*)(*$3));
- PyArrayObject * array = (PyArrayObject*) obj;
- if (!array || require_fortran(array)) SWIG_fail;
- $result = SWIG_Python_AppendOutput($result,obj);
-}
-
-%enddef /* %numpy_typemaps() macro */
-/* *************************************************************** */
-
-/* Concrete instances of the %numpy_typemaps() macro: Each invocation
- * below applies all of the typemaps above to the specified data type.
- */
-%numpy_typemaps(signed char , NPY_BYTE , int)
-%numpy_typemaps(unsigned char , NPY_UBYTE , int)
-%numpy_typemaps(short , NPY_SHORT , int)
-%numpy_typemaps(unsigned short , NPY_USHORT , int)
-%numpy_typemaps(int , NPY_INT , int)
-%numpy_typemaps(unsigned int , NPY_UINT , int)
-%numpy_typemaps(long , NPY_LONG , int)
-%numpy_typemaps(unsigned long , NPY_ULONG , int)
-%numpy_typemaps(long long , NPY_LONGLONG , int)
-%numpy_typemaps(unsigned long long, NPY_ULONGLONG, int)
-%numpy_typemaps(float , NPY_FLOAT , int)
-%numpy_typemaps(double , NPY_DOUBLE , int)
-
-/* ***************************************************************
- * The follow macro expansion does not work, because C++ bool is 4
- * bytes and NPY_BOOL is 1 byte
- *
- * %numpy_typemaps(bool, NPY_BOOL, int)
- */
-
-/* ***************************************************************
- * On my Mac, I get the following warning for this macro expansion:
- * 'swig/python detected a memory leak of type 'long double *', no destructor found.'
- *
- * %numpy_typemaps(long double, NPY_LONGDOUBLE, int)
- */
-
-/* ***************************************************************
- * Swig complains about a syntax error for the following macro
- * expansions:
- *
- * %numpy_typemaps(complex float, NPY_CFLOAT , int)
- *
- * %numpy_typemaps(complex double, NPY_CDOUBLE, int)
- *
- * %numpy_typemaps(complex long double, NPY_CLONGDOUBLE, int)
- */
-
-#endif /* SWIGPYTHON */
diff --git a/pymolfile/libpymolfile-old/python_molfile.i b/pymolfile/libpymolfile-old/python_molfile.i
deleted file mode 100644
index 5b041181d1894e9efaa5df64dd52b5a3658ac8e5..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/python_molfile.i
+++ /dev/null
@@ -1,386 +0,0 @@
-
-/* SWIG interface for libvmdmolfile of VMD molfile_plugins
- Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
- Published under the GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
- swig -python -outdir MDAnalysis/coordinates/xdrfile src/xdrfile/libxdrfile2.i
-*/
-%define DOCSTRING
-"
-:Author: Berk Onat <b.onat@warwick.ac.uk>
-:Year: 2017
-:Licence: GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
-"
-%enddef
-
-%module(docstring=DOCSTRING) libvmdmolfile
-
-
-
-/************************************************************
- * the molfile f77 interface in VMD plugins distribution *
- ************************************************************/
-
-/*
- * molfile fortran interface
- * $Id: f77_molfile.c,v 1.1 2006/03/10 22:48:49 johns Exp $
- * (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <string.h>
-
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
-
-#define F77TESTME 1
-
-/* fortran name mangling */
-#if defined(_F77_NO_UNDERSCORE)
-#define FNAME(n) n
-#elif defined(_F77_F2C_UNDERSCORE)
-#define FNAME(n) n ## __
-#else
-#define FNAME(n) n ## _
-#endif
-
-/* interface typedef magic */
-typedef int int4;
-
-struct molfile_f77_handle
-{
- void *handle;
- const char *fname;
- const char *ftype;
- molfile_plugin_t *plugin;
-};
-typedef struct molfile_f77_handle f77_fd;
-
-/* plugin list */
-#ifndef MAXPLUGINS
-#define MAXPLUGINS 200
-#endif
-static int numplugins=0;
-static molfile_plugin_t *plugin_list[MAXPLUGINS];
-
-/* we maintain a static list of assigned handles */
-#ifndef MAXHADNLES
-#define MAXHANDLES 200
-#endif
-static int4 numhandles=0;
-static f77_fd handle_list[MAXHANDLES];
-
-/* helper functions */
-/* helper function to copy fortran style (a la sun fortran) strings into
- * valid c style strings. just using the string pointers will not work,
- * since the strings are NOT zero terminated.
- *
- * WARNING: do not forget to free(2) them later,
- * or you'll have a memory leak!
- */
-static char *f77strdup(const char *s,const int sz)
-{
- char *r;
-
- r = (char *)malloc(sz + 1);
- r = (char *)memcpy(r, s, sz);
- r[sz] = '\0';
- return r;
-}
-
-/* trim off whitespace at the end of a string */
-static void f77trim(char *s,const int sz)
-{
- int i;
-
- i=1;
- while( (i++ < sz) && isspace(s[sz-i]) ) {
- s[sz-i] ='\0';
- }
-}
-
-/* get the filename extension */
-static const char *f77getfnext(const char *s)
-{
- int i,len;
-
- len = strlen(s);
- for (i=len; i>=0; --i) {
- if(s[i] == '.') {
- return &s[i+1];
- }
- }
- return NULL;
-}
-
-/* check validity of plugins and register them. */
-static int f77register(void *ptr, vmdplugin_t *plugin) {
-
- if (!plugin->type || !plugin->name || !plugin->author) {
- fprintf(stderr," skipping plugin with incomplete header\n");
- return -1;
- }
-
-#if F77TESTME
- fprintf(stderr, " trying to register plugin #%d: %s, type: %s/%d\n"
- " written by: %s\n\n", numplugins+1, plugin->name,
- plugin->type, plugin->abiversion, plugin->author);
-#endif
-
- if (plugin->abiversion != vmdplugin_ABIVERSION) {
- fprintf(stderr, " skipping plugin with incompatible ABI:%d/%d\n",
- plugin->abiversion, vmdplugin_ABIVERSION);
- return -2;
- }
-
- if (0 != strncmp(plugin->type, "mol file", 8)) {
- fprintf(stderr, " skipping plugin of incompatible type:%s\n",
- plugin->type);
- return -3;
- }
-
- if (numplugins < MAXPLUGINS) {
- plugin_list[numplugins] = (molfile_plugin_t *) plugin;
- ++numplugins;
- return 0;
- }
-
- fprintf(stderr, " too many plugins: %d. increase MAXPLUGINS, "
- "recompile, and try again.\n", numplugins);
-
- return -4;
-}
-
-
-/* the official fortran API */
-
-/* register all available plugins and clear handles. */
-void FNAME(f77_molfile_init)(void)
-{
- int i;
-
- MOLFILE_INIT_ALL;
-
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i].handle = NULL;
- }
-
- MOLFILE_REGISTER_ALL(NULL,f77register);
-
- /*
- * FIXME: check all plugins and make
- * sure the babel plugin(s) are last.
- */
-}
-
-/* unregister all available plugins */
-void FNAME(f77_molfile_finish)(void)
-{
-#if 0
- int i;
-
- /* FIXME: add code to close and nullify all open handles */
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i] = NULL;
- }
-#endif
-
- MOLFILE_FINI_ALL;
-}
-
-
-/* open a file and provide file descriptor */
-void FNAME(f77_molfile_open_read)(int4 *handle, int4 *natoms,
- const char *infile, const char *intype,
- const int len_if, const int len_it)
-{
- char *fname, *ftype;
- molfile_plugin_t *plugin;
- int i;
-
- if (numhandles >= MAXHANDLES) {
- fprintf(stderr, "too many molfile f77 handles.\n");
- *handle = -666;
- return;
- }
-
- fname = f77strdup(infile, len_if);
- f77trim(fname,len_if);
-
- ftype = f77strdup(intype, len_it);
- f77trim(ftype,len_it);
-
- fprintf(stderr, " %s: trying for: %s/%d, %s/%d\n",
- __FUNCTION__, fname, len_if, ftype, len_it);
-
- plugin = NULL;
- /* determine plugin type automatically */
- if(0 == strncmp(intype, "auto", 4)) {
- const char *fext;
-
- fext = f77getfnext(fname);
- if (fext == NULL) {
- fprintf(stderr, " could not determine file name extension "
- "for automatic plugin guess\n");
- *handle = -111;
- return;
- }
-#if F77TESTME
- fprintf(stderr, " filename extension: %s\n", fext);
-#endif
-
- for (i=0; (i<numplugins) && plugin==NULL; ++i) {
-#if F77TESTME
- fprintf(stderr, " tying filename extension: %s\n",
- plugin_list[i]->filename_extension);
-#endif
- if (0 == strcmp(plugin_list[i]->filename_extension, fext)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
-
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not determine matching plugin type"
- "from file name extension\n");
- *handle = -222;
- return;
- }
- } else {
-
- for (i=0; (i<numplugins) && (plugin==NULL); ++i) {
-#if F77TESTME
- fprintf(stderr, " tying plugin type: %s\n",
- plugin_list[i]->name);
-#endif
- if (0 == strcmp(plugin_list[i]->name, ftype)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not find plugin for type %s\n",ftype);
- *handle = -333;
- return;
- }
- }
-
- if(plugin == NULL) { /* this should not happen, but... */
- fprintf(stderr, " no plugin found.\n");
- *handle = -444;
- return;
- }
-
- /* build handle */
- ++numhandles;
- for (i=0; i<numhandles; ++i) {
- if(handle_list[i].plugin == NULL) {
- *handle = i;
- handle_list[i].fname=fname;
- handle_list[i].ftype=plugin->name;
- handle_list[i].plugin=plugin;
- }
- }
-
- /* open file for reading and detect number of atoms */
- *natoms=MOLFILE_NUMATOMS_UNKNOWN;
- handle_list[*handle].handle=
- plugin->open_file_read(fname,plugin->name,natoms);
- if(handle_list[*handle].handle == NULL) {
- fprintf(stderr, " open of %s-plugin for file %s failed\n",
- plugin->type, fname);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-777;
- return;
- }
-
- return;
-}
-
-/* read next time step */
-void FNAME(f77_molfile_read_next)(int4 *handle, int4 *natoms, float *xyz,
- float *box, int4 *status)
-{
- molfile_plugin_t *plugin;
- molfile_timestep_t step;
- int retval;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- /* skip or read the timestep as demanded */
- if(status == 0) {
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, NULL);
- } else {
- step.coords = xyz;
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, &step);
- }
-
- /* copy the box parameters */
- if (retval == MOLFILE_SUCCESS) {
- *status = 1;
- box[0]=step.A;
- box[1]=step.B;
- box[2]=step.C;
- box[3]=step.alpha;
- box[4]=step.beta;
- box[5]=step.gamma;
- } else {
- *status = 0;
- }
-}
-
-/* close a read file descriptor */
-void FNAME(f77_molfile_close_read)(int4 *handle)
-{
- molfile_plugin_t *plugin;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -111;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -222;
- return;
- }
-
-#if F77TESTME
- fprintf(stderr, " %s: trying to close handle %d"
- " for file %s\n", __FUNCTION__, *handle,
- handle_list[*handle].fname);
-#endif
-
- plugin->close_file_read(handle_list[*handle].handle);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-1;
-}
diff --git a/pymolfile/libpymolfile-old/xdrfile.c b/pymolfile/libpymolfile-old/xdrfile.c
deleted file mode 100644
index 4aa69ce7acb88664b70717f7a6d0114084c0a357..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile.c
+++ /dev/null
@@ -1,2624 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-/* Get HAVE_RPC_XDR_H, F77_FUNC from config.h if available */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <limits.h>
-
-/* get fixed-width types if we are using ANSI C99 */
-#ifdef HAVE_STDINT_H
-# include <stdint.h>
-#elif (defined HAVE_INTTYPES_H)
-# include <inttypes.h>
-#endif
-
-#ifdef HAVE_RPC_XDR_H
-# include <rpc/rpc.h>
-# include <rpc/xdr.h>
-#endif
-
-#include "xdrfile.h"
-
-/* Default FORTRAN name mangling is: lower case name, append underscore */
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
-#endif
-
-char *exdr_message[exdrNR] = {
- "OK",
- "Header",
- "String",
- "Double",
- "Integer",
- "Float",
- "Unsigned integer",
- "Compressed 3D coordinate",
- "Closing file",
- "Magic number",
- "Not enough memory",
- "End of file",
- "File not found"
-};
-
-/*
- * Declare our own XDR routines statically if no libraries are present.
- * Actual implementation is at the end of this file.
- *
- * We don't want the low-level XDR implementation as part of the Gromacs
- * documentation, so skip it for doxygen too...
- */
-#if (!defined HAVE_RPC_XDR_H && !defined DOXYGEN)
-
-enum xdr_op
-{
- XDR_ENCODE = 0,
- XDR_DECODE = 1,
- XDR_FREE = 2
-};
-
-
-/* We need integer types that are guaranteed to be 4 bytes wide.
- * If ANSI C99 headers were included they are already defined
- * as int32_t and uint32_t. Check, and if not define them ourselves.
- * Since it is just our workaround for missing ANSI C99 types, avoid adding
- * it to the doxygen documentation.
- */
-#if !(defined INT32_MAX || defined DOXYGEN)
-# if (INT_MAX == 2147483647)
-# define int32_t int
-# define uint32_t unsigned int
-# define INT32_MAX 2147483647
-# elif (LONG_MAX == 2147483647)
-# define int32_t long
-# define uint32_t unsigned long
-# define INT32_MAX 2147483647L
-# else
-# error ERROR: No 32 bit wide integer type found!
-# error Use system XDR libraries instead, or update xdrfile.c
-# endif
-#endif
-
-typedef struct XDR XDR;
-
-struct XDR
-{
- enum xdr_op x_op;
- struct xdr_ops
- {
- int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
- int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
- int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
- int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
- /* two next routines are not 64-bit IO safe - don't use! */
- unsigned int (*x_getpostn) (XDR *__xdrs);
- int (*x_setpostn) (XDR *__xdrs, off_t __pos);
- void (*x_destroy) (XDR *__xdrs);
- }
- *x_ops;
- char *x_private;
-};
-
-static int xdr_char (XDR *xdrs, char *ip);
-static int xdr_u_char (XDR *xdrs, unsigned char *ip);
-static int xdr_short (XDR *xdrs, short *ip);
-static int xdr_u_short (XDR *xdrs, unsigned short *ip);
-static int xdr_int (XDR *xdrs, int *ip);
-static int xdr_u_int (XDR *xdrs, unsigned int *ip);
-static int xdr_float (XDR *xdrs, float *ip);
-static int xdr_double (XDR *xdrs, double *ip);
-static int xdr_string (XDR *xdrs, char **ip, unsigned int maxsize);
-static int xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt);
-static void xdrstdio_create (XDR *xdrs, FILE *fp, enum xdr_op xop);
-
-#define xdr_getpos(xdrs) \
- (*(xdrs)->x_ops->x_getpostn)(xdrs)
-#define xdr_setpos(xdrs, pos) \
- (*(xdrs)->x_ops->x_setpostn)(xdrs, pos)
-#define xdr_destroy(xdrs) \
- do { \
- if ((xdrs)->x_ops->x_destroy) \
- (*(xdrs)->x_ops->x_destroy)(xdrs); \
- } while (0)
-#endif /* end of our own XDR declarations */
-
-
-
-
-
-/** Contents of the abstract XDRFILE data structure.
- *
- * @internal
- *
- * This structure is used to provide an XDR file interface that is
- * virtual identical to the standard UNIX fopen/fread/fwrite/fclose.
- */
-struct XDRFILE
-{
- FILE * fp; /**< pointer to standard C library file handle */
- XDR * xdr; /**< pointer to corresponding XDR handle */
- char mode; /**< r=read, w=write, a=append */
- int * buf1; /**< Buffer for internal use */
- int buf1size; /**< Current allocated length of buf1 */
- int * buf2; /**< Buffer for internal use */
- int buf2size; /**< Current allocated length of buf2 */
-};
-
-
-
-
-/*************************************************************
- * Implementation of higher-level routines to read/write *
- * portable data based on the XDR standard. These should be *
- * called from C - see further down for Fortran77 wrappers. *
- *************************************************************/
-
-XDRFILE *
-xdrfile_open(const char *path, const char *mode)
-{
- char newmode[5];
- enum xdr_op xdrmode;
- XDRFILE *xfp;
-
- /* make sure XDR files are opened in binary mode... */
- if(*mode=='w' || *mode=='W')
- {
- sprintf(newmode,"wb+");
- xdrmode=XDR_ENCODE;
- } else if(*mode == 'a' || *mode == 'A')
- {
- sprintf(newmode,"ab+");
- xdrmode = XDR_ENCODE;
- } else if(*mode == 'r' || *mode == 'R')
- {
- sprintf(newmode,"rb");
- xdrmode = XDR_DECODE;
- } else /* cannot determine mode */
- return NULL;
-
- if((xfp=(XDRFILE *)malloc(sizeof(XDRFILE)))==NULL)
- return NULL;
- if((xfp->fp=fopen(path,newmode))==NULL)
- {
- free(xfp);
- return NULL;
- }
- if((xfp->xdr=(XDR *)malloc(sizeof(XDR)))==NULL)
- {
- fclose(xfp->fp);
- free(xfp);
- return NULL;
- }
- xfp->mode=*mode;
- xdrstdio_create((XDR *)(xfp->xdr),xfp->fp,xdrmode);
- xfp->buf1 = xfp->buf2 = NULL;
- xfp->buf1size = xfp->buf2size = 0;
- return xfp;
-}
-
-int
-xdrfile_close(XDRFILE *xfp)
-{
- int ret=exdrCLOSE;
- if(xfp)
- {
- /* flush and destroy XDR stream */
- if(xfp->xdr)
- xdr_destroy((XDR *)(xfp->xdr));
- free(xfp->xdr);
- /* close the file */
- ret=fclose(xfp->fp);
- if(xfp->buf1size)
- free(xfp->buf1);
- if(xfp->buf2size)
- free(xfp->buf2);
- free(xfp);
- }
- return ret; /* return 0 if ok */
-}
-
-
-
-int
-xdrfile_read_int(int *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_int(int *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-
-int
-xdrfile_read_uint(unsigned int *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_int((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_uint(unsigned int *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_int((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_read_char(char *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_char((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_char(char *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_char((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-
-int
-xdrfile_read_uchar(unsigned char *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_char((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_uchar(unsigned char *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_char((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_read_short(short *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_short((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_short(short *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_short((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-
-int
-xdrfile_read_ushort(unsigned short *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_short((XDR *)(xfp->xdr),ptr+i))
- i++;
-
- return i;
-}
-
-int
-xdrfile_write_ushort(unsigned short *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
-
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_u_short((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_read_float(float *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_float((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_write_float(float *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_float((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_read_double(double *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_double((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_write_double(double *ptr, int ndata, XDRFILE* xfp)
-{
- int i=0;
- /* read write is encoded in the XDR struct */
- while(i<ndata && xdr_double((XDR *)(xfp->xdr),ptr+i))
- i++;
- return i;
-}
-
-int
-xdrfile_read_string(char *ptr, int maxlen, XDRFILE* xfp)
-{
- int i;
- if(xdr_string((XDR *)(xfp->xdr),&ptr,maxlen)) {
- i=0;
- while(i<maxlen && ptr[i]!=0)
- i++;
- if(i==maxlen)
- return maxlen;
- else
- return i+1;
- } else
- return 0;
-}
-
-int
-xdrfile_write_string(char *ptr, XDRFILE* xfp)
-{
- int len=strlen(ptr)+1;
-
- if(xdr_string((XDR *)(xfp->xdr),&ptr,len))
- return len;
- else
- return 0;
-}
-
-
-int
-xdrfile_read_opaque(char *ptr, int cnt, XDRFILE* xfp)
-{
- if(xdr_opaque((XDR *)(xfp->xdr),ptr,cnt))
- return cnt;
- else
- return 0;
-}
-
-
-int
-xdrfile_write_opaque(char *ptr, int cnt, XDRFILE* xfp)
-{
- if(xdr_opaque((XDR *)(xfp->xdr),ptr,cnt))
- return cnt;
- else
- return 0;
-}
-
-
-/* Internal support routines for reading/writing compressed coordinates
- * sizeofint - calculate smallest number of bits necessary
- * to represent a certain integer.
- */
-static int
-sizeofint(int size) {
- unsigned int num = 1;
- int num_of_bits = 0;
-
- while (size >= num && num_of_bits < 32)
- {
- num_of_bits++;
- num <<= 1;
- }
- return num_of_bits;
-}
-
-
-/*
- * sizeofints - calculate 'bitsize' of compressed ints
- *
- * given a number of small unsigned integers and the maximum value
- * return the number of bits needed to read or write them with the
- * routines encodeints/decodeints. You need this parameter when
- * calling those routines.
- * (However, in some cases we can just use the variable 'smallidx'
- * which is the exact number of bits, and them we dont need to call
- * this routine).
- */
-static int
-sizeofints(int num_of_ints, unsigned int sizes[])
-{
- int i, num;
- unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
- num_of_bytes = 1;
- bytes[0] = 1;
- num_of_bits = 0;
- for (i=0; i < num_of_ints; i++)
- {
- tmp = 0;
- for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++)
- {
- tmp = bytes[bytecnt] * sizes[i] + tmp;
- bytes[bytecnt] = tmp & 0xff;
- tmp >>= 8;
- }
- while (tmp != 0)
- {
- bytes[bytecnt++] = tmp & 0xff;
- tmp >>= 8;
- }
- num_of_bytes = bytecnt;
- }
- num = 1;
- num_of_bytes--;
- while (bytes[num_of_bytes] >= num)
- {
- num_of_bits++;
- num *= 2;
- }
- return num_of_bits + num_of_bytes * 8;
-
-}
-
-
-/*
- * encodebits - encode num into buf using the specified number of bits
- *
- * This routines appends the value of num to the bits already present in
- * the array buf. You need to give it the number of bits to use and you had
- * better make sure that this number of bits is enough to hold the value.
- * Num must also be positive.
- */
-static void
-encodebits(int buf[], int num_of_bits, int num)
-{
-
- unsigned int cnt, lastbyte;
- int lastbits;
- unsigned char * cbuf;
-
- cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
- cnt = (unsigned int) buf[0];
- lastbits = buf[1];
- lastbyte =(unsigned int) buf[2];
- while (num_of_bits >= 8)
- {
- lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
- cbuf[cnt++] = lastbyte >> lastbits;
- num_of_bits -= 8;
- }
- if (num_of_bits > 0)
- {
- lastbyte = (lastbyte << num_of_bits) | num;
- lastbits += num_of_bits;
- if (lastbits >= 8)
- {
- lastbits -= 8;
- cbuf[cnt++] = lastbyte >> lastbits;
- }
- }
- buf[0] = cnt;
- buf[1] = lastbits;
- buf[2] = lastbyte;
- if (lastbits>0)
- {
- cbuf[cnt] = lastbyte << (8 - lastbits);
- }
-}
-
-/*
- * encodeints - encode a small set of small integers in compressed format
- *
- * this routine is used internally by xdr3dfcoord, to encode a set of
- * small integers to the buffer for writing to a file.
- * Multiplication with fixed (specified maximum) sizes is used to get
- * to one big, multibyte integer. Allthough the routine could be
- * modified to handle sizes bigger than 16777216, or more than just
- * a few integers, this is not done because the gain in compression
- * isn't worth the effort. Note that overflowing the multiplication
- * or the byte buffer (32 bytes) is unchecked and whould cause bad results.
- * THese things are checked in the calling routines, so make sure not
- * to remove those checks...
- */
-
-static void
-encodeints(int buf[], int num_of_ints, int num_of_bits,
- unsigned int sizes[], unsigned int nums[])
-{
-
- int i;
- unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
-
- tmp = nums[0];
- num_of_bytes = 0;
- do
- {
- bytes[num_of_bytes++] = tmp & 0xff;
- tmp >>= 8;
- } while (tmp != 0);
-
- for (i = 1; i < num_of_ints; i++)
- {
- if (nums[i] >= sizes[i])
- {
- fprintf(stderr,"major breakdown in encodeints - num %u doesn't "
- "match size %u\n", nums[i], sizes[i]);
- abort();
- }
- /* use one step multiply */
- tmp = nums[i];
- for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++)
- {
- tmp = bytes[bytecnt] * sizes[i] + tmp;
- bytes[bytecnt] = tmp & 0xff;
- tmp >>= 8;
- }
- while (tmp != 0)
- {
- bytes[bytecnt++] = tmp & 0xff;
- tmp >>= 8;
- }
- num_of_bytes = bytecnt;
- }
- if (num_of_bits >= num_of_bytes * 8)
- {
- for (i = 0; i < num_of_bytes; i++)
- {
- encodebits(buf, 8, bytes[i]);
- }
- encodebits(buf, num_of_bits - num_of_bytes * 8, 0);
- }
- else
- {
- for (i = 0; i < num_of_bytes-1; i++)
- {
- encodebits(buf, 8, bytes[i]);
- }
- encodebits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
- }
-}
-
-
-/*
- * decodebits - decode number from buf using specified number of bits
- *
- * extract the number of bits from the array buf and construct an integer
- * from it. Return that value.
- *
- */
-
-static int
-decodebits(int buf[], int num_of_bits)
-{
-
- int cnt, num;
- unsigned int lastbits, lastbyte;
- unsigned char * cbuf;
- int mask = (1 << num_of_bits) -1;
-
- cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
- cnt = buf[0];
- lastbits = (unsigned int) buf[1];
- lastbyte = (unsigned int) buf[2];
-
- num = 0;
- while (num_of_bits >= 8)
- {
- lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
- num |= (lastbyte >> lastbits) << (num_of_bits - 8);
- num_of_bits -=8;
- }
- if (num_of_bits > 0)
- {
- if (lastbits < num_of_bits)
- {
- lastbits += 8;
- lastbyte = (lastbyte << 8) | cbuf[cnt++];
- }
- lastbits -= num_of_bits;
- num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
- }
- num &= mask;
- buf[0] = cnt;
- buf[1] = lastbits;
- buf[2] = lastbyte;
- return num;
-}
-
-/*
- * decodeints - decode 'small' integers from the buf array
- *
- * this routine is the inverse from encodeints() and decodes the small integers
- * written to buf by calculating the remainder and doing divisions with
- * the given sizes[]. You need to specify the total number of bits to be
- * used from buf in num_of_bits.
- *
- */
-
-static void
-decodeints(int buf[], int num_of_ints, int num_of_bits,
- unsigned int sizes[], int nums[])
-{
-
- int bytes[32];
- int i, j, num_of_bytes, p, num;
-
- bytes[1] = bytes[2] = bytes[3] = 0;
- num_of_bytes = 0;
- while (num_of_bits > 8)
- {
- bytes[num_of_bytes++] = decodebits(buf, 8);
- num_of_bits -= 8;
- }
- if (num_of_bits > 0)
- {
- bytes[num_of_bytes++] = decodebits(buf, num_of_bits);
- }
- for (i = num_of_ints-1; i > 0; i--)
- {
- num = 0;
- for (j = num_of_bytes-1; j >=0; j--)
- {
- num = (num << 8) | bytes[j];
- p = num / sizes[i];
- bytes[j] = p;
- num = num - p * sizes[i];
- }
- nums[i] = num;
- }
- nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
-}
-
-
-static const int magicints[] =
-{
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
- 80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,
- 1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003,
- 16384, 20642, 26007, 32768, 41285, 52015, 65536,82570, 104031,
- 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
- 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021,
- 4194304, 5284491, 6658042, 8388607, 10568983, 13316085, 16777216
-};
-
-#define FIRSTIDX 9
-/* note that magicints[FIRSTIDX-1] == 0 */
-#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
-
-/* Compressed coordinate routines - modified from the original
- * implementation by Frans v. Hoesel to make them threadsafe.
- */
-int
-xdrfile_decompress_coord_float(float *ptr,
- int *size,
- float *precision,
- XDRFILE* xfp)
-{
- int minint[3], maxint[3], *lip;
- int smallidx, minidx, maxidx;
- unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;
- int k, *buf1, *buf2, lsize, flag;
- int smallnum, smaller, larger, i, is_smaller, run;
- float *lfp, inv_precision;
- int tmp, *thiscoord, prevcoord[3];
- unsigned int bitsize;
-
- bitsizeint[0] = 0;
- bitsizeint[1] = 0;
- bitsizeint[2] = 0;
-
- if(xfp==NULL || ptr==NULL)
- return -1;
- tmp=xdrfile_read_int(&lsize,1,xfp);
- if(tmp==0)
- return -1; /* return if we could not read size */
- if (*size < lsize)
- {
- fprintf(stderr, "Requested to decompress %d coords, file contains %d\n",
- *size, lsize);
- return -1;
- }
- *size = lsize;
- size3 = *size * 3;
- if(size3>xfp->buf1size)
- {
- if((xfp->buf1=(int *)malloc(sizeof(int)*size3))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
- return -1;
- }
- xfp->buf1size=size3;
- xfp->buf2size=size3*1.2;
- if((xfp->buf2=(int *)malloc(sizeof(int)*xfp->buf2size))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
- return -1;
- }
- }
- /* Dont bother with compression for three atoms or less */
- if(*size<=9)
- {
- return xdrfile_read_float(ptr,size3,xfp)/3;
- /* return number of coords, not floats */
- }
- /* Compression-time if we got here. Read precision first */
- xdrfile_read_float(precision,1,xfp);
-
- /* avoid repeated pointer dereferencing. */
- buf1=xfp->buf1;
- buf2=xfp->buf2;
- /* buf2[0-2] are special and do not contain actual data */
- buf2[0] = buf2[1] = buf2[2] = 0;
- xdrfile_read_int(minint,3,xfp);
- xdrfile_read_int(maxint,3,xfp);
-
- sizeint[0] = maxint[0] - minint[0]+1;
- sizeint[1] = maxint[1] - minint[1]+1;
- sizeint[2] = maxint[2] - minint[2]+1;
-
- /* check if one of the sizes is to big to be multiplied */
- if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff)
- {
- bitsizeint[0] = sizeofint(sizeint[0]);
- bitsizeint[1] = sizeofint(sizeint[1]);
- bitsizeint[2] = sizeofint(sizeint[2]);
- bitsize = 0; /* flag the use of large sizes */
- }
- else
- {
- bitsize = sizeofints(3, sizeint);
- }
-
- if (xdrfile_read_int(&smallidx,1,xfp) == 0)
- return 0; /* not sure what has happened here or why we return... */
- tmp=smallidx+8;
- maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
- minidx = maxidx - 8; /* often this equal smallidx */
- tmp = smallidx-1;
- tmp = (FIRSTIDX>tmp) ? FIRSTIDX : tmp;
- smaller = magicints[tmp] / 2;
- smallnum = magicints[smallidx] / 2;
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
- larger = magicints[maxidx];
-
- /* buf2[0] holds the length in bytes */
-
- if (xdrfile_read_int(buf2,1,xfp) == 0)
- return 0;
- if (xdrfile_read_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp) == 0)
- return 0;
- buf2[0] = buf2[1] = buf2[2] = 0;
-
- lfp = ptr;
- inv_precision = 1.0 / * precision;
- run = 0;
- i = 0;
- lip = buf1;
- while ( i < lsize )
- {
- thiscoord = (int *)(lip) + i * 3;
-
- if (bitsize == 0)
- {
- thiscoord[0] = decodebits(buf2, bitsizeint[0]);
- thiscoord[1] = decodebits(buf2, bitsizeint[1]);
- thiscoord[2] = decodebits(buf2, bitsizeint[2]);
- }
- else
- {
- decodeints(buf2, 3, bitsize, sizeint, thiscoord);
- }
-
- i++;
- thiscoord[0] += minint[0];
- thiscoord[1] += minint[1];
- thiscoord[2] += minint[2];
-
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
-
- flag = decodebits(buf2, 1);
- is_smaller = 0;
- if (flag == 1)
- {
- run = decodebits(buf2, 5);
- is_smaller = run % 3;
- run -= is_smaller;
- is_smaller--;
- }
- if (run > 0)
- {
- thiscoord += 3;
- for (k = 0; k < run; k+=3)
- {
- decodeints(buf2, 3, smallidx, sizesmall, thiscoord);
- i++;
- thiscoord[0] += prevcoord[0] - smallnum;
- thiscoord[1] += prevcoord[1] - smallnum;
- thiscoord[2] += prevcoord[2] - smallnum;
- if (k == 0) {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
- prevcoord[0] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
- prevcoord[1] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
- prevcoord[2] = tmp;
- *lfp++ = prevcoord[0] * inv_precision;
- *lfp++ = prevcoord[1] * inv_precision;
- *lfp++ = prevcoord[2] * inv_precision;
- } else {
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
- }
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
- }
- }
- else
- {
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
- }
- smallidx += is_smaller;
- if (is_smaller < 0)
- {
- smallnum = smaller;
-
- if (smallidx > FIRSTIDX)
- {
- smaller = magicints[smallidx - 1] /2;
- }
- else
- {
- smaller = 0;
- }
- }
- else if (is_smaller > 0)
- {
- smaller = smallnum;
- smallnum = magicints[smallidx] / 2;
- }
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
- }
- return *size;
-}
-
-int
-xdrfile_compress_coord_float(float *ptr,
- int size,
- float precision,
- XDRFILE* xfp)
-{
- int minint[3], maxint[3], mindiff, *lip, diff;
- int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
- int minidx, maxidx;
- unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
- int k, *buf1, *buf2;
- int smallnum, smaller, larger, i, j, is_small, is_smaller, run, prevrun;
- float *lfp, lf;
- int tmp, tmpsum, *thiscoord, prevcoord[3];
- unsigned int tmpcoord[30];
- int errval=1;
- unsigned int bitsize;
-
- if(xfp==NULL)
- return -1;
- size3=3*size;
-
- bitsizeint[0] = 0;
- bitsizeint[1] = 0;
- bitsizeint[2] = 0;
-
- if(size3>xfp->buf1size)
- {
- if((xfp->buf1=(int *)malloc(sizeof(int)*size3))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
- return -1;
- }
- xfp->buf1size=size3;
- xfp->buf2size=size3*1.2;
- if((xfp->buf2=(int *)malloc(sizeof(int)*xfp->buf2size))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
- return -1;
- }
- }
- if(xdrfile_write_int(&size,1,xfp)==0)
- return -1; /* return if we could not write size */
- /* Dont bother with compression for three atoms or less */
- if(size<=9)
- {
- return xdrfile_write_float(ptr,size3,xfp)/3;
- /* return number of coords, not floats */
- }
- /* Compression-time if we got here. Write precision first */
- if (precision <= 0)
- precision = 1000;
- xdrfile_write_float(&precision,1,xfp);
- /* avoid repeated pointer dereferencing. */
- buf1=xfp->buf1;
- buf2=xfp->buf2;
- /* buf2[0-2] are special and do not contain actual data */
- buf2[0] = buf2[1] = buf2[2] = 0;
- minint[0] = minint[1] = minint[2] = INT_MAX;
- maxint[0] = maxint[1] = maxint[2] = INT_MIN;
- prevrun = -1;
- lfp = ptr;
- lip = buf1;
- mindiff = INT_MAX;
- oldlint1 = oldlint2 = oldlint3 = 0;
- while(lfp < ptr + size3 )
- {
- /* find nearest integer */
- if (*lfp >= 0.0)
- lf = *lfp * precision + 0.5;
- else
- lf = *lfp * precision - 0.5;
- if (fabs(lf) > INT_MAX-2)
- {
- /* scaling would cause overflow */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- lint1 = lf;
- if (lint1 < minint[0]) minint[0] = lint1;
- if (lint1 > maxint[0]) maxint[0] = lint1;
- *lip++ = lint1;
- lfp++;
- if (*lfp >= 0.0)
- lf = *lfp * precision + 0.5;
- else
- lf = *lfp * precision - 0.5;
- if (fabs(lf) > INT_MAX-2)
- {
- /* scaling would cause overflow */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- lint2 = lf;
- if (lint2 < minint[1]) minint[1] = lint2;
- if (lint2 > maxint[1]) maxint[1] = lint2;
- *lip++ = lint2;
- lfp++;
- if (*lfp >= 0.0)
- lf = *lfp * precision + 0.5;
- else
- lf = *lfp * precision - 0.5;
- if (fabs(lf) > INT_MAX-2)
- {
- errval=0;
- }
- lint3 = lf;
- if (lint3 < minint[2]) minint[2] = lint3;
- if (lint3 > maxint[2]) maxint[2] = lint3;
- *lip++ = lint3;
- lfp++;
- diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
- if (diff < mindiff && lfp > ptr + 3)
- mindiff = diff;
- oldlint1 = lint1;
- oldlint2 = lint2;
- oldlint3 = lint3;
- }
- xdrfile_write_int(minint,3,xfp);
- xdrfile_write_int(maxint,3,xfp);
-
- if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
- (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
- (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
- /* turning value in unsigned by subtracting minint
- * would cause overflow
- */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- sizeint[0] = maxint[0] - minint[0]+1;
- sizeint[1] = maxint[1] - minint[1]+1;
- sizeint[2] = maxint[2] - minint[2]+1;
-
- /* check if one of the sizes is to big to be multiplied */
- if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff)
- {
- bitsizeint[0] = sizeofint(sizeint[0]);
- bitsizeint[1] = sizeofint(sizeint[1]);
- bitsizeint[2] = sizeofint(sizeint[2]);
- bitsize = 0; /* flag the use of large sizes */
- }
- else
- {
- bitsize = sizeofints(3, sizeint);
- }
- lip = buf1;
- luip = (unsigned int *) buf1;
- smallidx = FIRSTIDX;
- while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
- {
- smallidx++;
- }
- xdrfile_write_int(&smallidx,1,xfp);
- tmp=smallidx+8;
- maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
- minidx = maxidx - 8; /* often this equal smallidx */
- tmp=smallidx-1;
- tmp= (FIRSTIDX>tmp) ? FIRSTIDX : tmp;
- smaller = magicints[tmp] / 2;
- smallnum = magicints[smallidx] / 2;
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
- larger = magicints[maxidx] / 2;
- i = 0;
- while (i < size)
- {
- is_small = 0;
- thiscoord = (int *)(luip) + i * 3;
- if (smallidx < maxidx && i >= 1 &&
- abs(thiscoord[0] - prevcoord[0]) < larger &&
- abs(thiscoord[1] - prevcoord[1]) < larger &&
- abs(thiscoord[2] - prevcoord[2]) < larger) {
- is_smaller = 1;
- }
- else if (smallidx > minidx)
- {
- is_smaller = -1;
- }
- else
- {
- is_smaller = 0;
- }
- if (i + 1 < size)
- {
- if (abs(thiscoord[0] - thiscoord[3]) < smallnum &&
- abs(thiscoord[1] - thiscoord[4]) < smallnum &&
- abs(thiscoord[2] - thiscoord[5]) < smallnum)
- {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
- thiscoord[3] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
- thiscoord[4] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
- thiscoord[5] = tmp;
- is_small = 1;
- }
- }
- tmpcoord[0] = thiscoord[0] - minint[0];
- tmpcoord[1] = thiscoord[1] - minint[1];
- tmpcoord[2] = thiscoord[2] - minint[2];
- if (bitsize == 0)
- {
- encodebits(buf2, bitsizeint[0], tmpcoord[0]);
- encodebits(buf2, bitsizeint[1], tmpcoord[1]);
- encodebits(buf2, bitsizeint[2], tmpcoord[2]);
- }
- else
- {
- encodeints(buf2, 3, bitsize, sizeint, tmpcoord);
- }
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
- thiscoord = thiscoord + 3;
- i++;
-
- run = 0;
- if (is_small == 0 && is_smaller == -1)
- is_smaller = 0;
- while (is_small && run < 8*3)
- {
- tmpsum=0;
- for(j=0;j<3;j++)
- {
- tmp=thiscoord[j] - prevcoord[j];
- tmpsum+=tmp*tmp;
- }
- if (is_smaller == -1 && tmpsum >= smaller * smaller)
- {
- is_smaller = 0;
- }
-
- tmpcoord[run++] = thiscoord[0] - prevcoord[0] + smallnum;
- tmpcoord[run++] = thiscoord[1] - prevcoord[1] + smallnum;
- tmpcoord[run++] = thiscoord[2] - prevcoord[2] + smallnum;
-
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
-
- i++;
- thiscoord = thiscoord + 3;
- is_small = 0;
- if (i < size &&
- abs(thiscoord[0] - prevcoord[0]) < smallnum &&
- abs(thiscoord[1] - prevcoord[1]) < smallnum &&
- abs(thiscoord[2] - prevcoord[2]) < smallnum)
- {
- is_small = 1;
- }
- }
- if (run != prevrun || is_smaller != 0)
- {
- prevrun = run;
- encodebits(buf2, 1, 1); /* flag the change in run-length */
- encodebits(buf2, 5, run+is_smaller+1);
- }
- else
- {
- encodebits(buf2, 1, 0); /* flag the fact that runlength did not change */
- }
- for (k=0; k < run; k+=3)
- {
- encodeints(buf2, 3, smallidx, sizesmall, &tmpcoord[k]);
- }
- if (is_smaller != 0)
- {
- smallidx += is_smaller;
- if (is_smaller < 0)
- {
- smallnum = smaller;
- smaller = magicints[smallidx-1] / 2;
- }
- else
- {
- smaller = smallnum;
- smallnum = magicints[smallidx] / 2;
- }
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
- }
- }
- if (buf2[1] != 0) buf2[0]++;
- xdrfile_write_int(buf2,1,xfp); /* buf2[0] holds the length in bytes */
- tmp=xdrfile_write_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp);
- if(tmp==(unsigned int)buf2[0])
- return size;
- else
- return -1;
-}
-
-
-int
-xdrfile_decompress_coord_double(double *ptr,
- int *size,
- double *precision,
- XDRFILE* xfp)
-{
- int minint[3], maxint[3], *lip;
- int smallidx, minidx, maxidx;
- unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;
- int k, *buf1, *buf2, lsize, flag;
- int smallnum, smaller, larger, i, is_smaller, run;
- double *lfp, inv_precision;
- float float_prec, tmpdata[30];
- int tmp, *thiscoord, prevcoord[3];
- unsigned int bitsize;
-
- bitsizeint[0] = 0;
- bitsizeint[1] = 0;
- bitsizeint[2] = 0;
-
- if(xfp==NULL || ptr==NULL)
- return -1;
- tmp=xdrfile_read_int(&lsize,1,xfp);
- if(tmp==0)
- return -1; /* return if we could not read size */
- if (*size < lsize)
- {
- fprintf(stderr, "Requested to decompress %d coords, file contains %d\n",
- *size, lsize);
- return -1;
- }
- *size = lsize;
- size3 = *size * 3;
- if(size3>xfp->buf1size)
- {
- if((xfp->buf1=(int *)malloc(sizeof(int)*size3))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for decompression coordinates.\n");
- return -1;
- }
- xfp->buf1size=size3;
- xfp->buf2size=size3*1.2;
- if((xfp->buf2=(int *)malloc(sizeof(int)*xfp->buf2size))==NULL)
- {
- fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
- return -1;
- }
- }
- /* Dont bother with compression for three atoms or less */
- if(*size<=9)
- {
- tmp=xdrfile_read_float(tmpdata,size3,xfp);
- for(i=0;i<9*3;i++)
- ptr[i]=tmpdata[i];
- return tmp/3;
- /* return number of coords, not floats */
- }
- /* Compression-time if we got here. Read precision first */
- xdrfile_read_float(&float_prec,1,xfp);
- *precision=float_prec;
- /* avoid repeated pointer dereferencing. */
- buf1=xfp->buf1;
- buf2=xfp->buf2;
- /* buf2[0-2] are special and do not contain actual data */
- buf2[0] = buf2[1] = buf2[2] = 0;
- xdrfile_read_int(minint,3,xfp);
- xdrfile_read_int(maxint,3,xfp);
-
- sizeint[0] = maxint[0] - minint[0]+1;
- sizeint[1] = maxint[1] - minint[1]+1;
- sizeint[2] = maxint[2] - minint[2]+1;
-
- /* check if one of the sizes is to big to be multiplied */
- if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff)
- {
- bitsizeint[0] = sizeofint(sizeint[0]);
- bitsizeint[1] = sizeofint(sizeint[1]);
- bitsizeint[2] = sizeofint(sizeint[2]);
- bitsize = 0; /* flag the use of large sizes */
- }
- else
- {
- bitsize = sizeofints(3, sizeint);
- }
-
- if (xdrfile_read_int(&smallidx,1,xfp) == 0)
- return 0;
- tmp=smallidx+8;
- maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
- minidx = maxidx - 8; /* often this equal smallidx */
- tmp = smallidx-1;
- tmp = (FIRSTIDX>tmp) ? FIRSTIDX : tmp;
- smaller = magicints[tmp] / 2;
- smallnum = magicints[smallidx] / 2;
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
- larger = magicints[maxidx];
-
- /* buf2[0] holds the length in bytes */
-
- if (xdrfile_read_int(buf2,1,xfp) == 0)
- return 0;
- if (xdrfile_read_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp) == 0)
- return 0;
- buf2[0] = buf2[1] = buf2[2] = 0;
-
- lfp = ptr;
- inv_precision = 1.0 / * precision;
- run = 0;
- i = 0;
- lip = buf1;
- while ( i < lsize )
- {
- thiscoord = (int *)(lip) + i * 3;
-
- if (bitsize == 0)
- {
- thiscoord[0] = decodebits(buf2, bitsizeint[0]);
- thiscoord[1] = decodebits(buf2, bitsizeint[1]);
- thiscoord[2] = decodebits(buf2, bitsizeint[2]);
- } else {
- decodeints(buf2, 3, bitsize, sizeint, thiscoord);
- }
-
- i++;
- thiscoord[0] += minint[0];
- thiscoord[1] += minint[1];
- thiscoord[2] += minint[2];
-
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
-
- flag = decodebits(buf2, 1);
- is_smaller = 0;
- if (flag == 1)
- {
- run = decodebits(buf2, 5);
- is_smaller = run % 3;
- run -= is_smaller;
- is_smaller--;
- }
- if (run > 0)
- {
- thiscoord += 3;
- for (k = 0; k < run; k+=3)
- {
- decodeints(buf2, 3, smallidx, sizesmall, thiscoord);
- i++;
- thiscoord[0] += prevcoord[0] - smallnum;
- thiscoord[1] += prevcoord[1] - smallnum;
- thiscoord[2] += prevcoord[2] - smallnum;
- if (k == 0)
- {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
- prevcoord[0] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
- prevcoord[1] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
- prevcoord[2] = tmp;
- *lfp++ = prevcoord[0] * inv_precision;
- *lfp++ = prevcoord[1] * inv_precision;
- *lfp++ = prevcoord[2] * inv_precision;
- }
- else
- {
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
- }
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
- }
- } else {
- *lfp++ = thiscoord[0] * inv_precision;
- *lfp++ = thiscoord[1] * inv_precision;
- *lfp++ = thiscoord[2] * inv_precision;
- }
- smallidx += is_smaller;
- if (is_smaller < 0) {
- smallnum = smaller;
- if (smallidx > FIRSTIDX) {
- smaller = magicints[smallidx - 1] /2;
- } else {
- smaller = 0;
- }
- } else if (is_smaller > 0) {
- smaller = smallnum;
- smallnum = magicints[smallidx] / 2;
- }
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
- }
- return *size;
-}
-
-int
-xdrfile_compress_coord_double(double *ptr,
- int size,
- double precision,
- XDRFILE* xfp)
-{
- int minint[3], maxint[3], mindiff, *lip, diff;
- int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
- int minidx, maxidx;
- unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
- int k, *buf1, *buf2;
- int smallnum, smaller, larger, i, j, is_small, is_smaller, run, prevrun;
- double *lfp;
- float float_prec, lf,tmpdata[30];
- int tmp, tmpsum, *thiscoord, prevcoord[3];
- unsigned int tmpcoord[30];
- int errval=1;
- unsigned int bitsize;
-
- bitsizeint[0] = 0;
- bitsizeint[1] = 0;
- bitsizeint[2] = 0;
-
- if(xfp==NULL)
- return -1;
- size3=3*size;
- if(size3>xfp->buf1size) {
- if((xfp->buf1=(int *)malloc(sizeof(int)*size3))==NULL) {
- fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
- return -1;
- }
- xfp->buf1size=size3;
- xfp->buf2size=size3*1.2;
- if((xfp->buf2=(int *)malloc(sizeof(int)*xfp->buf2size))==NULL) {
- fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
- return -1;
- }
- }
- if(xdrfile_write_int(&size,1,xfp)==0)
- return -1; /* return if we could not write size */
- /* Dont bother with compression for three atoms or less */
- if(size<=9) {
- for(i=0;i<9*3;i++)
- tmpdata[i]=ptr[i];
- return xdrfile_write_float(tmpdata,size3,xfp)/3;
- /* return number of coords, not floats */
- }
- /* Compression-time if we got here. Write precision first */
- if (precision <= 0)
- precision = 1000;
- float_prec=precision;
- xdrfile_write_float(&float_prec,1,xfp);
- /* avoid repeated pointer dereferencing. */
- buf1=xfp->buf1;
- buf2=xfp->buf2;
- /* buf2[0-2] are special and do not contain actual data */
- buf2[0] = buf2[1] = buf2[2] = 0;
- minint[0] = minint[1] = minint[2] = INT_MAX;
- maxint[0] = maxint[1] = maxint[2] = INT_MIN;
- prevrun = -1;
- lfp = ptr;
- lip = buf1;
- mindiff = INT_MAX;
- oldlint1 = oldlint2 = oldlint3 = 0;
- while(lfp < ptr + size3 ) {
- /* find nearest integer */
- if (*lfp >= 0.0)
- lf = (float)*lfp * float_prec + 0.5;
- else
- lf = (float)*lfp * float_prec - 0.5;
- if (fabs(lf) > INT_MAX-2) {
- /* scaling would cause overflow */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- lint1 = lf;
- if (lint1 < minint[0]) minint[0] = lint1;
- if (lint1 > maxint[0]) maxint[0] = lint1;
- *lip++ = lint1;
- lfp++;
- if (*lfp >= 0.0)
- lf = (float)*lfp * float_prec + 0.5;
- else
- lf = (float)*lfp * float_prec - 0.5;
- if (fabs(lf) > INT_MAX-2) {
- /* scaling would cause overflow */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- lint2 = lf;
- if (lint2 < minint[1]) minint[1] = lint2;
- if (lint2 > maxint[1]) maxint[1] = lint2;
- *lip++ = lint2;
- lfp++;
- if (*lfp >= 0.0)
- lf = (float)*lfp * float_prec + 0.5;
- else
- lf = (float)*lfp * float_prec - 0.5;
- if (fabs(lf) > INT_MAX-2) {
- errval=0;
- }
- lint3 = lf;
- if (lint3 < minint[2]) minint[2] = lint3;
- if (lint3 > maxint[2]) maxint[2] = lint3;
- *lip++ = lint3;
- lfp++;
- diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
- if (diff < mindiff && lfp > ptr + 3)
- mindiff = diff;
- oldlint1 = lint1;
- oldlint2 = lint2;
- oldlint3 = lint3;
- }
- xdrfile_write_int(minint,3,xfp);
- xdrfile_write_int(maxint,3,xfp);
-
- if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
- (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
- (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
- /* turning value in unsigned by subtracting minint
- * would cause overflow
- */
- fprintf(stderr,"Internal overflow compressing coordinates.\n");
- errval=0;
- }
- sizeint[0] = maxint[0] - minint[0]+1;
- sizeint[1] = maxint[1] - minint[1]+1;
- sizeint[2] = maxint[2] - minint[2]+1;
-
- /* check if one of the sizes is to big to be multiplied */
- if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
- bitsizeint[0] = sizeofint(sizeint[0]);
- bitsizeint[1] = sizeofint(sizeint[1]);
- bitsizeint[2] = sizeofint(sizeint[2]);
- bitsize = 0; /* flag the use of large sizes */
- } else {
- bitsize = sizeofints(3, sizeint);
- }
- lip = buf1;
- luip = (unsigned int *) buf1;
- smallidx = FIRSTIDX;
- while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
- smallidx++;
- }
- xdrfile_write_int(&smallidx,1,xfp);
- tmp=smallidx+8;
- maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
- minidx = maxidx - 8; /* often this equal smallidx */
- tmp=smallidx-1;
- tmp= (FIRSTIDX>tmp) ? FIRSTIDX : tmp;
- smaller = magicints[tmp] / 2;
- smallnum = magicints[smallidx] / 2;
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
- larger = magicints[maxidx] / 2;
- i = 0;
- while (i < size) {
- is_small = 0;
- thiscoord = (int *)(luip) + i * 3;
- if (smallidx < maxidx && i >= 1 &&
- abs(thiscoord[0] - prevcoord[0]) < larger &&
- abs(thiscoord[1] - prevcoord[1]) < larger &&
- abs(thiscoord[2] - prevcoord[2]) < larger) {
- is_smaller = 1;
- } else if (smallidx > minidx) {
- is_smaller = -1;
- } else {
- is_smaller = 0;
- }
- if (i + 1 < size) {
- if (abs(thiscoord[0] - thiscoord[3]) < smallnum &&
- abs(thiscoord[1] - thiscoord[4]) < smallnum &&
- abs(thiscoord[2] - thiscoord[5]) < smallnum) {
- /* interchange first with second atom for better
- * compression of water molecules
- */
- tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
- thiscoord[3] = tmp;
- tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
- thiscoord[4] = tmp;
- tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
- thiscoord[5] = tmp;
- is_small = 1;
- }
- }
- tmpcoord[0] = thiscoord[0] - minint[0];
- tmpcoord[1] = thiscoord[1] - minint[1];
- tmpcoord[2] = thiscoord[2] - minint[2];
- if (bitsize == 0) {
- encodebits(buf2, bitsizeint[0], tmpcoord[0]);
- encodebits(buf2, bitsizeint[1], tmpcoord[1]);
- encodebits(buf2, bitsizeint[2], tmpcoord[2]);
- } else {
- encodeints(buf2, 3, bitsize, sizeint, tmpcoord);
- }
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
- thiscoord = thiscoord + 3;
- i++;
-
- run = 0;
- if (is_small == 0 && is_smaller == -1)
- is_smaller = 0;
- while (is_small && run < 8*3) {
- tmpsum=0;
- for(j=0;j<3;j++) {
- tmp=thiscoord[j] - prevcoord[j];
- tmpsum+=tmp*tmp;
- }
- if (is_smaller == -1 && tmpsum >= smaller * smaller) {
- is_smaller = 0;
- }
-
- tmpcoord[run++] = thiscoord[0] - prevcoord[0] + smallnum;
- tmpcoord[run++] = thiscoord[1] - prevcoord[1] + smallnum;
- tmpcoord[run++] = thiscoord[2] - prevcoord[2] + smallnum;
-
- prevcoord[0] = thiscoord[0];
- prevcoord[1] = thiscoord[1];
- prevcoord[2] = thiscoord[2];
-
- i++;
- thiscoord = thiscoord + 3;
- is_small = 0;
- if (i < size &&
- abs(thiscoord[0] - prevcoord[0]) < smallnum &&
- abs(thiscoord[1] - prevcoord[1]) < smallnum &&
- abs(thiscoord[2] - prevcoord[2]) < smallnum) {
- is_small = 1;
- }
- }
- if (run != prevrun || is_smaller != 0) {
- prevrun = run;
- encodebits(buf2, 1, 1); /* flag the change in run-length */
- encodebits(buf2, 5, run+is_smaller+1);
- } else {
- encodebits(buf2, 1, 0); /* flag the fact that runlength did not change */
- }
- for (k=0; k < run; k+=3) {
- encodeints(buf2, 3, smallidx, sizesmall, &tmpcoord[k]);
- }
- if (is_smaller != 0) {
- smallidx += is_smaller;
- if (is_smaller < 0) {
- smallnum = smaller;
- smaller = magicints[smallidx-1] / 2;
- } else {
- smaller = smallnum;
- smallnum = magicints[smallidx] / 2;
- }
- sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
- }
- }
- if (buf2[1] != 0) buf2[0]++;
- xdrfile_write_int(buf2,1,xfp); /* buf2[0] holds the length in bytes */
- tmp=xdrfile_write_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp);
- if(tmp==(unsigned int)buf2[0])
- return size;
- else
- return -1;
-}
-
-
-/* Dont try do document Fortran interface, since
- * Doxygen barfs at the F77_FUNC macro
- */
-#ifndef DOXYGEN
-
-/*************************************************************
- * Fortran77 interface for reading/writing portable data *
- * The routine are not threadsafe when called from Fortran *
- * (as they are when called from C) unless you compile with *
- * this file with posix thread support. *
- * Note that these are not multithread-safe. *
- *************************************************************/
-#define MAX_FORTRAN_XDR 1024
-static XDRFILE *f77xdr[MAX_FORTRAN_XDR]; /* array of file handles */
-static int f77init = 1; /* zero array first time */
-
-/* internal to this file: C<-->Fortran string conversion */
-static int ftocstr(char *dest, int dest_len, char *src, int src_len);
-static int ctofstr(char *dest, int dest_len, char *src);
-
-
-void
-F77_FUNC(xdropen,XDROPEN)(int *fid, char *filename, char *mode,
- int fn_len, int mode_len)
-{
- char cfilename[512];
- char cmode[5];
- int i;
-
- /* zero array at first invocation */
- if(f77init) {
- for(i=0;i<MAX_FORTRAN_XDR;i++)
- f77xdr[i]=NULL;
- f77init=0;
- }
- i=0;
-
- /* nf77xdr is always smaller or equal to MAX_FORTRAN_XDR */
- while(i<MAX_FORTRAN_XDR && f77xdr[i]!=NULL)
- i++;
- if(i==MAX_FORTRAN_XDR) {
- *fid = -1;
- } else if (ftocstr(cfilename, sizeof(cfilename), filename, fn_len)) {
- *fid = -1;
- } else if (ftocstr(cmode, sizeof(cmode), mode,mode_len)) {
- *fid = -1;
- } else {
- f77xdr[i]=xdrfile_open(cfilename,cmode);
- /* return the index in the array as a fortran file handle */
- *fid=i;
- }
-}
-
-void
-F77_FUNC(xdrclose,XDRCLOSE)(int *fid)
-{
- /* first close it */
- xdrfile_close(f77xdr[*fid]);
- /* the remove it from file handle list */
- f77xdr[*fid]=NULL;
-}
-
-
-void
-F77_FUNC(xdrrint,XDRRINT)(int *fid, int *data, int *ndata, int *ret)
-{
- *ret = xdrfile_read_int(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwint,XDRWINT)(int *fid, int *data, int *ndata, int *ret)
-{
- *ret = xdrfile_write_int(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrruint,XDRRUINT)(int *fid, unsigned int *data, int *ndata, int *ret)
-{
- *ret = xdrfile_read_uint(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwuint,XDRWUINT)(int *fid, unsigned int *data, int *ndata, int *ret)
-{
- *ret = xdrfile_write_uint(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrrchar,XDRRCHAR)(int *fid, char *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_read_char(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwchar,XDRWCHAR)(int *fid, char *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_write_char(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrruchar,XDRRUCHAR)(int *fid, unsigned char *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_read_uchar(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwuchar,XDRWUCHAR)(int *fid, unsigned char *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_write_uchar(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrrshort,XDRRSHORT)(int *fid, short *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_read_short(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwshort,XDRWSHORT)(int *fid, short *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_write_short(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrrushort,XDRRUSHORT)(int *fid, unsigned short *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_read_ushort(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwushort,XDRWUSHORT)(int *fid, unsigned short *ip, int *ndata, int *ret)
-{
- *ret = xdrfile_write_ushort(ip,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrrsingle,XDRRSINGLE)(int *fid, float *data, int *ndata, int *ret)
-{
- *ret = xdrfile_read_float(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwsingle,XDRWSINGLE)(int *fid, float *data, int *ndata, int *ret)
-{
- *ret = xdrfile_write_float(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrrdouble,XDRRDOUBLE)(int *fid, double *data, int *ndata, int *ret)
-{
- *ret = xdrfile_read_double(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwdouble,XDRWDOUBLE)(int *fid, double *data, int *ndata, int *ret)
-{
- *ret = xdrfile_write_double(data,*ndata,f77xdr[*fid]);
-}
-
-static int ftocstr(char *dest, int destlen, char *src, int srclen)
-{
- char *p;
-
- p = src + srclen;
- while ( --p >= src && *p == ' ' );
- srclen = p - src + 1;
- destlen--;
- dest[0] = 0;
- if (srclen > destlen)
- return 1;
- while (srclen--)
- (*dest++ = *src++);
- *dest = '\0';
- return 0;
-}
-
-
-static int ctofstr(char *dest, int destlen, char *src)
-{
- while (destlen && *src) {
- *dest++ = *src++;
- destlen--;
- }
- while (destlen--)
- *dest++ = ' ';
- return 0;
-}
-
-
-void
-F77_FUNC(xdrrstring,XDRRSTRING)(int *fid, char *str, int *ret, int len)
-{
- char *cstr;
-
- if((cstr=(char*)malloc((len+1)*sizeof(char)))==NULL) {
- *ret = 0;
- return;
- }
- if (ftocstr(cstr, len+1, str, len)) {
- *ret = 0;
- free(cstr);
- return;
- }
-
- *ret = xdrfile_read_string(cstr, len+1,f77xdr[*fid]);
- ctofstr( str, len , cstr);
- free(cstr);
-}
-
-void
-F77_FUNC(xdrwstring,XDRWSTRING)(int *fid, char *str, int *ret, int len)
-{
- char *cstr;
-
- if((cstr=(char*)malloc((len+1)*sizeof(char)))==NULL) {
- *ret = 0;
- return;
- }
- if (ftocstr(cstr, len+1, str, len)) {
- *ret = 0;
- free(cstr);
- return;
- }
-
- *ret = xdrfile_write_string(cstr, f77xdr[*fid]);
- ctofstr( str, len , cstr);
- free(cstr);
-}
-
-void
-F77_FUNC(xdrropaque,XDRROPAQUE)(int *fid, char *data, int *ndata, int *ret)
-{
- *ret = xdrfile_read_opaque(data,*ndata,f77xdr[*fid]);
-}
-
-void
-F77_FUNC(xdrwopaque,XDRWOPAQUE)(int *fid, char *data, int *ndata, int *ret)
-{
- *ret = xdrfile_write_opaque(data,*ndata,f77xdr[*fid]);
-}
-
-
-/* Write single-precision compressed 3d coordinates */
-void
-F77_FUNC(xdrccs,XDRCCS)(int *fid, float *data, int *ncoord,
- float *precision, int *ret)
-{
- *ret = xdrfile_compress_coord_float(data,*ncoord,*precision,f77xdr[*fid]);
-}
-
-
-/* Read single-precision compressed 3d coordinates */
-void
-F77_FUNC(xdrdcs,XDRDCS)(int *fid, float *data, int *ncoord,
- float *precision, int *ret)
-{
- *ret = xdrfile_decompress_coord_float(data,ncoord,precision,f77xdr[*fid]);
-}
-
-
-/* Write compressed 3d coordinates from double precision data */
-void
-F77_FUNC(xdrccd,XDRCCD)(int *fid, double *data, int *ncoord,
- double *precision, int *ret)
-{
- *ret = xdrfile_compress_coord_double(data,*ncoord,*precision,f77xdr[*fid]);
-}
-
-/* Read compressed 3d coordinates into double precision data */
-void
-F77_FUNC(xddcd,XDRDCD)(int *fid, double *data, int *ncoord,
- double *precision, int *ret)
-{
- *ret = xdrfile_decompress_coord_double(data,ncoord,precision,f77xdr[*fid]);
-}
-
-
-
-
-
-
-
-#endif /* DOXYGEN */
-
-/*************************************************************
- * End of higher-level routines - dont change things below! *
- *************************************************************/
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/*************************************************************
- * The rest of this file contains our own implementation *
- * of the XDR calls in case you are compiling without them. *
- * You do NOT want to change things here since it would make *
- * things incompatible with the standard RPC/XDR routines. *
- *************************************************************/
-#ifndef HAVE_RPC_XDR_H
-
-/*
- * What follows is a modified version of the Sun XDR code. For reference
- * we include their copyright and license:
- *
- * Sun RPC is a product of Sun Microsystems, Inc. and is provided for
- * unrestricted use provided that this legend is included on all tape
- * media and as a part of the software program in whole or part. Users
- * may copy or modify Sun RPC without charge, but are not authorized
- * to license or distribute it to anyone else except as part of a product or
- * program developed by the user.
- *
- * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
- * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
- * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.
- *
- * Sun RPC is provided with no support and without any obligation on the
- * part of Sun Microsystems, Inc. to assist in its use, correction,
- * modification or enhancement.
- *
- * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
- * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
- * OR ANY PART THEREOF.
- *
- * In no event will Sun Microsystems, Inc. be liable for any lost revenue
- * or profits or other special, indirect and consequential damages, even if
- * Sun has been advised of the possibility of such damages.
- *
- * Sun Microsystems, Inc.
- * 2550 Garcia Avenue
- * Mountain View, California 94043
- */
-
-/* INT_MAX is defined in limits.h according to ANSI C */
-#if (INT_MAX > 2147483647)
-# error Error: Cannot use builtin XDR support when size of int
-# error is larger than 4 bytes. Use your system XDR libraries
-# error instead, or modify the source code in xdrfile.c
-#endif /* Check for 4 byte int type */
-
-
-
-
-
-typedef int (*xdrproc_t) (XDR *, void *,...);
-
-#define xdr_getlong(xdrs, longp) \
- (*(xdrs)->x_ops->x_getlong)(xdrs, longp)
-#define xdr_putlong(xdrs, longp) \
- (*(xdrs)->x_ops->x_putlong)(xdrs, longp)
-#define xdr_getbytes(xdrs, addr, len) \
- (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len)
-#define xdr_putbytes(xdrs, addr, len) \
- (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len)
-
-#define BYTES_PER_XDR_UNIT 4
-static char xdr_zero[BYTES_PER_XDR_UNIT] = {0, 0, 0, 0};
-
-static int32_t
-xdr_swapbytes(int32_t x)
-{
- int32_t y,i;
- char *px=(char *)&x;
- char *py=(char *)&y;
-
- for(i=0;i<4;i++)
- py[i]=px[3-i];
-
- return y;
-}
-
-static int32_t
-xdr_htonl(int32_t x)
-{
- int s=0x1234;
- if( *((char *)&s)==(char)0x34) {
- /* smallendian,swap bytes */
- return xdr_swapbytes(x);
- } else {
- /* bigendian, do nothing */
- return x;
- }
-}
-
-static int32_t
-xdr_ntohl(int x)
-{
- int s=0x1234;
- if( *((char *)&s)==(char)0x34) {
- /* smallendian, swap bytes */
- return xdr_swapbytes(x);
- } else {
- /* bigendian, do nothing */
- return x;
- }
-}
-
-static int
-xdr_int (XDR *xdrs, int *ip)
-{
- int32_t i32;
-
- switch (xdrs->x_op)
- {
- case XDR_ENCODE:
- i32 = (int32_t) *ip;
- return xdr_putlong (xdrs, &i32);
-
- case XDR_DECODE:
- if (!xdr_getlong (xdrs, &i32))
- {
- return 0;
- }
- *ip = (int) i32;
- case XDR_FREE:
- return 1;
- }
- return 0;
-}
-
-static int
-xdr_u_int (XDR *xdrs, unsigned int *up)
-{
- uint32_t ui32;
-
- switch (xdrs->x_op)
- {
- case XDR_ENCODE:
- ui32 = (uint32_t) * up;
- return xdr_putlong (xdrs, (int32_t *)&ui32);
-
- case XDR_DECODE:
- if (!xdr_getlong (xdrs, (int32_t *)&ui32))
- {
- return 0;
- }
- *up = (uint32_t) ui32;
- case XDR_FREE:
- return 1;
- }
- return 0;
-}
-
-static int
-xdr_short (XDR *xdrs, short *sp)
-{
- int32_t i32;
-
- switch (xdrs->x_op)
- {
- case XDR_ENCODE:
- i32 = (int32_t) *sp;
- return xdr_putlong (xdrs, &i32);
-
- case XDR_DECODE:
- if (!xdr_getlong (xdrs, &i32))
- {
- return 0;
- }
- *sp = (short) i32;
- return 1;
-
- case XDR_FREE:
- return 1;
- }
- return 0;
-}
-
-static int
-xdr_u_short (XDR *xdrs, unsigned short *sp)
-{
- uint32_t ui32;
-
- switch (xdrs->x_op)
- {
- case XDR_ENCODE:
- ui32 = (uint32_t) *sp;
- return xdr_putlong (xdrs, (int32_t *)&ui32);
-
- case XDR_DECODE:
- if (!xdr_getlong (xdrs, (int32_t *)&ui32))
- {
- return 0;
- }
- *sp = (unsigned short) ui32;
- return 1;
-
- case XDR_FREE:
- return 1;
- }
- return 0;
-}
-
-static int
-xdr_char (XDR *xdrs, char *cp)
-{
- int i;
-
- i = (*cp);
- if (!xdr_int (xdrs, &i))
- {
- return 0;
- }
- *cp = i;
- return 1;
-}
-
-static int
-xdr_u_char (XDR *xdrs, unsigned char *cp)
-{
- unsigned int u;
-
- u = (*cp);
- if (!xdr_u_int (xdrs, &u))
- {
- return 0;
- }
- *cp = u;
- return 1;
-}
-
-/*
- * XDR opaque data
- * Allows the specification of a fixed size sequence of opaque bytes.
- * cp points to the opaque object and cnt gives the byte length.
- */
-static int
-xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
-{
- unsigned int rndup;
- static char crud[BYTES_PER_XDR_UNIT];
-
- /*
- * if no data we are done
- */
- if (cnt == 0)
- return 1;
-
- /*
- * round byte count to full xdr units
- */
- rndup = cnt % BYTES_PER_XDR_UNIT;
- if (rndup > 0)
- rndup = BYTES_PER_XDR_UNIT - rndup;
-
- switch (xdrs->x_op)
- {
- case XDR_DECODE:
- if (!xdr_getbytes (xdrs, cp, cnt))
- {
- return 0;
- }
- if (rndup == 0)
- return 1;
- return xdr_getbytes (xdrs, (char *)crud, rndup);
-
- case XDR_ENCODE:
- if (!xdr_putbytes (xdrs, cp, cnt))
- {
- return 0;
- }
- if (rndup == 0)
- return 1;
- return xdr_putbytes (xdrs, xdr_zero, rndup);
-
- case XDR_FREE:
- return 1;
- }
-#undef BYTES_PER_XDR_UNIT
- return 0;
-}
-
-
-/*
- * XDR null terminated ASCII strings
- */
-static int
-xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
-{
- char *sp = *cpp; /* sp is the actual string pointer */
- unsigned int size;
- unsigned int nodesize;
-
- /*
- * first deal with the length since xdr strings are counted-strings
- */
- switch (xdrs->x_op)
- {
- case XDR_FREE:
- if (sp == NULL)
- {
- return 1; /* already free */
- }
- /* fall through... */
- case XDR_ENCODE:
- if (sp == NULL)
- return 0;
- size = strlen (sp);
- break;
- case XDR_DECODE:
- break;
- }
- if (!xdr_u_int (xdrs, &size))
- {
- return 0;
- }
- if (size > maxsize)
- {
- return 0;
- }
- nodesize = size + 1;
-
- /*
- * now deal with the actual bytes
- */
- switch (xdrs->x_op)
- {
- case XDR_DECODE:
- if (nodesize == 0)
- {
- return 1;
- }
- if (sp == NULL)
- *cpp = sp = (char *) malloc (nodesize);
- if (sp == NULL)
- {
- (void) fputs ("xdr_string: out of memory\n", stderr);
- return 0;
- }
- sp[size] = 0;
- /* fall into ... */
-
- case XDR_ENCODE:
- return xdr_opaque (xdrs, sp, size);
-
- case XDR_FREE:
- free (sp);
- *cpp = NULL;
- return 1;
- }
- return 0;
-}
-
-
-
-/* Floating-point stuff */
-
-static int
-xdr_float(XDR *xdrs, float *fp)
-{
- switch (xdrs->x_op) {
-
- case XDR_ENCODE:
- if (sizeof(float) == sizeof(int32_t))
- return (xdr_putlong(xdrs, (int32_t *)fp));
- else if (sizeof(float) == sizeof(int)) {
- int32_t tmp = *(int *)fp;
- return (xdr_putlong(xdrs, &tmp));
- }
- break;
-
- case XDR_DECODE:
- if (sizeof(float) == sizeof(int32_t))
- return (xdr_getlong(xdrs, (int32_t *)fp));
- else if (sizeof(float) == sizeof(int)) {
- int32_t tmp;
- if (xdr_getlong(xdrs, &tmp)) {
- *(int *)fp = tmp;
- return (1);
- }
- }
- break;
-
- case XDR_FREE:
- return (1);
- }
- return (0);
-}
-
-
-static int
-xdr_double(XDR *xdrs, double *dp)
-{
- /* Gromacs detects floating-point stuff at compile time, which is faster */
-#ifdef GROMACS
-# ifndef FLOAT_FORMAT_IEEE754
-# error non-IEEE floating point system, or you defined GROMACS yourself...
-# endif
- int LSW;
-# ifdef IEEE754_BIG_ENDIAN_WORD_ORDER
- int LSW=1;
-# else
- int LSW=0;
-# endif /* Big endian word order */
-#else
- /* Outside Gromacs we rely on dynamic detection of FP order. */
- int LSW; /* Least significant fp word */
-
- double x=0.987654321; /* Just a number */
- unsigned char ix = *((char *)&x);
-
- /* Possible representations in IEEE double precision:
- * (S=small endian, B=big endian)
- *
- * Byte order, Word order, Hex
- * S S b8 56 0e 3c dd 9a ef 3f
- * B S 3c 0e 56 b8 3f ef 9a dd
- * S B dd 9a ef 3f b8 56 0e 3c
- * B B 3f ef 9a dd 3c 0e 56 b8
- */
- if(ix==0xdd || ix==0x3f)
- LSW=1; /* Big endian word order */
- else if(ix==0xb8 || ix==0x3c)
- LSW=0; /* Small endian word order */
- else { /* Catch strange errors */
- fprintf(stderr,"Cannot detect floating-point word order.\n"
- "Do you have a non-IEEE system?\n"
- "Use system XDR libraries or fix xdr_double().\n");
- abort();
- }
-#endif /* end of dynamic detection of fp word order */
-
- switch (xdrs->x_op) {
-
- case XDR_ENCODE:
- if (2*sizeof(int32_t) == sizeof(double)) {
- int32_t *lp = (int32_t *)dp;
- return (xdr_putlong(xdrs, lp+!LSW) &&
- xdr_putlong(xdrs, lp+LSW));
- } else if (2*sizeof(int) == sizeof(double)) {
- int *ip = (int *)dp;
- int32_t tmp[2];
- tmp[0] = ip[!LSW];
- tmp[1] = ip[LSW];
- return (xdr_putlong(xdrs, tmp) &&
- xdr_putlong(xdrs, tmp+1));
- }
- break;
-
- case XDR_DECODE:
- if (2*sizeof(int32_t) == sizeof(double)) {
- int32_t *lp = (int32_t *)dp;
- return (xdr_getlong(xdrs, lp+!LSW) &&
- xdr_getlong(xdrs, lp+LSW));
- } else if (2*sizeof(int) == sizeof(double)) {
- int *ip = (int *)dp;
- int32_t tmp[2];
- if (xdr_getlong(xdrs, tmp+!LSW) &&
- xdr_getlong(xdrs, tmp+LSW)) {
- ip[0] = tmp[0];
- ip[1] = tmp[1];
- return (1);
- }
- }
- break;
-
- case XDR_FREE:
- return (1);
- }
- return (0);
-}
-
-
-static int xdrstdio_getlong (XDR *, int32_t *);
-static int xdrstdio_putlong (XDR *, int32_t *);
-static int xdrstdio_getbytes (XDR *, char *, unsigned int);
-static int xdrstdio_putbytes (XDR *, char *, unsigned int);
-static off_t xdrstdio_getpos (XDR *);
-static int xdrstdio_setpos (XDR *, off_t, int);
-static void xdrstdio_destroy (XDR *);
-
-/*
- * Ops vector for stdio type XDR
- */
-static const struct xdr_ops xdrstdio_ops =
- {
- xdrstdio_getlong, /* deserialize a long int */
- xdrstdio_putlong, /* serialize a long int */
- xdrstdio_getbytes, /* deserialize counted bytes */
- xdrstdio_putbytes, /* serialize counted bytes */
- xdrstdio_getpos, /* get offset in the stream */
- xdrstdio_setpos, /* set offset in the stream */
- xdrstdio_destroy, /* destroy stream */
- };
-
-/*
- * Initialize a stdio xdr stream.
- * Sets the xdr stream handle xdrs for use on the stream file.
- * Operation flag is set to op.
- */
-static void
-xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)
-{
- xdrs->x_op = op;
-
- xdrs->x_ops = (struct xdr_ops *) &xdrstdio_ops;
- xdrs->x_private = (char *) file;
-}
-
-/*
- * Destroy a stdio xdr stream.
- * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create.
- */
-static void
-xdrstdio_destroy (XDR *xdrs)
-{
- (void) fflush ((FILE *) xdrs->x_private);
- /* xx should we close the file ?? */
-}
-
-static int
-xdrstdio_getlong (XDR *xdrs, int32_t *lp)
-{
- int32_t mycopy;
-
- if (fread ((char *) & mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
- return 0;
- *lp = (int32_t) xdr_ntohl (mycopy);
- return 1;
-}
-
-static int
-xdrstdio_putlong (XDR *xdrs, int32_t *lp)
-{
- int32_t mycopy = xdr_htonl (*lp);
- lp = &mycopy;
- if (fwrite ((char *) lp, 4, 1, (FILE *) xdrs->x_private) != 1)
- return 0;
- return 1;
-}
-
-static int
-xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
-{
- if ((len != 0) && (fread (addr, (int) len, 1,
- (FILE *) xdrs->x_private) != 1))
- return 0;
- return 1;
-}
-
-static int
-xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
-{
- if ((len != 0) && (fwrite (addr, (int) len, 1,
- (FILE *) xdrs->x_private) != 1))
- return 0;
- return 1;
-}
-
-
-static off_t
-xdrstdio_getpos (XDR *xdrs)
-{
- return ftello((FILE *) xdrs->x_private);
-}
-
-static int
-xdrstdio_setpos (XDR *xdrs, off_t pos, int whence)
-{
- return fseeko((FILE *) xdrs->x_private, pos, whence) < 0 ? exdrNR : exdrOK;
-}
-
-
-int64_t xdr_tell(XDRFILE *xd)
-/* Reads position in file */
-{
- return (int64_t)xdrstdio_getpos(xd->xdr);
-}
-
-int xdr_seek(XDRFILE *xd, int64_t pos, int whence)
-/* Seeks to position in file */
-{
- int result;
- if ((result = xdrstdio_setpos(xd->xdr, (off_t) pos, whence)) != exdrOK)
- return result;
-
- return exdrOK;
-}
-
-
-#endif /* HAVE_RPC_XDR_H not defined */
diff --git a/pymolfile/libpymolfile-old/xdrfile.h b/pymolfile/libpymolfile-old/xdrfile.h
deleted file mode 100644
index 1d1d6c5d90e0b7cd11726e2f2721011c6e4180c1..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile.h
+++ /dev/null
@@ -1,631 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-/*! \file xdrfile.h
- * \brief Interface to read/write portabile binary files using XDR.
- *
- * This file provides an interface to read & write portably binary files,
- * using XDR - the external data representation standard defined in RFC 1014.
- *
- * There are several advantages to the XDR approach:
- *
- * -# It is portable. And not just portable between big/small integer endian,
- * but truly portable if you have system XDR routines. For example:
- * - It doesn't matter if the character representation is ASCII or EBCDIC.
- * - Some systems are small endian but use big endian order of the two
- * dword in a double precision floating-point variable. The system XDR
- * libraries will read/write this correctly.
- * - Some systems (VAX...) don't use IEEE floating point. Their system
- * XDR libraries will convert to/from this automatically.
- * -# XDR libraries are required for NFS and lots of other network functions.
- * This means there isn't a single Unix-like system that doesn't have them.
- * -# There is NO extra metadata whatsoever, and we write plain XDR files.
- * If you write a float, it will take exactly 4 bytes in the file.
- * (All basic datatypes are 4 bytes, double fp 8 bytes).
- * -# You can read/write the files by calling the system XDR routines directly
- * too - you don't have to use the routines defined in this file.
- * -# It is no problem if your system doesn't have XDR libraries (MS Windows).
- * We have written our own versions of the necessary routines that work if
- * your system uses ASCII for strings and IEEE floating-point. All types
- * of byte and dword endian for integer and floating-point are supported.
- * -# You can use these routines for any type of data, but since we designed
- * them for Gromacs we also provide a special routine to write coordinates
- * with (adjustable) lossy compression. The default precision will give you
- * three decimals guaranteed accuracy, and reduces the filesize to 1/10th
- * of normal binary data.
- *
- * We do not support getting or setting positions in XDR files, since it can
- * break in horrible ways for large (64-bit) files, resulting in silent data
- * corruption. Note that it works great to open/read/write 64-bit files if
- * your system supports it; it is just the random access we cannot trust!
- *
- * We also provide wrapper routines so this module can be used from FORTRAN -
- * see the file xdrfile_fortran.txt in the Gromacs distribution for
- * documentation on the FORTRAN interface!
- */
-
-
-#ifndef _XDRFILE_H_
-#define _XDRFILE_H_
-
-#ifdef __cplusplus
-extern "C"
-{
-#endif
-
- /*! \brief Abstract datatype for an portable binary file handle
- *
- * This datatype essentially works just like the standard FILE type in C.
- * The actual contents is hidden in the implementation, so you can only
- * define pointers to it, for use with the xdrfile routines.
- *
- * If you \a really need to see the definition it is in xdrfile.c, but you
- * cannot access elements of the structure outside that file.
- *
- * \warning The implementation is completely different from the C standard
- * library FILE, so don't even think about using an XDRFILE pointer as an
- * argument to a routine that needs a standard FILE pointer.
- */
- typedef struct XDRFILE XDRFILE;
-
- enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
- exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
- exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
-
- extern char *exdr_message[exdrNR];
-
-#define DIM 3
- typedef float matrix[DIM][DIM];
- typedef float rvec[DIM];
- typedef int mybool;
-
-
- /*! \brief Open a portable binary file, just like fopen()
- *
- * Use this routine much like calls to the standard library function
- * fopen(). The only difference is that the returned pointer should only
- * be used with routines defined in this header.
- *
- * \param path Full or relative path (including name) of the file
- * \param mode "r" for reading, "w" for writing, "a" for append.
- *
- * \return Pointer to abstract xdr file datatype, or NULL if an error occurs.
- *
- */
- XDRFILE *
- xdrfile_open (const char * path,
- const char * mode);
-
-
- /*! \brief Close a previously opened portable binary file, just like fclose()
- *
- * Use this routine much like calls to the standard library function
- * fopen(). The only difference is that it is used for an XDRFILE handle
- * instead of a FILE handle.
- *
- * \param xfp Pointer to an abstract XDRFILE datatype
- *
- * \return 0 on success, non-zero on error.
- */
- int
- xdrfile_close (XDRFILE * xfp);
-
-
-
-
- /*! \brief Read one or more \a char type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of characters to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of characters read
- */
- int
- xdrfile_read_char(char * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a characters type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of characters to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of characters written
- */
- int
- xdrfile_write_char(char * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read one or more \a unsigned \a char type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of unsigned characters to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned characters read
- */
- int
- xdrfile_read_uchar(unsigned char * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a unsigned \a characters type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of unsigned characters to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned characters written
- */
- int
- xdrfile_write_uchar(unsigned char * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read one or more \a short type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of shorts to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of shorts read
- */
- int
- xdrfile_read_short(short * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a short type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of shorts to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of shorts written
- */
- int
- xdrfile_write_short(short * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read one or more \a unsigned \a short type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of unsigned shorts to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned shorts read
- */
- int
- xdrfile_read_ushort(unsigned short * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a unsigned \a short type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of unsigned shorts to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned shorts written
- */
- int
- xdrfile_write_ushort(unsigned short * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
- /*! \brief Read one or more \a integer type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of integers to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of integers read
- *
- * The integer data type is assumed to be less than or equal to 32 bits.
- *
- * We do not provide any routines for reading/writing 64-bit integers, since
- * - Not all XDR implementations support it
- * - Not all machines have 64-bit integers
- *
- * Split your 64-bit data into two 32-bit integers for portability!
- */
- int
- xdrfile_read_int(int * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a integer type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of integers to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of integers written
- *
- * The integer data type is assumed to be less than or equal to 32 bits.
- *
- * We do not provide any routines for reading/writing 64-bit integers, since
- * - Not all XDR implementations support it
- * - Not all machines have 64-bit integers
- *
- * Split your 64-bit data into two 32-bit integers for portability!
- */
- int
- xdrfile_write_int(int * ptr,
- int ndata,
- XDRFILE * xfp);
-
- /*! \brief Read one or more \a unsigned \a integers type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of unsigned integers to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned integers read
- *
- * The integer data type is assumed to be less than or equal to 32 bits.
- *
- * We do not provide any routines for reading/writing 64-bit integers, since
- * - Not all XDR implementations support it
- * - Not all machines have 64-bit integers
- *
- * Split your 64-bit data into two 32-bit integers for portability!
- */
- int
- xdrfile_read_uint(unsigned int * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a unsigned \a integer type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of unsigned integers to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of unsigned integers written
- *
- * The integer data type is assumed to be less than or equal to 32 bits.
- *
- * We do not provide any routines for reading/writing 64-bit integers, since
- * - Not all XDR implementations support it
- * - Not all machines have 64-bit integers
- *
- * Split your 64-bit data into two 32-bit integers for portability!
- */
- int
- xdrfile_write_uint(unsigned int * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read one or more \a float type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of floats to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of floats read
- */
- int
- xdrfile_read_float(float * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a float type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of floats to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of floats written
- */
- int
- xdrfile_write_float(float * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read one or more \a double type variable(s)
- *
- * \param ptr Pointer to memory where data should be written
- * \param ndata Number of doubles to read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of doubles read
- */
- int
- xdrfile_read_double(double * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write one or more \a double type variable(s)
- *
- * \param ptr Pointer to memory where data should be read
- * \param ndata Number of double to write.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of doubles written
- */
- int
- xdrfile_write_double(double * ptr,
- int ndata,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read a string (array of characters)
- *
- * \param ptr Pointer to memory where data should be written
- * \param maxlen Maximum length of string. If no end-of-string is encountered,
- * one byte less than this is read and end-of-string appended.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of characters read, including end-of-string
- */
- int
- xdrfile_read_string(char * ptr,
- int maxlen,
- XDRFILE * xfp);
-
-
-
- /*! \brief Write a string (array of characters)
- *
- * \param ptr Pointer to memory where data should be read
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of characters written, including end-of-string
- */
- int
- xdrfile_write_string(char * ptr,
- XDRFILE * xfp);
-
-
-
- /*! \brief Read raw bytes from file (unknown datatype)
- *
- * \param ptr Pointer to memory where data should be written
- * \param nbytes Number of bytes to read. No conversion whatsoever is done.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of bytes read from file
- */
- int
- xdrfile_read_opaque(char * ptr,
- int nbytes,
- XDRFILE * xfp);
-
-
-
-
- /*! \brief Write raw bytes to file (unknown datatype)
- *
- * \param ptr Pointer to memory where data should be read
- * \param nbytes Number of bytes to write. No conversion whatsoever is done.
- * \param xfp Handle to portable binary file, created with xdrfile_open()
- *
- * \return Number of bytes written to file
- */
- int
- xdrfile_write_opaque(char * ptr,
- int nbytes,
- XDRFILE * xfp);
-
-
-
-
-
-
- /*! \brief Compress coordiates in a float array to XDR file
- *
- * This routine will perform \a lossy compression on the three-dimensional
- * coordinate data data specified and store it in the XDR file.
- *
- * The lossy part of the compression consists of multiplying each
- * coordinate with the precision argument and then rounding to integers.
- * We suggest a default value of 1000.0, which means you are guaranteed
- * three decimals of accuracy. The only limitation is that scaled coordinates
- * must still fit in an integer variable, so if the precision is 1000.0 the
- * coordinate magnitudes must be less than +-2e6.
- *
- * \param ptr Pointer to coordinates to compress (length 3*ncoord)
- * \param ncoord Number of coordinate triplets in data
- * \param precision Scaling factor for lossy compression. If it is <=0,
- * the default value of 1000.0 is used.
- * \param xfp Handle to portably binary file
- *
- * \return Number of coordinate triplets written.
- * IMPORTANT: Check that this is equal to ncoord - if it is
- * negative, an error occured. This should not happen with
- * normal data, but if your coordinates are NaN or very
- * large (>1e6) it is not possible to use the compression.
- *
- * \warning The compression algorithm is not part of the XDR standard,
- * and very complicated, so you will need this xdrfile module
- * to read it later.
- */
- int
- xdrfile_compress_coord_float(float * ptr,
- int ncoord,
- float precision,
- XDRFILE * xfp);
-
-
-
-
- /*! \brief Decompress coordiates from XDR file to array of floats
- *
- * This routine will decompress three-dimensional coordinate data previously
- * stored in an XDR file and store it in the specified array of floats.
- *
- * The precision used during the earlier compression is read from the file
- * and returned - you cannot adjust the accuracy at this stage.
- *
- * \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
- * \param ncoord Max number of coordinate triplets to read on input, actual
- * number of coordinate triplets read on return. If this
- * is smaller than the number of coordinates in the frame an
- * error will occur.
- * \param precision The precision used in the previous compression will be
- * written to this variable on return.
- * \param xfp Handle to portably binary file
- *
- * \return Number of coordinate triplets read. If this is negative,
- * an error occured.
- *
- * \warning Since we cannot count on being able to set/get the
- * position of large files (>2Gb), it is not possible to
- * recover from errors by re-reading the frame if the
- * storage area you provided was too small. To avoid this
- * from happening, we recommend that you store the number of
- * coordinates triplet as an integer either in a header or
- * just before the compressed coordinate data, so you can
- * read it first and allocated enough memory.
- */
- int
- xdrfile_decompress_coord_float(float * ptr,
- int * ncoord,
- float * precision,
- XDRFILE * xfp);
-
-
-
-
- /*! \brief Compress coordiates in a double array to XDR file
- *
- * This routine will perform \a lossy compression on the three-dimensional
- * coordinate data data specified and store it in the XDR file. Double will
- * NOT give you any extra precision since the coordinates are compressed. This
- * routine just avoids allocating a temporary array of floats.
- *
- * The lossy part of the compression consists of multiplying each
- * coordinate with the precision argument and then rounding to integers.
- * We suggest a default value of 1000.0, which means you are guaranteed
- * three decimals of accuracy. The only limitation is that scaled coordinates
- * must still fit in an integer variable, so if the precision is 1000.0 the
- * coordinate magnitudes must be less than +-2e6.
- *
- * \param ptr Pointer to coordinates to compress (length 3*ncoord)
- * \param ncoord Number of coordinate triplets in data
- * \param precision Scaling factor for lossy compression. If it is <=0, the
- * default value of 1000.0 is used.
- * \param xfp Handle to portably binary file
- *
- * \return Number of coordinate triplets written.
- * IMPORTANT: Check that this is equal to ncoord - if it is
- * negative, an error occured. This should not happen with
- * normal data, but if your coordinates are NaN or very
- * large (>1e6) it is not possible to use the compression.
- *
- * \warning The compression algorithm is not part of the XDR standard,
- * and very complicated, so you will need this xdrfile module
- * to read it later.
- */
- int
- xdrfile_compress_coord_double(double * ptr,
- int ncoord,
- double precision,
- XDRFILE * xfp);
-
-
-
-
- /*! \brief Decompress coordiates from XDR file to array of doubles
- *
- * This routine will decompress three-dimensional coordinate data previously
- * stored in an XDR file and store it in the specified array of doubles.
- * Double will NOT give you any extra precision since the coordinates are
- * compressed. This routine just avoids allocating a temporary array of floats.
- *
- * The precision used during the earlier compression is read from the file
- * and returned - you cannot adjust the accuracy at this stage.
- *
- * \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
- * \param ncoord Max number of coordinate triplets to read on input, actual
- * number of coordinate triplets read on return. If this
- * is smaller than the number of coordinates in the frame an
- * error will occur.
- * \param precision The precision used in the previous compression will be
- * written to this variable on return.
- * \param xfp Handle to portably binary file
- *
- * \return Number of coordinate triplets read. If this is negative,
- * an error occured.
- *
- * \warning Since we cannot count on being able to set/get the
- * position of large files (>2Gb), it is not possible to
- * recover from errors by re-reading the frame if the
- * storage area you provided was too small. To avoid this
- * from happening, we recommend that you store the number of
- * coordinates triplet as an integer either in a header or
- * just before the compressed coordinate data, so you can
- * read it first and allocated enough memory.
- */
- int
- xdrfile_decompress_coord_double(double * ptr,
- int * ncoord,
- double * precision,
- XDRFILE * xfp);
-
- int64_t xdr_tell(XDRFILE *xd);
- int xdr_seek(XDRFILE *xd, int64_t pos, int whence);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _XDRFILE_H_ */
-
diff --git a/pymolfile/libpymolfile-old/xdrfile_trr.c b/pymolfile/libpymolfile-old/xdrfile_trr.c
deleted file mode 100644
index 17597699486d69c31969f46f5d8b69ac0cc4fde3..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile_trr.c
+++ /dev/null
@@ -1,577 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-
-#include "xdrfile.h"
-#include "xdrfile_trr.h"
-
-#define BUFSIZE 128
-#define GROMACS_MAGIC 1993
-
-typedef struct /* This struct describes the order and the */
-/* sizes of the structs in a trjfile, sizes are given in bytes. */
-{
- mybool bDouble; /* Double precision? */
- int ir_size; /* Backward compatibility */
- int e_size; /* Backward compatibility */
- int box_size; /* Non zero if a box is present */
- int vir_size; /* Backward compatibility */
- int pres_size; /* Backward compatibility */
- int top_size; /* Backward compatibility */
- int sym_size; /* Backward compatibility */
- int x_size; /* Non zero if coordinates are present */
- int v_size; /* Non zero if velocities are present */
- int f_size; /* Non zero if forces are present */
-
- int natoms; /* The total number of atoms */
- int step; /* Current step number */
- int nre; /* Backward compatibility */
- float tf; /* Current time */
- float lambdaf; /* Current value of lambda */
- double td; /* Current time */
- double lambdad; /* Current value of lambda */
-} t_trnheader;
-
-static int nFloatSize(t_trnheader *sh,int *nflsz)
-{
- int nflsize=0;
-
- if (sh->box_size)
- nflsize = sh->box_size/(DIM*DIM);
- else if (sh->x_size)
- nflsize = sh->x_size/(sh->natoms*DIM);
- else if (sh->v_size)
- nflsize = sh->v_size/(sh->natoms*DIM);
- else if (sh->f_size)
- nflsize = sh->f_size/(sh->natoms*DIM);
- else
- return exdrHEADER;
-
- if (((nflsize != sizeof(float)) && (nflsize != sizeof(double))))
- return exdrHEADER;
-
- *nflsz = nflsize;
-
- return exdrOK;
-}
-
-static int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh)
-{
- int magic=GROMACS_MAGIC;
- int nflsz,slen,result;
- char *version = "GMX_trn_file";
- char buf[BUFSIZE];
-
- if (xdrfile_read_int(&magic,1,xd) != 1)
- return exdrINT;
-
- if (bRead)
- {
- if (xdrfile_read_int(&slen,1,xd) != 1)
- return exdrINT;
- if (slen != strlen(version)+1)
- return exdrSTRING;
- if (xdrfile_read_string(buf,BUFSIZE,xd) <= 0)
- return exdrSTRING;
- }
- else
- {
- slen = strlen(version)+1;
- if (xdrfile_read_int(&slen,1,xd) != 1)
- return exdrINT;
- if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
- return exdrSTRING;
- }
- if (xdrfile_read_int(&sh->ir_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->e_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->box_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->vir_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->pres_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->top_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->sym_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->x_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->v_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->f_size,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->natoms,1,xd) != 1)
- return exdrINT;
-
- if ((result = nFloatSize(sh,&nflsz)) != exdrOK)
- return result;
- sh->bDouble = (nflsz == sizeof(double));
-
- if (xdrfile_read_int(&sh->step,1,xd) != 1)
- return exdrINT;
- if (xdrfile_read_int(&sh->nre,1,xd) != 1)
- return exdrINT;
- if (sh->bDouble)
- {
- if (xdrfile_read_double(&sh->td,1,xd) != 1)
- return exdrDOUBLE;
- sh->tf = sh->td;
- if (xdrfile_read_double(&sh->lambdad,1,xd) != 1)
- return exdrDOUBLE;
- sh->lambdaf = sh->lambdad;
- }
- else
- {
- if (xdrfile_read_float(&sh->tf,1,xd) != 1)
- return exdrFLOAT;
- sh->td = sh->tf;
- if (xdrfile_read_float(&sh->lambdaf,1,xd) != 1)
- return exdrFLOAT;
- sh->lambdad = sh->lambdaf;
- }
-
- return exdrOK;
-}
-
-static int do_htrn(XDRFILE *xd,mybool bRead,t_trnheader *sh,
- matrix box,rvec *x,rvec *v,rvec *f)
-{
- double pvd[DIM*DIM];
- double *dx=NULL;
- float pvf[DIM*DIM];
- float *fx=NULL;
- int i,j;
-
- if (sh->bDouble)
- {
- if (sh->box_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<DIM); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != box)
- {
- pvd[i*DIM+j] = box[i][j];
- }
- }
- if (xdrfile_read_double(pvd,DIM*DIM,xd) == DIM*DIM)
- {
- for(i=0; (i<DIM); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != box)
- {
- box[i][j] = pvd[i*DIM+j];
- }
- }
- else
- return exdrDOUBLE;
- }
-
- if (sh->vir_size != 0)
- {
- if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM)
- return exdrDOUBLE;
- }
-
- if (sh->pres_size!= 0)
- {
- if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM)
- return exdrDOUBLE;
- }
-
- if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
- dx = (double *)calloc(sh->natoms*DIM,sizeof(dx[0]));
- if (NULL == dx)
- return exdrNOMEM;
- }
- if (sh->x_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- dx[i*DIM+j] = x[i][j];
- }
- }
- if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- if (bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- x[i][j] = dx[i*DIM+j];
- }
- }
- }
- else
- return exdrDOUBLE;
- }
- if (sh->v_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- dx[i*DIM+j] = v[i][j];
- }
- }
- if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != v)
- {
- v[i][j] = dx[i*DIM+j];
- }
- }
- else
- return exdrDOUBLE;
- }
- if (sh->f_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- dx[i*DIM+j] = f[i][j];
- }
- }
- if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- for(i=0; (i<sh->natoms); i++)
- {
- for(j=0; (j<DIM); j++)
- {
- if (NULL != f)
- {
- f[i][j] = dx[i*DIM+j];
- }
- }
- }
- }
- else
- return exdrDOUBLE;
- }
- if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
- free(dx);
- }
- }
- else
- /* Float */
- {
- if (sh->box_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<DIM); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != box)
- {
- pvf[i*DIM+j] = box[i][j];
- }
- }
- if (xdrfile_read_float(pvf,DIM*DIM,xd) == DIM*DIM)
- {
- for(i=0; (i<DIM); i++)
- {
- for(j=0; (j<DIM); j++)
- {
- if (NULL != box)
- {
- box[i][j] = pvf[i*DIM+j];
- }
- }
- }
- }
- else
- return exdrFLOAT;
- }
-
- if (sh->vir_size != 0)
- {
- if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM)
- return exdrFLOAT;
- }
-
- if (sh->pres_size!= 0)
- {
- if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM)
- return exdrFLOAT;
- }
-
- if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
- fx = (float *)calloc(sh->natoms*DIM,sizeof(fx[0]));
- if (NULL == fx)
- return exdrNOMEM;
- }
- if (sh->x_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- fx[i*DIM+j] = x[i][j];
- }
- }
- if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- if (bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- x[i][j] = fx[i*DIM+j];
- }
- }
- else
- return exdrFLOAT;
- }
- if (sh->v_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- fx[i*DIM+j] = v[i][j];
- }
- }
- if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != v)
- v[i][j] = fx[i*DIM+j];
- }
- else
- return exdrFLOAT;
- }
- if (sh->f_size != 0)
- {
- if (!bRead)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != x)
- {
- fx[i*DIM+j] = f[i][j];
- }
- }
- if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
- {
- for(i=0; (i<sh->natoms); i++)
- for(j=0; (j<DIM); j++)
- if (NULL != f)
- f[i][j] = fx[i*DIM+j];
- }
- else
- return exdrFLOAT;
- }
- if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
- free(fx);
- }
- }
- return exdrOK;
-}
-
-static int do_trn(XDRFILE *xd,mybool bRead,int *step,float *t,float *lambda,
- matrix box,int *natoms,rvec *x,rvec *v,rvec *f, int *has_prop)
-{
- t_trnheader *sh;
- int result;
-
- sh = (t_trnheader *)calloc(1,sizeof(*sh));
-
- if (!bRead) {
- sh->box_size = (NULL != box) ? sizeof(matrix):0;
- sh->x_size = ((NULL != x) ? (*natoms*sizeof(x[0])):0);
- sh->v_size = ((NULL != v) ? (*natoms*sizeof(v[0])):0);
- sh->f_size = ((NULL != f) ? (*natoms*sizeof(f[0])):0);
- sh->natoms = *natoms;
- sh->step = *step;
- sh->nre = 0;
- sh->td = *t;
- sh->lambdad = *lambda;
- sh->tf = *t;
- sh->lambdaf = *lambda;
- }
- if ((result = do_trnheader(xd,bRead,sh)) != exdrOK)
- return result;
- if (bRead) {
- *natoms = sh->natoms;
- *step = sh->step;
- *t = sh->td;
- *lambda = sh->lambdad;
- /* Flag what we read */
- if (sh->x_size)
- *has_prop |= HASX;
- if (sh->v_size)
- *has_prop |= HASV;
- if (sh->f_size)
- *has_prop |= HASF;
- }
- if ((result = do_htrn(xd,bRead,sh,box,x,v,f)) != exdrOK)
- return result;
-
- free(sh);
-
- return exdrOK;
-}
-
-/************************************************************
- *
- * The following routines are the exported ones
- *
- ************************************************************/
-
-int read_trr_natoms(char *fn,int *natoms)
-{
- XDRFILE *xd;
- t_trnheader sh;
- int result;
-
- xd = xdrfile_open(fn,"r");
- if (NULL == xd)
- return exdrFILENOTFOUND;
- if ((result = do_trnheader(xd,1,&sh)) != exdrOK)
- return result;
- xdrfile_close(xd);
- *natoms = sh.natoms;
-
- return exdrOK;
-}
-
-int read_trr_numframes(char *fn, int *numframes, int64_t **offsets)
-{
- XDRFILE *xd;
- t_trnheader sh;
- float time, lambda;
- int result, framebytes, est_nframes, totalframebytes;
- int64_t filesize, frame_offset;
-
- if ((xd = xdrfile_open(fn,"r"))==NULL)
- return exdrFILENOTFOUND;
- if (xdr_seek(xd, 0L, SEEK_END) != exdrOK)
- {
- xdrfile_close(xd);
- return exdrNR;
- }
- filesize = xdr_tell(xd);
- if (xdr_seek(xd, 0L, SEEK_SET) != exdrOK)
- {
- xdrfile_close(xd);
- return exdrNR;
- }
-
- if ((result = do_trnheader(xd,1,&sh)) != exdrOK)
- {
- xdrfile_close(xd);
- return result;
- }
-
- framebytes = sh.ir_size + sh.e_size + sh.box_size +
- sh.vir_size + sh.pres_size + sh.top_size +
- sh.sym_size + sh.x_size + sh.v_size + sh.f_size;
-
- est_nframes = (int) (filesize/((int64_t) (framebytes + TRR_MIN_HEADER_SIZE)) + 1); // add one because it'd be easy to underestimate low frame numbers.
- est_nframes += est_nframes/5;
-
- /* Allocate memory for the frame index array */
- if ((*offsets=(int64_t *)malloc(sizeof(int64_t)*est_nframes))==NULL)
- {
- xdrfile_close(xd);
- return exdrNOMEM;
- }
-
- (*offsets)[0] = 0L;
- *numframes = 1;
- while (1)
- {
- if (xdr_seek(xd, (int64_t) (framebytes), SEEK_CUR) != exdrOK) {
- free(*offsets);
- xdrfile_close(xd);
- return exdrNR;
- }
- frame_offset = xdr_tell(xd); /* Store it now, before we read the header */
- if ((result = do_trnheader(xd,1,&sh)) != exdrOK) /* Interpreting as EOF */
- break;
- /* Read was successful; this is another frame */
- /* Check if we need to enlarge array */
- if (*numframes == est_nframes){
- est_nframes += est_nframes/5 + 1; // Increase in 20% stretches
- if ((*offsets = realloc(*offsets, sizeof(int64_t)*est_nframes))==NULL)
- {
- xdrfile_close(xd);
- return exdrNOMEM;
- }
- }
- (*offsets)[*numframes] = frame_offset;
- (*numframes)++;
- /* Calculate how much to skip this time */
- framebytes = sh.ir_size + sh.e_size + sh.box_size +
- sh.vir_size + sh.pres_size + sh.top_size +
- sh.sym_size + sh.x_size + sh.v_size + sh.f_size;
- }
- xdrfile_close(xd);
- return exdrOK;
-}
-
-
-int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,
- matrix box,rvec *x,rvec *v,rvec *f)
-{
- int *plcholder;
- return do_trn(xd,0,&step,&t,&lambda,box,&natoms,x,v,f, plcholder);
-}
-
-int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,
- matrix box,rvec *x,rvec *v,rvec *f, int *has_prop)
-{
- return do_trn(xd,1,step,t,lambda,box,&natoms,x,v,f,has_prop);
-}
-
diff --git a/pymolfile/libpymolfile-old/xdrfile_trr.h b/pymolfile/libpymolfile-old/xdrfile_trr.h
deleted file mode 100644
index f3dc01c8a0c4f765408bd0f42f11f406a1ec40e7..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile_trr.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-#ifndef _xdrfile_trr_h
-#define _xdrfile_trr_h
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include "xdrfile.h"
-
- /* All functions return exdrOK if succesfull.
- * (error codes defined in xdrfile.h).
- */
-
- /* This function returns the number of atoms in the xtc file in *natoms */
- extern int read_trr_natoms(char *fn,int *natoms);
-
- /* Skip through trajectory, reading headers, obtain the total number of frames in the trr */
- extern int read_trr_numframes(char *fn, int *numframes, int64_t **offsets);
-
- /* Read one frame of an open trr file. If either of x,v,f,box are
- NULL the arrays will be read from the file but not used. */
- extern int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,
- matrix box,rvec *x,rvec *v,rvec *f, int *has_prop);
-
- /* Write a frame to trr file */
- extern int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,
- matrix box,rvec *x,rvec *v,rvec *f);
-
-/* Minimum TRR header size. It can have 8 bytes more if we have double time and lambda. */
-#define TRR_MIN_HEADER_SIZE 54
-#define TRR_DOUBLE_XTRA_HEADER 8
-
-/* Flags to signal the update of pos/vel/forces */
-#define HASX 1
-#define HASV 2
-#define HASF 4
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/pymolfile/libpymolfile-old/xdrfile_xtc.c b/pymolfile/libpymolfile-old/xdrfile_xtc.c
deleted file mode 100644
index 58a65eb6d3c009afb1cc2538aa1a5dbab7072aea..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile_xtc.c
+++ /dev/null
@@ -1,230 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include "xdrfile.h"
-#include "xdrfile_xtc.h"
-
-#define MAGIC 1995
-
-enum { FALSE, TRUE };
-
-static int xtc_header(XDRFILE *xd,int *natoms,int *step,float *time,mybool bRead)
-{
- int result,magic,n=1;
-
- /* Note: read is same as write. He he he */
- magic = MAGIC;
- if ((result = xdrfile_write_int(&magic,n,xd)) != n)
- {
- if (bRead)
- return exdrENDOFFILE;
- else
- return exdrINT;
- }
- if (magic != MAGIC)
- return exdrMAGIC;
- if ((result = xdrfile_write_int(natoms,n,xd)) != n)
- return exdrINT;
- if ((result = xdrfile_write_int(step,n,xd)) != n)
- return exdrINT;
- if ((result = xdrfile_write_float(time,n,xd)) != n)
- return exdrFLOAT;
-
- return exdrOK;
-}
-
-static int xtc_coord(XDRFILE *xd,int *natoms,matrix box,rvec *x,float *prec,
- mybool bRead)
-{
- int result;
-
- /* box */
- result = xdrfile_read_float(box[0],DIM*DIM,xd);
- if (DIM*DIM != result)
- return exdrFLOAT;
- else
- {
- if (bRead)
- {
- result = xdrfile_decompress_coord_float(x[0],natoms,prec,xd);
- if (result != *natoms)
- return exdr3DX;
- }
- else
- {
- result = xdrfile_compress_coord_float(x[0],*natoms,*prec,xd);
- if (result != *natoms)
- return exdr3DX;
- }
- }
- return exdrOK;
-}
-
-int read_xtc_natoms(char *fn,int *natoms)
-{
- XDRFILE *xd;
- int step,result;
- float time;
-
- xd = xdrfile_open(fn,"r");
- if (NULL == xd)
- return exdrFILENOTFOUND;
- result = xtc_header(xd,natoms,&step,&time,TRUE);
- xdrfile_close(xd);
-
- return result;
-}
-
-int read_xtc(XDRFILE *xd,
- int natoms,int *step,float *time,
- matrix box,rvec *x,float *prec)
-/* Read subsequent frames */
-{
- int result;
-
- if ((result = xtc_header(xd,&natoms,step,time,TRUE)) != exdrOK)
- return result;
-
- if ((result = xtc_coord(xd,&natoms,box,x,prec,1)) != exdrOK)
- return result;
-
- return exdrOK;
-}
-
-int read_xtc_numframes(char *fn, int *numframes, int64_t **offsets)
-{
- XDRFILE *xd;
- int framebytes, natoms, step;
- float time;
- int64_t filesize;
-
- if ((xd = xdrfile_open(fn,"r"))==NULL)
- return exdrFILENOTFOUND;
-
- if (xtc_header(xd,&natoms,&step,&time,TRUE) != exdrOK)
- {
- xdrfile_close(xd);
- return exdrHEADER;
- }
-
- if (xdr_seek(xd, 0L, SEEK_END) != exdrOK)
- {
- xdrfile_close(xd);
- return exdrNR;
- }
- filesize = xdr_tell(xd);
-
- /* Case of fewer than 10 atoms. Framesize known. */
- if (natoms < 10)
- {
- int i;
- xdrfile_close(xd);
- framebytes = XTC_SHORTHEADER_SIZE + XTC_SHORT_BYTESPERATOM*natoms;
- *numframes = filesize/framebytes; /* Should we complain if framesize doesn't divide filesize? */
- /* Allocate memory for the frame index array */
- if ((*offsets=(int64_t *)malloc(sizeof(int64_t)*(*numframes)))==NULL)
- return exdrNOMEM;
- for (i=0; i<*numframes; i++)
- {
- (*offsets)[i] = i*framebytes;
- }
- return exdrOK;
- }
- else /* No easy way out. We must iterate. */
- {
- int est_nframes;
- /* Estimation of number of frames, with 20% allowance for error. */
- if (xdr_seek(xd, (int64_t) XTC_HEADER_SIZE, SEEK_SET) != exdrOK)
- {
- xdrfile_close(xd);
- return exdrNR;
- }
- if (xdrfile_read_int(&framebytes,1,xd) == 0)
- {
- xdrfile_close(xd);
- return exdrENDOFFILE;
- }
- framebytes = (framebytes + 3) & ~0x03; //Rounding to the next 32-bit boundary
- est_nframes = (int) (filesize/((int64_t) (framebytes+XTC_HEADER_SIZE)) + 1); // add one because it'd be easy to underestimate low frame numbers.
- est_nframes += est_nframes/5;
-
- /* Allocate memory for the frame index array */
- if ((*offsets=(int64_t *)malloc(sizeof(int64_t)*est_nframes))==NULL)
- {
- xdrfile_close(xd);
- return exdrNOMEM;
- }
- (*offsets)[0] = 0L;
- *numframes = 1;
- while (1)
- {
- if (xdr_seek(xd, (int64_t) (framebytes+XTC_HEADER_SIZE), SEEK_CUR) != exdrOK) {
- free(*offsets);
- xdrfile_close(xd);
- return exdrNR;
- }
- if (xdrfile_read_int(&framebytes,1,xd) == 0)
- break;
- /* Read was successful; this is another frame */
- /* Check if we need to enlarge array */
- if (*numframes == est_nframes){
- est_nframes += est_nframes/5 + 1; // Increase in 20% stretches
- if ((*offsets = realloc(*offsets, sizeof(int64_t)*est_nframes))==NULL)
- {
- free(*offsets);
- xdrfile_close(xd);
- return exdrNOMEM;
- }
- }
- (*offsets)[*numframes] = xdr_tell(xd) - 4L - (int64_t) (XTC_HEADER_SIZE); //Account for the header and the nbytes bytes we read.
- (*numframes)++;
- framebytes = (framebytes + 3) & ~0x03; //Rounding to the next 32-bit boundary
- }
- xdrfile_close(xd);
- return exdrOK;
- }
-}
-
-
-int write_xtc(XDRFILE *xd,
- int natoms,int step,float time,
- matrix box,rvec *x,float prec)
-/* Write a frame to xtc file */
-{
- int result;
-
- if ((result = xtc_header(xd,&natoms,&step,&time,FALSE)) != exdrOK)
- return result;
-
- if ((result = xtc_coord(xd,&natoms,box,x,&prec,0)) != exdrOK)
- return result;
-
- return exdrOK;
-}
-
diff --git a/pymolfile/libpymolfile-old/xdrfile_xtc.h b/pymolfile/libpymolfile-old/xdrfile_xtc.h
deleted file mode 100644
index a99135c5baebeef36c8638bbb41b1832c80ae32d..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile-old/xdrfile_xtc.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
- *
- * $Id$
- *
- * Copyright (c) Erik Lindahl, David van der Spoel 2003,2004.
- * Copyright (c) Manuel Melo <manuel.nuno.melo@gmail.com> 2013,2014.
- * Coordinate compression (c) by Frans van Hoesel.
- * XTC/TRR seeking and indexing (c) Manuel Melo.
- *
- * This file is part of libxdrfile2.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,
- * USA.
- */
-
-#ifndef _xdrfile_xtc_h
-#define _xdrfile_xtc_h
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include "xdrfile.h"
-
- /* All functions return exdrOK if succesfull.
- * (error codes defined in xdrfile.h).
- */
-
- /* This function returns the number of atoms in the xtc file in *natoms */
- extern int read_xtc_natoms(char *fn,int *natoms);
-
- /* Seek through trajectory counting and indexing frames */
- extern int read_xtc_numframes(char *fn, int *numframes, int64_t **offsets);
-
- /* Read one frame of an open xtc file */
- extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
- matrix box,rvec *x,float *prec);
-
- /* Write a frame to xtc file */
- extern int write_xtc(XDRFILE *xd,
- int natoms,int step,float time,
- matrix box,rvec *x,float prec);
-
-/* XTC header fields until coord floats: *** only for trajectories of less than 10 atoms! *** */
-/* magic natoms step time DIM*DIM_box_vecs natoms */
-#define XTC_SHORTHEADER_SIZE (20 + DIM*DIM*4)
-/* Short XTCs store each coordinate as a 32-bit float. */
-#define XTC_SHORT_BYTESPERATOM 12
-/* XTC header fields until frame bytes: *** only for trajectories of more than 9 atoms! *** */
-/* magic natoms step time DIM*DIM_box_vecs natoms prec DIM_min_xyz DIM_max_xyz smallidx */
-#define XTC_HEADER_SIZE (DIM*DIM*4 + DIM*2 + 46)
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/pymolfile/libpymolfile/f77_molfile.c b/pymolfile/libpymolfile/f77_molfile.c
deleted file mode 100644
index 1bb6aee33f8e61628d32f88fa160be5f8813234f..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile/f77_molfile.c
+++ /dev/null
@@ -1,363 +0,0 @@
-
-/*
- * molfile fortran interface
- * $Id: f77_molfile.c,v 1.1 2006/03/10 22:48:49 johns Exp $
- * (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <string.h>
-
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
-
-#define F77TESTME 1
-
-/* fortran name mangling */
-#if defined(_F77_NO_UNDERSCORE)
-#define FNAME(n) n
-#elif defined(_F77_F2C_UNDERSCORE)
-#define FNAME(n) n ## __
-#else
-#define FNAME(n) n ## _
-#endif
-
-/* interface typedef magic */
-typedef int int4;
-
-struct molfile_f77_handle
-{
- void *handle;
- const char *fname;
- const char *ftype;
- molfile_plugin_t *plugin;
-};
-typedef struct molfile_f77_handle f77_fd;
-
-/* plugin list */
-#ifndef MAXPLUGINS
-#define MAXPLUGINS 200
-#endif
-static int numplugins=0;
-static molfile_plugin_t *plugin_list[MAXPLUGINS];
-
-/* we maintain a static list of assigned handles */
-#ifndef MAXHADNLES
-#define MAXHANDLES 200
-#endif
-static int4 numhandles=0;
-static f77_fd handle_list[MAXHANDLES];
-
-/* helper functions */
-/* helper function to copy fortran style (a la sun fortran) strings into
- * valid c style strings. just using the string pointers will not work,
- * since the strings are NOT zero terminated.
- *
- * WARNING: do not forget to free(2) them later,
- * or you'll have a memory leak!
- */
-static char *f77strdup(const char *s,const int sz)
-{
- char *r;
-
- r = (char *)malloc(sz + 1);
- r = (char *)memcpy(r, s, sz);
- r[sz] = '\0';
- return r;
-}
-
-/* trim off whitespace at the end of a string */
-static void f77trim(char *s,const int sz)
-{
- int i;
-
- i=1;
- while( (i++ < sz) && isspace(s[sz-i]) ) {
- s[sz-i] ='\0';
- }
-}
-
-/* get the filename extension */
-static const char *f77getfnext(const char *s)
-{
- int i,len;
-
- len = strlen(s);
- for (i=len; i>=0; --i) {
- if(s[i] == '.') {
- return &s[i+1];
- }
- }
- return NULL;
-}
-
-/* check validity of plugins and register them. */
-static int f77register(void *ptr, vmdplugin_t *plugin) {
-
- if (!plugin->type || !plugin->name || !plugin->author) {
- fprintf(stderr," skipping plugin with incomplete header\n");
- return -1;
- }
-
-#if F77TESTME
- fprintf(stderr, " trying to register plugin #%d: %s, type: %s/%d\n"
- " written by: %s\n\n", numplugins+1, plugin->name,
- plugin->type, plugin->abiversion, plugin->author);
-#endif
-
- if (plugin->abiversion != vmdplugin_ABIVERSION) {
- fprintf(stderr, " skipping plugin with incompatible ABI:%d/%d\n",
- plugin->abiversion, vmdplugin_ABIVERSION);
- return -2;
- }
-
- if (0 != strncmp(plugin->type, "mol file", 8)) {
- fprintf(stderr, " skipping plugin of incompatible type:%s\n",
- plugin->type);
- return -3;
- }
-
- if (numplugins < MAXPLUGINS) {
- plugin_list[numplugins] = (molfile_plugin_t *) plugin;
- ++numplugins;
- return 0;
- }
-
- fprintf(stderr, " too many plugins: %d. increase MAXPLUGINS, "
- "recompile, and try again.\n", numplugins);
-
- return -4;
-}
-
-
-/* the official fortran API */
-
-/* register all available plugins and clear handles. */
-void FNAME(f77_molfile_init)(void)
-{
- int i;
-
- MOLFILE_INIT_ALL;
-
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i].handle = NULL;
- }
-
- MOLFILE_REGISTER_ALL(NULL,f77register);
-
- /*
- * FIXME: check all plugins and make
- * sure the babel plugin(s) are last.
- */
-}
-
-/* unregister all available plugins */
-void FNAME(f77_molfile_finish)(void)
-{
-#if 0
- int i;
-
- /* FIXME: add code to close and nullify all open handles */
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i] = NULL;
- }
-#endif
-
- MOLFILE_FINI_ALL;
-}
-
-
-/* open a file and provide file descriptor */
-void FNAME(f77_molfile_open_read)(int4 *handle, int4 *natoms,
- const char *infile, const char *intype,
- const int len_if, const int len_it)
-{
- char *fname, *ftype;
- molfile_plugin_t *plugin;
- int i;
-
- if (numhandles >= MAXHANDLES) {
- fprintf(stderr, "too many molfile f77 handles.\n");
- *handle = -666;
- return;
- }
-
- fname = f77strdup(infile, len_if);
- f77trim(fname,len_if);
-
- ftype = f77strdup(intype, len_it);
- f77trim(ftype,len_it);
-
- fprintf(stderr, " %s: trying for: %s/%d, %s/%d\n",
- __FUNCTION__, fname, len_if, ftype, len_it);
-
- plugin = NULL;
- /* determine plugin type automatically */
- if(0 == strncmp(intype, "auto", 4)) {
- const char *fext;
-
- fext = f77getfnext(fname);
- if (fext == NULL) {
- fprintf(stderr, " could not determine file name extension "
- "for automatic plugin guess\n");
- *handle = -111;
- return;
- }
-#if F77TESTME
- fprintf(stderr, " filename extension: %s\n", fext);
-#endif
-
- for (i=0; (i<numplugins) && plugin==NULL; ++i) {
-#if F77TESTME
- fprintf(stderr, " tying filename extension: %s\n",
- plugin_list[i]->filename_extension);
-#endif
- if (0 == strcmp(plugin_list[i]->filename_extension, fext)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
-
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not determine matching plugin type"
- "from file name extension\n");
- *handle = -222;
- return;
- }
- } else {
-
- for (i=0; (i<numplugins) && (plugin==NULL); ++i) {
-#if F77TESTME
- fprintf(stderr, " tying plugin type: %s\n",
- plugin_list[i]->name);
-#endif
- if (0 == strcmp(plugin_list[i]->name, ftype)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not find plugin for type %s\n",ftype);
- *handle = -333;
- return;
- }
- }
-
- if(plugin == NULL) { /* this should not happen, but... */
- fprintf(stderr, " no plugin found.\n");
- *handle = -444;
- return;
- }
-
- /* build handle */
- ++numhandles;
- for (i=0; i<numhandles; ++i) {
- if(handle_list[i].plugin == NULL) {
- *handle = i;
- handle_list[i].fname=fname;
- handle_list[i].ftype=plugin->name;
- handle_list[i].plugin=plugin;
- }
- }
-
- /* open file for reading and detect number of atoms */
- *natoms=MOLFILE_NUMATOMS_UNKNOWN;
- handle_list[*handle].handle=
- plugin->open_file_read(fname,plugin->name,natoms);
- if(handle_list[*handle].handle == NULL) {
- fprintf(stderr, " open of %s-plugin for file %s failed\n",
- plugin->type, fname);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-777;
- return;
- }
-
- return;
-}
-
-/* read next time step */
-void FNAME(f77_molfile_read_next)(int4 *handle, int4 *natoms, float *xyz,
- float *box, int4 *status)
-{
- molfile_plugin_t *plugin;
- molfile_timestep_t step;
- int retval;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- /* skip or read the timestep as demanded */
- if(status == 0) {
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, NULL);
- } else {
- step.coords = xyz;
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, &step);
- }
-
- /* copy the box parameters */
- if (retval == MOLFILE_SUCCESS) {
- *status = 1;
- box[0]=step.A;
- box[1]=step.B;
- box[2]=step.C;
- box[3]=step.alpha;
- box[4]=step.beta;
- box[5]=step.gamma;
- } else {
- *status = 0;
- }
-}
-
-/* close a read file descriptor */
-void FNAME(f77_molfile_close_read)(int4 *handle)
-{
- molfile_plugin_t *plugin;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -111;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -222;
- return;
- }
-
-#if F77TESTME
- fprintf(stderr, " %s: trying to close handle %d"
- " for file %s\n", __FUNCTION__, *handle,
- handle_list[*handle].fname);
-#endif
-
- plugin->close_file_read(handle_list[*handle].handle);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-1;
-}
diff --git a/pymolfile/libpymolfile/libvmdmolfile.i b/pymolfile/libpymolfile/libvmdmolfile.i
deleted file mode 100644
index e5314f178c70209e9765dcabcf1f04f68f8a798b..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile/libvmdmolfile.i
+++ /dev/null
@@ -1,298 +0,0 @@
-/* -*- C -*- (not really, but good for syntax highlighting) */
-/* SWIG interface for libvmdmolfile of VMD molfile_plugins
- Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
- Published under BSD LICENSE
-
- swig -python -outdir . src/xdrfile/libxdrfile2.i
-*/
-%define DOCSTRING
-"
-:Author: Berk Onat <b.onat@warwick.ac.uk>
-:Year: 2017
-:Licence: BSD LICENSE
-
-
-"
-%enddef
-
-%module(docstring=DOCSTRING) libvmdmolfile
-
-
-%{
-/* Python SWIG interface to libvmdmolfile
- Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
- Published under BSD LICENSE
- */
-#define SWIG_FILE_WITH_INIT
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <string.h>
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
-%}
-
-%include "numpy.i"
-
-%init %{
-import_array();
-%}
-
-
-/*
- Wrapping only high-level plugin functions to register VMD
- plugins and to retrive the data through molfile_plugin interface.
-
- Only modifing call signatures. This will help one to access functions
- without dealing with pointers from python.
-*/
-
-
-/* status codes */
-enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
- exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
- exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
-
-/* These com from stdio.h, for file seeking. Gives all the flexibility to _fseek(). */
-enum { SEEK_SET, SEEK_CUR, SEEK_END };
-
-/* open/close xdr files */
-%feature("autodoc", "0") xdrfile_open;
-extern XDRFILE* xdrfile_open(const char *path, const char *mode);
-
-%feature("autodoc", "0") xdrfile_close;
-extern int xdrfile_close(XDRFILE *fp);
-
-
-/* from xdrfile_xtc.c */
-/* This function returns the number of atoms in the xtc file in *natoms
- extern int read_xtc_natoms(char *fn,int *natoms);
- ... but the wrapped function returns natoms as the python return value
-*/
-%feature("autodoc", "0") my_read_xtc_natoms;
-%rename (read_xtc_natoms) my_read_xtc_natoms;
-%exception my_read_xtc_natoms {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
- int my_read_xtc_natoms(char *fn) {
- int natoms;
- int status;
- status = read_xtc_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from xtc '%s'", status, fn);
- return 0;
- }
- return natoms;
- }
-%}
-
-%feature("autodoc", "0") my_read_xtc_numframes;
-%rename (read_xtc_numframes) my_read_xtc_numframes;
-%exception my_read_xtc_numframes {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
-PyObject * my_read_xtc_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_xtc_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through xtc '%s'", status, fn);
- return 0;
- }
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
- }
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
- }
-%}
-
-
-/* This function returns the number of atoms in the trr file in *natoms
- extern int read_trr_natoms(char *fn,int *natoms);
- ... but the wrapped function returns natoms as the python return value
-*/
-%feature("autodoc", "0") my_read_trr_natoms;
-%rename (read_trr_natoms) my_read_trr_natoms;
-%exception my_read_trr_natoms {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
- int my_read_trr_natoms(char *fn) {
- int natoms;
- int status;
- status = read_trr_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from trr '%s'", status, fn);
- return 0;
- }
- return natoms;
- }
-%}
-
-
-%feature("autodoc", "0") my_read_trr_numframes;
-%rename (read_trr_numframes) my_read_trr_numframes;
-%exception my_read_trr_numframes {
- $action
- if (PyErr_Occurred()) SWIG_fail;
-}
-%inline %{
-PyObject * my_read_trr_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_trr_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through trr '%s'", status, fn);
- return 0;
- }
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
- }
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
- }
-%}
-
-
-
-#define DIM 3
-typedef float matrix[DIM][DIM];
-typedef float rvec[DIM];
-
-
-/* Reading from xdr files */
-
-%apply (float INPLACE_ARRAY2[ANY][ANY]) {(matrix box)}
-%apply (int DIM1, int DIM2, float* INPLACE_ARRAY2) {(int natoms, int _DIM, float *x),
- (int vnatoms, int v_DIM, float *v),
- (int fnatoms, int f_DIM, float *f)}
-
-/* Read one frame of an open xtc file */
-/*
-extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
- matrix box,rvec *x,float *prec);
-*/
-%feature("autodoc", "read_xtc(XDRFILE, box, x) -> (status, step, time, precision)") my_read_xtc;
-%rename (read_xtc) my_read_xtc;
-%inline %{
-PyObject * my_read_xtc(XDRFILE *xd, matrix box, int natoms, int _DIM, float *x) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step;
- float time, prec;
- PyObject *tuple = PyTuple_New(4);
- status = read_xtc(xd, natoms, &step, &time, box, (rvec *)x, &prec);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)prec));
- return tuple; // return (status, step, time, prec)
-}
-%}
-
-%feature("autodoc", "read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)") my_read_trr;
-%rename (read_trr) my_read_trr;
-%inline %{
-PyObject * my_read_trr(XDRFILE *xd, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step, has_prop=0;
- float time, lmbda;
- PyObject *tuple = PyTuple_New(7);
- status = read_trr(xd, natoms, &step, &time, &lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f, &has_prop);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)lmbda));
- PyTuple_SET_ITEM(tuple, 4, PyBool_FromLong((long)(has_prop & HASX)));
- PyTuple_SET_ITEM(tuple, 5, PyBool_FromLong((long)(has_prop & HASV)));
- PyTuple_SET_ITEM(tuple, 6, PyBool_FromLong((long)(has_prop & HASF)));
- return tuple; // return (status, step, time, lmbda, has_x, has_v, has_f)
-}
-%}
-
-%clear (matrix box);
-%clear (int natoms, int _DIM, float *x);
-%clear (int vnatoms, int v_DIM, float *v);
-%clear (int fnatoms, int f_DIM, float *f);
-
-
-/* Writing of xdr files */
-
-%apply (float IN_ARRAY2[ANY][ANY]) {(matrix box)}
-%apply (int DIM1, int DIM2, float* IN_ARRAY2) {(int natoms, int _DIM, float *x),
- (int vnatoms, int v_DIM, float *v),
- (int fnatoms, int f_DIM, float *f)}
-
-/* Write a frame to xtc file */
-/*
-extern int write_xtc(XDRFILE *xd, int natoms,int step,float time,
- matrix box,rvec *x,float prec);
-*/
-%feature("autodoc", "write_xtc(XDRFILE, step, time, box, x, prec) -> status") my_write_xtc;
-%rename (write_xtc) my_write_xtc;
-%inline %{
-int my_write_xtc(XDRFILE *xd, int step, float time,
- matrix box, int natoms, int _DIM, float *x, float prec) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- return write_xtc(xd, natoms, step, time, box, (rvec *)x, prec);
-}
-%}
-
-%feature("autodoc", "write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status") my_write_trr;
-%rename (write_trr) my_write_trr;
-%inline %{
-int my_write_trr(XDRFILE *xd, int step, float time, float lmbda, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* Preparing for the case of empty arrays - NULL pointers tell the library to skip this property. */
- if (_DIM == 0) x = NULL;
- if (v_DIM == 0) v = NULL;
- if (f_DIM == 0) f = NULL;
- return write_trr(xd, natoms, step, time, lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f);
-}
-%}
-
-%feature("autodoc", "0") xdr_seek;
-extern int xdr_seek(XDRFILE *xd, long long pos, int whence);
-
-%feature("autodoc", "0") xdr_tell;
-extern long long xdr_tell(XDRFILE *xd);
-
-%clear (matrix box);
-%clear (int natoms, int _DIM, float *x);
-%clear (int vnatoms, int v_DIM, float *v);
-%clear (int fnatoms, int f_DIM, float *f);
-
-
diff --git a/pymolfile/libpymolfile/libvmdmolfile.py b/pymolfile/libpymolfile/libvmdmolfile.py
deleted file mode 100644
index 87a2c6692427936a46427739df076f2582fc4fef..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile/libvmdmolfile.py
+++ /dev/null
@@ -1,487 +0,0 @@
-# This file was automatically generated by SWIG (http://www.swig.org).
-# Version 2.0.11
-#
-# Do not make changes to this file unless you know what you are doing--modify
-# the SWIG interface file instead.
-
-
-
-
-"""
-
-:Author: Oliver Beckstein <orbeckst@gmail.com>
-:Author: Manuel Melo <manuel.nuno.melo@gmail.com>
-:Year: 2014
-:Licence: GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-
-
-The Gromacs XTC/TRR library :mod:`libxdrfile2`
-==============================================
-
-:mod:`libxdrfile2`, a derivative of the Gromacs_ `libxdrfile library`_, provides an
-interface to some high-level functions for XTC/TRR trajectory handling.
-Only functions required for reading and processing whole trajectories are exposed at
-the moment; low-level routines to read individual numbers are not provided. In
-addition, :mod:`libxdrfile2` exposes functions to allow fast frame indexing and XDR
-file seeking.
-
-The functions querying the numbers of atoms in a trajectory frame
-(:func:`read_xtc_natoms` and :func:`read_trr_natoms`) open a file themselves and
-only require the file name.
-
-All other functions operate on a *XDRFILE* object, which is a special file
-handle for xdr files. Any xdr-based trajectory file (XTC or TRR format) always
-has to be opened with :func:`xdrfile_open`. When done, close the trajectory
-with :func:`xdrfile_close`.
-
-The functions fill or read existing arrays of coordinates; they never allocate
-these arrays themselves. Hence they need to be setup outside libxdrfile2 as
-numpy arrays. The exception to these are the indexing ones functions that take
-care of array allocation and transference to a garbage-collectable memory object.
-
-
-.. _Gromacs: http://www.gromacs.org
-.. _libxdrfile library: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
-
-.. versionchanged:: 0.8.0
- :mod:`libxdrfile2` is now used instead of :mod:`libxdrfile`. :mod:`libxdrfile2` is
- based on :mod:`libxdrfile` but has xdr seeking and indexing capabilities.
- Unlike :mod:`libxdrfile` before it, :mod:`libxdrfile2` is distributed under the GNU
- GENERAL PUBLIC LICENSE, version 2 (or higher).
-
-
-Example: Reading from a XTC
----------------------------
-
-In the example we read coordinate frames from an existing XTC trajectory::
-
- import numpy as np
- from libxdrfile2 import xdrfile_open, xdrfile_close, read_xtc_natoms, read_xtc, DIM, exdrOK
- xtc = 'md.xtc'
-
- # get number of atoms
- natoms = read_xtc_natoms(xtc)
-
- # allocate coordinate array of the right size and type
- # (the type float32 is crucial to match the underlying C-code!!)
- x = np.zeros((natoms, DIM), dtype=np.float32)
- # allocate unit cell box
- box = np.zeros((DIM, DIM), dtype=np.float32)
-
- # open file
- XTC = xdrfile_open(xtc, 'r')
-
- # loop through file until return status signifies end or a problem
- # (it should become exdrENDOFFILE on the last iteration)
- status = exdrOK
- while status == exdrOK:
- status,step,time,prec = read_xtc(XTC, box, x)
- # do something with x
- centre = x.mean(axis=0)
- print 'Centre of geometry at %(time)g ps: %(centre)r' % vars()
-
- # finally close file
- xdrfile_close(XTC)
-
-Note that only the *contents* of the coordinate and unitcell arrays *x* and
-*box* change.
-
-
-Functions and constants
------------------------
-
-The module defines a number of constants such as :data:`DIM` or the
-`Status symbols`_.
-
-.. data:: DIM
-
- The number of cartesian dimensions for which the underlying C-code
- was compiled; this is most certainly 3.
-
-
-Status symbols
-~~~~~~~~~~~~~~
-
-A number of symbols are exported; they all start with the letters
-``exdr``. Important ones are listed here:
-
-.. data:: exdrOK
-
- Success of xdr file read/write operation.
-
-.. data:: exdrCLOSE
-
- xdr file is closed
-
-.. data:: exdrENDOFFILE
-
- end of file was reached (response of :func:`read_xtc` and
- :func:`read_trr` after the last read frame)
-
-.. data:: exdrFILENOTFOUND
-
- :func:`xdrfile_open` cannot find the requested file
-
-
-Opening and closing of XDR files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Two low-level functions are used to obtain a *XDRFILE* object (a file handle)
-to access xdr files such as XTC or TRR trajectories.
-
-.. function:: xdrfile_open(path, mode) -> XDRFILE
-
- Open *path* and returns a *XDRFILE* handle that is required by other
- functions.
-
- :Arguments:
- *path*
- file name
- *mode*
- 'r' for reading and 'w' for writing
- :Returns: *XDRFILE* handle
-
-.. function:: xdrfile_close(XDRFILE) -> status
-
- Close the xdrfile pointed to by *XDRFILE*.
-
- .. Warning:: Closing an already closed file will lead to a
- crash with a double-free pointer error.
-
-XTC functions
-~~~~~~~~~~~~~
-
-The XTC trajectory format is a lossy compression format that only stores
-coordinates. Compression level is determined by the *precision* argument to the
-:func:`write_xtc` function. Coordinates (Gromacs_ uses nm natively) are
-multiplied by *precision* and truncated to the integer part. A typical value is
-1000.0, which gives an accuracy of 1/100 of an Angstroem.
-
-The advantage of XTC over TRR is its significantly reduced size.
-
-
-.. function:: read_xtc_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a xtc file *fn*.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a XTC
- or if it is not readable.
-
-.. function:: read_xtc(XDRFILE, box, x) -> (status, step, time, precision)
-
- Read the next frame from the opened xtc trajectory into *x*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=numpy.float32)``
- which is updated with the coordinates from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see `Status symbols`_ for other
- values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
-.. function:: write_xtc(XDRFILE, step, time, box, x, prec) -> status
-
- Write the next frame *x* to the opened xtc trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the coordinates from the frame
- *precision*
- precision of the lossy xtc format (typically 1000.0)
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-TRR functions
-~~~~~~~~~~~~~
-
-TRR is the Gromacs_ native full-feature trajectory storage format. It can contain position
-coordinates, velocities and forces, and the lambda value for free energy perturbation
-calculations. Velocities and forces are optional in the sense that they can be all zero.
-
-.. function:: read_trr_natoms(fn) -> natoms
-
- Read the number of atoms *natoms* from a trr file *fn*.
-
- :Arguments:
- *fn*
- file name of a trr file
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR
- or if it is not readable.
-
-.. function:: read_trr_numframes(fn) -> (numframes, offsets)
-
- Read through the whole trajectory headers to obtain the total number of frames.
- The process is speeded up by reading frame headers for the amount of data in the frame,
- and then skipping directly to the next header. An array of frame offsets is also
- returned, which can later be used to seek direcly to arbitrary frames in the trajectory.
-
- :Arguments:
- *fn*
- file name of an xtc file
-
- :Returns:
- a tuple containing:
- *numframes*
- an int with the total frame count in the trajectory
- *offsets*
- a numpy array of int64 recording the starting byte offset of each frame
-
- :Raises: :exc:`IOError` if the supplied filed is not a TRR or if it is not readable.
-
-.. function:: read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)
-
- Read the next frame from the opened trr trajectory into *x*, *v*, and *f*.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object
- *box*
- pre-allocated numpy ``array((DIM,DIM),dtype=numpy.float32)`` which
- is filled with the unit cell box vectors
- *x*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **coordinates** from the frame
- *v*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **velocities** from the frame
- *f*
- pre-allocated numpy ``array((natoms, DIM),dtype=nump.float32)``
- which is updated with the **forces** from the frame
-
- :Returns:
- a tuple containing:
- *status*
- integer status (0 = exdrOK), see the ``libxdrfile2.exdr*`` constants
- under `Status symbols`_ for other values)
- *step*
- simulation step
- *time*
- simulation time in ps
- *lambda*
- current lambda value (only interesting for free energy perturbation)
- *has_x*
- boolean indicating whether coordinates were read from the TRR
- *has_v*
- boolean indicating whether velocities were read from the TRR
- *has_f*
- boolean indicating whether forces were read from the TRR
-
-.. function:: write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status
-
- Write the next frame to the opened trr trajectory.
-
- :Arguments:
- *XDRFILE*
- open *XDRFILE* object (writable)
- *step*
- simulation step
- *time*
- time step in ps
- *lambda*
- free energy lambda value (typically 0.0)
- *box*
- numpy ``array((DIM,DIM),dtype=numpy.float32)`` which contains
- the unit cell box vectors
- *x*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **coordinates** from the frame
- *v*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **velocities** from the frame
- *f*
- numpy ``array((natoms, DIM),dtype=nump.float32)``
- which contains the **forces** from the frame
-
- .. versionchanged:: 0.8.0
- either one of *x*, *v*, or *f* can now be set as a natom,0-DIM
- numpy ``array((natom, 0),dtype=nump.float32)``. This will cause the
- corresponding property to be skipped when writing to file.
-
- :Returns: *status*, integer status (0 = OK), see the ``libxdrfile2.exdr*``
- constants under `Status symbols`_ for other values)
-
-
-"""
-
-
-from sys import version_info
-if version_info >= (2,6,0):
- def swig_import_helper():
- from os.path import dirname
- import imp
- fp = None
- try:
- fp, pathname, description = imp.find_module('_libxdrfile2', [dirname(__file__)])
- except ImportError:
- import _libxdrfile2
- return _libxdrfile2
- if fp is not None:
- try:
- _mod = imp.load_module('_libxdrfile2', fp, pathname, description)
- finally:
- fp.close()
- return _mod
- _libxdrfile2 = swig_import_helper()
- del swig_import_helper
-else:
- import _libxdrfile2
-del version_info
-try:
- _swig_property = property
-except NameError:
- pass # Python < 2.2 doesn't have 'property'.
-def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
- if (name == "thisown"): return self.this.own(value)
- if (name == "this"):
- if type(value).__name__ == 'SwigPyObject':
- self.__dict__[name] = value
- return
- method = class_type.__swig_setmethods__.get(name,None)
- if method: return method(self,value)
- if (not static):
- self.__dict__[name] = value
- else:
- raise AttributeError("You cannot add attributes to %s" % self)
-
-def _swig_setattr(self,class_type,name,value):
- return _swig_setattr_nondynamic(self,class_type,name,value,0)
-
-def _swig_getattr(self,class_type,name):
- if (name == "thisown"): return self.this.own()
- method = class_type.__swig_getmethods__.get(name,None)
- if method: return method(self)
- raise AttributeError(name)
-
-def _swig_repr(self):
- try: strthis = "proxy of " + self.this.__repr__()
- except: strthis = ""
- return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
-
-try:
- _object = object
- _newclass = 1
-except AttributeError:
- class _object : pass
- _newclass = 0
-
-
-exdrOK = _libxdrfile2.exdrOK
-exdrHEADER = _libxdrfile2.exdrHEADER
-exdrSTRING = _libxdrfile2.exdrSTRING
-exdrDOUBLE = _libxdrfile2.exdrDOUBLE
-exdrINT = _libxdrfile2.exdrINT
-exdrFLOAT = _libxdrfile2.exdrFLOAT
-exdrUINT = _libxdrfile2.exdrUINT
-exdr3DX = _libxdrfile2.exdr3DX
-exdrCLOSE = _libxdrfile2.exdrCLOSE
-exdrMAGIC = _libxdrfile2.exdrMAGIC
-exdrNOMEM = _libxdrfile2.exdrNOMEM
-exdrENDOFFILE = _libxdrfile2.exdrENDOFFILE
-exdrFILENOTFOUND = _libxdrfile2.exdrFILENOTFOUND
-exdrNR = _libxdrfile2.exdrNR
-SEEK_SET = _libxdrfile2.SEEK_SET
-SEEK_CUR = _libxdrfile2.SEEK_CUR
-SEEK_END = _libxdrfile2.SEEK_END
-
-def xdrfile_open(*args):
- """xdrfile_open(path, mode) -> XDRFILE *"""
- return _libxdrfile2.xdrfile_open(*args)
-
-def xdrfile_close(*args):
- """xdrfile_close(fp) -> int"""
- return _libxdrfile2.xdrfile_close(*args)
-
-def read_xtc_natoms(*args):
- """read_xtc_natoms(fn) -> int"""
- return _libxdrfile2.read_xtc_natoms(*args)
-
-def read_xtc_numframes(*args):
- """read_xtc_numframes(fn) -> PyObject *"""
- return _libxdrfile2.read_xtc_numframes(*args)
-
-def read_trr_natoms(*args):
- """read_trr_natoms(fn) -> int"""
- return _libxdrfile2.read_trr_natoms(*args)
-
-def read_trr_numframes(*args):
- """read_trr_numframes(fn) -> PyObject *"""
- return _libxdrfile2.read_trr_numframes(*args)
-DIM = _libxdrfile2.DIM
-
-def read_xtc(*args):
- """read_xtc(XDRFILE, box, x) -> (status, step, time, precision)"""
- return _libxdrfile2.read_xtc(*args)
-
-def read_trr(*args):
- """read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)"""
- return _libxdrfile2.read_trr(*args)
-
-def write_xtc(*args):
- """write_xtc(XDRFILE, step, time, box, x, prec) -> status"""
- return _libxdrfile2.write_xtc(*args)
-
-def write_trr(*args):
- """write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status"""
- return _libxdrfile2.write_trr(*args)
-
-def xdr_seek(*args):
- """xdr_seek(xd, pos, whence) -> int"""
- return _libxdrfile2.xdr_seek(*args)
-
-def xdr_tell(*args):
- """xdr_tell(xd) -> long long"""
- return _libxdrfile2.xdr_tell(*args)
-# This file is compatible with both classic and new-style classes.
-
-
diff --git a/pymolfile/libpymolfile/tester.f b/pymolfile/libpymolfile/tester.f
deleted file mode 100644
index 40e250bb80cc1ad0d8446dd5d37f2726679b5636..0000000000000000000000000000000000000000
--- a/pymolfile/libpymolfile/tester.f
+++ /dev/null
@@ -1,110 +0,0 @@
-c testing frontend for the molfile plugin fortran interface
-c $Id: tester.f,v 1.1 2006/03/10 22:48:49 johns Exp $
-c (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
-
- program molfile
- implicit none
-
- integer*4 natom, maxatom, handle(4), status
- parameter (maxatom=3000*3)
- real*4 xyz(maxatom), box(6)
-
- character infile*200, intype*10
- integer i,j
-
- print*,'molfile fortran tester v0.01'
-
-C set some default values
- infile = 'TRAJEC.dcd'
- intype = 'auto'
- natom = -1
- handle(1) = -1
- handle(2) = -1
- handle(3) = -1
- handle(4) = -1
-
- print*,'filename: ', infile
- print*,'type: ', intype
-
-C set up everything and
-C register all static plugins
- call f77_molfile_init
-
- call f77_molfile_open_read(handle(1),natom,infile,intype)
-
- if (handle(1).lt.0) then
- print*,'file type unknown or not registered'
- else
- print*,'file successfully opened:'
- print*,'handle:',handle(1)
- print*,'natom: ',natom
- end if
-
- do i=1,2000
- status = 1 ! status=1 on entry means read
- call f77_molfile_read_next(handle(1),natom,xyz(1),box,status);
- print*,'read ',i,' status:',status
- print*,'atom(1)', (xyz(j),j=1,3)
- print*,'atom(10)',(xyz(j),j=31,33)
- print*,'atom(100)',(xyz(j),j=301,303)
- print*,'box',box
- if(status.eq.0) go to 666
- status = 0 ! status=0 on entry means skip
- call f77_molfile_read_next(handle(1),natom,xyz,box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 666
- end do
- 666 continue
-
- infile='li-nh3_4-end.pdb'
- intype='pdb'
- call f77_molfile_open_read(handle(2),natom,infile,intype)
-
- if (handle(2).lt.0) then
- print*,'file type unknown or not registered'
- else
- print*,'file successfully opened:'
- print*,'handle:',handle(2)
- print*,'natom: ',natom
- end if
-
- do i=1,2000
- status = 1 ! status=1 on entry means read
- call f77_molfile_read_next(handle(2),natom,xyz(1),box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 6666
- print*,'atom(1)', (xyz(j),j=1,3)
- print*,'atom(10)', (xyz(j),j=31,33)
- print*,'atom(100)',(xyz(j),j=301,303)
- print*,'box',box
- status = 0 ! status=0 on entry means skip
- call f77_molfile_read_next(handle(2),natom,xyz,box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 6666
- end do
- 6666 continue
- call f77_molfile_open_read(handle(3),natom,infile,intype)
- print*,'handle:',handle(3)
-
- call f77_molfile_close_read(handle(1),status)
- print*,'handle:',handle(1)
- call f77_molfile_open_read(handle(1),natom,infile,intype)
- print*,'handle:',handle(1)
- call f77_molfile_open_read(handle(4),natom,infile,intype)
- print*,'handle:',handle(4)
-
-
- call f77_molfile_close_read(handle(2),status)
- print*,'handle:',handle(2)
- call f77_molfile_close_read(handle(1),status)
- print*,'handle:',handle(1)
- call f77_molfile_close_read(handle(3),status)
- print*,'handle:',handle(3)
- call f77_molfile_close_read(handle(2),status)
- print*,'handle:',handle(2)
- call f77_molfile_close_read(handle(4),status)
- print*,'handle:',handle(4)
-
- call f77_molfile_finish
-
- end
diff --git a/pymolfile/molfile/.lipo b/pymolfile/molfile/.lipo
new file mode 100644
index 0000000000000000000000000000000000000000..6203b131c0616fd693c105831a2b1b23fb8fa669
Binary files /dev/null and b/pymolfile/molfile/.lipo differ
diff --git a/pymolfile/libpymolfile/__init__.py b/pymolfile/molfile/__init__.py
similarity index 50%
rename from pymolfile/libpymolfile/__init__.py
rename to pymolfile/molfile/__init__.py
index 584c3db77a365e537797219d8d866cef43fdd84e..2fa350890c2794810c7356d8e44d2271788527c6 100644
--- a/pymolfile/libpymolfile/__init__.py
+++ b/pymolfile/molfile/__init__.py
@@ -1,7 +1,7 @@
# Stand-alone python bindings for libvmdmolfile
# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
-# Published under the GNU GENERAL PUBLIC LICENSE Version 2 (or higher)
-"""Stand-alone vmdmolfile library.
+# Published under the BSD LICENSE
+"""libpymolfile library.
"""
diff --git a/pymolfile/molfile/__init__.pyc b/pymolfile/molfile/__init__.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..43a135fa7d8f6c90ddc870cad60f1cee52dd6933
Binary files /dev/null and b/pymolfile/molfile/__init__.pyc differ
diff --git a/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc b/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..3aaa7daa4aa032356318545e3c703ed00ac0ac6e
Binary files /dev/null and b/pymolfile/molfile/__pycache__/__init__.cpython-36.pyc differ
diff --git a/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..270df113f6d58296d31053c92d6273f8773ff8e6
Binary files /dev/null and b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc differ
diff --git a/pymolfile/molfile/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so
new file mode 100755
index 0000000000000000000000000000000000000000..5f16657f992bcb5f73c8572738446d8880bc9afd
Binary files /dev/null and b/pymolfile/molfile/_libpymolfile.so differ
diff --git a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Info.plist b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Info.plist
new file mode 100644
index 0000000000000000000000000000000000000000..a1ee3c17acbea1c02095f00322512685cdd3490d
--- /dev/null
+++ b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Info.plist
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+ <dict>
+ <key>CFBundleDevelopmentRegion</key>
+ <string>English</string>
+ <key>CFBundleIdentifier</key>
+ <string>com.apple.xcode.dsym._libpymolfile.so</string>
+ <key>CFBundleInfoDictionaryVersion</key>
+ <string>6.0</string>
+ <key>CFBundlePackageType</key>
+ <string>dSYM</string>
+ <key>CFBundleSignature</key>
+ <string>????</string>
+ <key>CFBundleShortVersionString</key>
+ <string>1.0</string>
+ <key>CFBundleVersion</key>
+ <string>1</string>
+ </dict>
+</plist>
diff --git a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so
new file mode 100644
index 0000000000000000000000000000000000000000..d66b822ee7cd1186e842d1ef8fbd9025fe68b6cb
Binary files /dev/null and b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so differ
diff --git a/pymolfile/molfile/compile.sh b/pymolfile/molfile/compile.sh
new file mode 100644
index 0000000000000000000000000000000000000000..0a16c41abea2454bf10bf092248037ae54376688
--- /dev/null
+++ b/pymolfile/molfile/compile.sh
@@ -0,0 +1,2 @@
+swig -Wall -c++ -python libpymolfile.i
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ -I. libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so -Ivmd_molfile_plugins/include/ -Ilib/ -L. lib/libmolfile_plugin.a -I/labEnv3/include/python3.6m/ -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.a b/pymolfile/molfile/lib/libmolfile_plugin.a
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.a
rename to pymolfile/molfile/lib/libmolfile_plugin.a
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.dylib b/pymolfile/molfile/lib/libmolfile_plugin.dylib
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.dylib
rename to pymolfile/molfile/lib/libmolfile_plugin.dylib
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.h b/pymolfile/molfile/lib/libmolfile_plugin.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.h
rename to pymolfile/molfile/lib/libmolfile_plugin.h
diff --git a/pymolfile/molfile/libpymolfile.i b/pymolfile/molfile/libpymolfile.i
new file mode 100644
index 0000000000000000000000000000000000000000..8ac048ba48bfa814e7b7b18b72dc212011b05ec2
--- /dev/null
+++ b/pymolfile/molfile/libpymolfile.i
@@ -0,0 +1,239 @@
+/* -*- C -*- (not really, but good for syntax highlighting) */
+/* SWIG interface for libvmdmolfile of VMD molfile_plugins
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under BSD LICENSE
+
+ swig -python -outdir pymolfile/lib/ pymolfile/src/libpymolfile.i
+*/
+%define DOCSTRING
+"
+:Author: Berk Onat <b.onat@warwick.ac.uk>
+:Year: 2017
+:Licence: BSD LICENSE
+
+
+"
+%enddef
+
+%module(docstring=DOCSTRING) libpymolfile
+
+
+%{
+/* Python SWIG interface to libpymolfile
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under BSD LICENSE
+ */
+#define SWIG_FILE_WITH_INIT
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+#include "pymolfile.h"
+%}
+
+%include "numpy.i"
+
+%init %{
+import_array();
+%}
+
+
+/*
+ Wrapping only high-level plugin functions to register VMD
+ plugins and to retrive the data through molfile_plugin interface.
+
+ Only modifing call signatures. This will help one to access functions
+ without dealing with pointers from python.
+*/
+
+
+/* plugin status codes for error handling */
+enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
+ pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
+
+/* pymolfile.c
+ initialize and finalize molfile plugins
+*/
+%feature("autodoc", "0") molfile_plugin_list;
+extern molfile_plugin_t** molfile_plugin_list(int maxsize);
+
+%feature("autodoc", "0") molfile_init;
+extern int molfile_init(void);
+
+%feature("autodoc", "0") molfile_finish;
+extern int molfile_finish(void);
+
+%feature("autodoc", "0") get_plugin;
+extern molfile_plugin_t* get_plugin(molfile_plugin_t** plugin_list, int plugin_no);
+
+%feature("autodoc", "0") molfile_plugin_info;
+%exception molfile_plugin_info {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
+ molfile_plugin_t *plugin;
+ int *plugno = &plugin_no;
+ int has_readstructure = 0;
+ int has_readbonds = 0;
+ int has_readangles = 0;
+ int has_writestructure = 0;
+ int has_writebonds = 0;
+ int has_writeangles = 0;
+ int has_readnexttimestep = 0;
+ int has_writetimestep = 0;
+ int plugin_list_size = sizeof(plugin_list) / sizeof(molfile_plugin_t**);
+ if (plugno==NULL || plugin_no<0){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin handle no should be given, be positive value and should not exceed the list length'%d'. You set '%d'", pluginNOINIT, plugin_list_size, plugin_no);
+ return 0;
+ }
+ plugin = plugin_list[plugin_no];
+ if(plugin==NULL || !plugin->open_file_read){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin '%d' is not initialized.", pluginNOINIT, plugin_no);
+ return 0;
+ }
+ if (plugin->read_structure) has_readstructure = 1;
+ if (plugin->read_bonds) has_readbonds = 1;
+ if (plugin->read_angles) has_readangles = 1;
+ if (plugin->read_next_timestep) has_readnexttimestep = 1;
+ if (plugin->write_structure) has_writestructure = 1;
+ if (plugin->write_bonds) has_writebonds = 1;
+ if (plugin->write_angles) has_writeangles = 1;
+ if (plugin->write_timestep) has_writetimestep = 1;
+ PyObject *tuple = PyTuple_New(17);
+ PyTuple_SET_ITEM(tuple, 0, PyString_FromString(plugin->filename_extension));
+ PyTuple_SET_ITEM(tuple, 1, PyString_FromString(plugin->name));
+ PyTuple_SET_ITEM(tuple, 2, PyInt_FromLong((long)has_readstructure));
+ PyTuple_SET_ITEM(tuple, 3, PyInt_FromLong((long)has_readbonds));
+ PyTuple_SET_ITEM(tuple, 4, PyInt_FromLong((long)has_readangles));
+ PyTuple_SET_ITEM(tuple, 5, PyInt_FromLong((long)has_readnexttimestep));
+ PyTuple_SET_ITEM(tuple, 6, PyInt_FromLong((long)has_writestructure));
+ PyTuple_SET_ITEM(tuple, 7, PyInt_FromLong((long)has_writebonds));
+ PyTuple_SET_ITEM(tuple, 8, PyInt_FromLong((long)has_writeangles));
+ PyTuple_SET_ITEM(tuple, 9, PyInt_FromLong((long)has_writetimestep));
+ PyTuple_SET_ITEM(tuple, 10, PyString_FromString(plugin->prettyname));
+ PyTuple_SET_ITEM(tuple, 11, PyString_FromString(plugin->type));
+ PyTuple_SET_ITEM(tuple, 12, PyString_FromString(plugin->author));
+ PyTuple_SET_ITEM(tuple, 13, PyInt_FromLong((long)plugin->majorv));
+ PyTuple_SET_ITEM(tuple, 14, PyInt_FromLong((long)plugin->minorv));
+ PyTuple_SET_ITEM(tuple, 15, PyInt_FromLong((long)plugin->abiversion));
+ PyTuple_SET_ITEM(tuple, 16, PyInt_FromLong((long)plugin->is_reentrant));
+ return tuple;
+ }
+%}
+
+/*
+%feature("autodoc", "0") molfile_open;
+%exception molfile_open {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * molfile_open(molfile_plugin_t* plugin, ) {
+ int *plugno = &plugin_no;
+ return plugin;
+ }
+%}
+*/
+
+/*
+ python wrappers for functions
+ and structure data in molfile_plugin.h
+*/
+
+/* molfile_atom_t
+
+ char name[16]; required atom name string
+ char type[16]; required atom type string
+ char resname[8]; required residue name string
+ int resid; required integer residue ID
+ char segid[8]; required segment name string, or ""
+ char chain[2]; required chain name, or ""
+ char altloc[2]; optional PDB alternate location code
+ char insertion[2]; optional PDB insertion code
+ float occupancy; optional occupancy value
+ float bfactor; optional B-factor value
+ float mass; optional mass value
+ float charge; optional charge value
+ float radius; optional radius value
+ int atomicnumber; optional element atomic number
+ int ctnumber; mae ct block, 0-based, including meta
+*/
+
+
+/* molfile_plugin_t */
+
+
+/* const char *filename_extension; */
+
+
+/*
+ void *(* open_file_read)(const char *filepath, const char *filetype,
+ int *natoms);
+ void (* close_file_read)(void *);
+ int (*read_structure)(void *, int *optflags, molfile_atom_t *atoms);
+ int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
+ int **bondtype, int *nbondtypes, char ***bondtypename);
+ int (* read_next_timestep)(void *, int natoms, molfile_timestep_t *);
+ void *(* open_file_write)(const char *filepath, const char *filetype,
+ int natoms);
+ int (* write_structure)(void *, int optflags, const molfile_atom_t *atoms);
+ int (* write_timestep)(void *, const molfile_timestep_t *);
+ void (* close_file_write)(void *);
+ int (* read_molecule_metadata)(void *, molfile_metadata_t **metadata);
+ int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
+ int *bondtype, int nbondtypes, char **bondtypename);
+ int (* read_angles)(void *handle, int *numangles, int **angles, int **angletypes,
+ int *numangletypes, char ***angletypenames, int *numdihedrals,
+ int **dihedrals, int **dihedraltypes, int *numdihedraltypes,
+ char ***dihedraltypenames, int *numimpropers, int **impropers,
+ int **impropertypes, int *numimpropertypes, char ***impropertypenames,
+ int *numcterms, int **cterms, int *ctermcols, int *ctermrows);
+ int (* write_angles)(void *handle, int numangles, const int *angles, const int *angletypes,
+ int numangletypes, const char **angletypenames, int numdihedrals,
+ const int *dihedrals, const int *dihedraltypes, int numdihedraltypes,
+ const char **dihedraltypenames, int numimpropers,
+ const int *impropers, const int *impropertypes, int numimpropertypes,
+ const char **impropertypenames, int numcterms, const int *cterms,
+ int ctermcols, int ctermrows);
+ int (* read_timestep)(void *, int natoms, molfile_timestep_t *,
+ molfile_qm_metadata_t *, molfile_qm_timestep_t *);
+ int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
+ int (* read_timestep2)(void *, molfile_ssize_t index, molfile_timestep_t *);
+ molfile_ssize_t (* read_times)( void *,
+ molfile_ssize_t start,
+ molfile_ssize_t count,
+ double * times );
+ int (* cons_fputs)(const int, const char*);
+*/
+
+
+/* molfile_timestep_t
+
+ float *coords; coordinates of all atoms, arranged xyzxyzxyz
+ float *velocities; space for velocities of all atoms; same layout
+ float A, B, C, alpha, beta, gamma;
+ double physical_time; physical time point associated with this frame
+
+ double total_energy;
+ double potential_energy;
+ double kinetic_energy;
+ double extended_energy;
+ double force_energy;
+ double total_pressure;
+*/
+
+
+/* molfile_timestep_metadata_t
+
+ unsigned int count; total # timesteps; -1 if unknown
+ unsigned int avg_bytes_per_timestep; bytes per timestep
+ int has_velocities; if timesteps have velocities
+*/
+
+
+
diff --git a/pymolfile/molfile/libpymolfile.py b/pymolfile/molfile/libpymolfile.py
new file mode 100644
index 0000000000000000000000000000000000000000..99826d44affeba9f88384ea9f7c7c7f98d6e0212
--- /dev/null
+++ b/pymolfile/molfile/libpymolfile.py
@@ -0,0 +1,138 @@
+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 3.0.12
+#
+# Do not make changes to this file unless you know what you are doing--modify
+# the SWIG interface file instead.
+
+"""
+
+:Author: Berk Onat <b.onat@warwick.ac.uk>
+:Year: 2017
+:Licence: BSD LICENSE
+
+
+
+"""
+
+
+from sys import version_info as _swig_python_version_info
+if _swig_python_version_info >= (2, 7, 0):
+ def swig_import_helper():
+ import importlib
+ pkg = __name__.rpartition('.')[0]
+ mname = '.'.join((pkg, '_libpymolfile')).lstrip('.')
+ try:
+ return importlib.import_module(mname)
+ except ImportError:
+ return importlib.import_module('_libpymolfile')
+ _libpymolfile = swig_import_helper()
+ del swig_import_helper
+elif _swig_python_version_info >= (2, 6, 0):
+ def swig_import_helper():
+ from os.path import dirname
+ import imp
+ fp = None
+ try:
+ fp, pathname, description = imp.find_module('_libpymolfile', [dirname(__file__)])
+ except ImportError:
+ import _libpymolfile
+ return _libpymolfile
+ try:
+ _mod = imp.load_module('_libpymolfile', fp, pathname, description)
+ finally:
+ if fp is not None:
+ fp.close()
+ return _mod
+ _libpymolfile = swig_import_helper()
+ del swig_import_helper
+else:
+ import _libpymolfile
+del _swig_python_version_info
+
+try:
+ _swig_property = property
+except NameError:
+ pass # Python < 2.2 doesn't have 'property'.
+
+try:
+ import builtins as __builtin__
+except ImportError:
+ import __builtin__
+
+def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
+ if (name == "thisown"):
+ return self.this.own(value)
+ if (name == "this"):
+ if type(value).__name__ == 'SwigPyObject':
+ self.__dict__[name] = value
+ return
+ method = class_type.__swig_setmethods__.get(name, None)
+ if method:
+ return method(self, value)
+ if (not static):
+ if _newclass:
+ object.__setattr__(self, name, value)
+ else:
+ self.__dict__[name] = value
+ else:
+ raise AttributeError("You cannot add attributes to %s" % self)
+
+
+def _swig_setattr(self, class_type, name, value):
+ return _swig_setattr_nondynamic(self, class_type, name, value, 0)
+
+
+def _swig_getattr(self, class_type, name):
+ if (name == "thisown"):
+ return self.this.own()
+ method = class_type.__swig_getmethods__.get(name, None)
+ if method:
+ return method(self)
+ raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
+
+
+def _swig_repr(self):
+ try:
+ strthis = "proxy of " + self.this.__repr__()
+ except __builtin__.Exception:
+ strthis = ""
+ return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
+
+try:
+ _object = object
+ _newclass = 1
+except __builtin__.Exception:
+ class _object:
+ pass
+ _newclass = 0
+
+pluginOK = _libpymolfile.pluginOK
+pluginNOINIT = _libpymolfile.pluginNOINIT
+pluginCLOSE = _libpymolfile.pluginCLOSE
+pluginNOMEM = _libpymolfile.pluginNOMEM
+pluginENDOFFILE = _libpymolfile.pluginENDOFFILE
+pluginFILENOTFOUND = _libpymolfile.pluginFILENOTFOUND
+pluginFORMATERROR = _libpymolfile.pluginFORMATERROR
+
+def molfile_plugin_list(maxsize):
+ """molfile_plugin_list(maxsize) -> molfile_plugin_t **"""
+ return _libpymolfile.molfile_plugin_list(maxsize)
+
+def molfile_init():
+ """molfile_init() -> int"""
+ return _libpymolfile.molfile_init()
+
+def molfile_finish():
+ """molfile_finish() -> int"""
+ return _libpymolfile.molfile_finish()
+
+def get_plugin(plugin_list, plugin_no):
+ """get_plugin(plugin_list, plugin_no) -> molfile_plugin_t *"""
+ return _libpymolfile.get_plugin(plugin_list, plugin_no)
+
+def molfile_plugin_info(plugin_list, plugin_no):
+ """molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"""
+ return _libpymolfile.molfile_plugin_info(plugin_list, plugin_no)
+# This file is compatible with both classic and new-style classes.
+
+
diff --git a/pymolfile/molfile/libpymolfile.pyc b/pymolfile/molfile/libpymolfile.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..f3736e9eb876d4d874db95272a6802c56f105570
Binary files /dev/null and b/pymolfile/molfile/libpymolfile.pyc differ
diff --git a/pymolfile/libpymolfile-old/libvmdmolfile_wrap.c b/pymolfile/molfile/libpymolfile_wrap.c
similarity index 67%
rename from pymolfile/libpymolfile-old/libvmdmolfile_wrap.c
rename to pymolfile/molfile/libpymolfile_wrap.c
index 4f6f3b412b63345876766b85352a020353acd7dc..6f1adbdcb0d89209aadcc05ce50230698c431e8d 100644
--- a/pymolfile/libpymolfile-old/libvmdmolfile_wrap.c
+++ b/pymolfile/molfile/libpymolfile_wrap.c
@@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------------
* This file was automatically generated by SWIG (http://www.swig.org).
- * Version 2.0.9
+ * Version 3.0.12
*
* This file is not intended to be easily readable and contains a number of
* coding conventions designed to improve portability and efficiency. Do not make
@@ -8,7 +8,11 @@
* interface file instead.
* ----------------------------------------------------------------------------- */
+
+#ifndef SWIGPYTHON
#define SWIGPYTHON
+#endif
+
#define SWIG_PYTHON_DIRECTOR_NO_VTABLE
/* -----------------------------------------------------------------------------
@@ -78,9 +82,11 @@
#endif
/* exporting methods */
-#if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
-# ifndef GCC_HASCLASSVISIBILITY
-# define GCC_HASCLASSVISIBILITY
+#if defined(__GNUC__)
+# if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
+# ifndef GCC_HASCLASSVISIBILITY
+# define GCC_HASCLASSVISIBILITY
+# endif
# endif
#endif
@@ -119,10 +125,29 @@
# define _SCL_SECURE_NO_DEPRECATE
#endif
+/* Deal with Apple's deprecated 'AssertMacros.h' from Carbon-framework */
+#if defined(__APPLE__) && !defined(__ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES)
+# define __ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES 0
+#endif
+
+/* Intel's compiler complains if a variable which was never initialised is
+ * cast to void, which is a common idiom which we use to indicate that we
+ * are aware a variable isn't used. So we just silence that warning.
+ * See: https://github.com/swig/swig/issues/192 for more discussion.
+ */
+#ifdef __INTEL_COMPILER
+# pragma warning disable 592
+#endif
-/* Python.h has to appear first */
-#include <Python.h>
+#if defined(_DEBUG) && defined(SWIG_PYTHON_INTERPRETER_NO_DEBUG)
+/* Use debug wrappers with the Python release dll */
+# undef _DEBUG
+# include <Python.h>
+# define _DEBUG
+#else
+# include <Python.h>
+#endif
/* -----------------------------------------------------------------------------
* swigrun.swg
@@ -294,7 +319,7 @@ SWIGINTERNINLINE int SWIG_CheckState(int r) {
return SWIG_IsOK(r) ? SWIG_CastRank(r) + 1 : 0;
}
#else /* no cast-rank mode */
-# define SWIG_AddCast
+# define SWIG_AddCast(r) (r)
# define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0)
#endif
@@ -358,18 +383,18 @@ SWIG_TypeNameComp(const char *f1, const char *l1,
/*
Check type equivalence in a name list like <name1>|<name2>|...
- Return 0 if not equal, 1 if equal
+ Return 0 if equal, -1 if nb < tb, 1 if nb > tb
*/
SWIGRUNTIME int
-SWIG_TypeEquiv(const char *nb, const char *tb) {
- int equiv = 0;
+SWIG_TypeCmp(const char *nb, const char *tb) {
+ int equiv = 1;
const char* te = tb + strlen(tb);
const char* ne = nb;
- while (!equiv && *ne) {
+ while (equiv != 0 && *ne) {
for (nb = ne; *ne; ++ne) {
if (*ne == '|') break;
}
- equiv = (SWIG_TypeNameComp(nb, ne, tb, te) == 0) ? 1 : 0;
+ equiv = SWIG_TypeNameComp(nb, ne, tb, te);
if (*ne) ++ne;
}
return equiv;
@@ -377,24 +402,13 @@ SWIG_TypeEquiv(const char *nb, const char *tb) {
/*
Check type equivalence in a name list like <name1>|<name2>|...
- Return 0 if equal, -1 if nb < tb, 1 if nb > tb
+ Return 0 if not equal, 1 if equal
*/
SWIGRUNTIME int
-SWIG_TypeCompare(const char *nb, const char *tb) {
- int equiv = 0;
- const char* te = tb + strlen(tb);
- const char* ne = nb;
- while (!equiv && *ne) {
- for (nb = ne; *ne; ++ne) {
- if (*ne == '|') break;
- }
- equiv = (SWIG_TypeNameComp(nb, ne, tb, te) == 0) ? 1 : 0;
- if (*ne) ++ne;
- }
- return equiv;
+SWIG_TypeEquiv(const char *nb, const char *tb) {
+ return SWIG_TypeCmp(nb, tb) == 0 ? 1 : 0;
}
-
/*
Check the typename
*/
@@ -541,14 +555,14 @@ SWIG_MangledTypeQueryModule(swig_module_info *start,
swig_module_info *iter = start;
do {
if (iter->size) {
- register size_t l = 0;
- register size_t r = iter->size - 1;
+ size_t l = 0;
+ size_t r = iter->size - 1;
do {
/* since l+r >= 0, we can (>> 1) instead (/ 2) */
- register size_t i = (l + r) >> 1;
+ size_t i = (l + r) >> 1;
const char *iname = iter->types[i]->name;
if (iname) {
- register int compare = strcmp(name, iname);
+ int compare = strcmp(name, iname);
if (compare == 0) {
return iter->types[i];
} else if (compare < 0) {
@@ -592,7 +606,7 @@ SWIG_TypeQueryModule(swig_module_info *start,
of the str field (the human readable name) */
swig_module_info *iter = start;
do {
- register size_t i = 0;
+ size_t i = 0;
for (; i < iter->size; ++i) {
if (iter->types[i]->str && (SWIG_TypeEquiv(iter->types[i]->str, name)))
return iter->types[i];
@@ -611,10 +625,10 @@ SWIG_TypeQueryModule(swig_module_info *start,
SWIGRUNTIME char *
SWIG_PackData(char *c, void *ptr, size_t sz) {
static const char hex[17] = "0123456789abcdef";
- register const unsigned char *u = (unsigned char *) ptr;
- register const unsigned char *eu = u + sz;
+ const unsigned char *u = (unsigned char *) ptr;
+ const unsigned char *eu = u + sz;
for (; u != eu; ++u) {
- register unsigned char uu = *u;
+ unsigned char uu = *u;
*(c++) = hex[(uu & 0xf0) >> 4];
*(c++) = hex[uu & 0xf];
}
@@ -626,22 +640,22 @@ SWIG_PackData(char *c, void *ptr, size_t sz) {
*/
SWIGRUNTIME const char *
SWIG_UnpackData(const char *c, void *ptr, size_t sz) {
- register unsigned char *u = (unsigned char *) ptr;
- register const unsigned char *eu = u + sz;
+ unsigned char *u = (unsigned char *) ptr;
+ const unsigned char *eu = u + sz;
for (; u != eu; ++u) {
- register char d = *(c++);
- register unsigned char uu;
+ char d = *(c++);
+ unsigned char uu;
if ((d >= '0') && (d <= '9'))
- uu = ((d - '0') << 4);
+ uu = (unsigned char)((d - '0') << 4);
else if ((d >= 'a') && (d <= 'f'))
- uu = ((d - ('a'-10)) << 4);
+ uu = (unsigned char)((d - ('a'-10)) << 4);
else
return (char *) 0;
d = *(c++);
if ((d >= '0') && (d <= '9'))
- uu |= (d - '0');
+ uu |= (unsigned char)(d - '0');
else if ((d >= 'a') && (d <= 'f'))
- uu |= (d - ('a'-10));
+ uu |= (unsigned char)(d - ('a'-10));
else
return (char *) 0;
*u = uu;
@@ -737,7 +751,7 @@ SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) {
#define PyString_FromString(x) PyUnicode_FromString(x)
#define PyString_Format(fmt, args) PyUnicode_Format(fmt, args)
#define PyString_AsString(str) PyBytes_AsString(str)
-#define PyString_Size(str) PyBytes_Size(str)
+#define PyString_Size(str) PyBytes_Size(str)
#define PyString_InternFromString(key) PyUnicode_InternFromString(key)
#define Py_TPFLAGS_HAVE_CLASS Py_TPFLAGS_BASETYPE
#define PyString_AS_STRING(x) PyUnicode_AS_STRING(x)
@@ -782,7 +796,7 @@ SWIG_Python_str_AsChar(PyObject *str)
#if PY_VERSION_HEX >= 0x03000000
# define SWIG_Python_str_DelForPy3(x) free( (void*) (x) )
#else
-# define SWIG_Python_str_DelForPy3(x)
+# define SWIG_Python_str_DelForPy3(x)
#endif
@@ -790,7 +804,7 @@ SWIGINTERN PyObject*
SWIG_Python_str_FromChar(const char *c)
{
#if PY_VERSION_HEX >= 0x03000000
- return PyUnicode_FromString(c);
+ return PyUnicode_FromString(c);
#else
return PyString_FromString(c);
#endif
@@ -824,10 +838,6 @@ PyString_FromFormat(const char *fmt, ...) {
}
#endif
-/* Add PyObject_Del for old Pythons */
-#if PY_VERSION_HEX < 0x01060000
-# define PyObject_Del(op) PyMem_DEL((op))
-#endif
#ifndef PyObject_DEL
# define PyObject_DEL PyObject_Del
#endif
@@ -942,6 +952,7 @@ typedef destructor freefunc;
#if PY_VERSION_HEX < 0x03020000
#define PyDescr_TYPE(x) (((PyDescrObject *)(x))->d_type)
#define PyDescr_NAME(x) (((PyDescrObject *)(x))->d_name)
+#define Py_hash_t long
#endif
/* -----------------------------------------------------------------------------
@@ -1028,7 +1039,7 @@ SWIG_Python_AddErrorMsg(const char* mesg)
# endif
# if defined(SWIG_PYTHON_USE_GIL) /* Use PyGILState threads calls */
# ifndef SWIG_PYTHON_INITIALIZE_THREADS
-# define SWIG_PYTHON_INITIALIZE_THREADS PyEval_InitThreads()
+# define SWIG_PYTHON_INITIALIZE_THREADS PyEval_InitThreads()
# endif
# ifdef __cplusplus /* C++ code */
class SWIG_Python_Thread_Block {
@@ -1154,7 +1165,7 @@ SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self),
#define SWIG_InternalNewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags)
-#define SWIG_CheckImplicit(ty) SWIG_Python_CheckImplicit(ty)
+#define SWIG_CheckImplicit(ty) SWIG_Python_CheckImplicit(ty)
#define SWIG_AcquirePtr(ptr, src) SWIG_Python_AcquirePtr(ptr, src)
#define swig_owntype int
@@ -1181,26 +1192,26 @@ SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self),
#define SWIG_SetModule(clientdata, pointer) SWIG_Python_SetModule(pointer)
#define SWIG_NewClientData(obj) SwigPyClientData_New(obj)
-#define SWIG_SetErrorObj SWIG_Python_SetErrorObj
-#define SWIG_SetErrorMsg SWIG_Python_SetErrorMsg
-#define SWIG_ErrorType(code) SWIG_Python_ErrorType(code)
-#define SWIG_Error(code, msg) SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg)
-#define SWIG_fail goto fail
+#define SWIG_SetErrorObj SWIG_Python_SetErrorObj
+#define SWIG_SetErrorMsg SWIG_Python_SetErrorMsg
+#define SWIG_ErrorType(code) SWIG_Python_ErrorType(code)
+#define SWIG_Error(code, msg) SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg)
+#define SWIG_fail goto fail
/* Runtime API implementation */
/* Error manipulation */
-SWIGINTERN void
+SWIGINTERN void
SWIG_Python_SetErrorObj(PyObject *errtype, PyObject *obj) {
- SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
PyErr_SetObject(errtype, obj);
Py_DECREF(obj);
SWIG_PYTHON_THREAD_END_BLOCK;
}
-SWIGINTERN void
+SWIGINTERN void
SWIG_Python_SetErrorMsg(PyObject *errtype, const char *msg) {
SWIG_PYTHON_THREAD_BEGIN_BLOCK;
PyErr_SetString(errtype, msg);
@@ -1221,7 +1232,7 @@ SwigPyBuiltin_AddPublicSymbol(PyObject *seq, const char *key) {
}
SWIGINTERN void
-SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *name, PyObject *obj) {
+SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *name, PyObject *obj) {
#if PY_VERSION_HEX < 0x02030000
PyDict_SetItemString(d, (char *)name, obj);
#else
@@ -1235,13 +1246,13 @@ SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *nam
#else
SWIGINTERN void
-SWIG_Python_SetConstant(PyObject *d, const char *name, PyObject *obj) {
+SWIG_Python_SetConstant(PyObject *d, const char *name, PyObject *obj) {
#if PY_VERSION_HEX < 0x02030000
PyDict_SetItemString(d, (char *)name, obj);
#else
PyDict_SetItemString(d, name, obj);
#endif
- Py_DECREF(obj);
+ Py_DECREF(obj);
}
#endif
@@ -1293,21 +1304,21 @@ SWIG_Python_AppendOutput(PyObject* result, PyObject* obj) {
/* Unpack the argument tuple */
-SWIGINTERN int
+SWIGINTERN Py_ssize_t
SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssize_t max, PyObject **objs)
{
if (!args) {
if (!min && !max) {
return 1;
} else {
- PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got none",
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got none",
name, (min == max ? "" : "at least "), (int)min);
return 0;
}
- }
+ }
if (!PyTuple_Check(args)) {
if (min <= 1 && max >= 1) {
- register int i;
+ Py_ssize_t i;
objs[0] = args;
for (i = 1; i < max; ++i) {
objs[i] = 0;
@@ -1317,17 +1328,17 @@ SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssi
PyErr_SetString(PyExc_SystemError, "UnpackTuple() argument list is not a tuple");
return 0;
} else {
- register Py_ssize_t l = PyTuple_GET_SIZE(args);
+ Py_ssize_t l = PyTuple_GET_SIZE(args);
if (l < min) {
- PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
name, (min == max ? "" : "at least "), (int)min, (int)l);
return 0;
} else if (l > max) {
- PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
name, (min == max ? "" : "at most "), (int)max, (int)l);
return 0;
} else {
- register int i;
+ Py_ssize_t i;
for (i = 0; i < l; ++i) {
objs[i] = PyTuple_GET_ITEM(args, i);
}
@@ -1335,7 +1346,7 @@ SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssi
objs[l] = 0;
}
return i + 1;
- }
+ }
}
}
@@ -1387,14 +1398,14 @@ extern "C" {
# undef Py_None
# define Py_None SWIG_Py_None()
# endif
-SWIGRUNTIMEINLINE PyObject *
+SWIGRUNTIMEINLINE PyObject *
_SWIG_Py_None(void)
{
PyObject *none = Py_BuildValue((char*)"");
Py_DECREF(none);
return none;
}
-SWIGRUNTIME PyObject *
+SWIGRUNTIME PyObject *
SWIG_Py_None(void)
{
static PyObject *SWIG_STATIC_POINTER(none) = _SWIG_Py_None();
@@ -1404,7 +1415,7 @@ SWIG_Py_None(void)
/* The python void return value */
-SWIGRUNTIMEINLINE PyObject *
+SWIGRUNTIMEINLINE PyObject *
SWIG_Py_Void(void)
{
PyObject *none = Py_None;
@@ -1424,7 +1435,7 @@ typedef struct {
PyTypeObject *pytype;
} SwigPyClientData;
-SWIGRUNTIMEINLINE int
+SWIGRUNTIMEINLINE int
SWIG_Python_CheckImplicit(swig_type_info *ty)
{
SwigPyClientData *data = (SwigPyClientData *)ty->clientdata;
@@ -1439,7 +1450,7 @@ SWIG_Python_ExceptionType(swig_type_info *desc) {
}
-SWIGRUNTIME SwigPyClientData *
+SWIGRUNTIME SwigPyClientData *
SwigPyClientData_New(PyObject* obj)
{
if (!obj) {
@@ -1493,7 +1504,7 @@ SwigPyClientData_New(PyObject* obj)
}
}
-SWIGRUNTIME void
+SWIGRUNTIME void
SwigPyClientData_Del(SwigPyClientData *data) {
Py_XDECREF(data->newraw);
Py_XDECREF(data->newargs);
@@ -1513,6 +1524,23 @@ typedef struct {
#endif
} SwigPyObject;
+
+#ifdef SWIGPYTHON_BUILTIN
+
+SWIGRUNTIME PyObject *
+SwigPyObject_get___dict__(PyObject *v, PyObject *SWIGUNUSEDPARM(args))
+{
+ SwigPyObject *sobj = (SwigPyObject *)v;
+
+ if (!sobj->dict)
+ sobj->dict = PyDict_New();
+
+ Py_INCREF(sobj->dict);
+ return sobj->dict;
+}
+
+#endif
+
SWIGRUNTIME PyObject *
SwigPyObject_long(SwigPyObject *v)
{
@@ -1577,35 +1605,7 @@ SwigPyObject_repr(SwigPyObject *v, PyObject *args)
PyString_ConcatAndDel(&repr,nrep);
# endif
}
- return repr;
-}
-
-SWIGRUNTIME int
-SwigPyObject_print(SwigPyObject *v, FILE *fp, int SWIGUNUSEDPARM(flags))
-{
- char *str;
-#ifdef METH_NOARGS
- PyObject *repr = SwigPyObject_repr(v);
-#else
- PyObject *repr = SwigPyObject_repr(v, NULL);
-#endif
- if (repr) {
- str = SWIG_Python_str_AsChar(repr);
- fputs(str, fp);
- SWIG_Python_str_DelForPy3(str);
- Py_DECREF(repr);
- return 0;
- } else {
- return 1;
- }
-}
-
-SWIGRUNTIME PyObject *
-SwigPyObject_str(SwigPyObject *v)
-{
- char result[SWIG_BUFFER_SIZE];
- return SWIG_PackVoidPtr(result, v->ptr, v->ty->name, sizeof(result)) ?
- SWIG_Python_str_FromChar(result) : 0;
+ return repr;
}
SWIGRUNTIME int
@@ -1626,7 +1626,7 @@ SwigPyObject_richcompare(SwigPyObject *v, SwigPyObject *w, int op)
return Py_NotImplemented;
}
res = PyBool_FromLong( (SwigPyObject_compare(v, w)==0) == (op == Py_EQ) ? 1 : 0);
- return res;
+ return res;
}
@@ -1679,30 +1679,46 @@ SwigPyObject_dealloc(PyObject *v)
if (destroy) {
/* destroy is always a VARARGS method */
PyObject *res;
+
+ /* PyObject_CallFunction() has the potential to silently drop
+ the active active exception. In cases of unnamed temporary
+ variable or where we just finished iterating over a generator
+ StopIteration will be active right now, and this needs to
+ remain true upon return from SwigPyObject_dealloc. So save
+ and restore. */
+
+ PyObject *val = NULL, *type = NULL, *tb = NULL;
+ PyErr_Fetch(&val, &type, &tb);
+
if (data->delargs) {
- /* we need to create a temporary object to carry the destroy operation */
- PyObject *tmp = SwigPyObject_New(sobj->ptr, ty, 0);
- res = SWIG_Python_CallFunctor(destroy, tmp);
- Py_DECREF(tmp);
+ /* we need to create a temporary object to carry the destroy operation */
+ PyObject *tmp = SwigPyObject_New(sobj->ptr, ty, 0);
+ res = SWIG_Python_CallFunctor(destroy, tmp);
+ Py_DECREF(tmp);
} else {
- PyCFunction meth = PyCFunction_GET_FUNCTION(destroy);
- PyObject *mself = PyCFunction_GET_SELF(destroy);
- res = ((*meth)(mself, v));
+ PyCFunction meth = PyCFunction_GET_FUNCTION(destroy);
+ PyObject *mself = PyCFunction_GET_SELF(destroy);
+ res = ((*meth)(mself, v));
}
+ if (!res)
+ PyErr_WriteUnraisable(destroy);
+
+ PyErr_Restore(val, type, tb);
+
Py_XDECREF(res);
- }
+ }
#if !defined(SWIG_PYTHON_SILENT_MEMLEAK)
else {
const char *name = SWIG_TypePrettyName(ty);
printf("swig/python detected a memory leak of type '%s', no destructor found.\n", (name ? name : "unknown"));
}
#endif
- }
+ }
Py_XDECREF(next);
PyObject_DEL(v);
}
-SWIGRUNTIME PyObject*
+SWIGRUNTIME PyObject*
SwigPyObject_append(PyObject* v, PyObject* next)
{
SwigPyObject *sobj = (SwigPyObject *) v;
@@ -1712,6 +1728,7 @@ SwigPyObject_append(PyObject* v, PyObject* next)
next = tmp;
#endif
if (!SwigPyObject_Check(next)) {
+ PyErr_SetString(PyExc_TypeError, "Attempt to append a non SwigPyObject");
return NULL;
}
sobj->next = next;
@@ -1719,7 +1736,7 @@ SwigPyObject_append(PyObject* v, PyObject* next)
return SWIG_Py_Void();
}
-SWIGRUNTIME PyObject*
+SWIGRUNTIME PyObject*
#ifdef METH_NOARGS
SwigPyObject_next(PyObject* v)
#else
@@ -1727,7 +1744,7 @@ SwigPyObject_next(PyObject* v, PyObject *SWIGUNUSEDPARM(args))
#endif
{
SwigPyObject *sobj = (SwigPyObject *) v;
- if (sobj->next) {
+ if (sobj->next) {
Py_INCREF(sobj->next);
return sobj->next;
} else {
@@ -1766,13 +1783,13 @@ SwigPyObject_own(PyObject *v, PyObject *args)
#if (PY_VERSION_HEX < 0x02020000)
if (!PyArg_ParseTuple(args,(char *)"|O:own",&val))
#elif (PY_VERSION_HEX < 0x02050000)
- if (!PyArg_UnpackTuple(args, (char *)"own", 0, 1, &val))
+ if (!PyArg_UnpackTuple(args, (char *)"own", 0, 1, &val))
#else
- if (!PyArg_UnpackTuple(args, "own", 0, 1, &val))
+ if (!PyArg_UnpackTuple(args, "own", 0, 1, &val))
#endif
{
return NULL;
- }
+ }
else
{
SwigPyObject *sobj = (SwigPyObject *)v;
@@ -1791,7 +1808,7 @@ SwigPyObject_own(PyObject *v, PyObject *args)
SwigPyObject_disown(v,args);
}
#endif
- }
+ }
return obj;
}
}
@@ -1800,23 +1817,23 @@ SwigPyObject_own(PyObject *v, PyObject *args)
static PyMethodDef
swigobject_methods[] = {
{(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_NOARGS, (char *)"releases ownership of the pointer"},
- {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_NOARGS, (char *)"aquires ownership of the pointer"},
+ {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_NOARGS, (char *)"acquires ownership of the pointer"},
{(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"},
{(char *)"append", (PyCFunction)SwigPyObject_append, METH_O, (char *)"appends another 'this' object"},
{(char *)"next", (PyCFunction)SwigPyObject_next, METH_NOARGS, (char *)"returns the next 'this' object"},
{(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_NOARGS, (char *)"returns object representation"},
- {0, 0, 0, 0}
+ {0, 0, 0, 0}
};
#else
static PyMethodDef
swigobject_methods[] = {
{(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_VARARGS, (char *)"releases ownership of the pointer"},
- {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_VARARGS, (char *)"aquires ownership of the pointer"},
+ {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_VARARGS, (char *)"acquires ownership of the pointer"},
{(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"},
{(char *)"append", (PyCFunction)SwigPyObject_append, METH_VARARGS, (char *)"appends another 'this' object"},
{(char *)"next", (PyCFunction)SwigPyObject_next, METH_VARARGS, (char *)"returns the next 'this' object"},
{(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_VARARGS, (char *)"returns object representation"},
- {0, 0, 0, 0}
+ {0, 0, 0, 0}
};
#endif
@@ -1867,7 +1884,9 @@ SwigPyObject_TypeOnce(void) {
(unaryfunc)SwigPyObject_oct, /*nb_oct*/
(unaryfunc)SwigPyObject_hex, /*nb_hex*/
#endif
-#if PY_VERSION_HEX >= 0x03000000 /* 3.0 */
+#if PY_VERSION_HEX >= 0x03050000 /* 3.5 */
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_matrix_multiply */
+#elif PY_VERSION_HEX >= 0x03000000 /* 3.0 */
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index, nb_inplace_divide removed */
#elif PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index */
@@ -1882,7 +1901,6 @@ SwigPyObject_TypeOnce(void) {
static int type_init = 0;
if (!type_init) {
const PyTypeObject tmp = {
- /* PyObject header changed in Python 3 */
#if PY_VERSION_HEX >= 0x03000000
PyVarObject_HEAD_INIT(NULL, 0)
#else
@@ -1893,7 +1911,7 @@ SwigPyObject_TypeOnce(void) {
sizeof(SwigPyObject), /* tp_basicsize */
0, /* tp_itemsize */
(destructor)SwigPyObject_dealloc, /* tp_dealloc */
- (printfunc)SwigPyObject_print, /* tp_print */
+ 0, /* tp_print */
#if PY_VERSION_HEX < 0x02020000
(getattrfunc)SwigPyObject_getattr, /* tp_getattr */
#else
@@ -1901,7 +1919,7 @@ SwigPyObject_TypeOnce(void) {
#endif
(setattrfunc)0, /* tp_setattr */
#if PY_VERSION_HEX >= 0x03000000
- 0, /* tp_reserved in 3.0.1, tp_compare in 3.0.0 but not used */
+ 0, /* tp_reserved in 3.0.1, tp_compare in 3.0.0 but not used */
#else
(cmpfunc)SwigPyObject_compare, /* tp_compare */
#endif
@@ -1911,7 +1929,7 @@ SwigPyObject_TypeOnce(void) {
0, /* tp_as_mapping */
(hashfunc)0, /* tp_hash */
(ternaryfunc)0, /* tp_call */
- (reprfunc)SwigPyObject_str, /* tp_str */
+ 0, /* tp_str */
PyObject_GenericGetAttr, /* tp_getattro */
0, /* tp_setattro */
0, /* tp_as_buffer */
@@ -1947,10 +1965,19 @@ SwigPyObject_TypeOnce(void) {
0, /* tp_del */
#endif
#if PY_VERSION_HEX >= 0x02060000
- 0, /* tp_version */
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
#endif
#ifdef COUNT_ALLOCS
- 0,0,0,0 /* tp_alloc -> tp_next */
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
#endif
};
swigpyobject_type = tmp;
@@ -1993,16 +2020,16 @@ SWIGRUNTIME int
SwigPyPacked_print(SwigPyPacked *v, FILE *fp, int SWIGUNUSEDPARM(flags))
{
char result[SWIG_BUFFER_SIZE];
- fputs("<Swig Packed ", fp);
+ fputs("<Swig Packed ", fp);
if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) {
- fputs("at ", fp);
- fputs(result, fp);
+ fputs("at ", fp);
+ fputs(result, fp);
}
- fputs(v->ty->name,fp);
+ fputs(v->ty->name,fp);
fputs(">", fp);
- return 0;
+ return 0;
}
-
+
SWIGRUNTIME PyObject *
SwigPyPacked_repr(SwigPyPacked *v)
{
@@ -2011,7 +2038,7 @@ SwigPyPacked_repr(SwigPyPacked *v)
return SWIG_Python_str_FromFormat("<Swig Packed at %s%s>", result, v->ty->name);
} else {
return SWIG_Python_str_FromFormat("<Swig Packed %s>", v->ty->name);
- }
+ }
}
SWIGRUNTIME PyObject *
@@ -2022,7 +2049,7 @@ SwigPyPacked_str(SwigPyPacked *v)
return SWIG_Python_str_FromFormat("%s%s", result, v->ty->name);
} else {
return SWIG_Python_str_FromChar(v->ty->name);
- }
+ }
}
SWIGRUNTIME int
@@ -2044,7 +2071,7 @@ SwigPyPacked_type(void) {
SWIGRUNTIMEINLINE int
SwigPyPacked_Check(PyObject *op) {
- return ((op)->ob_type == SwigPyPacked_TypeOnce())
+ return ((op)->ob_type == SwigPyPacked_TypeOnce())
|| (strcmp((op)->ob_type->tp_name,"SwigPyPacked") == 0);
}
@@ -2065,7 +2092,6 @@ SwigPyPacked_TypeOnce(void) {
static int type_init = 0;
if (!type_init) {
const PyTypeObject tmp = {
- /* PyObject header changed in Python 3 */
#if PY_VERSION_HEX>=0x03000000
PyVarObject_HEAD_INIT(NULL, 0)
#else
@@ -2126,10 +2152,19 @@ SwigPyPacked_TypeOnce(void) {
0, /* tp_del */
#endif
#if PY_VERSION_HEX >= 0x02060000
- 0, /* tp_version */
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
#endif
#ifdef COUNT_ALLOCS
- 0,0,0,0 /* tp_alloc -> tp_next */
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
#endif
};
swigpypacked_type = tmp;
@@ -2200,11 +2235,11 @@ SWIG_This(void)
/* TODO: I don't know how to implement the fast getset in Python 3 right now */
#if PY_VERSION_HEX>=0x03000000
-#define SWIG_PYTHON_SLOW_GETSET_THIS
+#define SWIG_PYTHON_SLOW_GETSET_THIS
#endif
SWIGRUNTIME SwigPyObject *
-SWIG_Python_GetSwigThis(PyObject *pyobj)
+SWIG_Python_GetSwigThis(PyObject *pyobj)
{
PyObject *obj;
@@ -2227,7 +2262,7 @@ SWIG_Python_GetSwigThis(PyObject *pyobj)
#if (!defined(SWIG_PYTHON_SLOW_GETSET_THIS) && (PY_VERSION_HEX >= 0x02030000))
if (PyInstance_Check(pyobj)) {
- obj = _PyInstance_Lookup(pyobj, SWIG_This());
+ obj = _PyInstance_Lookup(pyobj, SWIG_This());
} else {
PyObject **dictptr = _PyObject_GetDictPtr(pyobj);
if (dictptr != NULL) {
@@ -2260,7 +2295,7 @@ SWIG_Python_GetSwigThis(PyObject *pyobj)
#endif
if (obj && !SwigPyObject_Check(obj)) {
/* a PyObject is called 'this', try to get the 'real this'
- SwigPyObject from it */
+ SwigPyObject from it */
return SWIG_Python_GetSwigThis(obj);
}
return (SwigPyObject *)obj;
@@ -2288,10 +2323,11 @@ SWIGRUNTIME int
SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int flags, int *own) {
int res;
SwigPyObject *sobj;
+ int implicit_conv = (flags & SWIG_POINTER_IMPLICIT_CONV) != 0;
if (!obj)
return SWIG_ERROR;
- if (obj == Py_None) {
+ if (obj == Py_None && !implicit_conv) {
if (ptr)
*ptr = 0;
return SWIG_OK;
@@ -2340,7 +2376,7 @@ SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int
}
res = SWIG_OK;
} else {
- if (flags & SWIG_POINTER_IMPLICIT_CONV) {
+ if (implicit_conv) {
SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0;
if (data && !data->implicitconv) {
PyObject *klass = data->klass;
@@ -2366,7 +2402,7 @@ SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int
res = SWIG_AddCast(res);
res = SWIG_AddNewMask(res);
} else {
- res = SWIG_AddCast(res);
+ res = SWIG_AddCast(res);
}
}
}
@@ -2375,6 +2411,13 @@ SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int
}
}
}
+ if (!SWIG_IsOK(res) && obj == Py_None) {
+ if (ptr)
+ *ptr = 0;
+ if (PyErr_Occurred())
+ PyErr_Clear();
+ res = SWIG_OK;
+ }
}
return res;
}
@@ -2387,13 +2430,13 @@ SWIG_Python_ConvertFunctionPtr(PyObject *obj, void **ptr, swig_type_info *ty) {
return SWIG_ConvertPtr(obj, ptr, ty, 0);
} else {
void *vptr = 0;
-
+
/* here we get the method pointer for callbacks */
const char *doc = (((PyCFunctionObject *)obj) -> m_ml -> ml_doc);
const char *desc = doc ? strstr(doc, "swig_ptr: ") : 0;
if (desc)
desc = ty ? SWIG_UnpackVoidPtr(desc + 10, &vptr, ty->name) : 0;
- if (!desc)
+ if (!desc)
return SWIG_ERROR;
if (ty) {
swig_cast_info *tc = SWIG_TypeCheck(desc,ty);
@@ -2425,7 +2468,7 @@ SWIG_Python_ConvertPacked(PyObject *obj, void *ptr, size_t sz, swig_type_info *t
}
}
return SWIG_OK;
-}
+}
/* -----------------------------------------------------------------------------
* Create a new pointer object
@@ -2436,7 +2479,7 @@ SWIG_Python_ConvertPacked(PyObject *obj, void *ptr, size_t sz, swig_type_info *t
'this' attribute.
*/
-SWIGRUNTIME PyObject*
+SWIGRUNTIME PyObject*
SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this)
{
#if (PY_VERSION_HEX >= 0x02020000)
@@ -2462,7 +2505,7 @@ SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this)
}
} else {
#if PY_VERSION_HEX >= 0x03000000
- inst = PyBaseObject_Type.tp_new((PyTypeObject*) data->newargs, Py_None, Py_None);
+ inst = ((PyTypeObject*) data->newargs)->tp_new((PyTypeObject*) data->newargs, Py_None, Py_None);
if (inst) {
PyObject_SetAttr(inst, SWIG_This(), swig_this);
Py_TYPE(inst)->tp_flags &= ~Py_TPFLAGS_VALID_VERSION_TAG;
@@ -2530,7 +2573,7 @@ SWIG_Python_SetSwigThis(PyObject *inst, PyObject *swig_this)
dict = PyObject_GetAttrString(inst, (char*)"__dict__");
PyDict_SetItem(dict, SWIG_This(), swig_this);
Py_DECREF(dict);
-}
+}
SWIGINTERN PyObject *
@@ -2572,18 +2615,21 @@ SWIG_Python_NewPointerObj(PyObject *self, void *ptr, swig_type_info *type, int f
newobj = (SwigPyObject *) newobj->next;
newobj->next = next_self;
newobj = (SwigPyObject *)next_self;
+#ifdef SWIGPYTHON_BUILTIN
+ newobj->dict = 0;
+#endif
}
} else {
newobj = PyObject_New(SwigPyObject, clientdata->pytype);
+#ifdef SWIGPYTHON_BUILTIN
+ newobj->dict = 0;
+#endif
}
if (newobj) {
newobj->ptr = ptr;
newobj->ty = type;
newobj->own = own;
newobj->next = 0;
-#ifdef SWIGPYTHON_BUILTIN
- newobj->dict = 0;
-#endif
return (PyObject*) newobj;
}
return SWIG_Py_Void();
@@ -2608,7 +2654,7 @@ SWIG_Python_NewPackedObj(void *ptr, size_t sz, swig_type_info *type) {
}
/* -----------------------------------------------------------------------------*
- * Get type list
+ * Get type list
* -----------------------------------------------------------------------------*/
#ifdef SWIG_LINK_RUNTIME
@@ -2646,16 +2692,14 @@ PyModule_AddObject(PyObject *m, char *name, PyObject *o)
{
PyObject *dict;
if (!PyModule_Check(m)) {
- PyErr_SetString(PyExc_TypeError,
- "PyModule_AddObject() needs module as first arg");
+ PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs module as first arg");
return SWIG_ERROR;
}
if (!o) {
- PyErr_SetString(PyExc_TypeError,
- "PyModule_AddObject() needs non-NULL value");
+ PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs non-NULL value");
return SWIG_ERROR;
}
-
+
dict = PyModule_GetDict(m);
if (dict == NULL) {
/* Internal error -- modules must have a dict! */
@@ -2732,7 +2776,7 @@ SWIGRUNTIME swig_type_info *
SWIG_Python_TypeQuery(const char *type)
{
PyObject *cache = SWIG_Python_TypeCache();
- PyObject *key = SWIG_Python_str_FromChar(type);
+ PyObject *key = SWIG_Python_str_FromChar(type);
PyObject *obj = PyDict_GetItem(cache, key);
swig_type_info *descriptor;
if (obj) {
@@ -2758,7 +2802,7 @@ SWIG_Python_TypeQuery(const char *type)
return descriptor;
}
-/*
+/*
For backward compatibility only
*/
#define SWIG_POINTER_EXCEPTION 0
@@ -2767,7 +2811,7 @@ SWIG_Python_TypeQuery(const char *type)
SWIGRUNTIME int
SWIG_Python_AddErrMesg(const char* mesg, int infront)
-{
+{
if (PyErr_Occurred()) {
PyObject *type = 0;
PyObject *value = 0;
@@ -2791,7 +2835,7 @@ SWIG_Python_AddErrMesg(const char* mesg, int infront)
return 0;
}
}
-
+
SWIGRUNTIME int
SWIG_Python_ArgFail(int argnum)
{
@@ -2825,10 +2869,10 @@ SWIG_Python_TypeError(const char *type, PyObject *obj)
type, otype);
return;
}
- } else
-#endif
+ } else
+#endif
{
- const char *otype = (obj ? obj->ob_type->tp_name : 0);
+ const char *otype = (obj ? obj->ob_type->tp_name : 0);
if (otype) {
PyObject *str = PyObject_Str(obj);
const char *cstr = str ? SWIG_Python_str_AsChar(str) : 0;
@@ -2843,7 +2887,7 @@ SWIG_Python_TypeError(const char *type, PyObject *obj)
Py_XDECREF(str);
return;
}
- }
+ }
PyErr_Format(PyExc_TypeError, "a '%s' is expected", type);
} else {
PyErr_Format(PyExc_TypeError, "unexpected type is received");
@@ -2874,7 +2918,7 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
PyObject *descr;
PyObject *encoded_name;
descrsetfunc f;
- int res;
+ int res = -1;
# ifdef Py_USING_UNICODE
if (PyString_Check(name)) {
@@ -2897,7 +2941,6 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
goto done;
}
- res = -1;
descr = _PyType_Lookup(tp, name);
f = NULL;
if (descr != NULL)
@@ -2914,7 +2957,7 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
} else {
res = f(descr, obj, value);
}
-
+
done:
Py_DECREF(name);
return res;
@@ -2928,20 +2971,19 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
-#define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0)
+#define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0)
-#define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else
+#define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else
/* -------- TYPES TABLE (BEGIN) -------- */
-#define SWIGTYPE_p_XDRFILE swig_types[0]
-#define SWIGTYPE_p_a_3__a_3__float swig_types[1]
-#define SWIGTYPE_p_a_3__float swig_types[2]
-#define SWIGTYPE_p_char swig_types[3]
-static swig_type_info *swig_types[5];
-static swig_module_info swig_module = {swig_types, 4, 0, 0, 0, 0};
+#define SWIGTYPE_p_char swig_types[0]
+#define SWIGTYPE_p_int swig_types[1]
+#define SWIGTYPE_p_molfile_plugin_t swig_types[2]
+static swig_type_info *swig_types[4];
+static swig_module_info swig_module = {swig_types, 3, 0, 0, 0, 0};
#define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name)
#define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name)
@@ -2954,41 +2996,45 @@ static swig_module_info swig_module = {swig_types, 4, 0, 0, 0, 0};
#endif
/*-----------------------------------------------
- @(target):= _libxdrfile2.so
+ @(target):= _libpymolfile.so
------------------------------------------------*/
#if PY_VERSION_HEX >= 0x03000000
-# define SWIG_init PyInit__libxdrfile2
+# define SWIG_init PyInit__libpymolfile
#else
-# define SWIG_init init_libxdrfile2
+# define SWIG_init init_libpymolfile
#endif
-#define SWIG_name "_libxdrfile2"
+#define SWIG_name "_libpymolfile"
-#define SWIGVERSION 0x020009
+#define SWIGVERSION 0x030012
#define SWIG_VERSION SWIGVERSION
-#define SWIG_as_voidptr(a) (void *)((const void *)(a))
-#define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),(void**)(a))
+#define SWIG_as_voidptr(a) (void *)((const void *)(a))
+#define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),(void**)(a))
-/* Python SWIG interface to some functions in Gromacs libxdr v 2.0
- Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
- Published under the GNU LESSER GENERAL PUBLIC LICENSE Version 3 (or higher)
- See http://mdanalysis.googlecode.com for details.
+/* Python SWIG interface to libpymolfile
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under BSD LICENSE
*/
#define SWIG_FILE_WITH_INIT
#include <stdio.h>
-#include "xdrfile.h"
-#include "xdrfile_trr.h"
-#include "xdrfile_xtc.h"
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+#include "pymolfile.h"
#ifndef SWIG_FILE_WITH_INIT
-# define NO_IMPORT_ARRAY
+#define NO_IMPORT_ARRAY
#endif
#include "stdio.h"
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
@@ -2999,1496 +3045,294 @@ SWIGINTERNINLINE PyObject*
}
-SWIGINTERN swig_type_info*
-SWIG_pchar_descriptor(void)
-{
- static int init = 0;
- static swig_type_info* info = 0;
- if (!init) {
- info = SWIG_TypeQuery("_p_char");
- init = 1;
+PyObject * molfile_plugin_info(molfile_plugin_t *plugin_list, int plugin_no) {
+ molfile_plugin_t *plugin;
+ void *plugin_handle;
+ int has_readstructure = 0;
+ int has_readbonds = 0;
+ int has_readangles = 0;
+ int has_writestructure = 0;
+ int has_writebonds = 0;
+ int has_writeangles = 0;
+ int has_readnexttimestep = 0;
+ int has_writetimestep = 0;
+ int plugin_list_size = sizeof(plugin_list) / sizeof(molfile_plugin_t*);
+ if (&plugin_no==NULL || plugin_no<0 || plugin_no>plugin_list_size){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin handle no should be given, be positive value and should not exceed the list length. You set '%d'", pluginNOINIT, plugin_no);
+ return 0;
+ }
+ plugin = plugin_list[plugin_no];
+ if(plugin==NULL || !plugin->open_file_read){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin '%d' is not initialized.", pluginNOINIT, plugin_no);
+ return 0;
+ }
+ if (plugin->read_structure) has_readstructure = 1;
+ if (plugin->read_bonds) has_readbonds = 1;
+ if (plugin->read_angles) has_readangles = 1;
+ if (plugin->read_next_timestep) has_readnexttimestep = 1;
+ if (plugin->write_structure) has_writestructure = 1;
+ if (plugin->write_bonds) has_writebonds = 1;
+ if (plugin->write_angles) has_writeangles = 1;
+ if (plugin->write_timestep) has_writetimestep = 1;
+ PyObject *tuple = PyTuple_New(16);
+ PyTuple_SET_ITEM(tuple, 0, PyString_FromString((const char)plugin->name));
+ PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)has_readstructure));
+ PyTuple_SET_ITEM(tuple, 2, PyInt_FromLong((long)has_readbonds));
+ PyTuple_SET_ITEM(tuple, 3, PyInt_FromLong((long)has_readangles));
+ PyTuple_SET_ITEM(tuple, 4, PyInt_FromLong((long)has_readnexttimestep));
+ PyTuple_SET_ITEM(tuple, 5, PyInt_FromLong((long)has_writestructure));
+ PyTuple_SET_ITEM(tuple, 6, PyInt_FromLong((long)has_writebonds));
+ PyTuple_SET_ITEM(tuple, 7, PyInt_FromLong((long)has_writeangles));
+ PyTuple_SET_ITEM(tuple, 8, PyInt_FromLong((long)has_writetimestep));
+ PyTuple_SET_ITEM(tuple, 9, PyString_FromString((const char)plugin->prettyname));
+ PyTuple_SET_ITEM(tuple, 10, PyString_FromString((const char)plugin->type));
+ PyTuple_SET_ITEM(tuple, 11, PyString_FromString((const char)plugin->author));
+ PyTuple_SET_ITEM(tuple, 12, PyInt_FromLong((long)plugin->majorv));
+ PyTuple_SET_ITEM(tuple, 13, PyInt_FromLong((long)plugin->minorv));
+ PyTuple_SET_ITEM(tuple, 14, PyInt_FromLong((long)plugin->abiversion));
+ PyTuple_SET_ITEM(tuple, 15, PyInt_FromLong((long)plugin->is_reentrant));
+ return tuple;
}
- return info;
-}
+
+
+#include <limits.h>
+#if !defined(SWIG_NO_LLONG_MAX)
+# if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__)
+# define LLONG_MAX __LONG_LONG_MAX__
+# define LLONG_MIN (-LLONG_MAX - 1LL)
+# define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL)
+# endif
+#endif
SWIGINTERN int
-SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc)
+SWIG_AsVal_double (PyObject *obj, double *val)
{
-#if PY_VERSION_HEX>=0x03000000
- if (PyUnicode_Check(obj))
-#else
- if (PyString_Check(obj))
+ int res = SWIG_TypeError;
+ if (PyFloat_Check(obj)) {
+ if (val) *val = PyFloat_AsDouble(obj);
+ return SWIG_OK;
+#if PY_VERSION_HEX < 0x03000000
+ } else if (PyInt_Check(obj)) {
+ if (val) *val = (double) PyInt_AsLong(obj);
+ return SWIG_OK;
#endif
+ } else if (PyLong_Check(obj)) {
+ double v = PyLong_AsDouble(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_OK;
+ } else {
+ PyErr_Clear();
+ }
+ }
+#ifdef SWIG_PYTHON_CAST_MODE
{
- char *cstr; Py_ssize_t len;
-#if PY_VERSION_HEX>=0x03000000
- if (!alloc && cptr) {
- /* We can't allow converting without allocation, since the internal
- representation of string in Python 3 is UCS-2/UCS-4 but we require
- a UTF-8 representation.
- TODO(bhy) More detailed explanation */
- return SWIG_RuntimeError;
+ int dispatch = 0;
+ double d = PyFloat_AsDouble(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = d;
+ return SWIG_AddCast(SWIG_OK);
+ } else {
+ PyErr_Clear();
}
- obj = PyUnicode_AsUTF8String(obj);
- PyBytes_AsStringAndSize(obj, &cstr, &len);
- if(alloc) *alloc = SWIG_NEWOBJ;
-#else
- PyString_AsStringAndSize(obj, &cstr, &len);
-#endif
- if (cptr) {
- if (alloc) {
- /*
- In python the user should not be able to modify the inner
- string representation. To warranty that, if you define
- SWIG_PYTHON_SAFE_CSTRINGS, a new/copy of the python string
- buffer is always returned.
-
- The default behavior is just to return the pointer value,
- so, be careful.
- */
-#if defined(SWIG_PYTHON_SAFE_CSTRINGS)
- if (*alloc != SWIG_OLDOBJ)
-#else
- if (*alloc == SWIG_NEWOBJ)
-#endif
- {
- *cptr = (char *)memcpy((char *)malloc((len + 1)*sizeof(char)), cstr, sizeof(char)*(len + 1));
- *alloc = SWIG_NEWOBJ;
- }
- else {
- *cptr = cstr;
- *alloc = SWIG_OLDOBJ;
- }
+ if (!dispatch) {
+ long v = PyLong_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_AddCast(SWIG_AddCast(SWIG_OK));
} else {
- #if PY_VERSION_HEX>=0x03000000
- assert(0); /* Should never reach here in Python 3 */
- #endif
- *cptr = SWIG_Python_str_AsChar(obj);
- }
- }
- if (psize) *psize = len + 1;
-#if PY_VERSION_HEX>=0x03000000
- Py_XDECREF(obj);
-#endif
- return SWIG_OK;
- } else {
- swig_type_info* pchar_descriptor = SWIG_pchar_descriptor();
- if (pchar_descriptor) {
- void* vptr = 0;
- if (SWIG_ConvertPtr(obj, &vptr, pchar_descriptor, 0) == SWIG_OK) {
- if (cptr) *cptr = (char *) vptr;
- if (psize) *psize = vptr ? (strlen((char *)vptr) + 1) : 0;
- if (alloc) *alloc = SWIG_OLDOBJ;
- return SWIG_OK;
+ PyErr_Clear();
}
}
}
- return SWIG_TypeError;
+#endif
+ return res;
}
+#include <float.h>
-
- int my_read_xtc_natoms(char *fn) {
- int natoms;
- int status;
- status = read_xtc_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from xtc '%s'", status, fn);
- return 0;
- }
- return natoms;
- }
+#include <math.h>
-PyObject * my_read_xtc_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_xtc_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through xtc '%s'", status, fn);
- return 0;
- }
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
- }
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- #if PY_MAJOR_VERSION < 3
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- #else
- PyArray_BASE(npoffsets) = PyCapsule_New(*offsets, NULL, NULL);
- #endif
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
+SWIGINTERNINLINE int
+SWIG_CanCastAsInteger(double *d, double min, double max) {
+ double x = *d;
+ if ((min <= x && x <= max)) {
+ double fx = floor(x);
+ double cx = ceil(x);
+ double rd = ((x - fx) < 0.5) ? fx : cx; /* simple rint */
+ if ((errno == EDOM) || (errno == ERANGE)) {
+ errno = 0;
+ } else {
+ double summ, reps, diff;
+ if (rd < x) {
+ diff = x - rd;
+ } else if (rd > x) {
+ diff = rd - x;
+ } else {
+ return 1;
+ }
+ summ = rd + x;
+ reps = diff/summ;
+ if (reps < 8*DBL_EPSILON) {
+ *d = rd;
+ return 1;
+ }
+ }
}
+ return 0;
+}
- int my_read_trr_natoms(char *fn) {
- int natoms;
- int status;
- status = read_trr_natoms(fn, &natoms);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading natoms from trr '%s'", status, fn);
- return 0;
+SWIGINTERN int
+SWIG_AsVal_long (PyObject *obj, long* val)
+{
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(obj)) {
+ if (val) *val = PyInt_AsLong(obj);
+ return SWIG_OK;
+ } else
+#endif
+ if (PyLong_Check(obj)) {
+ long v = PyLong_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_OK;
+ } else {
+ PyErr_Clear();
+ return SWIG_OverflowError;
}
- return natoms;
}
-
-
-PyObject * my_read_trr_numframes(char *fn) {
- int numframes, status;
- int64_t *offsets[1];
- PyObject *npoffsets = NULL;
- status = read_trr_numframes(fn, &numframes, offsets);
- if (status != exdrOK) {
- PyErr_Format(PyExc_IOError, "[%d] Error reading numframes by seeking through trr '%s'", status, fn);
- return 0;
+#ifdef SWIG_PYTHON_CAST_MODE
+ {
+ int dispatch = 0;
+ long v = PyInt_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_AddCast(SWIG_OK);
+ } else {
+ PyErr_Clear();
}
- npy_intp nfrms[1] = { numframes };
- npoffsets = PyArray_SimpleNewFromData(1, nfrms, NPY_INT64, *offsets);
- if (npoffsets==NULL)
- {
- free(*offsets);
- Py_XDECREF(npoffsets);
- PyErr_Format(PyExc_IOError, "Error copying frame index into Python.");
- return 0;
+ if (!dispatch) {
+ double d;
+ int res = SWIG_AddCast(SWIG_AsVal_double (obj,&d));
+ if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, LONG_MIN, LONG_MAX)) {
+ if (val) *val = (long)(d);
+ return res;
+ }
}
- /* From http://web.archive.org/web/20130304224839/http://blog.enthought.com/python/numpy/simplified-creation-of-numpy-arrays-from-pre-allocated-memory/ */
- #if PY_MAJOR_VERSION < 3
- PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free);
- #else
- PyArray_BASE(npoffsets) = PyCapsule_New(*offsets, NULL, NULL);
- #endif
- PyObject *tuple = PyTuple_New(2);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)numframes));
- PyTuple_SET_ITEM(tuple, 1, npoffsets);
- return tuple;
}
-
-
-PyObject * my_read_xtc(XDRFILE *xd, matrix box, int natoms, int _DIM, float *x) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step;
- float time, prec;
- PyObject *tuple = PyTuple_New(4);
- status = read_xtc(xd, natoms, &step, &time, box, (rvec *)x, &prec);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)prec));
- return tuple; // return (status, step, time, prec)
+#endif
+ return SWIG_TypeError;
}
-/* Support older NumPy data type names
-*/
-#if NDARRAY_VERSION < 0x01000000
-#define NPY_BOOL PyArray_BOOL
-#define NPY_BYTE PyArray_BYTE
-#define NPY_UBYTE PyArray_UBYTE
-#define NPY_SHORT PyArray_SHORT
-#define NPY_USHORT PyArray_USHORT
-#define NPY_INT PyArray_INT
-#define NPY_UINT PyArray_UINT
-#define NPY_LONG PyArray_LONG
-#define NPY_ULONG PyArray_ULONG
-#define NPY_LONGLONG PyArray_LONGLONG
-#define NPY_ULONGLONG PyArray_ULONGLONG
-#define NPY_FLOAT PyArray_FLOAT
-#define NPY_DOUBLE PyArray_DOUBLE
-#define NPY_LONGDOUBLE PyArray_LONGDOUBLE
-#define NPY_CFLOAT PyArray_CFLOAT
-#define NPY_CDOUBLE PyArray_CDOUBLE
-#define NPY_CLONGDOUBLE PyArray_CLONGDOUBLE
-#define NPY_OBJECT PyArray_OBJECT
-#define NPY_STRING PyArray_STRING
-#define NPY_UNICODE PyArray_UNICODE
-#define NPY_VOID PyArray_VOID
-#define NPY_NTYPES PyArray_NTYPES
-#define NPY_NOTYPE PyArray_NOTYPE
-#define NPY_CHAR PyArray_CHAR
-#define NPY_USERDEF PyArray_USERDEF
-#define npy_intp intp
-
-#define NPY_MAX_BYTE MAX_BYTE
-#define NPY_MIN_BYTE MIN_BYTE
-#define NPY_MAX_UBYTE MAX_UBYTE
-#define NPY_MAX_SHORT MAX_SHORT
-#define NPY_MIN_SHORT MIN_SHORT
-#define NPY_MAX_USHORT MAX_USHORT
-#define NPY_MAX_INT MAX_INT
-#define NPY_MIN_INT MIN_INT
-#define NPY_MAX_UINT MAX_UINT
-#define NPY_MAX_LONG MAX_LONG
-#define NPY_MIN_LONG MIN_LONG
-#define NPY_MAX_ULONG MAX_ULONG
-#define NPY_MAX_LONGLONG MAX_LONGLONG
-#define NPY_MIN_LONGLONG MIN_LONGLONG
-#define NPY_MAX_ULONGLONG MAX_ULONGLONG
-#define NPY_MAX_INTP MAX_INTP
-#define NPY_MIN_INTP MIN_INTP
-
-#define NPY_FARRAY FARRAY
-#define NPY_F_CONTIGUOUS F_CONTIGUOUS
-#endif
-
-
-/* Macros to extract array attributes.
- */
-#define is_array(a) ((a) && PyArray_Check((PyArrayObject *)a))
-#define array_type(a) (int)(PyArray_TYPE(a))
-#define array_numdims(a) (((PyArrayObject *)a)->nd)
-#define array_dimensions(a) (((PyArrayObject *)a)->dimensions)
-#define array_size(a,i) (((PyArrayObject *)a)->dimensions[i])
-#define array_data(a) (((PyArrayObject *)a)->data)
-#define array_is_contiguous(a) (PyArray_ISCONTIGUOUS(a))
-#define array_is_native(a) (PyArray_ISNOTSWAPPED(a))
-#define array_is_fortran(a) (PyArray_ISFORTRAN(a))
-
-
- /* Given a PyObject, return a string describing its type.
- */
- const char* pytype_string(PyObject* py_obj) {
- if (py_obj == NULL ) return "C NULL value";
- if (py_obj == Py_None ) return "Python None" ;
- if (PyCallable_Check(py_obj)) return "callable" ;
- if (PyString_Check( py_obj)) return "string" ;
- if (PyInt_Check( py_obj)) return "int" ;
- if (PyFloat_Check( py_obj)) return "float" ;
- if (PyDict_Check( py_obj)) return "dict" ;
- if (PyList_Check( py_obj)) return "list" ;
- if (PyTuple_Check( py_obj)) return "tuple" ;
- #if PY_MAJOR_VERSION < 3
- if (PyFile_Check( py_obj)) return "file" ;
- #endif
- if (PyModule_Check( py_obj)) return "module" ;
- #if PY_MAJOR_VERSION < 3
- if (PyInstance_Check(py_obj)) return "instance" ;
- #endif
-
- return "unkown type";
- }
-
- /* Given a NumPy typecode, return a string describing the type.
- */
- const char* typecode_string(int typecode) {
- static const char* type_names[25] = {"bool", "byte", "unsigned byte",
- "short", "unsigned short", "int",
- "unsigned int", "long", "unsigned long",
- "long long", "unsigned long long",
- "float", "double", "long double",
- "complex float", "complex double",
- "complex long double", "object",
- "string", "unicode", "void", "ntypes",
- "notype", "char", "unknown"};
- return typecode < 24 ? type_names[typecode] : type_names[24];
- }
-
- /* Make sure input has correct numpy type. Allow character and byte
- * to match. Also allow int and long to match. This is deprecated.
- * You should use PyArray_EquivTypenums() instead.
- */
- int type_match(int actual_type, int desired_type) {
- return PyArray_EquivTypenums(actual_type, desired_type);
- }
-
-
- /* Given a PyObject pointer, cast it to a PyArrayObject pointer if
- * legal. If not, set the python error string appropriately and
- * return NULL.
- */
- PyArrayObject* obj_to_array_no_conversion(PyObject* input, int typecode)
- {
- PyArrayObject* ary = NULL;
- if (is_array(input) && (typecode == NPY_NOTYPE ||
- PyArray_EquivTypenums(array_type(input), typecode)))
- {
- ary = (PyArrayObject*) input;
- }
- else if is_array(input)
- {
- const char* desired_type = typecode_string(typecode);
- const char* actual_type = typecode_string(array_type(input));
- PyErr_Format(PyExc_TypeError,
- "Array of type '%s' required. Array of type '%s' given",
- desired_type, actual_type);
- ary = NULL;
- }
- else
- {
- const char * desired_type = typecode_string(typecode);
- const char * actual_type = pytype_string(input);
- PyErr_Format(PyExc_TypeError,
- "Array of type '%s' required. A '%s' was given",
- desired_type, actual_type);
- ary = NULL;
- }
- return ary;
- }
-
- /* Convert the given PyObject to a NumPy array with the given
- * typecode. On success, return a valid PyArrayObject* with the
- * correct type. On failure, the python error string will be set and
- * the routine returns NULL.
- */
- PyArrayObject* obj_to_array_allow_conversion(PyObject* input, int typecode,
- int* is_new_object)
- {
- PyArrayObject* ary = NULL;
- PyObject* py_obj;
- if (is_array(input) && (typecode == NPY_NOTYPE ||
- PyArray_EquivTypenums(array_type(input),typecode)))
- {
- ary = (PyArrayObject*) input;
- *is_new_object = 0;
- }
- else
- {
- py_obj = PyArray_FROMANY(input, typecode, 0, 0, NPY_DEFAULT);
- /* If NULL, PyArray_FromObject will have set python error value.*/
- ary = (PyArrayObject*) py_obj;
- *is_new_object = 1;
- }
- return ary;
- }
-
- /* Given a PyArrayObject, check to see if it is contiguous. If so,
- * return the input pointer and flag it as not a new object. If it is
- * not contiguous, create a new PyArrayObject using the original data,
- * flag it as a new object and return the pointer.
- */
- PyArrayObject* make_contiguous(PyArrayObject* ary, int* is_new_object,
- int min_dims, int max_dims)
- {
- PyArrayObject* result;
- if (array_is_contiguous(ary))
- {
- result = ary;
- *is_new_object = 0;
- }
- else
- {
- result = (PyArrayObject*) PyArray_ContiguousFromObject((PyObject*)ary,
- array_type(ary),
- min_dims,
- max_dims);
- *is_new_object = 1;
- }
- return result;
- }
-
- /* Given a PyArrayObject, check to see if it is Fortran-contiguous.
- * If so, return the input pointer, but do not flag it as not a new
- * object. If it is not Fortran-contiguous, create a new
- * PyArrayObject using the original data, flag it as a new object
- * and return the pointer.
- */
- PyArrayObject* make_fortran(PyArrayObject* ary, int* is_new_object,
- int min_dims, int max_dims)
- {
- PyArrayObject* result;
- if (array_is_fortran(ary))
- {
- result = ary;
- *is_new_object = 0;
- }
- else
- {
- Py_INCREF(ary->descr);
- result = (PyArrayObject*) PyArray_FromArray(ary, ary->descr, NPY_FORTRAN);
- *is_new_object = 1;
- }
- return result;
- }
-
- /* Convert a given PyObject to a contiguous PyArrayObject of the
- * specified type. If the input object is not a contiguous
- * PyArrayObject, a new one will be created and the new object flag
- * will be set.
- */
- PyArrayObject* obj_to_array_contiguous_allow_conversion(PyObject* input,
- int typecode,
- int* is_new_object)
- {
- int is_new1 = 0;
- int is_new2 = 0;
- PyArrayObject* ary2;
- PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode,
- &is_new1);
- if (ary1)
- {
- ary2 = make_contiguous(ary1, &is_new2, 0, 0);
- if ( is_new1 && is_new2)
- {
- Py_DECREF(ary1);
- }
- ary1 = ary2;
- }
- *is_new_object = is_new1 || is_new2;
- return ary1;
- }
-
- /* Convert a given PyObject to a Fortran-ordered PyArrayObject of the
- * specified type. If the input object is not a Fortran-ordered
- * PyArrayObject, a new one will be created and the new object flag
- * will be set.
- */
- PyArrayObject* obj_to_array_fortran_allow_conversion(PyObject* input,
- int typecode,
- int* is_new_object)
- {
- int is_new1 = 0;
- int is_new2 = 0;
- PyArrayObject* ary2;
- PyArrayObject* ary1 = obj_to_array_allow_conversion(input, typecode,
- &is_new1);
- if (ary1)
- {
- ary2 = make_fortran(ary1, &is_new2, 0, 0);
- if (is_new1 && is_new2)
- {
- Py_DECREF(ary1);
- }
- ary1 = ary2;
- }
- *is_new_object = is_new1 || is_new2;
- return ary1;
- }
-
-
-
- /* Test whether a python object is contiguous. If array is
- * contiguous, return 1. Otherwise, set the python error string and
- * return 0.
- */
- int require_contiguous(PyArrayObject* ary)
- {
- int contiguous = 1;
- if (!array_is_contiguous(ary))
- {
- PyErr_SetString(PyExc_TypeError,
- "Array must be contiguous. A non-contiguous array was given");
- contiguous = 0;
- }
- return contiguous;
- }
-
- /* Require that a numpy array is not byte-swapped. If the array is
- * not byte-swapped, return 1. Otherwise, set the python error string
- * and return 0.
- */
- int require_native(PyArrayObject* ary)
- {
- int native = 1;
- if (!array_is_native(ary))
- {
- PyErr_SetString(PyExc_TypeError,
- "Array must have native byteorder. "
- "A byte-swapped array was given");
- native = 0;
- }
- return native;
- }
-
- /* Require the given PyArrayObject to have a specified number of
- * dimensions. If the array has the specified number of dimensions,
- * return 1. Otherwise, set the python error string and return 0.
- */
- int require_dimensions(PyArrayObject* ary, int exact_dimensions)
- {
- int success = 1;
- if (array_numdims(ary) != exact_dimensions)
- {
- PyErr_Format(PyExc_TypeError,
- "Array must have %d dimensions. Given array has %d dimensions",
- exact_dimensions, array_numdims(ary));
- success = 0;
- }
- return success;
- }
-
- /* Require the given PyArrayObject to have one of a list of specified
- * number of dimensions. If the array has one of the specified number
- * of dimensions, return 1. Otherwise, set the python error string
- * and return 0.
- */
- int require_dimensions_n(PyArrayObject* ary, int* exact_dimensions, int n)
- {
- int success = 0;
- int i;
- char dims_str[255] = "";
- char s[255];
- for (i = 0; i < n && !success; i++)
- {
- if (array_numdims(ary) == exact_dimensions[i])
- {
- success = 1;
- }
- }
- if (!success)
- {
- for (i = 0; i < n-1; i++)
- {
- sprintf(s, "%d, ", exact_dimensions[i]);
- strcat(dims_str,s);
- }
- sprintf(s, " or %d", exact_dimensions[n-1]);
- strcat(dims_str,s);
- PyErr_Format(PyExc_TypeError,
- "Array must have %s dimensions. Given array has %d dimensions",
- dims_str, array_numdims(ary));
- }
- return success;
- }
-
- /* Require the given PyArrayObject to have a specified shape. If the
- * array has the specified shape, return 1. Otherwise, set the python
- * error string and return 0.
- */
- int require_size(PyArrayObject* ary, npy_intp* size, int n)
- {
- int i;
- int success = 1;
- int len;
- char desired_dims[255] = "[";
- char s[255];
- char actual_dims[255] = "[";
- for(i=0; i < n;i++)
- {
- if (size[i] != -1 && size[i] != array_size(ary,i))
- {
- success = 0;
- }
- }
- if (!success)
- {
- for (i = 0; i < n; i++)
- {
- if (size[i] == -1)
- {
- sprintf(s, "*,");
- }
- else
- {
- sprintf(s, "%ld,", (long int)size[i]);
- }
- strcat(desired_dims,s);
- }
- len = strlen(desired_dims);
- desired_dims[len-1] = ']';
- for (i = 0; i < n; i++)
- {
- sprintf(s, "%ld,", (long int)array_size(ary,i));
- strcat(actual_dims,s);
- }
- len = strlen(actual_dims);
- actual_dims[len-1] = ']';
- PyErr_Format(PyExc_TypeError,
- "Array must have shape of %s. Given array has shape of %s",
- desired_dims, actual_dims);
- }
- return success;
- }
-
- /* Require the given PyArrayObject to to be FORTRAN ordered. If the
- * the PyArrayObject is already FORTRAN ordered, do nothing. Else,
- * set the FORTRAN ordering flag and recompute the strides.
- */
- int require_fortran(PyArrayObject* ary)
- {
- int success = 1;
- int nd = array_numdims(ary);
- int i;
- if (array_is_fortran(ary)) return success;
- /* Set the FORTRAN ordered flag */
- ary->flags = NPY_FARRAY;
- /* Recompute the strides */
- ary->strides[0] = ary->strides[nd-1];
- for (i=1; i < nd; ++i)
- ary->strides[i] = ary->strides[i-1] * array_size(ary,i-1);
- return success;
- }
-
-
-
-PyObject * my_read_trr(XDRFILE *xd, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- int status, step, has_prop=0;
- float time, lmbda;
- PyObject *tuple = PyTuple_New(7);
- status = read_trr(xd, natoms, &step, &time, &lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f, &has_prop);
- PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)status));
- PyTuple_SET_ITEM(tuple, 1, PyInt_FromLong((long)step));
- PyTuple_SET_ITEM(tuple, 2, PyFloat_FromDouble((double)time));
- PyTuple_SET_ITEM(tuple, 3, PyFloat_FromDouble((double)lmbda));
- PyTuple_SET_ITEM(tuple, 4, PyBool_FromLong((long)(has_prop & HASX)));
- PyTuple_SET_ITEM(tuple, 5, PyBool_FromLong((long)(has_prop & HASV)));
- PyTuple_SET_ITEM(tuple, 6, PyBool_FromLong((long)(has_prop & HASF)));
- return tuple; // return (status, step, time, lmbda, has_x, has_v, has_f)
-}
-
-
-int my_write_xtc(XDRFILE *xd, int step, float time,
- matrix box, int natoms, int _DIM, float *x, float prec) {
- /* _DIM = 3 always, need to reorder for numpy.i SWIG */
- return write_xtc(xd, natoms, step, time, box, (rvec *)x, prec);
-}
-
-
-#include <limits.h>
-#if !defined(SWIG_NO_LLONG_MAX)
-# if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__)
-# define LLONG_MAX __LONG_LONG_MAX__
-# define LLONG_MIN (-LLONG_MAX - 1LL)
-# define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL)
-# endif
-#endif
-
-
-SWIGINTERN int
-SWIG_AsVal_double (PyObject *obj, double *val)
-{
- int res = SWIG_TypeError;
- if (PyFloat_Check(obj)) {
- if (val) *val = PyFloat_AsDouble(obj);
- return SWIG_OK;
- } else if (PyInt_Check(obj)) {
- if (val) *val = PyInt_AsLong(obj);
- return SWIG_OK;
- } else if (PyLong_Check(obj)) {
- double v = PyLong_AsDouble(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = v;
- return SWIG_OK;
- } else {
- PyErr_Clear();
- }
- }
-#ifdef SWIG_PYTHON_CAST_MODE
- {
- int dispatch = 0;
- double d = PyFloat_AsDouble(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = d;
- return SWIG_AddCast(SWIG_OK);
- } else {
- PyErr_Clear();
- }
- if (!dispatch) {
- long v = PyLong_AsLong(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = v;
- return SWIG_AddCast(SWIG_AddCast(SWIG_OK));
- } else {
- PyErr_Clear();
- }
- }
- }
-#endif
- return res;
-}
-
-
-#include <float.h>
-
-
-#include <math.h>
-
-
-SWIGINTERNINLINE int
-SWIG_CanCastAsInteger(double *d, double min, double max) {
- double x = *d;
- if ((min <= x && x <= max)) {
- double fx = floor(x);
- double cx = ceil(x);
- double rd = ((x - fx) < 0.5) ? fx : cx; /* simple rint */
- if ((errno == EDOM) || (errno == ERANGE)) {
- errno = 0;
- } else {
- double summ, reps, diff;
- if (rd < x) {
- diff = x - rd;
- } else if (rd > x) {
- diff = rd - x;
- } else {
- return 1;
- }
- summ = rd + x;
- reps = diff/summ;
- if (reps < 8*DBL_EPSILON) {
- *d = rd;
- return 1;
- }
- }
- }
- return 0;
-}
-
-
-SWIGINTERN int
-SWIG_AsVal_long (PyObject *obj, long* val)
-{
- if (PyInt_Check(obj)) {
- if (val) *val = PyInt_AsLong(obj);
- return SWIG_OK;
- } else if (PyLong_Check(obj)) {
- long v = PyLong_AsLong(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = v;
- return SWIG_OK;
- } else {
- PyErr_Clear();
- }
- }
-#ifdef SWIG_PYTHON_CAST_MODE
- {
- int dispatch = 0;
- long v = PyInt_AsLong(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = v;
- return SWIG_AddCast(SWIG_OK);
- } else {
- PyErr_Clear();
- }
- if (!dispatch) {
- double d;
- int res = SWIG_AddCast(SWIG_AsVal_double (obj,&d));
- if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, LONG_MIN, LONG_MAX)) {
- if (val) *val = (long)(d);
- return res;
- }
- }
- }
-#endif
- return SWIG_TypeError;
-}
-
-
-SWIGINTERN int
-SWIG_AsVal_int (PyObject * obj, int *val)
-{
- long v;
- int res = SWIG_AsVal_long (obj, &v);
- if (SWIG_IsOK(res)) {
- if ((v < INT_MIN || v > INT_MAX)) {
- return SWIG_OverflowError;
- } else {
- if (val) *val = (int)(v);
- }
- }
- return res;
-}
-
-
-SWIGINTERN int
-SWIG_AsVal_float (PyObject * obj, float *val)
-{
- double v;
- int res = SWIG_AsVal_double (obj, &v);
- if (SWIG_IsOK(res)) {
- if ((v < -FLT_MAX || v > FLT_MAX)) {
- return SWIG_OverflowError;
- } else {
- if (val) *val = (float)(v);
- }
- }
- return res;
-}
-
-
-int my_write_trr(XDRFILE *xd, int step, float time, float lmbda, matrix box,
- int natoms, int _DIM, float *x,
- int vnatoms, int v_DIM, float *v,
- int fnatoms, int f_DIM, float *f) {
- /* Preparing for the case of empty arrays - NULL pointers tell the library to skip this property. */
- if (_DIM == 0) x = NULL;
- if (v_DIM == 0) v = NULL;
- if (f_DIM == 0) f = NULL;
- return write_trr(xd, natoms, step, time, lmbda, box, (rvec *)x, (rvec *)v, (rvec *)f);
-}
-
-
-SWIGINTERN int
-SWIG_AsVal_long_SS_long (PyObject *obj, long long *val)
-{
- int res = SWIG_TypeError;
- if (PyLong_Check(obj)) {
- long long v = PyLong_AsLongLong(obj);
- if (!PyErr_Occurred()) {
- if (val) *val = v;
- return SWIG_OK;
- } else {
- PyErr_Clear();
- }
- } else {
- long v;
- res = SWIG_AsVal_long (obj,&v);
- if (SWIG_IsOK(res)) {
- if (val) *val = v;
- return res;
- }
- }
-#ifdef SWIG_PYTHON_CAST_MODE
- {
- const double mant_max = 1LL << DBL_MANT_DIG;
- const double mant_min = -mant_max;
- double d;
- res = SWIG_AsVal_double (obj,&d);
- if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, mant_min, mant_max)) {
- if (val) *val = (long long)(d);
- return SWIG_AddCast(res);
- }
- res = SWIG_TypeError;
- }
-#endif
- return res;
-}
-
-
- #define SWIG_From_long PyLong_FromLong
-
-
-SWIGINTERNINLINE PyObject*
-SWIG_From_long_SS_long (long long value)
-{
- return ((value < LONG_MIN) || (value > LONG_MAX)) ?
- PyLong_FromLongLong(value) : PyLong_FromLong((long)(value));
-}
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-SWIGINTERN PyObject *_wrap_xdrfile_open(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- char *arg1 = (char *) 0 ;
- char *arg2 = (char *) 0 ;
- int res1 ;
- char *buf1 = 0 ;
- int alloc1 = 0 ;
- int res2 ;
- char *buf2 = 0 ;
- int alloc2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- XDRFILE *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:xdrfile_open",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_AsCharPtrAndSize(obj0, &buf1, NULL, &alloc1);
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xdrfile_open" "', argument " "1"" of type '" "char const *""'");
- }
- arg1 = (char *)(buf1);
- res2 = SWIG_AsCharPtrAndSize(obj1, &buf2, NULL, &alloc2);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "xdrfile_open" "', argument " "2"" of type '" "char const *""'");
- }
- arg2 = (char *)(buf2);
- result = (XDRFILE *)xdrfile_open((char const *)arg1,(char const *)arg2);
- resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_XDRFILE, 0 | 0 );
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- if (alloc2 == SWIG_NEWOBJ) free((char*)buf2);
- return resultobj;
-fail:
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- if (alloc2 == SWIG_NEWOBJ) free((char*)buf2);
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_xdrfile_close(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:xdrfile_close",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xdrfile_close" "', argument " "1"" of type '" "XDRFILE *""'");
- }
- arg1 = (XDRFILE *)(argp1);
- result = (int)xdrfile_close(arg1);
- resultobj = SWIG_From_int((int)(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_read_xtc_natoms(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- char *arg1 = (char *) 0 ;
- int res1 ;
- char *buf1 = 0 ;
- int alloc1 = 0 ;
- PyObject * obj0 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:read_xtc_natoms",&obj0)) SWIG_fail;
- res1 = SWIG_AsCharPtrAndSize(obj0, &buf1, NULL, &alloc1);
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_xtc_natoms" "', argument " "1"" of type '" "char *""'");
- }
- arg1 = (char *)(buf1);
- {
- result = (int)my_read_xtc_natoms(arg1);
- if (PyErr_Occurred()) SWIG_fail;
- }
- resultobj = SWIG_From_int((int)(result));
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return resultobj;
-fail:
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_read_xtc_numframes(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- char *arg1 = (char *) 0 ;
- int res1 ;
- char *buf1 = 0 ;
- int alloc1 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:read_xtc_numframes",&obj0)) SWIG_fail;
- res1 = SWIG_AsCharPtrAndSize(obj0, &buf1, NULL, &alloc1);
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_xtc_numframes" "', argument " "1"" of type '" "char *""'");
- }
- arg1 = (char *)(buf1);
- {
- result = (PyObject *)my_read_xtc_numframes(arg1);
- if (PyErr_Occurred()) SWIG_fail;
- }
- resultobj = result;
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return resultobj;
-fail:
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_read_trr_natoms(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- char *arg1 = (char *) 0 ;
- int res1 ;
- char *buf1 = 0 ;
- int alloc1 = 0 ;
- PyObject * obj0 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:read_trr_natoms",&obj0)) SWIG_fail;
- res1 = SWIG_AsCharPtrAndSize(obj0, &buf1, NULL, &alloc1);
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_trr_natoms" "', argument " "1"" of type '" "char *""'");
- }
- arg1 = (char *)(buf1);
- {
- result = (int)my_read_trr_natoms(arg1);
- if (PyErr_Occurred()) SWIG_fail;
- }
- resultobj = SWIG_From_int((int)(result));
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return resultobj;
-fail:
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_read_trr_numframes(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- char *arg1 = (char *) 0 ;
- int res1 ;
- char *buf1 = 0 ;
- int alloc1 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:read_trr_numframes",&obj0)) SWIG_fail;
- res1 = SWIG_AsCharPtrAndSize(obj0, &buf1, NULL, &alloc1);
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_trr_numframes" "', argument " "1"" of type '" "char *""'");
- }
- arg1 = (char *)(buf1);
- {
- result = (PyObject *)my_read_trr_numframes(arg1);
- if (PyErr_Occurred()) SWIG_fail;
- }
- resultobj = result;
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return resultobj;
-fail:
- if (alloc1 == SWIG_NEWOBJ) free((char*)buf1);
- return NULL;
+SWIGINTERN int
+SWIG_AsVal_int (PyObject * obj, int *val)
+{
+ long v;
+ int res = SWIG_AsVal_long (obj, &v);
+ if (SWIG_IsOK(res)) {
+ if ((v < INT_MIN || v > INT_MAX)) {
+ return SWIG_OverflowError;
+ } else {
+ if (val) *val = (int)(v);
+ }
+ }
+ return res;
}
-
-SWIGINTERN PyObject *_wrap_read_xtc(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+#ifdef __cplusplus
+extern "C" {
+#endif
+SWIGINTERN PyObject *_wrap_molfile_plugin_list(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- float (*arg2)[3] ;
- int arg3 ;
- int arg4 ;
- float *arg5 = (float *) 0 ;
+ int *arg1 = (int *) 0 ;
void *argp1 = 0 ;
int res1 = 0 ;
- PyArrayObject *array2 = NULL ;
- PyArrayObject *array3 = NULL ;
PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- PyObject * obj2 = 0 ;
- PyObject *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OOO:read_xtc",&obj0,&obj1,&obj2)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
+ molfile_plugin_t *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:molfile_plugin_list",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_int, 0 | 0 );
if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_xtc" "', argument " "1"" of type '" "XDRFILE *""'");
- }
- arg1 = (XDRFILE *)(argp1);
- {
- npy_intp size[2] = {
- 3, 3
- };
- array2 = obj_to_array_no_conversion(obj1, NPY_FLOAT);
- if (!array2 || !require_dimensions(array2,2) || !require_size(array2, size, 2) ||
- !require_contiguous(array2) || !require_native(array2)) SWIG_fail;
- arg2 = (float (*)[3]) array_data(array2);
- }
- {
- array3 = obj_to_array_no_conversion(obj2, NPY_FLOAT);
- if (!array3 || !require_dimensions(array3,2) || !require_contiguous(array3) ||
- !require_native(array3)) SWIG_fail;
- arg3 = (int) array_size(array3,0);
- arg4 = (int) array_size(array3,1);
- arg5 = (float*) array_data(array3);
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "molfile_plugin_list" "', argument " "1"" of type '" "int *""'");
}
- result = (PyObject *)my_read_xtc(arg1,(float (*)[3])arg2,arg3,arg4,arg5);
- resultobj = result;
+ arg1 = (int *)(argp1);
+ result = (molfile_plugin_t *)molfile_plugin_list(arg1);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
return resultobj;
fail:
return NULL;
}
-SWIGINTERN PyObject *_wrap_read_trr(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+SWIGINTERN PyObject *_wrap_molfile_init(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- float (*arg2)[3] ;
- int arg3 ;
- int arg4 ;
- float *arg5 = (float *) 0 ;
- int arg6 ;
- int arg7 ;
- float *arg8 = (float *) 0 ;
- int arg9 ;
- int arg10 ;
- float *arg11 = (float *) 0 ;
+ molfile_plugin_t *arg1 = (molfile_plugin_t *) 0 ;
void *argp1 = 0 ;
int res1 = 0 ;
- PyArrayObject *array2 = NULL ;
- PyArrayObject *array3 = NULL ;
- PyArrayObject *array6 = NULL ;
- PyArrayObject *array9 = NULL ;
PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- PyObject * obj2 = 0 ;
- PyObject * obj3 = 0 ;
- PyObject * obj4 = 0 ;
- PyObject *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OOOOO:read_trr",&obj0,&obj1,&obj2,&obj3,&obj4)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
+ int result;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:molfile_init",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "read_trr" "', argument " "1"" of type '" "XDRFILE *""'");
- }
- arg1 = (XDRFILE *)(argp1);
- {
- npy_intp size[2] = {
- 3, 3
- };
- array2 = obj_to_array_no_conversion(obj1, NPY_FLOAT);
- if (!array2 || !require_dimensions(array2,2) || !require_size(array2, size, 2) ||
- !require_contiguous(array2) || !require_native(array2)) SWIG_fail;
- arg2 = (float (*)[3]) array_data(array2);
- }
- {
- array3 = obj_to_array_no_conversion(obj2, NPY_FLOAT);
- if (!array3 || !require_dimensions(array3,2) || !require_contiguous(array3) ||
- !require_native(array3)) SWIG_fail;
- arg3 = (int) array_size(array3,0);
- arg4 = (int) array_size(array3,1);
- arg5 = (float*) array_data(array3);
- }
- {
- array6 = obj_to_array_no_conversion(obj3, NPY_FLOAT);
- if (!array6 || !require_dimensions(array6,2) || !require_contiguous(array6) ||
- !require_native(array6)) SWIG_fail;
- arg6 = (int) array_size(array6,0);
- arg7 = (int) array_size(array6,1);
- arg8 = (float*) array_data(array6);
- }
- {
- array9 = obj_to_array_no_conversion(obj4, NPY_FLOAT);
- if (!array9 || !require_dimensions(array9,2) || !require_contiguous(array9) ||
- !require_native(array9)) SWIG_fail;
- arg9 = (int) array_size(array9,0);
- arg10 = (int) array_size(array9,1);
- arg11 = (float*) array_data(array9);
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "molfile_init" "', argument " "1"" of type '" "molfile_plugin_t *""'");
}
- result = (PyObject *)my_read_trr(arg1,(float (*)[3])arg2,arg3,arg4,arg5,arg6,arg7,arg8,arg9,arg10,arg11);
- resultobj = result;
+ arg1 = (molfile_plugin_t *)(argp1);
+ result = (int)molfile_init(arg1);
+ resultobj = SWIG_From_int((int)(result));
return resultobj;
fail:
return NULL;
}
-SWIGINTERN PyObject *_wrap_write_xtc(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+SWIGINTERN PyObject *_wrap_molfile_finish(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- int arg2 ;
- float arg3 ;
- float (*arg4)[3] ;
- int arg5 ;
- int arg6 ;
- float *arg7 = (float *) 0 ;
- float arg8 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- int val2 ;
- int ecode2 = 0 ;
- float val3 ;
- int ecode3 = 0 ;
- PyArrayObject *array4 = NULL ;
- int is_new_object4 = 0 ;
- PyArrayObject *array5 = NULL ;
- int is_new_object5 = 0 ;
- float val8 ;
- int ecode8 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- PyObject * obj2 = 0 ;
- PyObject * obj3 = 0 ;
- PyObject * obj4 = 0 ;
- PyObject * obj5 = 0 ;
int result;
-
- if (!PyArg_ParseTuple(args,(char *)"OOOOOO:write_xtc",&obj0,&obj1,&obj2,&obj3,&obj4,&obj5)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "write_xtc" "', argument " "1"" of type '" "XDRFILE *""'");
- }
- arg1 = (XDRFILE *)(argp1);
- ecode2 = SWIG_AsVal_int(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "write_xtc" "', argument " "2"" of type '" "int""'");
- }
- arg2 = (int)(val2);
- ecode3 = SWIG_AsVal_float(obj2, &val3);
- if (!SWIG_IsOK(ecode3)) {
- SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "write_xtc" "', argument " "3"" of type '" "float""'");
- }
- arg3 = (float)(val3);
- {
- npy_intp size[2] = {
- 3, 3
- };
- array4 = obj_to_array_contiguous_allow_conversion(obj3, NPY_FLOAT,
- &is_new_object4);
- if (!array4 || !require_dimensions(array4, 2) ||
- !require_size(array4, size, 2)) SWIG_fail;
- arg4 = (float (*)[3]) array_data(array4);
- }
- {
- npy_intp size[2] = {
- -1, -1
- };
- array5 = obj_to_array_contiguous_allow_conversion(obj4, NPY_FLOAT,
- &is_new_object5);
- if (!array5 || !require_dimensions(array5, 2) ||
- !require_size(array5, size, 2)) SWIG_fail;
- arg5 = (int) array_size(array5,0);
- arg6 = (int) array_size(array5,1);
- arg7 = (float*) array_data(array5);
- }
- ecode8 = SWIG_AsVal_float(obj5, &val8);
- if (!SWIG_IsOK(ecode8)) {
- SWIG_exception_fail(SWIG_ArgError(ecode8), "in method '" "write_xtc" "', argument " "8"" of type '" "float""'");
- }
- arg8 = (float)(val8);
- result = (int)my_write_xtc(arg1,arg2,arg3,(float (*)[3])arg4,arg5,arg6,arg7,arg8);
+
+ if (!PyArg_ParseTuple(args,(char *)":molfile_finish")) SWIG_fail;
+ result = (int)molfile_finish();
resultobj = SWIG_From_int((int)(result));
- {
- if (is_new_object4 && array4)
- {
- Py_DECREF(array4);
- }
- }
- {
- if (is_new_object5 && array5)
- {
- Py_DECREF(array5);
- }
- }
return resultobj;
fail:
- {
- if (is_new_object4 && array4)
- {
- Py_DECREF(array4);
- }
- }
- {
- if (is_new_object5 && array5)
- {
- Py_DECREF(array5);
- }
- }
return NULL;
}
-SWIGINTERN PyObject *_wrap_write_trr(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+SWIGINTERN PyObject *_wrap_molfile_plugin_info(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
+ molfile_plugin_t *arg1 = (molfile_plugin_t *) 0 ;
int arg2 ;
- float arg3 ;
- float arg4 ;
- float (*arg5)[3] ;
- int arg6 ;
- int arg7 ;
- float *arg8 = (float *) 0 ;
- int arg9 ;
- int arg10 ;
- float *arg11 = (float *) 0 ;
- int arg12 ;
- int arg13 ;
- float *arg14 = (float *) 0 ;
void *argp1 = 0 ;
int res1 = 0 ;
int val2 ;
int ecode2 = 0 ;
- float val3 ;
- int ecode3 = 0 ;
- float val4 ;
- int ecode4 = 0 ;
- PyArrayObject *array5 = NULL ;
- int is_new_object5 = 0 ;
- PyArrayObject *array6 = NULL ;
- int is_new_object6 = 0 ;
- PyArrayObject *array9 = NULL ;
- int is_new_object9 = 0 ;
- PyArrayObject *array12 = NULL ;
- int is_new_object12 = 0 ;
PyObject * obj0 = 0 ;
PyObject * obj1 = 0 ;
- PyObject * obj2 = 0 ;
- PyObject * obj3 = 0 ;
- PyObject * obj4 = 0 ;
- PyObject * obj5 = 0 ;
- PyObject * obj6 = 0 ;
- PyObject * obj7 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"OOOOOOOO:write_trr",&obj0,&obj1,&obj2,&obj3,&obj4,&obj5,&obj6,&obj7)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:molfile_plugin_info",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "write_trr" "', argument " "1"" of type '" "XDRFILE *""'");
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "molfile_plugin_info" "', argument " "1"" of type '" "molfile_plugin_t *""'");
}
- arg1 = (XDRFILE *)(argp1);
+ arg1 = (molfile_plugin_t *)(argp1);
ecode2 = SWIG_AsVal_int(obj1, &val2);
if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "write_trr" "', argument " "2"" of type '" "int""'");
- }
+ SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "molfile_plugin_info" "', argument " "2"" of type '" "int""'");
+ }
arg2 = (int)(val2);
- ecode3 = SWIG_AsVal_float(obj2, &val3);
- if (!SWIG_IsOK(ecode3)) {
- SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "write_trr" "', argument " "3"" of type '" "float""'");
- }
- arg3 = (float)(val3);
- ecode4 = SWIG_AsVal_float(obj3, &val4);
- if (!SWIG_IsOK(ecode4)) {
- SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "write_trr" "', argument " "4"" of type '" "float""'");
- }
- arg4 = (float)(val4);
- {
- npy_intp size[2] = {
- 3, 3
- };
- array5 = obj_to_array_contiguous_allow_conversion(obj4, NPY_FLOAT,
- &is_new_object5);
- if (!array5 || !require_dimensions(array5, 2) ||
- !require_size(array5, size, 2)) SWIG_fail;
- arg5 = (float (*)[3]) array_data(array5);
- }
- {
- npy_intp size[2] = {
- -1, -1
- };
- array6 = obj_to_array_contiguous_allow_conversion(obj5, NPY_FLOAT,
- &is_new_object6);
- if (!array6 || !require_dimensions(array6, 2) ||
- !require_size(array6, size, 2)) SWIG_fail;
- arg6 = (int) array_size(array6,0);
- arg7 = (int) array_size(array6,1);
- arg8 = (float*) array_data(array6);
- }
- {
- npy_intp size[2] = {
- -1, -1
- };
- array9 = obj_to_array_contiguous_allow_conversion(obj6, NPY_FLOAT,
- &is_new_object9);
- if (!array9 || !require_dimensions(array9, 2) ||
- !require_size(array9, size, 2)) SWIG_fail;
- arg9 = (int) array_size(array9,0);
- arg10 = (int) array_size(array9,1);
- arg11 = (float*) array_data(array9);
- }
- {
- npy_intp size[2] = {
- -1, -1
- };
- array12 = obj_to_array_contiguous_allow_conversion(obj7, NPY_FLOAT,
- &is_new_object12);
- if (!array12 || !require_dimensions(array12, 2) ||
- !require_size(array12, size, 2)) SWIG_fail;
- arg12 = (int) array_size(array12,0);
- arg13 = (int) array_size(array12,1);
- arg14 = (float*) array_data(array12);
- }
- result = (int)my_write_trr(arg1,arg2,arg3,arg4,(float (*)[3])arg5,arg6,arg7,arg8,arg9,arg10,arg11,arg12,arg13,arg14);
- resultobj = SWIG_From_int((int)(result));
- {
- if (is_new_object5 && array5)
- {
- Py_DECREF(array5);
- }
- }
- {
- if (is_new_object6 && array6)
- {
- Py_DECREF(array6);
- }
- }
- {
- if (is_new_object9 && array9)
- {
- Py_DECREF(array9);
- }
- }
- {
- if (is_new_object12 && array12)
- {
- Py_DECREF(array12);
- }
- }
- return resultobj;
-fail:
- {
- if (is_new_object5 && array5)
- {
- Py_DECREF(array5);
- }
- }
- {
- if (is_new_object6 && array6)
- {
- Py_DECREF(array6);
- }
- }
- {
- if (is_new_object9 && array9)
- {
- Py_DECREF(array9);
- }
- }
{
- if (is_new_object12 && array12)
- {
- Py_DECREF(array12);
- }
- }
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_xdr_seek(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- long long arg2 ;
- int arg3 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- long long val2 ;
- int ecode2 = 0 ;
- int val3 ;
- int ecode3 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- PyObject * obj2 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"OOO:xdr_seek",&obj0,&obj1,&obj2)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xdr_seek" "', argument " "1"" of type '" "XDRFILE *""'");
- }
- arg1 = (XDRFILE *)(argp1);
- ecode2 = SWIG_AsVal_long_SS_long(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "xdr_seek" "', argument " "2"" of type '" "long long""'");
- }
- arg2 = (long long)(val2);
- ecode3 = SWIG_AsVal_int(obj2, &val3);
- if (!SWIG_IsOK(ecode3)) {
- SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "xdr_seek" "', argument " "3"" of type '" "int""'");
- }
- arg3 = (int)(val3);
- result = (int)xdr_seek(arg1,arg2,arg3);
- resultobj = SWIG_From_int((int)(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_xdr_tell(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- XDRFILE *arg1 = (XDRFILE *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- long long result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:xdr_tell",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_XDRFILE, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "xdr_tell" "', argument " "1"" of type '" "XDRFILE *""'");
+ result = (PyObject *)molfile_plugin_info(arg1,arg2);
+ if (PyErr_Occurred()) SWIG_fail;
}
- arg1 = (XDRFILE *)(argp1);
- result = (long long)xdr_tell(arg1);
- resultobj = SWIG_From_long_SS_long((long long)(result));
+ resultobj = result;
return resultobj;
fail:
return NULL;
@@ -4497,46 +3341,34 @@ fail:
static PyMethodDef SwigMethods[] = {
{ (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL},
- { (char *)"xdrfile_open", _wrap_xdrfile_open, METH_VARARGS, (char *)"xdrfile_open(path, mode) -> XDRFILE *"},
- { (char *)"xdrfile_close", _wrap_xdrfile_close, METH_VARARGS, (char *)"xdrfile_close(fp) -> int"},
- { (char *)"read_xtc_natoms", _wrap_read_xtc_natoms, METH_VARARGS, (char *)"read_xtc_natoms(fn) -> int"},
- { (char *)"read_xtc_numframes", _wrap_read_xtc_numframes, METH_VARARGS, (char *)"read_xtc_numframes(fn) -> PyObject *"},
- { (char *)"read_trr_natoms", _wrap_read_trr_natoms, METH_VARARGS, (char *)"read_trr_natoms(fn) -> int"},
- { (char *)"read_trr_numframes", _wrap_read_trr_numframes, METH_VARARGS, (char *)"read_trr_numframes(fn) -> PyObject *"},
- { (char *)"read_xtc", _wrap_read_xtc, METH_VARARGS, (char *)"read_xtc(XDRFILE, box, x) -> (status, step, time, precision)"},
- { (char *)"read_trr", _wrap_read_trr, METH_VARARGS, (char *)"read_trr(XDRFILE, box, x, v, f) -> (status, step, time, lambda)"},
- { (char *)"write_xtc", _wrap_write_xtc, METH_VARARGS, (char *)"write_xtc(XDRFILE, step, time, box, x, prec) -> status"},
- { (char *)"write_trr", _wrap_write_trr, METH_VARARGS, (char *)"write_trr(XDRFILE, step, time, lambda, box, x, v, f) -> status"},
- { (char *)"xdr_seek", _wrap_xdr_seek, METH_VARARGS, (char *)"xdr_seek(xd, pos, whence) -> int"},
- { (char *)"xdr_tell", _wrap_xdr_tell, METH_VARARGS, (char *)"xdr_tell(xd) -> long long"},
+ { (char *)"molfile_plugin_list", _wrap_molfile_plugin_list, METH_VARARGS, (char *)"molfile_plugin_list(maxsize) -> molfile_plugin_t *"},
+ { (char *)"molfile_init", _wrap_molfile_init, METH_VARARGS, (char *)"molfile_init(plugin_list) -> int"},
+ { (char *)"molfile_finish", _wrap_molfile_finish, METH_VARARGS, (char *)"molfile_finish() -> int"},
+ { (char *)"molfile_plugin_info", _wrap_molfile_plugin_info, METH_VARARGS, (char *)"molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"},
{ NULL, NULL, 0, NULL }
};
/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
-static swig_type_info _swigt__p_XDRFILE = {"_p_XDRFILE", "XDRFILE *", 0, 0, (void*)0, 0};
-static swig_type_info _swigt__p_a_3__a_3__float = {"_p_a_3__a_3__float", "matrix *|float (*)[3][3]", 0, 0, (void*)0, 0};
-static swig_type_info _swigt__p_a_3__float = {"_p_a_3__float", "float (*)[3]|rvec *", 0, 0, (void*)0, 0};
static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0};
+static swig_type_info _swigt__p_int = {"_p_int", "int *", 0, 0, (void*)0, 0};
+static swig_type_info _swigt__p_molfile_plugin_t = {"_p_molfile_plugin_t", "molfile_plugin_t *", 0, 0, (void*)0, 0};
static swig_type_info *swig_type_initial[] = {
- &_swigt__p_XDRFILE,
- &_swigt__p_a_3__a_3__float,
- &_swigt__p_a_3__float,
&_swigt__p_char,
+ &_swigt__p_int,
+ &_swigt__p_molfile_plugin_t,
};
-static swig_cast_info _swigc__p_XDRFILE[] = { {&_swigt__p_XDRFILE, 0, 0, 0},{0, 0, 0, 0}};
-static swig_cast_info _swigc__p_a_3__a_3__float[] = { {&_swigt__p_a_3__a_3__float, 0, 0, 0},{0, 0, 0, 0}};
-static swig_cast_info _swigc__p_a_3__float[] = { {&_swigt__p_a_3__float, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}};
+static swig_cast_info _swigc__p_int[] = { {&_swigt__p_int, 0, 0, 0},{0, 0, 0, 0}};
+static swig_cast_info _swigc__p_molfile_plugin_t[] = { {&_swigt__p_molfile_plugin_t, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info *swig_cast_initial[] = {
- _swigc__p_XDRFILE,
- _swigc__p_a_3__a_3__float,
- _swigc__p_a_3__float,
_swigc__p_char,
+ _swigc__p_int,
+ _swigc__p_molfile_plugin_t,
};
@@ -4561,7 +3393,7 @@ static swig_const_info swig_const_table[] = {
* array with the correct data and linking the correct swig_cast_info
* structures together.
*
- * The generated swig_type_info structures are assigned staticly to an initial
+ * The generated swig_type_info structures are assigned statically to an initial
* array. We just loop through that array, and handle each type individually.
* First we lookup if this type has been already loaded, and if so, use the
* loaded structure instead of the generated one. Then we have to fill in the
@@ -4605,8 +3437,8 @@ SWIGRUNTIME void
SWIG_InitializeModule(void *clientdata) {
size_t i;
swig_module_info *module_head, *iter;
- int found, init;
-
+ int init;
+
/* check to see if the circular list has been setup, if not, set it up */
if (swig_module.next==0) {
/* Initialize the swig_module */
@@ -4617,39 +3449,35 @@ SWIG_InitializeModule(void *clientdata) {
} else {
init = 0;
}
-
+
/* Try and load any already created modules */
module_head = SWIG_GetModule(clientdata);
if (!module_head) {
/* This is the first module loaded for this interpreter */
/* so set the swig module into the interpreter */
SWIG_SetModule(clientdata, &swig_module);
- module_head = &swig_module;
} else {
/* the interpreter has loaded a SWIG module, but has it loaded this one? */
- found=0;
iter=module_head;
do {
if (iter==&swig_module) {
- found=1;
- break;
+ /* Our module is already in the list, so there's nothing more to do. */
+ return;
}
iter=iter->next;
} while (iter!= module_head);
-
- /* if the is found in the list, then all is done and we may leave */
- if (found) return;
- /* otherwise we must add out module into the list */
+
+ /* otherwise we must add our module into the list */
swig_module.next = module_head->next;
module_head->next = &swig_module;
}
-
- /* When multiple interpeters are used, a module could have already been initialized in
+
+ /* When multiple interpreters are used, a module could have already been initialized in
a different interpreter, but not yet have a pointer in this interpreter.
In this case, we do not want to continue adding types... everything should be
set up already */
if (init == 0) return;
-
+
/* Now work on filling in swig_module.types */
#ifdef SWIGRUNTIME_DEBUG
printf("SWIG_InitializeModule: size %d\n", swig_module.size);
@@ -4658,11 +3486,11 @@ SWIG_InitializeModule(void *clientdata) {
swig_type_info *type = 0;
swig_type_info *ret;
swig_cast_info *cast;
-
+
#ifdef SWIGRUNTIME_DEBUG
printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name);
#endif
-
+
/* if there is another module already loaded */
if (swig_module.next != &swig_module) {
type = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, swig_module.type_initial[i]->name);
@@ -4681,7 +3509,7 @@ SWIG_InitializeModule(void *clientdata) {
} else {
type = swig_module.type_initial[i];
}
-
+
/* Insert casting types */
cast = swig_module.cast_initial[i];
while (cast->type) {
@@ -4712,7 +3540,7 @@ SWIG_InitializeModule(void *clientdata) {
if (!ocast) ret = 0;
}
}
-
+
if (!ret) {
#ifdef SWIGRUNTIME_DEBUG
printf("SWIG_InitializeModule: adding cast %s\n", cast->type->name);
@@ -4729,7 +3557,7 @@ SWIG_InitializeModule(void *clientdata) {
swig_module.types[i] = type;
}
swig_module.types[i] = 0;
-
+
#ifdef SWIGRUNTIME_DEBUG
printf("**** SWIG_InitializeModule: Cast List ******\n");
for (i = 0; i < swig_module.size; ++i) {
@@ -4757,10 +3585,10 @@ SWIG_PropagateClientData(void) {
size_t i;
swig_cast_info *equiv;
static int init_run = 0;
-
+
if (init_run) return;
init_run = 1;
-
+
for (i = 0; i < swig_module.size; i++) {
if (swig_module.types[i]->clientdata) {
equiv = swig_module.types[i]->cast;
@@ -4788,28 +3616,28 @@ SWIG_PropagateClientData(void) {
#ifdef __cplusplus
extern "C" {
#endif
-
+
/* Python-specific SWIG API */
#define SWIG_newvarlink() SWIG_Python_newvarlink()
#define SWIG_addvarlink(p, name, get_attr, set_attr) SWIG_Python_addvarlink(p, name, get_attr, set_attr)
#define SWIG_InstallConstants(d, constants) SWIG_Python_InstallConstants(d, constants)
-
+
/* -----------------------------------------------------------------------------
* global variable support code.
* ----------------------------------------------------------------------------- */
-
+
typedef struct swig_globalvar {
char *name; /* Name of global variable */
PyObject *(*get_attr)(void); /* Return the current value */
int (*set_attr)(PyObject *); /* Set the value */
struct swig_globalvar *next;
} swig_globalvar;
-
+
typedef struct swig_varlinkobject {
PyObject_HEAD
swig_globalvar *vars;
} swig_varlinkobject;
-
+
SWIGINTERN PyObject *
swig_varlink_repr(swig_varlinkobject *SWIGUNUSEDPARM(v)) {
#if PY_VERSION_HEX >= 0x03000000
@@ -4818,7 +3646,7 @@ extern "C" {
return PyString_FromString("<Swig global variables>");
#endif
}
-
+
SWIGINTERN PyObject *
swig_varlink_str(swig_varlinkobject *v) {
#if PY_VERSION_HEX >= 0x03000000
@@ -4856,7 +3684,7 @@ extern "C" {
#endif
return str;
}
-
+
SWIGINTERN int
swig_varlink_print(swig_varlinkobject *v, FILE *fp, int SWIGUNUSEDPARM(flags)) {
char *tmp;
@@ -4867,7 +3695,7 @@ extern "C" {
Py_DECREF(str);
return 0;
}
-
+
SWIGINTERN void
swig_varlink_dealloc(swig_varlinkobject *v) {
swig_globalvar *var = v->vars;
@@ -4878,7 +3706,7 @@ extern "C" {
var = n;
}
}
-
+
SWIGINTERN PyObject *
swig_varlink_getattr(swig_varlinkobject *v, char *n) {
PyObject *res = NULL;
@@ -4891,11 +3719,11 @@ extern "C" {
var = var->next;
}
if (res == NULL && !PyErr_Occurred()) {
- PyErr_SetString(PyExc_NameError,"Unknown C global variable");
+ PyErr_Format(PyExc_AttributeError, "Unknown C global variable '%s'", n);
}
return res;
}
-
+
SWIGINTERN int
swig_varlink_setattr(swig_varlinkobject *v, char *n, PyObject *p) {
int res = 1;
@@ -4908,11 +3736,11 @@ extern "C" {
var = var->next;
}
if (res == 1 && !PyErr_Occurred()) {
- PyErr_SetString(PyExc_NameError,"Unknown C global variable");
+ PyErr_Format(PyExc_AttributeError, "Unknown C global variable '%s'", n);
}
return res;
}
-
+
SWIGINTERN PyTypeObject*
swig_varlink_type(void) {
static char varlink__doc__[] = "Swig var link object";
@@ -4920,7 +3748,6 @@ extern "C" {
static int type_init = 0;
if (!type_init) {
const PyTypeObject tmp = {
- /* PyObject header changed in Python 3 */
#if PY_VERSION_HEX >= 0x03000000
PyVarObject_HEAD_INIT(NULL, 0)
#else
@@ -4958,10 +3785,19 @@ extern "C" {
0, /* tp_del */
#endif
#if PY_VERSION_HEX >= 0x02060000
- 0, /* tp_version */
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
#endif
#ifdef COUNT_ALLOCS
- 0,0,0,0 /* tp_alloc -> tp_next */
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
#endif
};
varlink_type = tmp;
@@ -4975,7 +3811,7 @@ extern "C" {
}
return &varlink_type;
}
-
+
/* Create a variable linking object for use later */
SWIGINTERN PyObject *
SWIG_Python_newvarlink(void) {
@@ -4985,8 +3821,8 @@ extern "C" {
}
return ((PyObject*) result);
}
-
- SWIGINTERN void
+
+ SWIGINTERN void
SWIG_Python_addvarlink(PyObject *p, char *name, PyObject *(*get_attr)(void), int (*set_attr)(PyObject *p)) {
swig_varlinkobject *v = (swig_varlinkobject *) p;
swig_globalvar *gv = (swig_globalvar *) malloc(sizeof(swig_globalvar));
@@ -5002,18 +3838,18 @@ extern "C" {
}
v->vars = gv;
}
-
+
SWIGINTERN PyObject *
SWIG_globals(void) {
- static PyObject *_SWIG_globals = 0;
- if (!_SWIG_globals) _SWIG_globals = SWIG_newvarlink();
+ static PyObject *_SWIG_globals = 0;
+ if (!_SWIG_globals) _SWIG_globals = SWIG_newvarlink();
return _SWIG_globals;
}
-
+
/* -----------------------------------------------------------------------------
* constants/methods manipulation
* ----------------------------------------------------------------------------- */
-
+
/* Install Constants */
SWIGINTERN void
SWIG_Python_InstallConstants(PyObject *d, swig_const_info constants[]) {
@@ -5037,11 +3873,11 @@ extern "C" {
}
}
}
-
+
/* -----------------------------------------------------------------------------*/
/* Fix SwigMethods to carry the callback ptrs when needed */
/* -----------------------------------------------------------------------------*/
-
+
SWIGINTERN void
SWIG_Python_FixMethods(PyMethodDef *methods,
swig_const_info *const_table,
@@ -5050,12 +3886,14 @@ extern "C" {
size_t i;
for (i = 0; methods[i].ml_name; ++i) {
const char *c = methods[i].ml_doc;
- if (c && (c = strstr(c, "swig_ptr: "))) {
+ if (!c) continue;
+ c = strstr(c, "swig_ptr: ");
+ if (c) {
int j;
swig_const_info *ci = 0;
const char *name = c + 10;
for (j = 0; const_table[j].type; ++j) {
- if (strncmp(const_table[j].name, name,
+ if (strncmp(const_table[j].name, name,
strlen(const_table[j].name)) == 0) {
ci = &(const_table[j]);
break;
@@ -5082,8 +3920,8 @@ extern "C" {
}
}
}
- }
-
+ }
+
#ifdef __cplusplus
}
#endif
@@ -5096,7 +3934,7 @@ extern "C" {
extern "C"
#endif
-SWIGEXPORT
+SWIGEXPORT
#if PY_VERSION_HEX >= 0x03000000
PyObject*
#else
@@ -5126,7 +3964,7 @@ SWIG_init(void) {
NULL
};
#endif
-
+
#if defined(SWIGPYTHON_BUILTIN)
static SwigPyClientData SwigPyObject_clientdata = {
0, 0, 0, 0, 0, 0, 0
@@ -5141,56 +3979,56 @@ SWIG_init(void) {
static PyGetSetDef thisown_getset_def = {
(char *)"thisown", SwigPyBuiltin_GetterClosure, SwigPyBuiltin_SetterClosure, NULL, &thisown_getset_closure
};
- PyObject *metatype_args;
PyTypeObject *builtin_pytype;
int builtin_base_count;
swig_type_info *builtin_basetype;
PyObject *tuple;
PyGetSetDescrObject *static_getset;
PyTypeObject *metatype;
+ PyTypeObject *swigpyobject;
SwigPyClientData *cd;
PyObject *public_interface, *public_symbol;
PyObject *this_descr;
PyObject *thisown_descr;
+ PyObject *self = 0;
int i;
-
+
(void)builtin_pytype;
(void)builtin_base_count;
(void)builtin_basetype;
(void)tuple;
(void)static_getset;
-
- /* metatype is used to implement static member variables. */
- metatype_args = Py_BuildValue("(s(O){})", "SwigPyObjectType", &PyType_Type);
- assert(metatype_args);
- metatype = (PyTypeObject *) PyType_Type.tp_call((PyObject *) &PyType_Type, metatype_args, NULL);
+ (void)self;
+
+ /* Metaclass is used to implement static member variables */
+ metatype = SwigPyObjectType();
assert(metatype);
- Py_DECREF(metatype_args);
- metatype->tp_setattro = (setattrofunc) &SwigPyObjectType_setattro;
- assert(PyType_Ready(metatype) >= 0);
#endif
-
+
/* Fix SwigMethods to carry the callback ptrs when needed */
SWIG_Python_FixMethods(SwigMethods, swig_const_table, swig_types, swig_type_initial);
-
+
#if PY_VERSION_HEX >= 0x03000000
m = PyModule_Create(&SWIG_module);
#else
m = Py_InitModule((char *) SWIG_name, SwigMethods);
#endif
+
md = d = PyModule_GetDict(m);
(void)md;
-
+
SWIG_InitializeModule(0);
-
+
#ifdef SWIGPYTHON_BUILTIN
+ swigpyobject = SwigPyObject_TypeOnce();
+
SwigPyObject_stype = SWIG_MangledTypeQuery("_p_SwigPyObject");
assert(SwigPyObject_stype);
cd = (SwigPyClientData*) SwigPyObject_stype->clientdata;
if (!cd) {
SwigPyObject_stype->clientdata = &SwigPyObject_clientdata;
- SwigPyObject_clientdata.pytype = SwigPyObject_TypeOnce();
- } else if (SwigPyObject_TypeOnce()->tp_basicsize != cd->pytype->tp_basicsize) {
+ SwigPyObject_clientdata.pytype = swigpyobject;
+ } else if (swigpyobject->tp_basicsize != cd->pytype->tp_basicsize) {
PyErr_SetString(PyExc_RuntimeError, "Import error: attempted to load two incompatible swig-generated modules.");
# if PY_VERSION_HEX >= 0x03000000
return NULL;
@@ -5198,19 +4036,19 @@ SWIG_init(void) {
return;
# endif
}
-
+
/* All objects have a 'this' attribute */
this_descr = PyDescr_NewGetSet(SwigPyObject_type(), &this_getset_def);
(void)this_descr;
-
+
/* All objects have a 'thisown' attribute */
thisown_descr = PyDescr_NewGetSet(SwigPyObject_type(), &thisown_getset_def);
(void)thisown_descr;
-
+
public_interface = PyList_New(0);
public_symbol = 0;
(void)public_symbol;
-
+
PyDict_SetItemString(md, "__all__", public_interface);
Py_DECREF(public_interface);
for (i = 0; SwigMethods[i].ml_name != NULL; ++i)
@@ -5218,30 +4056,22 @@ SWIG_init(void) {
for (i = 0; swig_const_table[i].name != 0; ++i)
SwigPyBuiltin_AddPublicSymbol(public_interface, swig_const_table[i].name);
#endif
-
+
SWIG_InstallConstants(d,swig_const_table);
-
-
+
+
import_array();
-
- SWIG_Python_SetConstant(d, "exdrOK",SWIG_From_int((int)(exdrOK)));
- SWIG_Python_SetConstant(d, "exdrHEADER",SWIG_From_int((int)(exdrHEADER)));
- SWIG_Python_SetConstant(d, "exdrSTRING",SWIG_From_int((int)(exdrSTRING)));
- SWIG_Python_SetConstant(d, "exdrDOUBLE",SWIG_From_int((int)(exdrDOUBLE)));
- SWIG_Python_SetConstant(d, "exdrINT",SWIG_From_int((int)(exdrINT)));
- SWIG_Python_SetConstant(d, "exdrFLOAT",SWIG_From_int((int)(exdrFLOAT)));
- SWIG_Python_SetConstant(d, "exdrUINT",SWIG_From_int((int)(exdrUINT)));
- SWIG_Python_SetConstant(d, "exdr3DX",SWIG_From_int((int)(exdr3DX)));
- SWIG_Python_SetConstant(d, "exdrCLOSE",SWIG_From_int((int)(exdrCLOSE)));
- SWIG_Python_SetConstant(d, "exdrMAGIC",SWIG_From_int((int)(exdrMAGIC)));
- SWIG_Python_SetConstant(d, "exdrNOMEM",SWIG_From_int((int)(exdrNOMEM)));
- SWIG_Python_SetConstant(d, "exdrENDOFFILE",SWIG_From_int((int)(exdrENDOFFILE)));
- SWIG_Python_SetConstant(d, "exdrFILENOTFOUND",SWIG_From_int((int)(exdrFILENOTFOUND)));
- SWIG_Python_SetConstant(d, "exdrNR",SWIG_From_int((int)(exdrNR)));
+
+ SWIG_Python_SetConstant(d, "pluginOK",SWIG_From_int((int)(pluginOK)));
+ SWIG_Python_SetConstant(d, "pluginNOINIT",SWIG_From_int((int)(pluginNOINIT)));
+ SWIG_Python_SetConstant(d, "pluginCLOSE",SWIG_From_int((int)(pluginCLOSE)));
+ SWIG_Python_SetConstant(d, "pluginNOMEM",SWIG_From_int((int)(pluginNOMEM)));
+ SWIG_Python_SetConstant(d, "pluginENDOFFILE",SWIG_From_int((int)(pluginENDOFFILE)));
+ SWIG_Python_SetConstant(d, "pluginFILENOTFOUND",SWIG_From_int((int)(pluginFILENOTFOUND)));
+ SWIG_Python_SetConstant(d, "pluginFORMATERROR",SWIG_From_int((int)(pluginFORMATERROR)));
SWIG_Python_SetConstant(d, "SEEK_SET",SWIG_From_int((int)(SEEK_SET)));
SWIG_Python_SetConstant(d, "SEEK_CUR",SWIG_From_int((int)(SEEK_CUR)));
SWIG_Python_SetConstant(d, "SEEK_END",SWIG_From_int((int)(SEEK_END)));
- SWIG_Python_SetConstant(d, "DIM",SWIG_From_int((int)(3)));
#if PY_VERSION_HEX >= 0x03000000
return m;
#else
diff --git a/pymolfile/molfile/libpymolfile_wrap.cxx b/pymolfile/molfile/libpymolfile_wrap.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..a29b996585521d9172c15dca7a7f2811c71dc908
--- /dev/null
+++ b/pymolfile/molfile/libpymolfile_wrap.cxx
@@ -0,0 +1,4202 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 3.0.12
+ *
+ * This file is not intended to be easily readable and contains a number of
+ * coding conventions designed to improve portability and efficiency. Do not make
+ * changes to this file unless you know what you are doing--modify the SWIG
+ * interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+
+#ifndef SWIGPYTHON
+#define SWIGPYTHON
+#endif
+
+#define SWIG_PYTHON_DIRECTOR_NO_VTABLE
+
+
+#ifdef __cplusplus
+/* SwigValueWrapper is described in swig.swg */
+template<typename T> class SwigValueWrapper {
+ struct SwigMovePointer {
+ T *ptr;
+ SwigMovePointer(T *p) : ptr(p) { }
+ ~SwigMovePointer() { delete ptr; }
+ SwigMovePointer& operator=(SwigMovePointer& rhs) { T* oldptr = ptr; ptr = 0; delete oldptr; ptr = rhs.ptr; rhs.ptr = 0; return *this; }
+ } pointer;
+ SwigValueWrapper& operator=(const SwigValueWrapper<T>& rhs);
+ SwigValueWrapper(const SwigValueWrapper<T>& rhs);
+public:
+ SwigValueWrapper() : pointer(0) { }
+ SwigValueWrapper& operator=(const T& t) { SwigMovePointer tmp(new T(t)); pointer = tmp; return *this; }
+ operator T&() const { return *pointer.ptr; }
+ T *operator&() { return pointer.ptr; }
+};
+
+template <typename T> T SwigValueInit() {
+ return T();
+}
+#endif
+
+/* -----------------------------------------------------------------------------
+ * This section contains generic SWIG labels for method/variable
+ * declarations/attributes, and other compiler dependent labels.
+ * ----------------------------------------------------------------------------- */
+
+/* template workaround for compilers that cannot correctly implement the C++ standard */
+#ifndef SWIGTEMPLATEDISAMBIGUATOR
+# if defined(__SUNPRO_CC) && (__SUNPRO_CC <= 0x560)
+# define SWIGTEMPLATEDISAMBIGUATOR template
+# elif defined(__HP_aCC)
+/* Needed even with `aCC -AA' when `aCC -V' reports HP ANSI C++ B3910B A.03.55 */
+/* If we find a maximum version that requires this, the test would be __HP_aCC <= 35500 for A.03.55 */
+# define SWIGTEMPLATEDISAMBIGUATOR template
+# else
+# define SWIGTEMPLATEDISAMBIGUATOR
+# endif
+#endif
+
+/* inline attribute */
+#ifndef SWIGINLINE
+# if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__))
+# define SWIGINLINE inline
+# else
+# define SWIGINLINE
+# endif
+#endif
+
+/* attribute recognised by some compilers to avoid 'unused' warnings */
+#ifndef SWIGUNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define SWIGUNUSED __attribute__ ((__unused__))
+# else
+# define SWIGUNUSED
+# endif
+# elif defined(__ICC)
+# define SWIGUNUSED __attribute__ ((__unused__))
+# else
+# define SWIGUNUSED
+# endif
+#endif
+
+#ifndef SWIG_MSC_UNSUPPRESS_4505
+# if defined(_MSC_VER)
+# pragma warning(disable : 4505) /* unreferenced local function has been removed */
+# endif
+#endif
+
+#ifndef SWIGUNUSEDPARM
+# ifdef __cplusplus
+# define SWIGUNUSEDPARM(p)
+# else
+# define SWIGUNUSEDPARM(p) p SWIGUNUSED
+# endif
+#endif
+
+/* internal SWIG method */
+#ifndef SWIGINTERN
+# define SWIGINTERN static SWIGUNUSED
+#endif
+
+/* internal inline SWIG method */
+#ifndef SWIGINTERNINLINE
+# define SWIGINTERNINLINE SWIGINTERN SWIGINLINE
+#endif
+
+/* exporting methods */
+#if defined(__GNUC__)
+# if (__GNUC__ >= 4) || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
+# ifndef GCC_HASCLASSVISIBILITY
+# define GCC_HASCLASSVISIBILITY
+# endif
+# endif
+#endif
+
+#ifndef SWIGEXPORT
+# if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
+# if defined(STATIC_LINKED)
+# define SWIGEXPORT
+# else
+# define SWIGEXPORT __declspec(dllexport)
+# endif
+# else
+# if defined(__GNUC__) && defined(GCC_HASCLASSVISIBILITY)
+# define SWIGEXPORT __attribute__ ((visibility("default")))
+# else
+# define SWIGEXPORT
+# endif
+# endif
+#endif
+
+/* calling conventions for Windows */
+#ifndef SWIGSTDCALL
+# if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
+# define SWIGSTDCALL __stdcall
+# else
+# define SWIGSTDCALL
+# endif
+#endif
+
+/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
+#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE)
+# define _CRT_SECURE_NO_DEPRECATE
+#endif
+
+/* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */
+#if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE)
+# define _SCL_SECURE_NO_DEPRECATE
+#endif
+
+/* Deal with Apple's deprecated 'AssertMacros.h' from Carbon-framework */
+#if defined(__APPLE__) && !defined(__ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES)
+# define __ASSERT_MACROS_DEFINE_VERSIONS_WITHOUT_UNDERSCORES 0
+#endif
+
+/* Intel's compiler complains if a variable which was never initialised is
+ * cast to void, which is a common idiom which we use to indicate that we
+ * are aware a variable isn't used. So we just silence that warning.
+ * See: https://github.com/swig/swig/issues/192 for more discussion.
+ */
+#ifdef __INTEL_COMPILER
+# pragma warning disable 592
+#endif
+
+
+#if defined(_DEBUG) && defined(SWIG_PYTHON_INTERPRETER_NO_DEBUG)
+/* Use debug wrappers with the Python release dll */
+# undef _DEBUG
+# include <Python.h>
+# define _DEBUG
+#else
+# include <Python.h>
+#endif
+
+/* -----------------------------------------------------------------------------
+ * swigrun.swg
+ *
+ * This file contains generic C API SWIG runtime support for pointer
+ * type checking.
+ * ----------------------------------------------------------------------------- */
+
+/* This should only be incremented when either the layout of swig_type_info changes,
+ or for whatever reason, the runtime changes incompatibly */
+#define SWIG_RUNTIME_VERSION "4"
+
+/* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */
+#ifdef SWIG_TYPE_TABLE
+# define SWIG_QUOTE_STRING(x) #x
+# define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x)
+# define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE)
+#else
+# define SWIG_TYPE_TABLE_NAME
+#endif
+
+/*
+ You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for
+ creating a static or dynamic library from the SWIG runtime code.
+ In 99.9% of the cases, SWIG just needs to declare them as 'static'.
+
+ But only do this if strictly necessary, ie, if you have problems
+ with your compiler or suchlike.
+*/
+
+#ifndef SWIGRUNTIME
+# define SWIGRUNTIME SWIGINTERN
+#endif
+
+#ifndef SWIGRUNTIMEINLINE
+# define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE
+#endif
+
+/* Generic buffer size */
+#ifndef SWIG_BUFFER_SIZE
+# define SWIG_BUFFER_SIZE 1024
+#endif
+
+/* Flags for pointer conversions */
+#define SWIG_POINTER_DISOWN 0x1
+#define SWIG_CAST_NEW_MEMORY 0x2
+
+/* Flags for new pointer objects */
+#define SWIG_POINTER_OWN 0x1
+
+
+/*
+ Flags/methods for returning states.
+
+ The SWIG conversion methods, as ConvertPtr, return an integer
+ that tells if the conversion was successful or not. And if not,
+ an error code can be returned (see swigerrors.swg for the codes).
+
+ Use the following macros/flags to set or process the returning
+ states.
+
+ In old versions of SWIG, code such as the following was usually written:
+
+ if (SWIG_ConvertPtr(obj,vptr,ty.flags) != -1) {
+ // success code
+ } else {
+ //fail code
+ }
+
+ Now you can be more explicit:
+
+ int res = SWIG_ConvertPtr(obj,vptr,ty.flags);
+ if (SWIG_IsOK(res)) {
+ // success code
+ } else {
+ // fail code
+ }
+
+ which is the same really, but now you can also do
+
+ Type *ptr;
+ int res = SWIG_ConvertPtr(obj,(void **)(&ptr),ty.flags);
+ if (SWIG_IsOK(res)) {
+ // success code
+ if (SWIG_IsNewObj(res) {
+ ...
+ delete *ptr;
+ } else {
+ ...
+ }
+ } else {
+ // fail code
+ }
+
+ I.e., now SWIG_ConvertPtr can return new objects and you can
+ identify the case and take care of the deallocation. Of course that
+ also requires SWIG_ConvertPtr to return new result values, such as
+
+ int SWIG_ConvertPtr(obj, ptr,...) {
+ if (<obj is ok>) {
+ if (<need new object>) {
+ *ptr = <ptr to new allocated object>;
+ return SWIG_NEWOBJ;
+ } else {
+ *ptr = <ptr to old object>;
+ return SWIG_OLDOBJ;
+ }
+ } else {
+ return SWIG_BADOBJ;
+ }
+ }
+
+ Of course, returning the plain '0(success)/-1(fail)' still works, but you can be
+ more explicit by returning SWIG_BADOBJ, SWIG_ERROR or any of the
+ SWIG errors code.
+
+ Finally, if the SWIG_CASTRANK_MODE is enabled, the result code
+ allows to return the 'cast rank', for example, if you have this
+
+ int food(double)
+ int fooi(int);
+
+ and you call
+
+ food(1) // cast rank '1' (1 -> 1.0)
+ fooi(1) // cast rank '0'
+
+ just use the SWIG_AddCast()/SWIG_CheckState()
+*/
+
+#define SWIG_OK (0)
+#define SWIG_ERROR (-1)
+#define SWIG_IsOK(r) (r >= 0)
+#define SWIG_ArgError(r) ((r != SWIG_ERROR) ? r : SWIG_TypeError)
+
+/* The CastRankLimit says how many bits are used for the cast rank */
+#define SWIG_CASTRANKLIMIT (1 << 8)
+/* The NewMask denotes the object was created (using new/malloc) */
+#define SWIG_NEWOBJMASK (SWIG_CASTRANKLIMIT << 1)
+/* The TmpMask is for in/out typemaps that use temporal objects */
+#define SWIG_TMPOBJMASK (SWIG_NEWOBJMASK << 1)
+/* Simple returning values */
+#define SWIG_BADOBJ (SWIG_ERROR)
+#define SWIG_OLDOBJ (SWIG_OK)
+#define SWIG_NEWOBJ (SWIG_OK | SWIG_NEWOBJMASK)
+#define SWIG_TMPOBJ (SWIG_OK | SWIG_TMPOBJMASK)
+/* Check, add and del mask methods */
+#define SWIG_AddNewMask(r) (SWIG_IsOK(r) ? (r | SWIG_NEWOBJMASK) : r)
+#define SWIG_DelNewMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_NEWOBJMASK) : r)
+#define SWIG_IsNewObj(r) (SWIG_IsOK(r) && (r & SWIG_NEWOBJMASK))
+#define SWIG_AddTmpMask(r) (SWIG_IsOK(r) ? (r | SWIG_TMPOBJMASK) : r)
+#define SWIG_DelTmpMask(r) (SWIG_IsOK(r) ? (r & ~SWIG_TMPOBJMASK) : r)
+#define SWIG_IsTmpObj(r) (SWIG_IsOK(r) && (r & SWIG_TMPOBJMASK))
+
+/* Cast-Rank Mode */
+#if defined(SWIG_CASTRANK_MODE)
+# ifndef SWIG_TypeRank
+# define SWIG_TypeRank unsigned long
+# endif
+# ifndef SWIG_MAXCASTRANK /* Default cast allowed */
+# define SWIG_MAXCASTRANK (2)
+# endif
+# define SWIG_CASTRANKMASK ((SWIG_CASTRANKLIMIT) -1)
+# define SWIG_CastRank(r) (r & SWIG_CASTRANKMASK)
+SWIGINTERNINLINE int SWIG_AddCast(int r) {
+ return SWIG_IsOK(r) ? ((SWIG_CastRank(r) < SWIG_MAXCASTRANK) ? (r + 1) : SWIG_ERROR) : r;
+}
+SWIGINTERNINLINE int SWIG_CheckState(int r) {
+ return SWIG_IsOK(r) ? SWIG_CastRank(r) + 1 : 0;
+}
+#else /* no cast-rank mode */
+# define SWIG_AddCast(r) (r)
+# define SWIG_CheckState(r) (SWIG_IsOK(r) ? 1 : 0)
+#endif
+
+
+#include <string.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef void *(*swig_converter_func)(void *, int *);
+typedef struct swig_type_info *(*swig_dycast_func)(void **);
+
+/* Structure to store information on one type */
+typedef struct swig_type_info {
+ const char *name; /* mangled name of this type */
+ const char *str; /* human readable name of this type */
+ swig_dycast_func dcast; /* dynamic cast function down a hierarchy */
+ struct swig_cast_info *cast; /* linked list of types that can cast into this type */
+ void *clientdata; /* language specific type data */
+ int owndata; /* flag if the structure owns the clientdata */
+} swig_type_info;
+
+/* Structure to store a type and conversion function used for casting */
+typedef struct swig_cast_info {
+ swig_type_info *type; /* pointer to type that is equivalent to this type */
+ swig_converter_func converter; /* function to cast the void pointers */
+ struct swig_cast_info *next; /* pointer to next cast in linked list */
+ struct swig_cast_info *prev; /* pointer to the previous cast */
+} swig_cast_info;
+
+/* Structure used to store module information
+ * Each module generates one structure like this, and the runtime collects
+ * all of these structures and stores them in a circularly linked list.*/
+typedef struct swig_module_info {
+ swig_type_info **types; /* Array of pointers to swig_type_info structures that are in this module */
+ size_t size; /* Number of types in this module */
+ struct swig_module_info *next; /* Pointer to next element in circularly linked list */
+ swig_type_info **type_initial; /* Array of initially generated type structures */
+ swig_cast_info **cast_initial; /* Array of initially generated casting structures */
+ void *clientdata; /* Language specific module data */
+} swig_module_info;
+
+/*
+ Compare two type names skipping the space characters, therefore
+ "char*" == "char *" and "Class<int>" == "Class<int >", etc.
+
+ Return 0 when the two name types are equivalent, as in
+ strncmp, but skipping ' '.
+*/
+SWIGRUNTIME int
+SWIG_TypeNameComp(const char *f1, const char *l1,
+ const char *f2, const char *l2) {
+ for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) {
+ while ((*f1 == ' ') && (f1 != l1)) ++f1;
+ while ((*f2 == ' ') && (f2 != l2)) ++f2;
+ if (*f1 != *f2) return (*f1 > *f2) ? 1 : -1;
+ }
+ return (int)((l1 - f1) - (l2 - f2));
+}
+
+/*
+ Check type equivalence in a name list like <name1>|<name2>|...
+ Return 0 if equal, -1 if nb < tb, 1 if nb > tb
+*/
+SWIGRUNTIME int
+SWIG_TypeCmp(const char *nb, const char *tb) {
+ int equiv = 1;
+ const char* te = tb + strlen(tb);
+ const char* ne = nb;
+ while (equiv != 0 && *ne) {
+ for (nb = ne; *ne; ++ne) {
+ if (*ne == '|') break;
+ }
+ equiv = SWIG_TypeNameComp(nb, ne, tb, te);
+ if (*ne) ++ne;
+ }
+ return equiv;
+}
+
+/*
+ Check type equivalence in a name list like <name1>|<name2>|...
+ Return 0 if not equal, 1 if equal
+*/
+SWIGRUNTIME int
+SWIG_TypeEquiv(const char *nb, const char *tb) {
+ return SWIG_TypeCmp(nb, tb) == 0 ? 1 : 0;
+}
+
+/*
+ Check the typename
+*/
+SWIGRUNTIME swig_cast_info *
+SWIG_TypeCheck(const char *c, swig_type_info *ty) {
+ if (ty) {
+ swig_cast_info *iter = ty->cast;
+ while (iter) {
+ if (strcmp(iter->type->name, c) == 0) {
+ if (iter == ty->cast)
+ return iter;
+ /* Move iter to the top of the linked list */
+ iter->prev->next = iter->next;
+ if (iter->next)
+ iter->next->prev = iter->prev;
+ iter->next = ty->cast;
+ iter->prev = 0;
+ if (ty->cast) ty->cast->prev = iter;
+ ty->cast = iter;
+ return iter;
+ }
+ iter = iter->next;
+ }
+ }
+ return 0;
+}
+
+/*
+ Identical to SWIG_TypeCheck, except strcmp is replaced with a pointer comparison
+*/
+SWIGRUNTIME swig_cast_info *
+SWIG_TypeCheckStruct(swig_type_info *from, swig_type_info *ty) {
+ if (ty) {
+ swig_cast_info *iter = ty->cast;
+ while (iter) {
+ if (iter->type == from) {
+ if (iter == ty->cast)
+ return iter;
+ /* Move iter to the top of the linked list */
+ iter->prev->next = iter->next;
+ if (iter->next)
+ iter->next->prev = iter->prev;
+ iter->next = ty->cast;
+ iter->prev = 0;
+ if (ty->cast) ty->cast->prev = iter;
+ ty->cast = iter;
+ return iter;
+ }
+ iter = iter->next;
+ }
+ }
+ return 0;
+}
+
+/*
+ Cast a pointer up an inheritance hierarchy
+*/
+SWIGRUNTIMEINLINE void *
+SWIG_TypeCast(swig_cast_info *ty, void *ptr, int *newmemory) {
+ return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr, newmemory);
+}
+
+/*
+ Dynamic pointer casting. Down an inheritance hierarchy
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) {
+ swig_type_info *lastty = ty;
+ if (!ty || !ty->dcast) return ty;
+ while (ty && (ty->dcast)) {
+ ty = (*ty->dcast)(ptr);
+ if (ty) lastty = ty;
+ }
+ return lastty;
+}
+
+/*
+ Return the name associated with this type
+*/
+SWIGRUNTIMEINLINE const char *
+SWIG_TypeName(const swig_type_info *ty) {
+ return ty->name;
+}
+
+/*
+ Return the pretty name associated with this type,
+ that is an unmangled type name in a form presentable to the user.
+*/
+SWIGRUNTIME const char *
+SWIG_TypePrettyName(const swig_type_info *type) {
+ /* The "str" field contains the equivalent pretty names of the
+ type, separated by vertical-bar characters. We choose
+ to print the last name, as it is often (?) the most
+ specific. */
+ if (!type) return NULL;
+ if (type->str != NULL) {
+ const char *last_name = type->str;
+ const char *s;
+ for (s = type->str; *s; s++)
+ if (*s == '|') last_name = s+1;
+ return last_name;
+ }
+ else
+ return type->name;
+}
+
+/*
+ Set the clientdata field for a type
+*/
+SWIGRUNTIME void
+SWIG_TypeClientData(swig_type_info *ti, void *clientdata) {
+ swig_cast_info *cast = ti->cast;
+ /* if (ti->clientdata == clientdata) return; */
+ ti->clientdata = clientdata;
+
+ while (cast) {
+ if (!cast->converter) {
+ swig_type_info *tc = cast->type;
+ if (!tc->clientdata) {
+ SWIG_TypeClientData(tc, clientdata);
+ }
+ }
+ cast = cast->next;
+ }
+}
+SWIGRUNTIME void
+SWIG_TypeNewClientData(swig_type_info *ti, void *clientdata) {
+ SWIG_TypeClientData(ti, clientdata);
+ ti->owndata = 1;
+}
+
+/*
+ Search for a swig_type_info structure only by mangled name
+ Search is a O(log #types)
+
+ We start searching at module start, and finish searching when start == end.
+ Note: if start == end at the beginning of the function, we go all the way around
+ the circular list.
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_MangledTypeQueryModule(swig_module_info *start,
+ swig_module_info *end,
+ const char *name) {
+ swig_module_info *iter = start;
+ do {
+ if (iter->size) {
+ size_t l = 0;
+ size_t r = iter->size - 1;
+ do {
+ /* since l+r >= 0, we can (>> 1) instead (/ 2) */
+ size_t i = (l + r) >> 1;
+ const char *iname = iter->types[i]->name;
+ if (iname) {
+ int compare = strcmp(name, iname);
+ if (compare == 0) {
+ return iter->types[i];
+ } else if (compare < 0) {
+ if (i) {
+ r = i - 1;
+ } else {
+ break;
+ }
+ } else if (compare > 0) {
+ l = i + 1;
+ }
+ } else {
+ break; /* should never happen */
+ }
+ } while (l <= r);
+ }
+ iter = iter->next;
+ } while (iter != end);
+ return 0;
+}
+
+/*
+ Search for a swig_type_info structure for either a mangled name or a human readable name.
+ It first searches the mangled names of the types, which is a O(log #types)
+ If a type is not found it then searches the human readable names, which is O(#types).
+
+ We start searching at module start, and finish searching when start == end.
+ Note: if start == end at the beginning of the function, we go all the way around
+ the circular list.
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeQueryModule(swig_module_info *start,
+ swig_module_info *end,
+ const char *name) {
+ /* STEP 1: Search the name field using binary search */
+ swig_type_info *ret = SWIG_MangledTypeQueryModule(start, end, name);
+ if (ret) {
+ return ret;
+ } else {
+ /* STEP 2: If the type hasn't been found, do a complete search
+ of the str field (the human readable name) */
+ swig_module_info *iter = start;
+ do {
+ size_t i = 0;
+ for (; i < iter->size; ++i) {
+ if (iter->types[i]->str && (SWIG_TypeEquiv(iter->types[i]->str, name)))
+ return iter->types[i];
+ }
+ iter = iter->next;
+ } while (iter != end);
+ }
+
+ /* neither found a match */
+ return 0;
+}
+
+/*
+ Pack binary data into a string
+*/
+SWIGRUNTIME char *
+SWIG_PackData(char *c, void *ptr, size_t sz) {
+ static const char hex[17] = "0123456789abcdef";
+ const unsigned char *u = (unsigned char *) ptr;
+ const unsigned char *eu = u + sz;
+ for (; u != eu; ++u) {
+ unsigned char uu = *u;
+ *(c++) = hex[(uu & 0xf0) >> 4];
+ *(c++) = hex[uu & 0xf];
+ }
+ return c;
+}
+
+/*
+ Unpack binary data from a string
+*/
+SWIGRUNTIME const char *
+SWIG_UnpackData(const char *c, void *ptr, size_t sz) {
+ unsigned char *u = (unsigned char *) ptr;
+ const unsigned char *eu = u + sz;
+ for (; u != eu; ++u) {
+ char d = *(c++);
+ unsigned char uu;
+ if ((d >= '0') && (d <= '9'))
+ uu = (unsigned char)((d - '0') << 4);
+ else if ((d >= 'a') && (d <= 'f'))
+ uu = (unsigned char)((d - ('a'-10)) << 4);
+ else
+ return (char *) 0;
+ d = *(c++);
+ if ((d >= '0') && (d <= '9'))
+ uu |= (unsigned char)(d - '0');
+ else if ((d >= 'a') && (d <= 'f'))
+ uu |= (unsigned char)(d - ('a'-10));
+ else
+ return (char *) 0;
+ *u = uu;
+ }
+ return c;
+}
+
+/*
+ Pack 'void *' into a string buffer.
+*/
+SWIGRUNTIME char *
+SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) {
+ char *r = buff;
+ if ((2*sizeof(void *) + 2) > bsz) return 0;
+ *(r++) = '_';
+ r = SWIG_PackData(r,&ptr,sizeof(void *));
+ if (strlen(name) + 1 > (bsz - (r - buff))) return 0;
+ strcpy(r,name);
+ return buff;
+}
+
+SWIGRUNTIME const char *
+SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) {
+ if (*c != '_') {
+ if (strcmp(c,"NULL") == 0) {
+ *ptr = (void *) 0;
+ return name;
+ } else {
+ return 0;
+ }
+ }
+ return SWIG_UnpackData(++c,ptr,sizeof(void *));
+}
+
+SWIGRUNTIME char *
+SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) {
+ char *r = buff;
+ size_t lname = (name ? strlen(name) : 0);
+ if ((2*sz + 2 + lname) > bsz) return 0;
+ *(r++) = '_';
+ r = SWIG_PackData(r,ptr,sz);
+ if (lname) {
+ strncpy(r,name,lname+1);
+ } else {
+ *r = 0;
+ }
+ return buff;
+}
+
+SWIGRUNTIME const char *
+SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) {
+ if (*c != '_') {
+ if (strcmp(c,"NULL") == 0) {
+ memset(ptr,0,sz);
+ return name;
+ } else {
+ return 0;
+ }
+ }
+ return SWIG_UnpackData(++c,ptr,sz);
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+/* Errors in SWIG */
+#define SWIG_UnknownError -1
+#define SWIG_IOError -2
+#define SWIG_RuntimeError -3
+#define SWIG_IndexError -4
+#define SWIG_TypeError -5
+#define SWIG_DivisionByZero -6
+#define SWIG_OverflowError -7
+#define SWIG_SyntaxError -8
+#define SWIG_ValueError -9
+#define SWIG_SystemError -10
+#define SWIG_AttributeError -11
+#define SWIG_MemoryError -12
+#define SWIG_NullReferenceError -13
+
+
+
+/* Compatibility macros for Python 3 */
+#if PY_VERSION_HEX >= 0x03000000
+
+#define PyClass_Check(obj) PyObject_IsInstance(obj, (PyObject *)&PyType_Type)
+#define PyInt_Check(x) PyLong_Check(x)
+#define PyInt_AsLong(x) PyLong_AsLong(x)
+#define PyInt_FromLong(x) PyLong_FromLong(x)
+#define PyInt_FromSize_t(x) PyLong_FromSize_t(x)
+#define PyString_Check(name) PyBytes_Check(name)
+#define PyString_FromString(x) PyUnicode_FromString(x)
+#define PyString_Format(fmt, args) PyUnicode_Format(fmt, args)
+#define PyString_AsString(str) PyBytes_AsString(str)
+#define PyString_Size(str) PyBytes_Size(str)
+#define PyString_InternFromString(key) PyUnicode_InternFromString(key)
+#define Py_TPFLAGS_HAVE_CLASS Py_TPFLAGS_BASETYPE
+#define PyString_AS_STRING(x) PyUnicode_AS_STRING(x)
+#define _PyLong_FromSsize_t(x) PyLong_FromSsize_t(x)
+
+#endif
+
+#ifndef Py_TYPE
+# define Py_TYPE(op) ((op)->ob_type)
+#endif
+
+/* SWIG APIs for compatibility of both Python 2 & 3 */
+
+#if PY_VERSION_HEX >= 0x03000000
+# define SWIG_Python_str_FromFormat PyUnicode_FromFormat
+#else
+# define SWIG_Python_str_FromFormat PyString_FromFormat
+#endif
+
+
+/* Warning: This function will allocate a new string in Python 3,
+ * so please call SWIG_Python_str_DelForPy3(x) to free the space.
+ */
+SWIGINTERN char*
+SWIG_Python_str_AsChar(PyObject *str)
+{
+#if PY_VERSION_HEX >= 0x03000000
+ char *cstr;
+ char *newstr;
+ Py_ssize_t len;
+ str = PyUnicode_AsUTF8String(str);
+ PyBytes_AsStringAndSize(str, &cstr, &len);
+ newstr = (char *) malloc(len+1);
+ memcpy(newstr, cstr, len+1);
+ Py_XDECREF(str);
+ return newstr;
+#else
+ return PyString_AsString(str);
+#endif
+}
+
+#if PY_VERSION_HEX >= 0x03000000
+# define SWIG_Python_str_DelForPy3(x) free( (void*) (x) )
+#else
+# define SWIG_Python_str_DelForPy3(x)
+#endif
+
+
+SWIGINTERN PyObject*
+SWIG_Python_str_FromChar(const char *c)
+{
+#if PY_VERSION_HEX >= 0x03000000
+ return PyUnicode_FromString(c);
+#else
+ return PyString_FromString(c);
+#endif
+}
+
+/* Add PyOS_snprintf for old Pythons */
+#if PY_VERSION_HEX < 0x02020000
+# if defined(_MSC_VER) || defined(__BORLANDC__) || defined(_WATCOM)
+# define PyOS_snprintf _snprintf
+# else
+# define PyOS_snprintf snprintf
+# endif
+#endif
+
+/* A crude PyString_FromFormat implementation for old Pythons */
+#if PY_VERSION_HEX < 0x02020000
+
+#ifndef SWIG_PYBUFFER_SIZE
+# define SWIG_PYBUFFER_SIZE 1024
+#endif
+
+static PyObject *
+PyString_FromFormat(const char *fmt, ...) {
+ va_list ap;
+ char buf[SWIG_PYBUFFER_SIZE * 2];
+ int res;
+ va_start(ap, fmt);
+ res = vsnprintf(buf, sizeof(buf), fmt, ap);
+ va_end(ap);
+ return (res < 0 || res >= (int)sizeof(buf)) ? 0 : PyString_FromString(buf);
+}
+#endif
+
+#ifndef PyObject_DEL
+# define PyObject_DEL PyObject_Del
+#endif
+
+/* A crude PyExc_StopIteration exception for old Pythons */
+#if PY_VERSION_HEX < 0x02020000
+# ifndef PyExc_StopIteration
+# define PyExc_StopIteration PyExc_RuntimeError
+# endif
+# ifndef PyObject_GenericGetAttr
+# define PyObject_GenericGetAttr 0
+# endif
+#endif
+
+/* Py_NotImplemented is defined in 2.1 and up. */
+#if PY_VERSION_HEX < 0x02010000
+# ifndef Py_NotImplemented
+# define Py_NotImplemented PyExc_RuntimeError
+# endif
+#endif
+
+/* A crude PyString_AsStringAndSize implementation for old Pythons */
+#if PY_VERSION_HEX < 0x02010000
+# ifndef PyString_AsStringAndSize
+# define PyString_AsStringAndSize(obj, s, len) {*s = PyString_AsString(obj); *len = *s ? strlen(*s) : 0;}
+# endif
+#endif
+
+/* PySequence_Size for old Pythons */
+#if PY_VERSION_HEX < 0x02000000
+# ifndef PySequence_Size
+# define PySequence_Size PySequence_Length
+# endif
+#endif
+
+/* PyBool_FromLong for old Pythons */
+#if PY_VERSION_HEX < 0x02030000
+static
+PyObject *PyBool_FromLong(long ok)
+{
+ PyObject *result = ok ? Py_True : Py_False;
+ Py_INCREF(result);
+ return result;
+}
+#endif
+
+/* Py_ssize_t for old Pythons */
+/* This code is as recommended by: */
+/* http://www.python.org/dev/peps/pep-0353/#conversion-guidelines */
+#if PY_VERSION_HEX < 0x02050000 && !defined(PY_SSIZE_T_MIN)
+typedef int Py_ssize_t;
+# define PY_SSIZE_T_MAX INT_MAX
+# define PY_SSIZE_T_MIN INT_MIN
+typedef inquiry lenfunc;
+typedef intargfunc ssizeargfunc;
+typedef intintargfunc ssizessizeargfunc;
+typedef intobjargproc ssizeobjargproc;
+typedef intintobjargproc ssizessizeobjargproc;
+typedef getreadbufferproc readbufferproc;
+typedef getwritebufferproc writebufferproc;
+typedef getsegcountproc segcountproc;
+typedef getcharbufferproc charbufferproc;
+static long PyNumber_AsSsize_t (PyObject *x, void *SWIGUNUSEDPARM(exc))
+{
+ long result = 0;
+ PyObject *i = PyNumber_Int(x);
+ if (i) {
+ result = PyInt_AsLong(i);
+ Py_DECREF(i);
+ }
+ return result;
+}
+#endif
+
+#if PY_VERSION_HEX < 0x02050000
+#define PyInt_FromSize_t(x) PyInt_FromLong((long)x)
+#endif
+
+#if PY_VERSION_HEX < 0x02040000
+#define Py_VISIT(op) \
+ do { \
+ if (op) { \
+ int vret = visit((op), arg); \
+ if (vret) \
+ return vret; \
+ } \
+ } while (0)
+#endif
+
+#if PY_VERSION_HEX < 0x02030000
+typedef struct {
+ PyTypeObject type;
+ PyNumberMethods as_number;
+ PyMappingMethods as_mapping;
+ PySequenceMethods as_sequence;
+ PyBufferProcs as_buffer;
+ PyObject *name, *slots;
+} PyHeapTypeObject;
+#endif
+
+#if PY_VERSION_HEX < 0x02030000
+typedef destructor freefunc;
+#endif
+
+#if ((PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 6) || \
+ (PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION > 0) || \
+ (PY_MAJOR_VERSION > 3))
+# define SWIGPY_USE_CAPSULE
+# define SWIGPY_CAPSULE_NAME ((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION ".type_pointer_capsule" SWIG_TYPE_TABLE_NAME)
+#endif
+
+#if PY_VERSION_HEX < 0x03020000
+#define PyDescr_TYPE(x) (((PyDescrObject *)(x))->d_type)
+#define PyDescr_NAME(x) (((PyDescrObject *)(x))->d_name)
+#define Py_hash_t long
+#endif
+
+/* -----------------------------------------------------------------------------
+ * error manipulation
+ * ----------------------------------------------------------------------------- */
+
+SWIGRUNTIME PyObject*
+SWIG_Python_ErrorType(int code) {
+ PyObject* type = 0;
+ switch(code) {
+ case SWIG_MemoryError:
+ type = PyExc_MemoryError;
+ break;
+ case SWIG_IOError:
+ type = PyExc_IOError;
+ break;
+ case SWIG_RuntimeError:
+ type = PyExc_RuntimeError;
+ break;
+ case SWIG_IndexError:
+ type = PyExc_IndexError;
+ break;
+ case SWIG_TypeError:
+ type = PyExc_TypeError;
+ break;
+ case SWIG_DivisionByZero:
+ type = PyExc_ZeroDivisionError;
+ break;
+ case SWIG_OverflowError:
+ type = PyExc_OverflowError;
+ break;
+ case SWIG_SyntaxError:
+ type = PyExc_SyntaxError;
+ break;
+ case SWIG_ValueError:
+ type = PyExc_ValueError;
+ break;
+ case SWIG_SystemError:
+ type = PyExc_SystemError;
+ break;
+ case SWIG_AttributeError:
+ type = PyExc_AttributeError;
+ break;
+ default:
+ type = PyExc_RuntimeError;
+ }
+ return type;
+}
+
+
+SWIGRUNTIME void
+SWIG_Python_AddErrorMsg(const char* mesg)
+{
+ PyObject *type = 0;
+ PyObject *value = 0;
+ PyObject *traceback = 0;
+
+ if (PyErr_Occurred()) PyErr_Fetch(&type, &value, &traceback);
+ if (value) {
+ char *tmp;
+ PyObject *old_str = PyObject_Str(value);
+ PyErr_Clear();
+ Py_XINCREF(type);
+
+ PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg);
+ SWIG_Python_str_DelForPy3(tmp);
+ Py_DECREF(old_str);
+ Py_DECREF(value);
+ } else {
+ PyErr_SetString(PyExc_RuntimeError, mesg);
+ }
+}
+
+#if defined(SWIG_PYTHON_NO_THREADS)
+# if defined(SWIG_PYTHON_THREADS)
+# undef SWIG_PYTHON_THREADS
+# endif
+#endif
+#if defined(SWIG_PYTHON_THREADS) /* Threading support is enabled */
+# if !defined(SWIG_PYTHON_USE_GIL) && !defined(SWIG_PYTHON_NO_USE_GIL)
+# if (PY_VERSION_HEX >= 0x02030000) /* For 2.3 or later, use the PyGILState calls */
+# define SWIG_PYTHON_USE_GIL
+# endif
+# endif
+# if defined(SWIG_PYTHON_USE_GIL) /* Use PyGILState threads calls */
+# ifndef SWIG_PYTHON_INITIALIZE_THREADS
+# define SWIG_PYTHON_INITIALIZE_THREADS PyEval_InitThreads()
+# endif
+# ifdef __cplusplus /* C++ code */
+ class SWIG_Python_Thread_Block {
+ bool status;
+ PyGILState_STATE state;
+ public:
+ void end() { if (status) { PyGILState_Release(state); status = false;} }
+ SWIG_Python_Thread_Block() : status(true), state(PyGILState_Ensure()) {}
+ ~SWIG_Python_Thread_Block() { end(); }
+ };
+ class SWIG_Python_Thread_Allow {
+ bool status;
+ PyThreadState *save;
+ public:
+ void end() { if (status) { PyEval_RestoreThread(save); status = false; }}
+ SWIG_Python_Thread_Allow() : status(true), save(PyEval_SaveThread()) {}
+ ~SWIG_Python_Thread_Allow() { end(); }
+ };
+# define SWIG_PYTHON_THREAD_BEGIN_BLOCK SWIG_Python_Thread_Block _swig_thread_block
+# define SWIG_PYTHON_THREAD_END_BLOCK _swig_thread_block.end()
+# define SWIG_PYTHON_THREAD_BEGIN_ALLOW SWIG_Python_Thread_Allow _swig_thread_allow
+# define SWIG_PYTHON_THREAD_END_ALLOW _swig_thread_allow.end()
+# else /* C code */
+# define SWIG_PYTHON_THREAD_BEGIN_BLOCK PyGILState_STATE _swig_thread_block = PyGILState_Ensure()
+# define SWIG_PYTHON_THREAD_END_BLOCK PyGILState_Release(_swig_thread_block)
+# define SWIG_PYTHON_THREAD_BEGIN_ALLOW PyThreadState *_swig_thread_allow = PyEval_SaveThread()
+# define SWIG_PYTHON_THREAD_END_ALLOW PyEval_RestoreThread(_swig_thread_allow)
+# endif
+# else /* Old thread way, not implemented, user must provide it */
+# if !defined(SWIG_PYTHON_INITIALIZE_THREADS)
+# define SWIG_PYTHON_INITIALIZE_THREADS
+# endif
+# if !defined(SWIG_PYTHON_THREAD_BEGIN_BLOCK)
+# define SWIG_PYTHON_THREAD_BEGIN_BLOCK
+# endif
+# if !defined(SWIG_PYTHON_THREAD_END_BLOCK)
+# define SWIG_PYTHON_THREAD_END_BLOCK
+# endif
+# if !defined(SWIG_PYTHON_THREAD_BEGIN_ALLOW)
+# define SWIG_PYTHON_THREAD_BEGIN_ALLOW
+# endif
+# if !defined(SWIG_PYTHON_THREAD_END_ALLOW)
+# define SWIG_PYTHON_THREAD_END_ALLOW
+# endif
+# endif
+#else /* No thread support */
+# define SWIG_PYTHON_INITIALIZE_THREADS
+# define SWIG_PYTHON_THREAD_BEGIN_BLOCK
+# define SWIG_PYTHON_THREAD_END_BLOCK
+# define SWIG_PYTHON_THREAD_BEGIN_ALLOW
+# define SWIG_PYTHON_THREAD_END_ALLOW
+#endif
+
+/* -----------------------------------------------------------------------------
+ * Python API portion that goes into the runtime
+ * ----------------------------------------------------------------------------- */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* -----------------------------------------------------------------------------
+ * Constant declarations
+ * ----------------------------------------------------------------------------- */
+
+/* Constant Types */
+#define SWIG_PY_POINTER 4
+#define SWIG_PY_BINARY 5
+
+/* Constant information structure */
+typedef struct swig_const_info {
+ int type;
+ char *name;
+ long lvalue;
+ double dvalue;
+ void *pvalue;
+ swig_type_info **ptype;
+} swig_const_info;
+
+
+/* -----------------------------------------------------------------------------
+ * Wrapper of PyInstanceMethod_New() used in Python 3
+ * It is exported to the generated module, used for -fastproxy
+ * ----------------------------------------------------------------------------- */
+#if PY_VERSION_HEX >= 0x03000000
+SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *func)
+{
+ return PyInstanceMethod_New(func);
+}
+#else
+SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *SWIGUNUSEDPARM(self), PyObject *SWIGUNUSEDPARM(func))
+{
+ return NULL;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+
+/* -----------------------------------------------------------------------------
+ * pyrun.swg
+ *
+ * This file contains the runtime support for Python modules
+ * and includes code for managing global variables and pointer
+ * type checking.
+ *
+ * ----------------------------------------------------------------------------- */
+
+/* Common SWIG API */
+
+/* for raw pointers */
+#define SWIG_Python_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, 0)
+#define SWIG_ConvertPtr(obj, pptr, type, flags) SWIG_Python_ConvertPtr(obj, pptr, type, flags)
+#define SWIG_ConvertPtrAndOwn(obj,pptr,type,flags,own) SWIG_Python_ConvertPtrAndOwn(obj, pptr, type, flags, own)
+
+#ifdef SWIGPYTHON_BUILTIN
+#define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(self, ptr, type, flags)
+#else
+#define SWIG_NewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags)
+#endif
+
+#define SWIG_InternalNewPointerObj(ptr, type, flags) SWIG_Python_NewPointerObj(NULL, ptr, type, flags)
+
+#define SWIG_CheckImplicit(ty) SWIG_Python_CheckImplicit(ty)
+#define SWIG_AcquirePtr(ptr, src) SWIG_Python_AcquirePtr(ptr, src)
+#define swig_owntype int
+
+/* for raw packed data */
+#define SWIG_ConvertPacked(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty)
+#define SWIG_NewPackedObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type)
+
+/* for class or struct pointers */
+#define SWIG_ConvertInstance(obj, pptr, type, flags) SWIG_ConvertPtr(obj, pptr, type, flags)
+#define SWIG_NewInstanceObj(ptr, type, flags) SWIG_NewPointerObj(ptr, type, flags)
+
+/* for C or C++ function pointers */
+#define SWIG_ConvertFunctionPtr(obj, pptr, type) SWIG_Python_ConvertFunctionPtr(obj, pptr, type)
+#define SWIG_NewFunctionPtrObj(ptr, type) SWIG_Python_NewPointerObj(NULL, ptr, type, 0)
+
+/* for C++ member pointers, ie, member methods */
+#define SWIG_ConvertMember(obj, ptr, sz, ty) SWIG_Python_ConvertPacked(obj, ptr, sz, ty)
+#define SWIG_NewMemberObj(ptr, sz, type) SWIG_Python_NewPackedObj(ptr, sz, type)
+
+
+/* Runtime API */
+
+#define SWIG_GetModule(clientdata) SWIG_Python_GetModule(clientdata)
+#define SWIG_SetModule(clientdata, pointer) SWIG_Python_SetModule(pointer)
+#define SWIG_NewClientData(obj) SwigPyClientData_New(obj)
+
+#define SWIG_SetErrorObj SWIG_Python_SetErrorObj
+#define SWIG_SetErrorMsg SWIG_Python_SetErrorMsg
+#define SWIG_ErrorType(code) SWIG_Python_ErrorType(code)
+#define SWIG_Error(code, msg) SWIG_Python_SetErrorMsg(SWIG_ErrorType(code), msg)
+#define SWIG_fail goto fail
+
+
+/* Runtime API implementation */
+
+/* Error manipulation */
+
+SWIGINTERN void
+SWIG_Python_SetErrorObj(PyObject *errtype, PyObject *obj) {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ PyErr_SetObject(errtype, obj);
+ Py_DECREF(obj);
+ SWIG_PYTHON_THREAD_END_BLOCK;
+}
+
+SWIGINTERN void
+SWIG_Python_SetErrorMsg(PyObject *errtype, const char *msg) {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ PyErr_SetString(errtype, msg);
+ SWIG_PYTHON_THREAD_END_BLOCK;
+}
+
+#define SWIG_Python_Raise(obj, type, desc) SWIG_Python_SetErrorObj(SWIG_Python_ExceptionType(desc), obj)
+
+/* Set a constant value */
+
+#if defined(SWIGPYTHON_BUILTIN)
+
+SWIGINTERN void
+SwigPyBuiltin_AddPublicSymbol(PyObject *seq, const char *key) {
+ PyObject *s = PyString_InternFromString(key);
+ PyList_Append(seq, s);
+ Py_DECREF(s);
+}
+
+SWIGINTERN void
+SWIG_Python_SetConstant(PyObject *d, PyObject *public_interface, const char *name, PyObject *obj) {
+#if PY_VERSION_HEX < 0x02030000
+ PyDict_SetItemString(d, (char *)name, obj);
+#else
+ PyDict_SetItemString(d, name, obj);
+#endif
+ Py_DECREF(obj);
+ if (public_interface)
+ SwigPyBuiltin_AddPublicSymbol(public_interface, name);
+}
+
+#else
+
+SWIGINTERN void
+SWIG_Python_SetConstant(PyObject *d, const char *name, PyObject *obj) {
+#if PY_VERSION_HEX < 0x02030000
+ PyDict_SetItemString(d, (char *)name, obj);
+#else
+ PyDict_SetItemString(d, name, obj);
+#endif
+ Py_DECREF(obj);
+}
+
+#endif
+
+/* Append a value to the result obj */
+
+SWIGINTERN PyObject*
+SWIG_Python_AppendOutput(PyObject* result, PyObject* obj) {
+#if !defined(SWIG_PYTHON_OUTPUT_TUPLE)
+ if (!result) {
+ result = obj;
+ } else if (result == Py_None) {
+ Py_DECREF(result);
+ result = obj;
+ } else {
+ if (!PyList_Check(result)) {
+ PyObject *o2 = result;
+ result = PyList_New(1);
+ PyList_SetItem(result, 0, o2);
+ }
+ PyList_Append(result,obj);
+ Py_DECREF(obj);
+ }
+ return result;
+#else
+ PyObject* o2;
+ PyObject* o3;
+ if (!result) {
+ result = obj;
+ } else if (result == Py_None) {
+ Py_DECREF(result);
+ result = obj;
+ } else {
+ if (!PyTuple_Check(result)) {
+ o2 = result;
+ result = PyTuple_New(1);
+ PyTuple_SET_ITEM(result, 0, o2);
+ }
+ o3 = PyTuple_New(1);
+ PyTuple_SET_ITEM(o3, 0, obj);
+ o2 = result;
+ result = PySequence_Concat(o2, o3);
+ Py_DECREF(o2);
+ Py_DECREF(o3);
+ }
+ return result;
+#endif
+}
+
+/* Unpack the argument tuple */
+
+SWIGINTERN Py_ssize_t
+SWIG_Python_UnpackTuple(PyObject *args, const char *name, Py_ssize_t min, Py_ssize_t max, PyObject **objs)
+{
+ if (!args) {
+ if (!min && !max) {
+ return 1;
+ } else {
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got none",
+ name, (min == max ? "" : "at least "), (int)min);
+ return 0;
+ }
+ }
+ if (!PyTuple_Check(args)) {
+ if (min <= 1 && max >= 1) {
+ Py_ssize_t i;
+ objs[0] = args;
+ for (i = 1; i < max; ++i) {
+ objs[i] = 0;
+ }
+ return 2;
+ }
+ PyErr_SetString(PyExc_SystemError, "UnpackTuple() argument list is not a tuple");
+ return 0;
+ } else {
+ Py_ssize_t l = PyTuple_GET_SIZE(args);
+ if (l < min) {
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
+ name, (min == max ? "" : "at least "), (int)min, (int)l);
+ return 0;
+ } else if (l > max) {
+ PyErr_Format(PyExc_TypeError, "%s expected %s%d arguments, got %d",
+ name, (min == max ? "" : "at most "), (int)max, (int)l);
+ return 0;
+ } else {
+ Py_ssize_t i;
+ for (i = 0; i < l; ++i) {
+ objs[i] = PyTuple_GET_ITEM(args, i);
+ }
+ for (; l < max; ++l) {
+ objs[l] = 0;
+ }
+ return i + 1;
+ }
+ }
+}
+
+/* A functor is a function object with one single object argument */
+#if PY_VERSION_HEX >= 0x02020000
+#define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunctionObjArgs(functor, obj, NULL);
+#else
+#define SWIG_Python_CallFunctor(functor, obj) PyObject_CallFunction(functor, "O", obj);
+#endif
+
+/*
+ Helper for static pointer initialization for both C and C++ code, for example
+ static PyObject *SWIG_STATIC_POINTER(MyVar) = NewSomething(...);
+*/
+#ifdef __cplusplus
+#define SWIG_STATIC_POINTER(var) var
+#else
+#define SWIG_STATIC_POINTER(var) var = 0; if (!var) var
+#endif
+
+/* -----------------------------------------------------------------------------
+ * Pointer declarations
+ * ----------------------------------------------------------------------------- */
+
+/* Flags for new pointer objects */
+#define SWIG_POINTER_NOSHADOW (SWIG_POINTER_OWN << 1)
+#define SWIG_POINTER_NEW (SWIG_POINTER_NOSHADOW | SWIG_POINTER_OWN)
+
+#define SWIG_POINTER_IMPLICIT_CONV (SWIG_POINTER_DISOWN << 1)
+
+#define SWIG_BUILTIN_TP_INIT (SWIG_POINTER_OWN << 2)
+#define SWIG_BUILTIN_INIT (SWIG_BUILTIN_TP_INIT | SWIG_POINTER_OWN)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* How to access Py_None */
+#if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
+# ifndef SWIG_PYTHON_NO_BUILD_NONE
+# ifndef SWIG_PYTHON_BUILD_NONE
+# define SWIG_PYTHON_BUILD_NONE
+# endif
+# endif
+#endif
+
+#ifdef SWIG_PYTHON_BUILD_NONE
+# ifdef Py_None
+# undef Py_None
+# define Py_None SWIG_Py_None()
+# endif
+SWIGRUNTIMEINLINE PyObject *
+_SWIG_Py_None(void)
+{
+ PyObject *none = Py_BuildValue((char*)"");
+ Py_DECREF(none);
+ return none;
+}
+SWIGRUNTIME PyObject *
+SWIG_Py_None(void)
+{
+ static PyObject *SWIG_STATIC_POINTER(none) = _SWIG_Py_None();
+ return none;
+}
+#endif
+
+/* The python void return value */
+
+SWIGRUNTIMEINLINE PyObject *
+SWIG_Py_Void(void)
+{
+ PyObject *none = Py_None;
+ Py_INCREF(none);
+ return none;
+}
+
+/* SwigPyClientData */
+
+typedef struct {
+ PyObject *klass;
+ PyObject *newraw;
+ PyObject *newargs;
+ PyObject *destroy;
+ int delargs;
+ int implicitconv;
+ PyTypeObject *pytype;
+} SwigPyClientData;
+
+SWIGRUNTIMEINLINE int
+SWIG_Python_CheckImplicit(swig_type_info *ty)
+{
+ SwigPyClientData *data = (SwigPyClientData *)ty->clientdata;
+ return data ? data->implicitconv : 0;
+}
+
+SWIGRUNTIMEINLINE PyObject *
+SWIG_Python_ExceptionType(swig_type_info *desc) {
+ SwigPyClientData *data = desc ? (SwigPyClientData *) desc->clientdata : 0;
+ PyObject *klass = data ? data->klass : 0;
+ return (klass ? klass : PyExc_RuntimeError);
+}
+
+
+SWIGRUNTIME SwigPyClientData *
+SwigPyClientData_New(PyObject* obj)
+{
+ if (!obj) {
+ return 0;
+ } else {
+ SwigPyClientData *data = (SwigPyClientData *)malloc(sizeof(SwigPyClientData));
+ /* the klass element */
+ data->klass = obj;
+ Py_INCREF(data->klass);
+ /* the newraw method and newargs arguments used to create a new raw instance */
+ if (PyClass_Check(obj)) {
+ data->newraw = 0;
+ data->newargs = obj;
+ Py_INCREF(obj);
+ } else {
+#if (PY_VERSION_HEX < 0x02020000)
+ data->newraw = 0;
+#else
+ data->newraw = PyObject_GetAttrString(data->klass, (char *)"__new__");
+#endif
+ if (data->newraw) {
+ Py_INCREF(data->newraw);
+ data->newargs = PyTuple_New(1);
+ PyTuple_SetItem(data->newargs, 0, obj);
+ } else {
+ data->newargs = obj;
+ }
+ Py_INCREF(data->newargs);
+ }
+ /* the destroy method, aka as the C++ delete method */
+ data->destroy = PyObject_GetAttrString(data->klass, (char *)"__swig_destroy__");
+ if (PyErr_Occurred()) {
+ PyErr_Clear();
+ data->destroy = 0;
+ }
+ if (data->destroy) {
+ int flags;
+ Py_INCREF(data->destroy);
+ flags = PyCFunction_GET_FLAGS(data->destroy);
+#ifdef METH_O
+ data->delargs = !(flags & (METH_O));
+#else
+ data->delargs = 0;
+#endif
+ } else {
+ data->delargs = 0;
+ }
+ data->implicitconv = 0;
+ data->pytype = 0;
+ return data;
+ }
+}
+
+SWIGRUNTIME void
+SwigPyClientData_Del(SwigPyClientData *data) {
+ Py_XDECREF(data->newraw);
+ Py_XDECREF(data->newargs);
+ Py_XDECREF(data->destroy);
+}
+
+/* =============== SwigPyObject =====================*/
+
+typedef struct {
+ PyObject_HEAD
+ void *ptr;
+ swig_type_info *ty;
+ int own;
+ PyObject *next;
+#ifdef SWIGPYTHON_BUILTIN
+ PyObject *dict;
+#endif
+} SwigPyObject;
+
+
+#ifdef SWIGPYTHON_BUILTIN
+
+SWIGRUNTIME PyObject *
+SwigPyObject_get___dict__(PyObject *v, PyObject *SWIGUNUSEDPARM(args))
+{
+ SwigPyObject *sobj = (SwigPyObject *)v;
+
+ if (!sobj->dict)
+ sobj->dict = PyDict_New();
+
+ Py_INCREF(sobj->dict);
+ return sobj->dict;
+}
+
+#endif
+
+SWIGRUNTIME PyObject *
+SwigPyObject_long(SwigPyObject *v)
+{
+ return PyLong_FromVoidPtr(v->ptr);
+}
+
+SWIGRUNTIME PyObject *
+SwigPyObject_format(const char* fmt, SwigPyObject *v)
+{
+ PyObject *res = NULL;
+ PyObject *args = PyTuple_New(1);
+ if (args) {
+ if (PyTuple_SetItem(args, 0, SwigPyObject_long(v)) == 0) {
+ PyObject *ofmt = SWIG_Python_str_FromChar(fmt);
+ if (ofmt) {
+#if PY_VERSION_HEX >= 0x03000000
+ res = PyUnicode_Format(ofmt,args);
+#else
+ res = PyString_Format(ofmt,args);
+#endif
+ Py_DECREF(ofmt);
+ }
+ Py_DECREF(args);
+ }
+ }
+ return res;
+}
+
+SWIGRUNTIME PyObject *
+SwigPyObject_oct(SwigPyObject *v)
+{
+ return SwigPyObject_format("%o",v);
+}
+
+SWIGRUNTIME PyObject *
+SwigPyObject_hex(SwigPyObject *v)
+{
+ return SwigPyObject_format("%x",v);
+}
+
+SWIGRUNTIME PyObject *
+#ifdef METH_NOARGS
+SwigPyObject_repr(SwigPyObject *v)
+#else
+SwigPyObject_repr(SwigPyObject *v, PyObject *args)
+#endif
+{
+ const char *name = SWIG_TypePrettyName(v->ty);
+ PyObject *repr = SWIG_Python_str_FromFormat("<Swig Object of type '%s' at %p>", (name ? name : "unknown"), (void *)v);
+ if (v->next) {
+# ifdef METH_NOARGS
+ PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next);
+# else
+ PyObject *nrep = SwigPyObject_repr((SwigPyObject *)v->next, args);
+# endif
+# if PY_VERSION_HEX >= 0x03000000
+ PyObject *joined = PyUnicode_Concat(repr, nrep);
+ Py_DecRef(repr);
+ Py_DecRef(nrep);
+ repr = joined;
+# else
+ PyString_ConcatAndDel(&repr,nrep);
+# endif
+ }
+ return repr;
+}
+
+SWIGRUNTIME int
+SwigPyObject_compare(SwigPyObject *v, SwigPyObject *w)
+{
+ void *i = v->ptr;
+ void *j = w->ptr;
+ return (i < j) ? -1 : ((i > j) ? 1 : 0);
+}
+
+/* Added for Python 3.x, would it also be useful for Python 2.x? */
+SWIGRUNTIME PyObject*
+SwigPyObject_richcompare(SwigPyObject *v, SwigPyObject *w, int op)
+{
+ PyObject* res;
+ if( op != Py_EQ && op != Py_NE ) {
+ Py_INCREF(Py_NotImplemented);
+ return Py_NotImplemented;
+ }
+ res = PyBool_FromLong( (SwigPyObject_compare(v, w)==0) == (op == Py_EQ) ? 1 : 0);
+ return res;
+}
+
+
+SWIGRUNTIME PyTypeObject* SwigPyObject_TypeOnce(void);
+
+#ifdef SWIGPYTHON_BUILTIN
+static swig_type_info *SwigPyObject_stype = 0;
+SWIGRUNTIME PyTypeObject*
+SwigPyObject_type(void) {
+ SwigPyClientData *cd;
+ assert(SwigPyObject_stype);
+ cd = (SwigPyClientData*) SwigPyObject_stype->clientdata;
+ assert(cd);
+ assert(cd->pytype);
+ return cd->pytype;
+}
+#else
+SWIGRUNTIME PyTypeObject*
+SwigPyObject_type(void) {
+ static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyObject_TypeOnce();
+ return type;
+}
+#endif
+
+SWIGRUNTIMEINLINE int
+SwigPyObject_Check(PyObject *op) {
+#ifdef SWIGPYTHON_BUILTIN
+ PyTypeObject *target_tp = SwigPyObject_type();
+ if (PyType_IsSubtype(op->ob_type, target_tp))
+ return 1;
+ return (strcmp(op->ob_type->tp_name, "SwigPyObject") == 0);
+#else
+ return (Py_TYPE(op) == SwigPyObject_type())
+ || (strcmp(Py_TYPE(op)->tp_name,"SwigPyObject") == 0);
+#endif
+}
+
+SWIGRUNTIME PyObject *
+SwigPyObject_New(void *ptr, swig_type_info *ty, int own);
+
+SWIGRUNTIME void
+SwigPyObject_dealloc(PyObject *v)
+{
+ SwigPyObject *sobj = (SwigPyObject *) v;
+ PyObject *next = sobj->next;
+ if (sobj->own == SWIG_POINTER_OWN) {
+ swig_type_info *ty = sobj->ty;
+ SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0;
+ PyObject *destroy = data ? data->destroy : 0;
+ if (destroy) {
+ /* destroy is always a VARARGS method */
+ PyObject *res;
+
+ /* PyObject_CallFunction() has the potential to silently drop
+ the active active exception. In cases of unnamed temporary
+ variable or where we just finished iterating over a generator
+ StopIteration will be active right now, and this needs to
+ remain true upon return from SwigPyObject_dealloc. So save
+ and restore. */
+
+ PyObject *val = NULL, *type = NULL, *tb = NULL;
+ PyErr_Fetch(&val, &type, &tb);
+
+ if (data->delargs) {
+ /* we need to create a temporary object to carry the destroy operation */
+ PyObject *tmp = SwigPyObject_New(sobj->ptr, ty, 0);
+ res = SWIG_Python_CallFunctor(destroy, tmp);
+ Py_DECREF(tmp);
+ } else {
+ PyCFunction meth = PyCFunction_GET_FUNCTION(destroy);
+ PyObject *mself = PyCFunction_GET_SELF(destroy);
+ res = ((*meth)(mself, v));
+ }
+ if (!res)
+ PyErr_WriteUnraisable(destroy);
+
+ PyErr_Restore(val, type, tb);
+
+ Py_XDECREF(res);
+ }
+#if !defined(SWIG_PYTHON_SILENT_MEMLEAK)
+ else {
+ const char *name = SWIG_TypePrettyName(ty);
+ printf("swig/python detected a memory leak of type '%s', no destructor found.\n", (name ? name : "unknown"));
+ }
+#endif
+ }
+ Py_XDECREF(next);
+ PyObject_DEL(v);
+}
+
+SWIGRUNTIME PyObject*
+SwigPyObject_append(PyObject* v, PyObject* next)
+{
+ SwigPyObject *sobj = (SwigPyObject *) v;
+#ifndef METH_O
+ PyObject *tmp = 0;
+ if (!PyArg_ParseTuple(next,(char *)"O:append", &tmp)) return NULL;
+ next = tmp;
+#endif
+ if (!SwigPyObject_Check(next)) {
+ PyErr_SetString(PyExc_TypeError, "Attempt to append a non SwigPyObject");
+ return NULL;
+ }
+ sobj->next = next;
+ Py_INCREF(next);
+ return SWIG_Py_Void();
+}
+
+SWIGRUNTIME PyObject*
+#ifdef METH_NOARGS
+SwigPyObject_next(PyObject* v)
+#else
+SwigPyObject_next(PyObject* v, PyObject *SWIGUNUSEDPARM(args))
+#endif
+{
+ SwigPyObject *sobj = (SwigPyObject *) v;
+ if (sobj->next) {
+ Py_INCREF(sobj->next);
+ return sobj->next;
+ } else {
+ return SWIG_Py_Void();
+ }
+}
+
+SWIGINTERN PyObject*
+#ifdef METH_NOARGS
+SwigPyObject_disown(PyObject *v)
+#else
+SwigPyObject_disown(PyObject* v, PyObject *SWIGUNUSEDPARM(args))
+#endif
+{
+ SwigPyObject *sobj = (SwigPyObject *)v;
+ sobj->own = 0;
+ return SWIG_Py_Void();
+}
+
+SWIGINTERN PyObject*
+#ifdef METH_NOARGS
+SwigPyObject_acquire(PyObject *v)
+#else
+SwigPyObject_acquire(PyObject* v, PyObject *SWIGUNUSEDPARM(args))
+#endif
+{
+ SwigPyObject *sobj = (SwigPyObject *)v;
+ sobj->own = SWIG_POINTER_OWN;
+ return SWIG_Py_Void();
+}
+
+SWIGINTERN PyObject*
+SwigPyObject_own(PyObject *v, PyObject *args)
+{
+ PyObject *val = 0;
+#if (PY_VERSION_HEX < 0x02020000)
+ if (!PyArg_ParseTuple(args,(char *)"|O:own",&val))
+#elif (PY_VERSION_HEX < 0x02050000)
+ if (!PyArg_UnpackTuple(args, (char *)"own", 0, 1, &val))
+#else
+ if (!PyArg_UnpackTuple(args, "own", 0, 1, &val))
+#endif
+ {
+ return NULL;
+ }
+ else
+ {
+ SwigPyObject *sobj = (SwigPyObject *)v;
+ PyObject *obj = PyBool_FromLong(sobj->own);
+ if (val) {
+#ifdef METH_NOARGS
+ if (PyObject_IsTrue(val)) {
+ SwigPyObject_acquire(v);
+ } else {
+ SwigPyObject_disown(v);
+ }
+#else
+ if (PyObject_IsTrue(val)) {
+ SwigPyObject_acquire(v,args);
+ } else {
+ SwigPyObject_disown(v,args);
+ }
+#endif
+ }
+ return obj;
+ }
+}
+
+#ifdef METH_O
+static PyMethodDef
+swigobject_methods[] = {
+ {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_NOARGS, (char *)"releases ownership of the pointer"},
+ {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_NOARGS, (char *)"acquires ownership of the pointer"},
+ {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"},
+ {(char *)"append", (PyCFunction)SwigPyObject_append, METH_O, (char *)"appends another 'this' object"},
+ {(char *)"next", (PyCFunction)SwigPyObject_next, METH_NOARGS, (char *)"returns the next 'this' object"},
+ {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_NOARGS, (char *)"returns object representation"},
+ {0, 0, 0, 0}
+};
+#else
+static PyMethodDef
+swigobject_methods[] = {
+ {(char *)"disown", (PyCFunction)SwigPyObject_disown, METH_VARARGS, (char *)"releases ownership of the pointer"},
+ {(char *)"acquire", (PyCFunction)SwigPyObject_acquire, METH_VARARGS, (char *)"acquires ownership of the pointer"},
+ {(char *)"own", (PyCFunction)SwigPyObject_own, METH_VARARGS, (char *)"returns/sets ownership of the pointer"},
+ {(char *)"append", (PyCFunction)SwigPyObject_append, METH_VARARGS, (char *)"appends another 'this' object"},
+ {(char *)"next", (PyCFunction)SwigPyObject_next, METH_VARARGS, (char *)"returns the next 'this' object"},
+ {(char *)"__repr__",(PyCFunction)SwigPyObject_repr, METH_VARARGS, (char *)"returns object representation"},
+ {0, 0, 0, 0}
+};
+#endif
+
+#if PY_VERSION_HEX < 0x02020000
+SWIGINTERN PyObject *
+SwigPyObject_getattr(SwigPyObject *sobj,char *name)
+{
+ return Py_FindMethod(swigobject_methods, (PyObject *)sobj, name);
+}
+#endif
+
+SWIGRUNTIME PyTypeObject*
+SwigPyObject_TypeOnce(void) {
+ static char swigobject_doc[] = "Swig object carries a C/C++ instance pointer";
+
+ static PyNumberMethods SwigPyObject_as_number = {
+ (binaryfunc)0, /*nb_add*/
+ (binaryfunc)0, /*nb_subtract*/
+ (binaryfunc)0, /*nb_multiply*/
+ /* nb_divide removed in Python 3 */
+#if PY_VERSION_HEX < 0x03000000
+ (binaryfunc)0, /*nb_divide*/
+#endif
+ (binaryfunc)0, /*nb_remainder*/
+ (binaryfunc)0, /*nb_divmod*/
+ (ternaryfunc)0,/*nb_power*/
+ (unaryfunc)0, /*nb_negative*/
+ (unaryfunc)0, /*nb_positive*/
+ (unaryfunc)0, /*nb_absolute*/
+ (inquiry)0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+#if PY_VERSION_HEX < 0x03000000
+ 0, /*nb_coerce*/
+#endif
+ (unaryfunc)SwigPyObject_long, /*nb_int*/
+#if PY_VERSION_HEX < 0x03000000
+ (unaryfunc)SwigPyObject_long, /*nb_long*/
+#else
+ 0, /*nb_reserved*/
+#endif
+ (unaryfunc)0, /*nb_float*/
+#if PY_VERSION_HEX < 0x03000000
+ (unaryfunc)SwigPyObject_oct, /*nb_oct*/
+ (unaryfunc)SwigPyObject_hex, /*nb_hex*/
+#endif
+#if PY_VERSION_HEX >= 0x03050000 /* 3.5 */
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_matrix_multiply */
+#elif PY_VERSION_HEX >= 0x03000000 /* 3.0 */
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index, nb_inplace_divide removed */
+#elif PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index */
+#elif PY_VERSION_HEX >= 0x02020000 /* 2.2.0 */
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_true_divide */
+#elif PY_VERSION_HEX >= 0x02000000 /* 2.0.0 */
+ 0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_or */
+#endif
+ };
+
+ static PyTypeObject swigpyobject_type;
+ static int type_init = 0;
+ if (!type_init) {
+ const PyTypeObject tmp = {
+#if PY_VERSION_HEX >= 0x03000000
+ PyVarObject_HEAD_INIT(NULL, 0)
+#else
+ PyObject_HEAD_INIT(NULL)
+ 0, /* ob_size */
+#endif
+ (char *)"SwigPyObject", /* tp_name */
+ sizeof(SwigPyObject), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)SwigPyObject_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+#if PY_VERSION_HEX < 0x02020000
+ (getattrfunc)SwigPyObject_getattr, /* tp_getattr */
+#else
+ (getattrfunc)0, /* tp_getattr */
+#endif
+ (setattrfunc)0, /* tp_setattr */
+#if PY_VERSION_HEX >= 0x03000000
+ 0, /* tp_reserved in 3.0.1, tp_compare in 3.0.0 but not used */
+#else
+ (cmpfunc)SwigPyObject_compare, /* tp_compare */
+#endif
+ (reprfunc)SwigPyObject_repr, /* tp_repr */
+ &SwigPyObject_as_number, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ (hashfunc)0, /* tp_hash */
+ (ternaryfunc)0, /* tp_call */
+ 0, /* tp_str */
+ PyObject_GenericGetAttr, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT, /* tp_flags */
+ swigobject_doc, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ (richcmpfunc)SwigPyObject_richcompare,/* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+#if PY_VERSION_HEX >= 0x02020000
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ swigobject_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ 0, /* tp_new */
+ 0, /* tp_free */
+ 0, /* tp_is_gc */
+ 0, /* tp_bases */
+ 0, /* tp_mro */
+ 0, /* tp_cache */
+ 0, /* tp_subclasses */
+ 0, /* tp_weaklist */
+#endif
+#if PY_VERSION_HEX >= 0x02030000
+ 0, /* tp_del */
+#endif
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
+#endif
+#ifdef COUNT_ALLOCS
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
+#endif
+ };
+ swigpyobject_type = tmp;
+ type_init = 1;
+#if PY_VERSION_HEX < 0x02020000
+ swigpyobject_type.ob_type = &PyType_Type;
+#else
+ if (PyType_Ready(&swigpyobject_type) < 0)
+ return NULL;
+#endif
+ }
+ return &swigpyobject_type;
+}
+
+SWIGRUNTIME PyObject *
+SwigPyObject_New(void *ptr, swig_type_info *ty, int own)
+{
+ SwigPyObject *sobj = PyObject_NEW(SwigPyObject, SwigPyObject_type());
+ if (sobj) {
+ sobj->ptr = ptr;
+ sobj->ty = ty;
+ sobj->own = own;
+ sobj->next = 0;
+ }
+ return (PyObject *)sobj;
+}
+
+/* -----------------------------------------------------------------------------
+ * Implements a simple Swig Packed type, and use it instead of string
+ * ----------------------------------------------------------------------------- */
+
+typedef struct {
+ PyObject_HEAD
+ void *pack;
+ swig_type_info *ty;
+ size_t size;
+} SwigPyPacked;
+
+SWIGRUNTIME int
+SwigPyPacked_print(SwigPyPacked *v, FILE *fp, int SWIGUNUSEDPARM(flags))
+{
+ char result[SWIG_BUFFER_SIZE];
+ fputs("<Swig Packed ", fp);
+ if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) {
+ fputs("at ", fp);
+ fputs(result, fp);
+ }
+ fputs(v->ty->name,fp);
+ fputs(">", fp);
+ return 0;
+}
+
+SWIGRUNTIME PyObject *
+SwigPyPacked_repr(SwigPyPacked *v)
+{
+ char result[SWIG_BUFFER_SIZE];
+ if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) {
+ return SWIG_Python_str_FromFormat("<Swig Packed at %s%s>", result, v->ty->name);
+ } else {
+ return SWIG_Python_str_FromFormat("<Swig Packed %s>", v->ty->name);
+ }
+}
+
+SWIGRUNTIME PyObject *
+SwigPyPacked_str(SwigPyPacked *v)
+{
+ char result[SWIG_BUFFER_SIZE];
+ if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))){
+ return SWIG_Python_str_FromFormat("%s%s", result, v->ty->name);
+ } else {
+ return SWIG_Python_str_FromChar(v->ty->name);
+ }
+}
+
+SWIGRUNTIME int
+SwigPyPacked_compare(SwigPyPacked *v, SwigPyPacked *w)
+{
+ size_t i = v->size;
+ size_t j = w->size;
+ int s = (i < j) ? -1 : ((i > j) ? 1 : 0);
+ return s ? s : strncmp((char *)v->pack, (char *)w->pack, 2*v->size);
+}
+
+SWIGRUNTIME PyTypeObject* SwigPyPacked_TypeOnce(void);
+
+SWIGRUNTIME PyTypeObject*
+SwigPyPacked_type(void) {
+ static PyTypeObject *SWIG_STATIC_POINTER(type) = SwigPyPacked_TypeOnce();
+ return type;
+}
+
+SWIGRUNTIMEINLINE int
+SwigPyPacked_Check(PyObject *op) {
+ return ((op)->ob_type == SwigPyPacked_TypeOnce())
+ || (strcmp((op)->ob_type->tp_name,"SwigPyPacked") == 0);
+}
+
+SWIGRUNTIME void
+SwigPyPacked_dealloc(PyObject *v)
+{
+ if (SwigPyPacked_Check(v)) {
+ SwigPyPacked *sobj = (SwigPyPacked *) v;
+ free(sobj->pack);
+ }
+ PyObject_DEL(v);
+}
+
+SWIGRUNTIME PyTypeObject*
+SwigPyPacked_TypeOnce(void) {
+ static char swigpacked_doc[] = "Swig object carries a C/C++ instance pointer";
+ static PyTypeObject swigpypacked_type;
+ static int type_init = 0;
+ if (!type_init) {
+ const PyTypeObject tmp = {
+#if PY_VERSION_HEX>=0x03000000
+ PyVarObject_HEAD_INIT(NULL, 0)
+#else
+ PyObject_HEAD_INIT(NULL)
+ 0, /* ob_size */
+#endif
+ (char *)"SwigPyPacked", /* tp_name */
+ sizeof(SwigPyPacked), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)SwigPyPacked_dealloc, /* tp_dealloc */
+ (printfunc)SwigPyPacked_print, /* tp_print */
+ (getattrfunc)0, /* tp_getattr */
+ (setattrfunc)0, /* tp_setattr */
+#if PY_VERSION_HEX>=0x03000000
+ 0, /* tp_reserved in 3.0.1 */
+#else
+ (cmpfunc)SwigPyPacked_compare, /* tp_compare */
+#endif
+ (reprfunc)SwigPyPacked_repr, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ (hashfunc)0, /* tp_hash */
+ (ternaryfunc)0, /* tp_call */
+ (reprfunc)SwigPyPacked_str, /* tp_str */
+ PyObject_GenericGetAttr, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT, /* tp_flags */
+ swigpacked_doc, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+#if PY_VERSION_HEX >= 0x02020000
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ 0, /* tp_new */
+ 0, /* tp_free */
+ 0, /* tp_is_gc */
+ 0, /* tp_bases */
+ 0, /* tp_mro */
+ 0, /* tp_cache */
+ 0, /* tp_subclasses */
+ 0, /* tp_weaklist */
+#endif
+#if PY_VERSION_HEX >= 0x02030000
+ 0, /* tp_del */
+#endif
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
+#endif
+#ifdef COUNT_ALLOCS
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
+#endif
+ };
+ swigpypacked_type = tmp;
+ type_init = 1;
+#if PY_VERSION_HEX < 0x02020000
+ swigpypacked_type.ob_type = &PyType_Type;
+#else
+ if (PyType_Ready(&swigpypacked_type) < 0)
+ return NULL;
+#endif
+ }
+ return &swigpypacked_type;
+}
+
+SWIGRUNTIME PyObject *
+SwigPyPacked_New(void *ptr, size_t size, swig_type_info *ty)
+{
+ SwigPyPacked *sobj = PyObject_NEW(SwigPyPacked, SwigPyPacked_type());
+ if (sobj) {
+ void *pack = malloc(size);
+ if (pack) {
+ memcpy(pack, ptr, size);
+ sobj->pack = pack;
+ sobj->ty = ty;
+ sobj->size = size;
+ } else {
+ PyObject_DEL((PyObject *) sobj);
+ sobj = 0;
+ }
+ }
+ return (PyObject *) sobj;
+}
+
+SWIGRUNTIME swig_type_info *
+SwigPyPacked_UnpackData(PyObject *obj, void *ptr, size_t size)
+{
+ if (SwigPyPacked_Check(obj)) {
+ SwigPyPacked *sobj = (SwigPyPacked *)obj;
+ if (sobj->size != size) return 0;
+ memcpy(ptr, sobj->pack, size);
+ return sobj->ty;
+ } else {
+ return 0;
+ }
+}
+
+/* -----------------------------------------------------------------------------
+ * pointers/data manipulation
+ * ----------------------------------------------------------------------------- */
+
+SWIGRUNTIMEINLINE PyObject *
+_SWIG_This(void)
+{
+ return SWIG_Python_str_FromChar("this");
+}
+
+static PyObject *swig_this = NULL;
+
+SWIGRUNTIME PyObject *
+SWIG_This(void)
+{
+ if (swig_this == NULL)
+ swig_this = _SWIG_This();
+ return swig_this;
+}
+
+/* #define SWIG_PYTHON_SLOW_GETSET_THIS */
+
+/* TODO: I don't know how to implement the fast getset in Python 3 right now */
+#if PY_VERSION_HEX>=0x03000000
+#define SWIG_PYTHON_SLOW_GETSET_THIS
+#endif
+
+SWIGRUNTIME SwigPyObject *
+SWIG_Python_GetSwigThis(PyObject *pyobj)
+{
+ PyObject *obj;
+
+ if (SwigPyObject_Check(pyobj))
+ return (SwigPyObject *) pyobj;
+
+#ifdef SWIGPYTHON_BUILTIN
+ (void)obj;
+# ifdef PyWeakref_CheckProxy
+ if (PyWeakref_CheckProxy(pyobj)) {
+ pyobj = PyWeakref_GET_OBJECT(pyobj);
+ if (pyobj && SwigPyObject_Check(pyobj))
+ return (SwigPyObject*) pyobj;
+ }
+# endif
+ return NULL;
+#else
+
+ obj = 0;
+
+#if (!defined(SWIG_PYTHON_SLOW_GETSET_THIS) && (PY_VERSION_HEX >= 0x02030000))
+ if (PyInstance_Check(pyobj)) {
+ obj = _PyInstance_Lookup(pyobj, SWIG_This());
+ } else {
+ PyObject **dictptr = _PyObject_GetDictPtr(pyobj);
+ if (dictptr != NULL) {
+ PyObject *dict = *dictptr;
+ obj = dict ? PyDict_GetItem(dict, SWIG_This()) : 0;
+ } else {
+#ifdef PyWeakref_CheckProxy
+ if (PyWeakref_CheckProxy(pyobj)) {
+ PyObject *wobj = PyWeakref_GET_OBJECT(pyobj);
+ return wobj ? SWIG_Python_GetSwigThis(wobj) : 0;
+ }
+#endif
+ obj = PyObject_GetAttr(pyobj,SWIG_This());
+ if (obj) {
+ Py_DECREF(obj);
+ } else {
+ if (PyErr_Occurred()) PyErr_Clear();
+ return 0;
+ }
+ }
+ }
+#else
+ obj = PyObject_GetAttr(pyobj,SWIG_This());
+ if (obj) {
+ Py_DECREF(obj);
+ } else {
+ if (PyErr_Occurred()) PyErr_Clear();
+ return 0;
+ }
+#endif
+ if (obj && !SwigPyObject_Check(obj)) {
+ /* a PyObject is called 'this', try to get the 'real this'
+ SwigPyObject from it */
+ return SWIG_Python_GetSwigThis(obj);
+ }
+ return (SwigPyObject *)obj;
+#endif
+}
+
+/* Acquire a pointer value */
+
+SWIGRUNTIME int
+SWIG_Python_AcquirePtr(PyObject *obj, int own) {
+ if (own == SWIG_POINTER_OWN) {
+ SwigPyObject *sobj = SWIG_Python_GetSwigThis(obj);
+ if (sobj) {
+ int oldown = sobj->own;
+ sobj->own = own;
+ return oldown;
+ }
+ }
+ return 0;
+}
+
+/* Convert a pointer value */
+
+SWIGRUNTIME int
+SWIG_Python_ConvertPtrAndOwn(PyObject *obj, void **ptr, swig_type_info *ty, int flags, int *own) {
+ int res;
+ SwigPyObject *sobj;
+ int implicit_conv = (flags & SWIG_POINTER_IMPLICIT_CONV) != 0;
+
+ if (!obj)
+ return SWIG_ERROR;
+ if (obj == Py_None && !implicit_conv) {
+ if (ptr)
+ *ptr = 0;
+ return SWIG_OK;
+ }
+
+ res = SWIG_ERROR;
+
+ sobj = SWIG_Python_GetSwigThis(obj);
+ if (own)
+ *own = 0;
+ while (sobj) {
+ void *vptr = sobj->ptr;
+ if (ty) {
+ swig_type_info *to = sobj->ty;
+ if (to == ty) {
+ /* no type cast needed */
+ if (ptr) *ptr = vptr;
+ break;
+ } else {
+ swig_cast_info *tc = SWIG_TypeCheck(to->name,ty);
+ if (!tc) {
+ sobj = (SwigPyObject *)sobj->next;
+ } else {
+ if (ptr) {
+ int newmemory = 0;
+ *ptr = SWIG_TypeCast(tc,vptr,&newmemory);
+ if (newmemory == SWIG_CAST_NEW_MEMORY) {
+ assert(own); /* badly formed typemap which will lead to a memory leak - it must set and use own to delete *ptr */
+ if (own)
+ *own = *own | SWIG_CAST_NEW_MEMORY;
+ }
+ }
+ break;
+ }
+ }
+ } else {
+ if (ptr) *ptr = vptr;
+ break;
+ }
+ }
+ if (sobj) {
+ if (own)
+ *own = *own | sobj->own;
+ if (flags & SWIG_POINTER_DISOWN) {
+ sobj->own = 0;
+ }
+ res = SWIG_OK;
+ } else {
+ if (implicit_conv) {
+ SwigPyClientData *data = ty ? (SwigPyClientData *) ty->clientdata : 0;
+ if (data && !data->implicitconv) {
+ PyObject *klass = data->klass;
+ if (klass) {
+ PyObject *impconv;
+ data->implicitconv = 1; /* avoid recursion and call 'explicit' constructors*/
+ impconv = SWIG_Python_CallFunctor(klass, obj);
+ data->implicitconv = 0;
+ if (PyErr_Occurred()) {
+ PyErr_Clear();
+ impconv = 0;
+ }
+ if (impconv) {
+ SwigPyObject *iobj = SWIG_Python_GetSwigThis(impconv);
+ if (iobj) {
+ void *vptr;
+ res = SWIG_Python_ConvertPtrAndOwn((PyObject*)iobj, &vptr, ty, 0, 0);
+ if (SWIG_IsOK(res)) {
+ if (ptr) {
+ *ptr = vptr;
+ /* transfer the ownership to 'ptr' */
+ iobj->own = 0;
+ res = SWIG_AddCast(res);
+ res = SWIG_AddNewMask(res);
+ } else {
+ res = SWIG_AddCast(res);
+ }
+ }
+ }
+ Py_DECREF(impconv);
+ }
+ }
+ }
+ }
+ if (!SWIG_IsOK(res) && obj == Py_None) {
+ if (ptr)
+ *ptr = 0;
+ if (PyErr_Occurred())
+ PyErr_Clear();
+ res = SWIG_OK;
+ }
+ }
+ return res;
+}
+
+/* Convert a function ptr value */
+
+SWIGRUNTIME int
+SWIG_Python_ConvertFunctionPtr(PyObject *obj, void **ptr, swig_type_info *ty) {
+ if (!PyCFunction_Check(obj)) {
+ return SWIG_ConvertPtr(obj, ptr, ty, 0);
+ } else {
+ void *vptr = 0;
+
+ /* here we get the method pointer for callbacks */
+ const char *doc = (((PyCFunctionObject *)obj) -> m_ml -> ml_doc);
+ const char *desc = doc ? strstr(doc, "swig_ptr: ") : 0;
+ if (desc)
+ desc = ty ? SWIG_UnpackVoidPtr(desc + 10, &vptr, ty->name) : 0;
+ if (!desc)
+ return SWIG_ERROR;
+ if (ty) {
+ swig_cast_info *tc = SWIG_TypeCheck(desc,ty);
+ if (tc) {
+ int newmemory = 0;
+ *ptr = SWIG_TypeCast(tc,vptr,&newmemory);
+ assert(!newmemory); /* newmemory handling not yet implemented */
+ } else {
+ return SWIG_ERROR;
+ }
+ } else {
+ *ptr = vptr;
+ }
+ return SWIG_OK;
+ }
+}
+
+/* Convert a packed value value */
+
+SWIGRUNTIME int
+SWIG_Python_ConvertPacked(PyObject *obj, void *ptr, size_t sz, swig_type_info *ty) {
+ swig_type_info *to = SwigPyPacked_UnpackData(obj, ptr, sz);
+ if (!to) return SWIG_ERROR;
+ if (ty) {
+ if (to != ty) {
+ /* check type cast? */
+ swig_cast_info *tc = SWIG_TypeCheck(to->name,ty);
+ if (!tc) return SWIG_ERROR;
+ }
+ }
+ return SWIG_OK;
+}
+
+/* -----------------------------------------------------------------------------
+ * Create a new pointer object
+ * ----------------------------------------------------------------------------- */
+
+/*
+ Create a new instance object, without calling __init__, and set the
+ 'this' attribute.
+*/
+
+SWIGRUNTIME PyObject*
+SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this)
+{
+#if (PY_VERSION_HEX >= 0x02020000)
+ PyObject *inst = 0;
+ PyObject *newraw = data->newraw;
+ if (newraw) {
+ inst = PyObject_Call(newraw, data->newargs, NULL);
+ if (inst) {
+#if !defined(SWIG_PYTHON_SLOW_GETSET_THIS)
+ PyObject **dictptr = _PyObject_GetDictPtr(inst);
+ if (dictptr != NULL) {
+ PyObject *dict = *dictptr;
+ if (dict == NULL) {
+ dict = PyDict_New();
+ *dictptr = dict;
+ PyDict_SetItem(dict, SWIG_This(), swig_this);
+ }
+ }
+#else
+ PyObject *key = SWIG_This();
+ PyObject_SetAttr(inst, key, swig_this);
+#endif
+ }
+ } else {
+#if PY_VERSION_HEX >= 0x03000000
+ inst = ((PyTypeObject*) data->newargs)->tp_new((PyTypeObject*) data->newargs, Py_None, Py_None);
+ if (inst) {
+ PyObject_SetAttr(inst, SWIG_This(), swig_this);
+ Py_TYPE(inst)->tp_flags &= ~Py_TPFLAGS_VALID_VERSION_TAG;
+ }
+#else
+ PyObject *dict = PyDict_New();
+ if (dict) {
+ PyDict_SetItem(dict, SWIG_This(), swig_this);
+ inst = PyInstance_NewRaw(data->newargs, dict);
+ Py_DECREF(dict);
+ }
+#endif
+ }
+ return inst;
+#else
+#if (PY_VERSION_HEX >= 0x02010000)
+ PyObject *inst = 0;
+ PyObject *dict = PyDict_New();
+ if (dict) {
+ PyDict_SetItem(dict, SWIG_This(), swig_this);
+ inst = PyInstance_NewRaw(data->newargs, dict);
+ Py_DECREF(dict);
+ }
+ return (PyObject *) inst;
+#else
+ PyInstanceObject *inst = PyObject_NEW(PyInstanceObject, &PyInstance_Type);
+ if (inst == NULL) {
+ return NULL;
+ }
+ inst->in_class = (PyClassObject *)data->newargs;
+ Py_INCREF(inst->in_class);
+ inst->in_dict = PyDict_New();
+ if (inst->in_dict == NULL) {
+ Py_DECREF(inst);
+ return NULL;
+ }
+#ifdef Py_TPFLAGS_HAVE_WEAKREFS
+ inst->in_weakreflist = NULL;
+#endif
+#ifdef Py_TPFLAGS_GC
+ PyObject_GC_Init(inst);
+#endif
+ PyDict_SetItem(inst->in_dict, SWIG_This(), swig_this);
+ return (PyObject *) inst;
+#endif
+#endif
+}
+
+SWIGRUNTIME void
+SWIG_Python_SetSwigThis(PyObject *inst, PyObject *swig_this)
+{
+ PyObject *dict;
+#if (PY_VERSION_HEX >= 0x02020000) && !defined(SWIG_PYTHON_SLOW_GETSET_THIS)
+ PyObject **dictptr = _PyObject_GetDictPtr(inst);
+ if (dictptr != NULL) {
+ dict = *dictptr;
+ if (dict == NULL) {
+ dict = PyDict_New();
+ *dictptr = dict;
+ }
+ PyDict_SetItem(dict, SWIG_This(), swig_this);
+ return;
+ }
+#endif
+ dict = PyObject_GetAttrString(inst, (char*)"__dict__");
+ PyDict_SetItem(dict, SWIG_This(), swig_this);
+ Py_DECREF(dict);
+}
+
+
+SWIGINTERN PyObject *
+SWIG_Python_InitShadowInstance(PyObject *args) {
+ PyObject *obj[2];
+ if (!SWIG_Python_UnpackTuple(args, "swiginit", 2, 2, obj)) {
+ return NULL;
+ } else {
+ SwigPyObject *sthis = SWIG_Python_GetSwigThis(obj[0]);
+ if (sthis) {
+ SwigPyObject_append((PyObject*) sthis, obj[1]);
+ } else {
+ SWIG_Python_SetSwigThis(obj[0], obj[1]);
+ }
+ return SWIG_Py_Void();
+ }
+}
+
+/* Create a new pointer object */
+
+SWIGRUNTIME PyObject *
+SWIG_Python_NewPointerObj(PyObject *self, void *ptr, swig_type_info *type, int flags) {
+ SwigPyClientData *clientdata;
+ PyObject * robj;
+ int own;
+
+ if (!ptr)
+ return SWIG_Py_Void();
+
+ clientdata = type ? (SwigPyClientData *)(type->clientdata) : 0;
+ own = (flags & SWIG_POINTER_OWN) ? SWIG_POINTER_OWN : 0;
+ if (clientdata && clientdata->pytype) {
+ SwigPyObject *newobj;
+ if (flags & SWIG_BUILTIN_TP_INIT) {
+ newobj = (SwigPyObject*) self;
+ if (newobj->ptr) {
+ PyObject *next_self = clientdata->pytype->tp_alloc(clientdata->pytype, 0);
+ while (newobj->next)
+ newobj = (SwigPyObject *) newobj->next;
+ newobj->next = next_self;
+ newobj = (SwigPyObject *)next_self;
+#ifdef SWIGPYTHON_BUILTIN
+ newobj->dict = 0;
+#endif
+ }
+ } else {
+ newobj = PyObject_New(SwigPyObject, clientdata->pytype);
+#ifdef SWIGPYTHON_BUILTIN
+ newobj->dict = 0;
+#endif
+ }
+ if (newobj) {
+ newobj->ptr = ptr;
+ newobj->ty = type;
+ newobj->own = own;
+ newobj->next = 0;
+ return (PyObject*) newobj;
+ }
+ return SWIG_Py_Void();
+ }
+
+ assert(!(flags & SWIG_BUILTIN_TP_INIT));
+
+ robj = SwigPyObject_New(ptr, type, own);
+ if (robj && clientdata && !(flags & SWIG_POINTER_NOSHADOW)) {
+ PyObject *inst = SWIG_Python_NewShadowInstance(clientdata, robj);
+ Py_DECREF(robj);
+ robj = inst;
+ }
+ return robj;
+}
+
+/* Create a new packed object */
+
+SWIGRUNTIMEINLINE PyObject *
+SWIG_Python_NewPackedObj(void *ptr, size_t sz, swig_type_info *type) {
+ return ptr ? SwigPyPacked_New((void *) ptr, sz, type) : SWIG_Py_Void();
+}
+
+/* -----------------------------------------------------------------------------*
+ * Get type list
+ * -----------------------------------------------------------------------------*/
+
+#ifdef SWIG_LINK_RUNTIME
+void *SWIG_ReturnGlobalTypeList(void *);
+#endif
+
+SWIGRUNTIME swig_module_info *
+SWIG_Python_GetModule(void *SWIGUNUSEDPARM(clientdata)) {
+ static void *type_pointer = (void *)0;
+ /* first check if module already created */
+ if (!type_pointer) {
+#ifdef SWIG_LINK_RUNTIME
+ type_pointer = SWIG_ReturnGlobalTypeList((void *)0);
+#else
+# ifdef SWIGPY_USE_CAPSULE
+ type_pointer = PyCapsule_Import(SWIGPY_CAPSULE_NAME, 0);
+# else
+ type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
+ (char*)"type_pointer" SWIG_TYPE_TABLE_NAME);
+# endif
+ if (PyErr_Occurred()) {
+ PyErr_Clear();
+ type_pointer = (void *)0;
+ }
+#endif
+ }
+ return (swig_module_info *) type_pointer;
+}
+
+#if PY_MAJOR_VERSION < 2
+/* PyModule_AddObject function was introduced in Python 2.0. The following function
+ is copied out of Python/modsupport.c in python version 2.3.4 */
+SWIGINTERN int
+PyModule_AddObject(PyObject *m, char *name, PyObject *o)
+{
+ PyObject *dict;
+ if (!PyModule_Check(m)) {
+ PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs module as first arg");
+ return SWIG_ERROR;
+ }
+ if (!o) {
+ PyErr_SetString(PyExc_TypeError, "PyModule_AddObject() needs non-NULL value");
+ return SWIG_ERROR;
+ }
+
+ dict = PyModule_GetDict(m);
+ if (dict == NULL) {
+ /* Internal error -- modules must have a dict! */
+ PyErr_Format(PyExc_SystemError, "module '%s' has no __dict__",
+ PyModule_GetName(m));
+ return SWIG_ERROR;
+ }
+ if (PyDict_SetItemString(dict, name, o))
+ return SWIG_ERROR;
+ Py_DECREF(o);
+ return SWIG_OK;
+}
+#endif
+
+SWIGRUNTIME void
+#ifdef SWIGPY_USE_CAPSULE
+SWIG_Python_DestroyModule(PyObject *obj)
+#else
+SWIG_Python_DestroyModule(void *vptr)
+#endif
+{
+#ifdef SWIGPY_USE_CAPSULE
+ swig_module_info *swig_module = (swig_module_info *) PyCapsule_GetPointer(obj, SWIGPY_CAPSULE_NAME);
+#else
+ swig_module_info *swig_module = (swig_module_info *) vptr;
+#endif
+ swig_type_info **types = swig_module->types;
+ size_t i;
+ for (i =0; i < swig_module->size; ++i) {
+ swig_type_info *ty = types[i];
+ if (ty->owndata) {
+ SwigPyClientData *data = (SwigPyClientData *) ty->clientdata;
+ if (data) SwigPyClientData_Del(data);
+ }
+ }
+ Py_DECREF(SWIG_This());
+ swig_this = NULL;
+}
+
+SWIGRUNTIME void
+SWIG_Python_SetModule(swig_module_info *swig_module) {
+#if PY_VERSION_HEX >= 0x03000000
+ /* Add a dummy module object into sys.modules */
+ PyObject *module = PyImport_AddModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION);
+#else
+ static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} }; /* Sentinel */
+ PyObject *module = Py_InitModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION, swig_empty_runtime_method_table);
+#endif
+#ifdef SWIGPY_USE_CAPSULE
+ PyObject *pointer = PyCapsule_New((void *) swig_module, SWIGPY_CAPSULE_NAME, SWIG_Python_DestroyModule);
+ if (pointer && module) {
+ PyModule_AddObject(module, (char*)"type_pointer_capsule" SWIG_TYPE_TABLE_NAME, pointer);
+ } else {
+ Py_XDECREF(pointer);
+ }
+#else
+ PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
+ if (pointer && module) {
+ PyModule_AddObject(module, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME, pointer);
+ } else {
+ Py_XDECREF(pointer);
+ }
+#endif
+}
+
+/* The python cached type query */
+SWIGRUNTIME PyObject *
+SWIG_Python_TypeCache(void) {
+ static PyObject *SWIG_STATIC_POINTER(cache) = PyDict_New();
+ return cache;
+}
+
+SWIGRUNTIME swig_type_info *
+SWIG_Python_TypeQuery(const char *type)
+{
+ PyObject *cache = SWIG_Python_TypeCache();
+ PyObject *key = SWIG_Python_str_FromChar(type);
+ PyObject *obj = PyDict_GetItem(cache, key);
+ swig_type_info *descriptor;
+ if (obj) {
+#ifdef SWIGPY_USE_CAPSULE
+ descriptor = (swig_type_info *) PyCapsule_GetPointer(obj, NULL);
+#else
+ descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
+#endif
+ } else {
+ swig_module_info *swig_module = SWIG_GetModule(0);
+ descriptor = SWIG_TypeQueryModule(swig_module, swig_module, type);
+ if (descriptor) {
+#ifdef SWIGPY_USE_CAPSULE
+ obj = PyCapsule_New((void*) descriptor, NULL, NULL);
+#else
+ obj = PyCObject_FromVoidPtr(descriptor, NULL);
+#endif
+ PyDict_SetItem(cache, key, obj);
+ Py_DECREF(obj);
+ }
+ }
+ Py_DECREF(key);
+ return descriptor;
+}
+
+/*
+ For backward compatibility only
+*/
+#define SWIG_POINTER_EXCEPTION 0
+#define SWIG_arg_fail(arg) SWIG_Python_ArgFail(arg)
+#define SWIG_MustGetPtr(p, type, argnum, flags) SWIG_Python_MustGetPtr(p, type, argnum, flags)
+
+SWIGRUNTIME int
+SWIG_Python_AddErrMesg(const char* mesg, int infront)
+{
+ if (PyErr_Occurred()) {
+ PyObject *type = 0;
+ PyObject *value = 0;
+ PyObject *traceback = 0;
+ PyErr_Fetch(&type, &value, &traceback);
+ if (value) {
+ char *tmp;
+ PyObject *old_str = PyObject_Str(value);
+ Py_XINCREF(type);
+ PyErr_Clear();
+ if (infront) {
+ PyErr_Format(type, "%s %s", mesg, tmp = SWIG_Python_str_AsChar(old_str));
+ } else {
+ PyErr_Format(type, "%s %s", tmp = SWIG_Python_str_AsChar(old_str), mesg);
+ }
+ SWIG_Python_str_DelForPy3(tmp);
+ Py_DECREF(old_str);
+ }
+ return 1;
+ } else {
+ return 0;
+ }
+}
+
+SWIGRUNTIME int
+SWIG_Python_ArgFail(int argnum)
+{
+ if (PyErr_Occurred()) {
+ /* add information about failing argument */
+ char mesg[256];
+ PyOS_snprintf(mesg, sizeof(mesg), "argument number %d:", argnum);
+ return SWIG_Python_AddErrMesg(mesg, 1);
+ } else {
+ return 0;
+ }
+}
+
+SWIGRUNTIMEINLINE const char *
+SwigPyObject_GetDesc(PyObject *self)
+{
+ SwigPyObject *v = (SwigPyObject *)self;
+ swig_type_info *ty = v ? v->ty : 0;
+ return ty ? ty->str : "";
+}
+
+SWIGRUNTIME void
+SWIG_Python_TypeError(const char *type, PyObject *obj)
+{
+ if (type) {
+#if defined(SWIG_COBJECT_TYPES)
+ if (obj && SwigPyObject_Check(obj)) {
+ const char *otype = (const char *) SwigPyObject_GetDesc(obj);
+ if (otype) {
+ PyErr_Format(PyExc_TypeError, "a '%s' is expected, 'SwigPyObject(%s)' is received",
+ type, otype);
+ return;
+ }
+ } else
+#endif
+ {
+ const char *otype = (obj ? obj->ob_type->tp_name : 0);
+ if (otype) {
+ PyObject *str = PyObject_Str(obj);
+ const char *cstr = str ? SWIG_Python_str_AsChar(str) : 0;
+ if (cstr) {
+ PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s(%s)' is received",
+ type, otype, cstr);
+ SWIG_Python_str_DelForPy3(cstr);
+ } else {
+ PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s' is received",
+ type, otype);
+ }
+ Py_XDECREF(str);
+ return;
+ }
+ }
+ PyErr_Format(PyExc_TypeError, "a '%s' is expected", type);
+ } else {
+ PyErr_Format(PyExc_TypeError, "unexpected type is received");
+ }
+}
+
+
+/* Convert a pointer value, signal an exception on a type mismatch */
+SWIGRUNTIME void *
+SWIG_Python_MustGetPtr(PyObject *obj, swig_type_info *ty, int SWIGUNUSEDPARM(argnum), int flags) {
+ void *result;
+ if (SWIG_Python_ConvertPtr(obj, &result, ty, flags) == -1) {
+ PyErr_Clear();
+#if SWIG_POINTER_EXCEPTION
+ if (flags) {
+ SWIG_Python_TypeError(SWIG_TypePrettyName(ty), obj);
+ SWIG_Python_ArgFail(argnum);
+ }
+#endif
+ }
+ return result;
+}
+
+#ifdef SWIGPYTHON_BUILTIN
+SWIGRUNTIME int
+SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
+ PyTypeObject *tp = obj->ob_type;
+ PyObject *descr;
+ PyObject *encoded_name;
+ descrsetfunc f;
+ int res = -1;
+
+# ifdef Py_USING_UNICODE
+ if (PyString_Check(name)) {
+ name = PyUnicode_Decode(PyString_AsString(name), PyString_Size(name), NULL, NULL);
+ if (!name)
+ return -1;
+ } else if (!PyUnicode_Check(name))
+# else
+ if (!PyString_Check(name))
+# endif
+ {
+ PyErr_Format(PyExc_TypeError, "attribute name must be string, not '%.200s'", name->ob_type->tp_name);
+ return -1;
+ } else {
+ Py_INCREF(name);
+ }
+
+ if (!tp->tp_dict) {
+ if (PyType_Ready(tp) < 0)
+ goto done;
+ }
+
+ descr = _PyType_Lookup(tp, name);
+ f = NULL;
+ if (descr != NULL)
+ f = descr->ob_type->tp_descr_set;
+ if (!f) {
+ if (PyString_Check(name)) {
+ encoded_name = name;
+ Py_INCREF(name);
+ } else {
+ encoded_name = PyUnicode_AsUTF8String(name);
+ }
+ PyErr_Format(PyExc_AttributeError, "'%.100s' object has no attribute '%.200s'", tp->tp_name, PyString_AsString(encoded_name));
+ Py_DECREF(encoded_name);
+ } else {
+ res = f(descr, obj, value);
+ }
+
+ done:
+ Py_DECREF(name);
+ return res;
+}
+#endif
+
+
+#ifdef __cplusplus
+}
+#endif
+
+
+
+#define SWIG_exception_fail(code, msg) do { SWIG_Error(code, msg); SWIG_fail; } while(0)
+
+#define SWIG_contract_assert(expr, msg) if (!(expr)) { SWIG_Error(SWIG_RuntimeError, msg); SWIG_fail; } else
+
+
+
+/* -------- TYPES TABLE (BEGIN) -------- */
+
+#define SWIGTYPE_p_char swig_types[0]
+#define SWIGTYPE_p_molfile_plugin_t swig_types[1]
+#define SWIGTYPE_p_p_molfile_plugin_t swig_types[2]
+static swig_type_info *swig_types[4];
+static swig_module_info swig_module = {swig_types, 3, 0, 0, 0, 0};
+#define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name)
+#define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name)
+
+/* -------- TYPES TABLE (END) -------- */
+
+#if (PY_VERSION_HEX <= 0x02000000)
+# if !defined(SWIG_PYTHON_CLASSIC)
+# error "This python version requires swig to be run with the '-classic' option"
+# endif
+#endif
+
+/*-----------------------------------------------
+ @(target):= _libpymolfile.so
+ ------------------------------------------------*/
+#if PY_VERSION_HEX >= 0x03000000
+# define SWIG_init PyInit__libpymolfile
+
+#else
+# define SWIG_init init_libpymolfile
+
+#endif
+#define SWIG_name "_libpymolfile"
+
+#define SWIGVERSION 0x030012
+#define SWIG_VERSION SWIGVERSION
+
+
+#define SWIG_as_voidptr(a) const_cast< void * >(static_cast< const void * >(a))
+#define SWIG_as_voidptrptr(a) ((void)SWIG_as_voidptr(*a),reinterpret_cast< void** >(a))
+
+
+#include <stdexcept>
+
+
+namespace swig {
+ class SwigPtr_PyObject {
+ protected:
+ PyObject *_obj;
+
+ public:
+ SwigPtr_PyObject() :_obj(0)
+ {
+ }
+
+ SwigPtr_PyObject(const SwigPtr_PyObject& item) : _obj(item._obj)
+ {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ Py_XINCREF(_obj);
+ SWIG_PYTHON_THREAD_END_BLOCK;
+ }
+
+ SwigPtr_PyObject(PyObject *obj, bool initial_ref = true) :_obj(obj)
+ {
+ if (initial_ref) {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ Py_XINCREF(_obj);
+ SWIG_PYTHON_THREAD_END_BLOCK;
+ }
+ }
+
+ SwigPtr_PyObject & operator=(const SwigPtr_PyObject& item)
+ {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ Py_XINCREF(item._obj);
+ Py_XDECREF(_obj);
+ _obj = item._obj;
+ SWIG_PYTHON_THREAD_END_BLOCK;
+ return *this;
+ }
+
+ ~SwigPtr_PyObject()
+ {
+ SWIG_PYTHON_THREAD_BEGIN_BLOCK;
+ Py_XDECREF(_obj);
+ SWIG_PYTHON_THREAD_END_BLOCK;
+ }
+
+ operator PyObject *() const
+ {
+ return _obj;
+ }
+
+ PyObject *operator->() const
+ {
+ return _obj;
+ }
+ };
+}
+
+
+namespace swig {
+ struct SwigVar_PyObject : SwigPtr_PyObject {
+ SwigVar_PyObject(PyObject* obj = 0) : SwigPtr_PyObject(obj, false) { }
+
+ SwigVar_PyObject & operator = (PyObject* obj)
+ {
+ Py_XDECREF(_obj);
+ _obj = obj;
+ return *this;
+ }
+ };
+}
+
+
+/* Python SWIG interface to libpymolfile
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under BSD LICENSE
+ */
+#define SWIG_FILE_WITH_INIT
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+#include "pymolfile.h"
+
+
+#ifndef SWIG_FILE_WITH_INIT
+#define NO_IMPORT_ARRAY
+#endif
+#include "stdio.h"
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#include <numpy/arrayobject.h>
+
+
+#include <complex>
+
+
+SWIGINTERNINLINE PyObject*
+ SWIG_From_int (int value)
+{
+ return PyInt_FromLong((long) value);
+}
+
+
+#include <limits.h>
+#if !defined(SWIG_NO_LLONG_MAX)
+# if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__)
+# define LLONG_MAX __LONG_LONG_MAX__
+# define LLONG_MIN (-LLONG_MAX - 1LL)
+# define ULLONG_MAX (LLONG_MAX * 2ULL + 1ULL)
+# endif
+#endif
+
+
+SWIGINTERN int
+SWIG_AsVal_double (PyObject *obj, double *val)
+{
+ int res = SWIG_TypeError;
+ if (PyFloat_Check(obj)) {
+ if (val) *val = PyFloat_AsDouble(obj);
+ return SWIG_OK;
+#if PY_VERSION_HEX < 0x03000000
+ } else if (PyInt_Check(obj)) {
+ if (val) *val = (double) PyInt_AsLong(obj);
+ return SWIG_OK;
+#endif
+ } else if (PyLong_Check(obj)) {
+ double v = PyLong_AsDouble(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_OK;
+ } else {
+ PyErr_Clear();
+ }
+ }
+#ifdef SWIG_PYTHON_CAST_MODE
+ {
+ int dispatch = 0;
+ double d = PyFloat_AsDouble(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = d;
+ return SWIG_AddCast(SWIG_OK);
+ } else {
+ PyErr_Clear();
+ }
+ if (!dispatch) {
+ long v = PyLong_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_AddCast(SWIG_AddCast(SWIG_OK));
+ } else {
+ PyErr_Clear();
+ }
+ }
+ }
+#endif
+ return res;
+}
+
+
+#include <float.h>
+
+
+#include <math.h>
+
+
+SWIGINTERNINLINE int
+SWIG_CanCastAsInteger(double *d, double min, double max) {
+ double x = *d;
+ if ((min <= x && x <= max)) {
+ double fx = floor(x);
+ double cx = ceil(x);
+ double rd = ((x - fx) < 0.5) ? fx : cx; /* simple rint */
+ if ((errno == EDOM) || (errno == ERANGE)) {
+ errno = 0;
+ } else {
+ double summ, reps, diff;
+ if (rd < x) {
+ diff = x - rd;
+ } else if (rd > x) {
+ diff = rd - x;
+ } else {
+ return 1;
+ }
+ summ = rd + x;
+ reps = diff/summ;
+ if (reps < 8*DBL_EPSILON) {
+ *d = rd;
+ return 1;
+ }
+ }
+ }
+ return 0;
+}
+
+
+SWIGINTERN int
+SWIG_AsVal_long (PyObject *obj, long* val)
+{
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(obj)) {
+ if (val) *val = PyInt_AsLong(obj);
+ return SWIG_OK;
+ } else
+#endif
+ if (PyLong_Check(obj)) {
+ long v = PyLong_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_OK;
+ } else {
+ PyErr_Clear();
+ return SWIG_OverflowError;
+ }
+ }
+#ifdef SWIG_PYTHON_CAST_MODE
+ {
+ int dispatch = 0;
+ long v = PyInt_AsLong(obj);
+ if (!PyErr_Occurred()) {
+ if (val) *val = v;
+ return SWIG_AddCast(SWIG_OK);
+ } else {
+ PyErr_Clear();
+ }
+ if (!dispatch) {
+ double d;
+ int res = SWIG_AddCast(SWIG_AsVal_double (obj,&d));
+ if (SWIG_IsOK(res) && SWIG_CanCastAsInteger(&d, LONG_MIN, LONG_MAX)) {
+ if (val) *val = (long)(d);
+ return res;
+ }
+ }
+ }
+#endif
+ return SWIG_TypeError;
+}
+
+
+SWIGINTERN int
+SWIG_AsVal_int (PyObject * obj, int *val)
+{
+ long v;
+ int res = SWIG_AsVal_long (obj, &v);
+ if (SWIG_IsOK(res)) {
+ if ((v < INT_MIN || v > INT_MAX)) {
+ return SWIG_OverflowError;
+ } else {
+ if (val) *val = static_cast< int >(v);
+ }
+ }
+ return res;
+}
+
+
+PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
+ molfile_plugin_t *plugin;
+ int *plugno = &plugin_no;
+ int has_readstructure = 0;
+ int has_readbonds = 0;
+ int has_readangles = 0;
+ int has_writestructure = 0;
+ int has_writebonds = 0;
+ int has_writeangles = 0;
+ int has_readnexttimestep = 0;
+ int has_writetimestep = 0;
+ int plugin_list_size = sizeof(plugin_list) / sizeof(molfile_plugin_t**);
+ if (plugno==NULL || plugin_no<0){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin handle no should be given, be positive value and should not exceed the list length'%d'. You set '%d'", pluginNOINIT, plugin_list_size, plugin_no);
+ return 0;
+ }
+ plugin = plugin_list[plugin_no];
+ if(plugin==NULL || !plugin->open_file_read){
+ PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin '%d' is not initialized.", pluginNOINIT, plugin_no);
+ return 0;
+ }
+ if (plugin->read_structure) has_readstructure = 1;
+ if (plugin->read_bonds) has_readbonds = 1;
+ if (plugin->read_angles) has_readangles = 1;
+ if (plugin->read_next_timestep) has_readnexttimestep = 1;
+ if (plugin->write_structure) has_writestructure = 1;
+ if (plugin->write_bonds) has_writebonds = 1;
+ if (plugin->write_angles) has_writeangles = 1;
+ if (plugin->write_timestep) has_writetimestep = 1;
+ PyObject *tuple = PyTuple_New(17);
+ PyTuple_SET_ITEM(tuple, 0, PyString_FromString(plugin->filename_extension));
+ PyTuple_SET_ITEM(tuple, 1, PyString_FromString(plugin->name));
+ PyTuple_SET_ITEM(tuple, 2, PyInt_FromLong((long)has_readstructure));
+ PyTuple_SET_ITEM(tuple, 3, PyInt_FromLong((long)has_readbonds));
+ PyTuple_SET_ITEM(tuple, 4, PyInt_FromLong((long)has_readangles));
+ PyTuple_SET_ITEM(tuple, 5, PyInt_FromLong((long)has_readnexttimestep));
+ PyTuple_SET_ITEM(tuple, 6, PyInt_FromLong((long)has_writestructure));
+ PyTuple_SET_ITEM(tuple, 7, PyInt_FromLong((long)has_writebonds));
+ PyTuple_SET_ITEM(tuple, 8, PyInt_FromLong((long)has_writeangles));
+ PyTuple_SET_ITEM(tuple, 9, PyInt_FromLong((long)has_writetimestep));
+ PyTuple_SET_ITEM(tuple, 10, PyString_FromString(plugin->prettyname));
+ PyTuple_SET_ITEM(tuple, 11, PyString_FromString(plugin->type));
+ PyTuple_SET_ITEM(tuple, 12, PyString_FromString(plugin->author));
+ PyTuple_SET_ITEM(tuple, 13, PyInt_FromLong((long)plugin->majorv));
+ PyTuple_SET_ITEM(tuple, 14, PyInt_FromLong((long)plugin->minorv));
+ PyTuple_SET_ITEM(tuple, 15, PyInt_FromLong((long)plugin->abiversion));
+ PyTuple_SET_ITEM(tuple, 16, PyInt_FromLong((long)plugin->is_reentrant));
+ return tuple;
+ }
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+SWIGINTERN PyObject *_wrap_molfile_plugin_list(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ int arg1 ;
+ int val1 ;
+ int ecode1 = 0 ;
+ PyObject * obj0 = 0 ;
+ molfile_plugin_t **result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:molfile_plugin_list",&obj0)) SWIG_fail;
+ ecode1 = SWIG_AsVal_int(obj0, &val1);
+ if (!SWIG_IsOK(ecode1)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "molfile_plugin_list" "', argument " "1"" of type '" "int""'");
+ }
+ arg1 = static_cast< int >(val1);
+ result = (molfile_plugin_t **)molfile_plugin_list(arg1);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_molfile_init(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ int result;
+
+ if (!PyArg_ParseTuple(args,(char *)":molfile_init")) SWIG_fail;
+ result = (int)molfile_init();
+ resultobj = SWIG_From_int(static_cast< int >(result));
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_molfile_finish(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ int result;
+
+ if (!PyArg_ParseTuple(args,(char *)":molfile_finish")) SWIG_fail;
+ result = (int)molfile_finish();
+ resultobj = SWIG_From_int(static_cast< int >(result));
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_get_plugin(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ molfile_plugin_t **arg1 = (molfile_plugin_t **) 0 ;
+ int arg2 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ int val2 ;
+ int ecode2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+ molfile_plugin_t *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:get_plugin",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_plugin" "', argument " "1"" of type '" "molfile_plugin_t **""'");
+ }
+ arg1 = reinterpret_cast< molfile_plugin_t ** >(argp1);
+ ecode2 = SWIG_AsVal_int(obj1, &val2);
+ if (!SWIG_IsOK(ecode2)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_plugin" "', argument " "2"" of type '" "int""'");
+ }
+ arg2 = static_cast< int >(val2);
+ result = (molfile_plugin_t *)get_plugin(arg1,arg2);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_molfile_plugin_info(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ molfile_plugin_t **arg1 = (molfile_plugin_t **) 0 ;
+ int arg2 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ int val2 ;
+ int ecode2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:molfile_plugin_info",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "molfile_plugin_info" "', argument " "1"" of type '" "molfile_plugin_t **""'");
+ }
+ arg1 = reinterpret_cast< molfile_plugin_t ** >(argp1);
+ ecode2 = SWIG_AsVal_int(obj1, &val2);
+ if (!SWIG_IsOK(ecode2)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "molfile_plugin_info" "', argument " "2"" of type '" "int""'");
+ }
+ arg2 = static_cast< int >(val2);
+ {
+ result = (PyObject *)molfile_plugin_info(arg1,arg2);
+ if (PyErr_Occurred()) SWIG_fail;
+ }
+ resultobj = result;
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+static PyMethodDef SwigMethods[] = {
+ { (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL},
+ { (char *)"molfile_plugin_list", _wrap_molfile_plugin_list, METH_VARARGS, (char *)"molfile_plugin_list(maxsize) -> molfile_plugin_t **"},
+ { (char *)"molfile_init", _wrap_molfile_init, METH_VARARGS, (char *)"molfile_init() -> int"},
+ { (char *)"molfile_finish", _wrap_molfile_finish, METH_VARARGS, (char *)"molfile_finish() -> int"},
+ { (char *)"get_plugin", _wrap_get_plugin, METH_VARARGS, (char *)"get_plugin(plugin_list, plugin_no) -> molfile_plugin_t *"},
+ { (char *)"molfile_plugin_info", _wrap_molfile_plugin_info, METH_VARARGS, (char *)"molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"},
+ { NULL, NULL, 0, NULL }
+};
+
+
+/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
+
+static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0};
+static swig_type_info _swigt__p_molfile_plugin_t = {"_p_molfile_plugin_t", "molfile_plugin_t *", 0, 0, (void*)0, 0};
+static swig_type_info _swigt__p_p_molfile_plugin_t = {"_p_p_molfile_plugin_t", "molfile_plugin_t **", 0, 0, (void*)0, 0};
+
+static swig_type_info *swig_type_initial[] = {
+ &_swigt__p_char,
+ &_swigt__p_molfile_plugin_t,
+ &_swigt__p_p_molfile_plugin_t,
+};
+
+static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}};
+static swig_cast_info _swigc__p_molfile_plugin_t[] = { {&_swigt__p_molfile_plugin_t, 0, 0, 0},{0, 0, 0, 0}};
+static swig_cast_info _swigc__p_p_molfile_plugin_t[] = { {&_swigt__p_p_molfile_plugin_t, 0, 0, 0},{0, 0, 0, 0}};
+
+static swig_cast_info *swig_cast_initial[] = {
+ _swigc__p_char,
+ _swigc__p_molfile_plugin_t,
+ _swigc__p_p_molfile_plugin_t,
+};
+
+
+/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */
+
+static swig_const_info swig_const_table[] = {
+{0, 0, 0, 0.0, 0, 0}};
+
+#ifdef __cplusplus
+}
+#endif
+/* -----------------------------------------------------------------------------
+ * Type initialization:
+ * This problem is tough by the requirement that no dynamic
+ * memory is used. Also, since swig_type_info structures store pointers to
+ * swig_cast_info structures and swig_cast_info structures store pointers back
+ * to swig_type_info structures, we need some lookup code at initialization.
+ * The idea is that swig generates all the structures that are needed.
+ * The runtime then collects these partially filled structures.
+ * The SWIG_InitializeModule function takes these initial arrays out of
+ * swig_module, and does all the lookup, filling in the swig_module.types
+ * array with the correct data and linking the correct swig_cast_info
+ * structures together.
+ *
+ * The generated swig_type_info structures are assigned statically to an initial
+ * array. We just loop through that array, and handle each type individually.
+ * First we lookup if this type has been already loaded, and if so, use the
+ * loaded structure instead of the generated one. Then we have to fill in the
+ * cast linked list. The cast data is initially stored in something like a
+ * two-dimensional array. Each row corresponds to a type (there are the same
+ * number of rows as there are in the swig_type_initial array). Each entry in
+ * a column is one of the swig_cast_info structures for that type.
+ * The cast_initial array is actually an array of arrays, because each row has
+ * a variable number of columns. So to actually build the cast linked list,
+ * we find the array of casts associated with the type, and loop through it
+ * adding the casts to the list. The one last trick we need to do is making
+ * sure the type pointer in the swig_cast_info struct is correct.
+ *
+ * First off, we lookup the cast->type name to see if it is already loaded.
+ * There are three cases to handle:
+ * 1) If the cast->type has already been loaded AND the type we are adding
+ * casting info to has not been loaded (it is in this module), THEN we
+ * replace the cast->type pointer with the type pointer that has already
+ * been loaded.
+ * 2) If BOTH types (the one we are adding casting info to, and the
+ * cast->type) are loaded, THEN the cast info has already been loaded by
+ * the previous module so we just ignore it.
+ * 3) Finally, if cast->type has not already been loaded, then we add that
+ * swig_cast_info to the linked list (because the cast->type) pointer will
+ * be correct.
+ * ----------------------------------------------------------------------------- */
+
+#ifdef __cplusplus
+extern "C" {
+#if 0
+} /* c-mode */
+#endif
+#endif
+
+#if 0
+#define SWIGRUNTIME_DEBUG
+#endif
+
+
+SWIGRUNTIME void
+SWIG_InitializeModule(void *clientdata) {
+ size_t i;
+ swig_module_info *module_head, *iter;
+ int init;
+
+ /* check to see if the circular list has been setup, if not, set it up */
+ if (swig_module.next==0) {
+ /* Initialize the swig_module */
+ swig_module.type_initial = swig_type_initial;
+ swig_module.cast_initial = swig_cast_initial;
+ swig_module.next = &swig_module;
+ init = 1;
+ } else {
+ init = 0;
+ }
+
+ /* Try and load any already created modules */
+ module_head = SWIG_GetModule(clientdata);
+ if (!module_head) {
+ /* This is the first module loaded for this interpreter */
+ /* so set the swig module into the interpreter */
+ SWIG_SetModule(clientdata, &swig_module);
+ } else {
+ /* the interpreter has loaded a SWIG module, but has it loaded this one? */
+ iter=module_head;
+ do {
+ if (iter==&swig_module) {
+ /* Our module is already in the list, so there's nothing more to do. */
+ return;
+ }
+ iter=iter->next;
+ } while (iter!= module_head);
+
+ /* otherwise we must add our module into the list */
+ swig_module.next = module_head->next;
+ module_head->next = &swig_module;
+ }
+
+ /* When multiple interpreters are used, a module could have already been initialized in
+ a different interpreter, but not yet have a pointer in this interpreter.
+ In this case, we do not want to continue adding types... everything should be
+ set up already */
+ if (init == 0) return;
+
+ /* Now work on filling in swig_module.types */
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: size %d\n", swig_module.size);
+#endif
+ for (i = 0; i < swig_module.size; ++i) {
+ swig_type_info *type = 0;
+ swig_type_info *ret;
+ swig_cast_info *cast;
+
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name);
+#endif
+
+ /* if there is another module already loaded */
+ if (swig_module.next != &swig_module) {
+ type = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, swig_module.type_initial[i]->name);
+ }
+ if (type) {
+ /* Overwrite clientdata field */
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: found type %s\n", type->name);
+#endif
+ if (swig_module.type_initial[i]->clientdata) {
+ type->clientdata = swig_module.type_initial[i]->clientdata;
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: found and overwrite type %s \n", type->name);
+#endif
+ }
+ } else {
+ type = swig_module.type_initial[i];
+ }
+
+ /* Insert casting types */
+ cast = swig_module.cast_initial[i];
+ while (cast->type) {
+ /* Don't need to add information already in the list */
+ ret = 0;
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: look cast %s\n", cast->type->name);
+#endif
+ if (swig_module.next != &swig_module) {
+ ret = SWIG_MangledTypeQueryModule(swig_module.next, &swig_module, cast->type->name);
+#ifdef SWIGRUNTIME_DEBUG
+ if (ret) printf("SWIG_InitializeModule: found cast %s\n", ret->name);
+#endif
+ }
+ if (ret) {
+ if (type == swig_module.type_initial[i]) {
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: skip old type %s\n", ret->name);
+#endif
+ cast->type = ret;
+ ret = 0;
+ } else {
+ /* Check for casting already in the list */
+ swig_cast_info *ocast = SWIG_TypeCheck(ret->name, type);
+#ifdef SWIGRUNTIME_DEBUG
+ if (ocast) printf("SWIG_InitializeModule: skip old cast %s\n", ret->name);
+#endif
+ if (!ocast) ret = 0;
+ }
+ }
+
+ if (!ret) {
+#ifdef SWIGRUNTIME_DEBUG
+ printf("SWIG_InitializeModule: adding cast %s\n", cast->type->name);
+#endif
+ if (type->cast) {
+ type->cast->prev = cast;
+ cast->next = type->cast;
+ }
+ type->cast = cast;
+ }
+ cast++;
+ }
+ /* Set entry in modules->types array equal to the type */
+ swig_module.types[i] = type;
+ }
+ swig_module.types[i] = 0;
+
+#ifdef SWIGRUNTIME_DEBUG
+ printf("**** SWIG_InitializeModule: Cast List ******\n");
+ for (i = 0; i < swig_module.size; ++i) {
+ int j = 0;
+ swig_cast_info *cast = swig_module.cast_initial[i];
+ printf("SWIG_InitializeModule: type %d %s\n", i, swig_module.type_initial[i]->name);
+ while (cast->type) {
+ printf("SWIG_InitializeModule: cast type %s\n", cast->type->name);
+ cast++;
+ ++j;
+ }
+ printf("---- Total casts: %d\n",j);
+ }
+ printf("**** SWIG_InitializeModule: Cast List ******\n");
+#endif
+}
+
+/* This function will propagate the clientdata field of type to
+* any new swig_type_info structures that have been added into the list
+* of equivalent types. It is like calling
+* SWIG_TypeClientData(type, clientdata) a second time.
+*/
+SWIGRUNTIME void
+SWIG_PropagateClientData(void) {
+ size_t i;
+ swig_cast_info *equiv;
+ static int init_run = 0;
+
+ if (init_run) return;
+ init_run = 1;
+
+ for (i = 0; i < swig_module.size; i++) {
+ if (swig_module.types[i]->clientdata) {
+ equiv = swig_module.types[i]->cast;
+ while (equiv) {
+ if (!equiv->converter) {
+ if (equiv->type && !equiv->type->clientdata)
+ SWIG_TypeClientData(equiv->type, swig_module.types[i]->clientdata);
+ }
+ equiv = equiv->next;
+ }
+ }
+ }
+}
+
+#ifdef __cplusplus
+#if 0
+{
+ /* c-mode */
+#endif
+}
+#endif
+
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /* Python-specific SWIG API */
+#define SWIG_newvarlink() SWIG_Python_newvarlink()
+#define SWIG_addvarlink(p, name, get_attr, set_attr) SWIG_Python_addvarlink(p, name, get_attr, set_attr)
+#define SWIG_InstallConstants(d, constants) SWIG_Python_InstallConstants(d, constants)
+
+ /* -----------------------------------------------------------------------------
+ * global variable support code.
+ * ----------------------------------------------------------------------------- */
+
+ typedef struct swig_globalvar {
+ char *name; /* Name of global variable */
+ PyObject *(*get_attr)(void); /* Return the current value */
+ int (*set_attr)(PyObject *); /* Set the value */
+ struct swig_globalvar *next;
+ } swig_globalvar;
+
+ typedef struct swig_varlinkobject {
+ PyObject_HEAD
+ swig_globalvar *vars;
+ } swig_varlinkobject;
+
+ SWIGINTERN PyObject *
+ swig_varlink_repr(swig_varlinkobject *SWIGUNUSEDPARM(v)) {
+#if PY_VERSION_HEX >= 0x03000000
+ return PyUnicode_InternFromString("<Swig global variables>");
+#else
+ return PyString_FromString("<Swig global variables>");
+#endif
+ }
+
+ SWIGINTERN PyObject *
+ swig_varlink_str(swig_varlinkobject *v) {
+#if PY_VERSION_HEX >= 0x03000000
+ PyObject *str = PyUnicode_InternFromString("(");
+ PyObject *tail;
+ PyObject *joined;
+ swig_globalvar *var;
+ for (var = v->vars; var; var=var->next) {
+ tail = PyUnicode_FromString(var->name);
+ joined = PyUnicode_Concat(str, tail);
+ Py_DecRef(str);
+ Py_DecRef(tail);
+ str = joined;
+ if (var->next) {
+ tail = PyUnicode_InternFromString(", ");
+ joined = PyUnicode_Concat(str, tail);
+ Py_DecRef(str);
+ Py_DecRef(tail);
+ str = joined;
+ }
+ }
+ tail = PyUnicode_InternFromString(")");
+ joined = PyUnicode_Concat(str, tail);
+ Py_DecRef(str);
+ Py_DecRef(tail);
+ str = joined;
+#else
+ PyObject *str = PyString_FromString("(");
+ swig_globalvar *var;
+ for (var = v->vars; var; var=var->next) {
+ PyString_ConcatAndDel(&str,PyString_FromString(var->name));
+ if (var->next) PyString_ConcatAndDel(&str,PyString_FromString(", "));
+ }
+ PyString_ConcatAndDel(&str,PyString_FromString(")"));
+#endif
+ return str;
+ }
+
+ SWIGINTERN int
+ swig_varlink_print(swig_varlinkobject *v, FILE *fp, int SWIGUNUSEDPARM(flags)) {
+ char *tmp;
+ PyObject *str = swig_varlink_str(v);
+ fprintf(fp,"Swig global variables ");
+ fprintf(fp,"%s\n", tmp = SWIG_Python_str_AsChar(str));
+ SWIG_Python_str_DelForPy3(tmp);
+ Py_DECREF(str);
+ return 0;
+ }
+
+ SWIGINTERN void
+ swig_varlink_dealloc(swig_varlinkobject *v) {
+ swig_globalvar *var = v->vars;
+ while (var) {
+ swig_globalvar *n = var->next;
+ free(var->name);
+ free(var);
+ var = n;
+ }
+ }
+
+ SWIGINTERN PyObject *
+ swig_varlink_getattr(swig_varlinkobject *v, char *n) {
+ PyObject *res = NULL;
+ swig_globalvar *var = v->vars;
+ while (var) {
+ if (strcmp(var->name,n) == 0) {
+ res = (*var->get_attr)();
+ break;
+ }
+ var = var->next;
+ }
+ if (res == NULL && !PyErr_Occurred()) {
+ PyErr_Format(PyExc_AttributeError, "Unknown C global variable '%s'", n);
+ }
+ return res;
+ }
+
+ SWIGINTERN int
+ swig_varlink_setattr(swig_varlinkobject *v, char *n, PyObject *p) {
+ int res = 1;
+ swig_globalvar *var = v->vars;
+ while (var) {
+ if (strcmp(var->name,n) == 0) {
+ res = (*var->set_attr)(p);
+ break;
+ }
+ var = var->next;
+ }
+ if (res == 1 && !PyErr_Occurred()) {
+ PyErr_Format(PyExc_AttributeError, "Unknown C global variable '%s'", n);
+ }
+ return res;
+ }
+
+ SWIGINTERN PyTypeObject*
+ swig_varlink_type(void) {
+ static char varlink__doc__[] = "Swig var link object";
+ static PyTypeObject varlink_type;
+ static int type_init = 0;
+ if (!type_init) {
+ const PyTypeObject tmp = {
+#if PY_VERSION_HEX >= 0x03000000
+ PyVarObject_HEAD_INIT(NULL, 0)
+#else
+ PyObject_HEAD_INIT(NULL)
+ 0, /* ob_size */
+#endif
+ (char *)"swigvarlink", /* tp_name */
+ sizeof(swig_varlinkobject), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor) swig_varlink_dealloc, /* tp_dealloc */
+ (printfunc) swig_varlink_print, /* tp_print */
+ (getattrfunc) swig_varlink_getattr, /* tp_getattr */
+ (setattrfunc) swig_varlink_setattr, /* tp_setattr */
+ 0, /* tp_compare */
+ (reprfunc) swig_varlink_repr, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ (reprfunc) swig_varlink_str, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ 0, /* tp_flags */
+ varlink__doc__, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+#if PY_VERSION_HEX >= 0x02020000
+ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, /* tp_iter -> tp_weaklist */
+#endif
+#if PY_VERSION_HEX >= 0x02030000
+ 0, /* tp_del */
+#endif
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /* tp_version_tag */
+#endif
+#if PY_VERSION_HEX >= 0x03040000
+ 0, /* tp_finalize */
+#endif
+#ifdef COUNT_ALLOCS
+ 0, /* tp_allocs */
+ 0, /* tp_frees */
+ 0, /* tp_maxalloc */
+#if PY_VERSION_HEX >= 0x02050000
+ 0, /* tp_prev */
+#endif
+ 0 /* tp_next */
+#endif
+ };
+ varlink_type = tmp;
+ type_init = 1;
+#if PY_VERSION_HEX < 0x02020000
+ varlink_type.ob_type = &PyType_Type;
+#else
+ if (PyType_Ready(&varlink_type) < 0)
+ return NULL;
+#endif
+ }
+ return &varlink_type;
+ }
+
+ /* Create a variable linking object for use later */
+ SWIGINTERN PyObject *
+ SWIG_Python_newvarlink(void) {
+ swig_varlinkobject *result = PyObject_NEW(swig_varlinkobject, swig_varlink_type());
+ if (result) {
+ result->vars = 0;
+ }
+ return ((PyObject*) result);
+ }
+
+ SWIGINTERN void
+ SWIG_Python_addvarlink(PyObject *p, char *name, PyObject *(*get_attr)(void), int (*set_attr)(PyObject *p)) {
+ swig_varlinkobject *v = (swig_varlinkobject *) p;
+ swig_globalvar *gv = (swig_globalvar *) malloc(sizeof(swig_globalvar));
+ if (gv) {
+ size_t size = strlen(name)+1;
+ gv->name = (char *)malloc(size);
+ if (gv->name) {
+ strncpy(gv->name,name,size);
+ gv->get_attr = get_attr;
+ gv->set_attr = set_attr;
+ gv->next = v->vars;
+ }
+ }
+ v->vars = gv;
+ }
+
+ SWIGINTERN PyObject *
+ SWIG_globals(void) {
+ static PyObject *_SWIG_globals = 0;
+ if (!_SWIG_globals) _SWIG_globals = SWIG_newvarlink();
+ return _SWIG_globals;
+ }
+
+ /* -----------------------------------------------------------------------------
+ * constants/methods manipulation
+ * ----------------------------------------------------------------------------- */
+
+ /* Install Constants */
+ SWIGINTERN void
+ SWIG_Python_InstallConstants(PyObject *d, swig_const_info constants[]) {
+ PyObject *obj = 0;
+ size_t i;
+ for (i = 0; constants[i].type; ++i) {
+ switch(constants[i].type) {
+ case SWIG_PY_POINTER:
+ obj = SWIG_InternalNewPointerObj(constants[i].pvalue, *(constants[i]).ptype,0);
+ break;
+ case SWIG_PY_BINARY:
+ obj = SWIG_NewPackedObj(constants[i].pvalue, constants[i].lvalue, *(constants[i].ptype));
+ break;
+ default:
+ obj = 0;
+ break;
+ }
+ if (obj) {
+ PyDict_SetItemString(d, constants[i].name, obj);
+ Py_DECREF(obj);
+ }
+ }
+ }
+
+ /* -----------------------------------------------------------------------------*/
+ /* Fix SwigMethods to carry the callback ptrs when needed */
+ /* -----------------------------------------------------------------------------*/
+
+ SWIGINTERN void
+ SWIG_Python_FixMethods(PyMethodDef *methods,
+ swig_const_info *const_table,
+ swig_type_info **types,
+ swig_type_info **types_initial) {
+ size_t i;
+ for (i = 0; methods[i].ml_name; ++i) {
+ const char *c = methods[i].ml_doc;
+ if (!c) continue;
+ c = strstr(c, "swig_ptr: ");
+ if (c) {
+ int j;
+ swig_const_info *ci = 0;
+ const char *name = c + 10;
+ for (j = 0; const_table[j].type; ++j) {
+ if (strncmp(const_table[j].name, name,
+ strlen(const_table[j].name)) == 0) {
+ ci = &(const_table[j]);
+ break;
+ }
+ }
+ if (ci) {
+ void *ptr = (ci->type == SWIG_PY_POINTER) ? ci->pvalue : 0;
+ if (ptr) {
+ size_t shift = (ci->ptype) - types;
+ swig_type_info *ty = types_initial[shift];
+ size_t ldoc = (c - methods[i].ml_doc);
+ size_t lptr = strlen(ty->name)+2*sizeof(void*)+2;
+ char *ndoc = (char*)malloc(ldoc + lptr + 10);
+ if (ndoc) {
+ char *buff = ndoc;
+ strncpy(buff, methods[i].ml_doc, ldoc);
+ buff += ldoc;
+ strncpy(buff, "swig_ptr: ", 10);
+ buff += 10;
+ SWIG_PackVoidPtr(buff, ptr, ty->name, lptr);
+ methods[i].ml_doc = ndoc;
+ }
+ }
+ }
+ }
+ }
+ }
+
+#ifdef __cplusplus
+}
+#endif
+
+/* -----------------------------------------------------------------------------*
+ * Partial Init method
+ * -----------------------------------------------------------------------------*/
+
+#ifdef __cplusplus
+extern "C"
+#endif
+
+SWIGEXPORT
+#if PY_VERSION_HEX >= 0x03000000
+PyObject*
+#else
+void
+#endif
+SWIG_init(void) {
+ PyObject *m, *d, *md;
+#if PY_VERSION_HEX >= 0x03000000
+ static struct PyModuleDef SWIG_module = {
+# if PY_VERSION_HEX >= 0x03020000
+ PyModuleDef_HEAD_INIT,
+# else
+ {
+ PyObject_HEAD_INIT(NULL)
+ NULL, /* m_init */
+ 0, /* m_index */
+ NULL, /* m_copy */
+ },
+# endif
+ (char *) SWIG_name,
+ NULL,
+ -1,
+ SwigMethods,
+ NULL,
+ NULL,
+ NULL,
+ NULL
+ };
+#endif
+
+#if defined(SWIGPYTHON_BUILTIN)
+ static SwigPyClientData SwigPyObject_clientdata = {
+ 0, 0, 0, 0, 0, 0, 0
+ };
+ static PyGetSetDef this_getset_def = {
+ (char *)"this", &SwigPyBuiltin_ThisClosure, NULL, NULL, NULL
+ };
+ static SwigPyGetSet thisown_getset_closure = {
+ (PyCFunction) SwigPyObject_own,
+ (PyCFunction) SwigPyObject_own
+ };
+ static PyGetSetDef thisown_getset_def = {
+ (char *)"thisown", SwigPyBuiltin_GetterClosure, SwigPyBuiltin_SetterClosure, NULL, &thisown_getset_closure
+ };
+ PyTypeObject *builtin_pytype;
+ int builtin_base_count;
+ swig_type_info *builtin_basetype;
+ PyObject *tuple;
+ PyGetSetDescrObject *static_getset;
+ PyTypeObject *metatype;
+ PyTypeObject *swigpyobject;
+ SwigPyClientData *cd;
+ PyObject *public_interface, *public_symbol;
+ PyObject *this_descr;
+ PyObject *thisown_descr;
+ PyObject *self = 0;
+ int i;
+
+ (void)builtin_pytype;
+ (void)builtin_base_count;
+ (void)builtin_basetype;
+ (void)tuple;
+ (void)static_getset;
+ (void)self;
+
+ /* Metaclass is used to implement static member variables */
+ metatype = SwigPyObjectType();
+ assert(metatype);
+#endif
+
+ /* Fix SwigMethods to carry the callback ptrs when needed */
+ SWIG_Python_FixMethods(SwigMethods, swig_const_table, swig_types, swig_type_initial);
+
+#if PY_VERSION_HEX >= 0x03000000
+ m = PyModule_Create(&SWIG_module);
+#else
+ m = Py_InitModule((char *) SWIG_name, SwigMethods);
+#endif
+
+ md = d = PyModule_GetDict(m);
+ (void)md;
+
+ SWIG_InitializeModule(0);
+
+#ifdef SWIGPYTHON_BUILTIN
+ swigpyobject = SwigPyObject_TypeOnce();
+
+ SwigPyObject_stype = SWIG_MangledTypeQuery("_p_SwigPyObject");
+ assert(SwigPyObject_stype);
+ cd = (SwigPyClientData*) SwigPyObject_stype->clientdata;
+ if (!cd) {
+ SwigPyObject_stype->clientdata = &SwigPyObject_clientdata;
+ SwigPyObject_clientdata.pytype = swigpyobject;
+ } else if (swigpyobject->tp_basicsize != cd->pytype->tp_basicsize) {
+ PyErr_SetString(PyExc_RuntimeError, "Import error: attempted to load two incompatible swig-generated modules.");
+# if PY_VERSION_HEX >= 0x03000000
+ return NULL;
+# else
+ return;
+# endif
+ }
+
+ /* All objects have a 'this' attribute */
+ this_descr = PyDescr_NewGetSet(SwigPyObject_type(), &this_getset_def);
+ (void)this_descr;
+
+ /* All objects have a 'thisown' attribute */
+ thisown_descr = PyDescr_NewGetSet(SwigPyObject_type(), &thisown_getset_def);
+ (void)thisown_descr;
+
+ public_interface = PyList_New(0);
+ public_symbol = 0;
+ (void)public_symbol;
+
+ PyDict_SetItemString(md, "__all__", public_interface);
+ Py_DECREF(public_interface);
+ for (i = 0; SwigMethods[i].ml_name != NULL; ++i)
+ SwigPyBuiltin_AddPublicSymbol(public_interface, SwigMethods[i].ml_name);
+ for (i = 0; swig_const_table[i].name != 0; ++i)
+ SwigPyBuiltin_AddPublicSymbol(public_interface, swig_const_table[i].name);
+#endif
+
+ SWIG_InstallConstants(d,swig_const_table);
+
+
+ import_array();
+
+ SWIG_Python_SetConstant(d, "pluginOK",SWIG_From_int(static_cast< int >(pluginOK)));
+ SWIG_Python_SetConstant(d, "pluginNOINIT",SWIG_From_int(static_cast< int >(pluginNOINIT)));
+ SWIG_Python_SetConstant(d, "pluginCLOSE",SWIG_From_int(static_cast< int >(pluginCLOSE)));
+ SWIG_Python_SetConstant(d, "pluginNOMEM",SWIG_From_int(static_cast< int >(pluginNOMEM)));
+ SWIG_Python_SetConstant(d, "pluginENDOFFILE",SWIG_From_int(static_cast< int >(pluginENDOFFILE)));
+ SWIG_Python_SetConstant(d, "pluginFILENOTFOUND",SWIG_From_int(static_cast< int >(pluginFILENOTFOUND)));
+ SWIG_Python_SetConstant(d, "pluginFORMATERROR",SWIG_From_int(static_cast< int >(pluginFORMATERROR)));
+#if PY_VERSION_HEX >= 0x03000000
+ return m;
+#else
+ return;
+#endif
+}
+
diff --git a/pymolfile/libpymolfile/numpy.i b/pymolfile/molfile/numpy.i
similarity index 100%
rename from pymolfile/libpymolfile/numpy.i
rename to pymolfile/molfile/numpy.i
diff --git a/pymolfile/molfile/pymolfile.c b/pymolfile/molfile/pymolfile.c
new file mode 100644
index 0000000000000000000000000000000000000000..5bae356ea6afb0e04d4b0c691d94da62c3ab41c6
--- /dev/null
+++ b/pymolfile/molfile/pymolfile.c
@@ -0,0 +1,248 @@
+/* Hey emacs this is -*- C -*- and this is my editor vim.
+ *
+ * molfile.c : C and Fortran interfaces for molfile_plugins
+ * Copyright (c) Berk Onat <b.onat@warwick.ac.uk> 2017
+ *
+ * This program is under BSD LICENSE
+ */
+
+/*
+ * The code is written following the plugin test
+ * context of f77_molfile.c by Axel Kohlmeyer and
+ * in molfile_plugin/src/f77 and catdcd.c by
+ * Justin Gullingsrud of VMD plugins.
+ */
+
+/* Get HAVE_CONFIG_H */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdbool.h>
+#include <ctype.h>
+
+/* get fixed-width types if we are using ANSI C99 */
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#elif (defined HAVE_INTTYPES_H)
+# include <inttypes.h>
+#endif
+
+#include "pymolfile.h"
+
+int numplugins=0;
+molfile_plugin_t** plugin_list;
+
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Helper functions to set and store plugins *
+ * * * * * * * * * * * * * * * * * * * * * * */
+#if 0
+void init_readwriteaccess(struct DICTHOLDER *dict);
+
+struct DICTHOLDER * plugin_find(struct DICTHOLDER *dict, const char *pluginname){
+ struct DICTHOLDER *dictitem;
+ dictitem = dict;
+ // search in dictionary linked list
+ while(dictitem != NULL){
+ if(strcmp(dictitem->key, pluginname) == 0){
+ return dictitem;
+ }
+ dictitem = dictitem->next;
+ }
+ return NULL;
+}
+#endif
+
+molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no)
+{
+ if(plug_no < 0){
+ return NULL;
+ } else {
+ return plug_list[plug_no];
+ }
+}
+
+#if 0
+void init_readwriteaccess(struct DICTHOLDER *dict){
+ struct DICTHOLDER *dictitem;
+ dictitem = dict;
+ // search in dictionary linked list
+ while(dictitem != NULL){
+ if(!dictitem->id){
+ if(plugin_list[dictitem->id]->read_next_timestep){
+ dictitem->read = 1;
+ }
+ if(plugin_list[dictitem->id]->write_timestep){
+ dictitem->write = 1;
+ }
+ }
+ dictitem = dictitem->next;
+ }
+}
+
+static int has_readsupport(const char *pluginname){
+ struct DICTHOLDER *item;
+ item = plugin_find(&plugindict, pluginname);
+ if (!item){
+ return item->read;
+ } else {
+ return 0;
+ }
+}
+
+static int has_writesupport(const char *pluginname){
+ struct DICTHOLDER *item;
+ item = plugin_find(&plugindict, pluginname);
+ if (!item){
+ return item->write;
+ } else {
+ return 0;
+ }
+}
+
+static int plugin_add(struct DICTHOLDER *dict, const char *key, int id){
+ struct DICTHOLDER *dictitem;
+ // Check list is empty or it already has the key
+ if (plugin_find(dict, key) == NULL){
+ dictitem = dict;
+ while(1){
+ // Find the empty next in the list and add item
+ if(dictitem == NULL){
+ struct DICTHOLDER *item = (struct DICTHOLDER*) malloc(sizeof(struct DICTHOLDER));
+ item->key = key;
+ item->id = id;
+ item->read = NULL;
+ item->write = NULL;
+ dictitem = &item;
+ return 0;
+ } else {
+ dictitem = dictitem->next;
+ }
+ }
+ } else {
+ return 1;
+ }
+}
+
+static int plugin_remove(struct DICTHOLDER *dict, const char *key){
+ struct DICTHOLDER *dictitem;
+ // Check list is empty or it already has the key
+ if (plugin_find(dict, key) == NULL){
+ // No key in the list. Nothing to remove.
+ return 1;
+ } else {
+ // Remove key in the list
+ dictitem = dict;
+ while(dictitem != NULL){
+ if(strcmp(dictitem->next->key, key) == 0){
+ struct DICTHOLDER *item = dictitem->next->next;
+ dictitem->next = item;
+ return 0;
+ }
+ dictitem = dictitem->next;
+ }
+ return 1;
+ }
+}
+#endif
+/* * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Interface functions to initialize molfile plugins *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/* check validity of plugins and register them. */
+static int molfile_register(void*, vmdplugin_t *plugin) {
+ if (!plugin->type || !plugin->name || !plugin->author) {
+ // skipping plugin with incomplete header
+ return VMDPLUGIN_ERROR;
+ }
+ else if (plugin->abiversion != vmdplugin_ABIVERSION) {
+ // skipping plugin with incompatible ABI
+ return VMDPLUGIN_ERROR;
+ }
+ else if (0 != strncmp(plugin->type, "mol file", 8)) {
+ // skipping plugin of incompatible type
+ return VMDPLUGIN_ERROR;
+ }
+ else if (numplugins >= MAXPLUGINS) {
+ // too many plugins: increase MAXPLUGINS
+ return VMDPLUGIN_ERROR;
+ }
+
+ //if (plugin_find(&plugindict, plugin->name) != NULL) {
+ // multiple plugins for file type
+ // return VMDPLUGIN_ERROR;
+ //} else {
+ plugin_list[numplugins] = (molfile_plugin_t *) plugin;
+ //plugin_add(&plugindict, plugin->name, numplugins);
+ ++numplugins;
+ return VMDPLUGIN_SUCCESS;
+ //}
+}
+
+molfile_plugin_t** molfile_plugin_list(int maxsize)
+{
+ if(maxsize < MAXPLUGINS){
+ maxsize = MAXPLUGINS;
+ }
+ plugin_list = (molfile_plugin_t**) malloc(sizeof(molfile_plugin_t*)*maxsize);
+ return plugin_list;
+}
+
+/* register all available plugins and clear handles. */
+int molfile_init(void)
+{
+#if 0
+ int molfile_internal_register(void *ptr, vmdplugin_t *plugin)
+ {
+ if (!plugin->type || !plugin->name || !plugin->author) {
+ // skipping plugin with incomplete header
+ return VMDPLUGIN_ERROR;
+ }
+ else if (plugin->abiversion != vmdplugin_ABIVERSION) {
+ // skipping plugin with incompatible ABI
+ return VMDPLUGIN_ERROR;
+ }
+ else if (0 != strncmp(plugin->type, "mol file", 8)) {
+ // skipping plugin of incompatible type
+ return VMDPLUGIN_ERROR;
+ }
+ else if (num_plugins >= MAX_PLUGINS) {
+ // too many plugins: increase MAXPLUGINS
+ return VMDPLUGIN_ERROR;
+ }
+
+ if (plugin_find(&plugindict, plugin->name) != NULL) {
+ // multiple plugins for file type
+ return VMDPLUGIN_ERROR;
+ } else {
+ plugin_list[numplugins] = (molfile_plugin_t *) plugin;
+ ++numplugins;
+ return VMDPLUGIN_SUCCESS;
+ }
+ }
+#endif
+ MOLFILE_INIT_ALL;
+ MOLFILE_REGISTER_ALL(NULL,molfile_register);
+ return numplugins;
+}
+
+/* unregister all available plugins */
+int molfile_finish(void)
+{
+ MOLFILE_FINI_ALL;
+ return 0;
+}
+
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Wrappers to directly access molfile plugin*
+ * functions and settings *
+ * * * * * * * * * * * * * * * * * * * * * * */
+
+/* molfile_plugin_t access */
+
+/* Functions in molfile_plugin_t */
+
+
diff --git a/pymolfile/molfile/pymolfile.h b/pymolfile/molfile/pymolfile.h
new file mode 100644
index 0000000000000000000000000000000000000000..e71a911f5bfbd883fa9506462e9d3214526572c9
--- /dev/null
+++ b/pymolfile/molfile/pymolfile.h
@@ -0,0 +1,72 @@
+/* Hey emacs this is -*- C -*- and this is my editor vim.
+ *
+ * molfile.c : C and Fortran interfaces for molfile_plugins
+ * Copyright (c) Berk Onat <b.onat@warwick.ac.uk> 2017
+ *
+ * This program is under BSD LICENSE
+ */
+
+/*
+ * The code is written following the plugin test
+ * context of f77_molfile.c by Axel Kohlmeyer and
+ * in molfile_plugin/src/f77 and catdcd.c by
+ * Justin Gullingsrud of VMD plugins.
+ */
+
+#ifndef _MOLFILE_H_
+#define _MOLFILE_H_
+
+#ifdef __cplusplus
+extern "C"
+{
+
+#endif
+
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+
+enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
+ pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
+
+#ifndef MAXPLUGINS
+#define MAXPLUGINS 200
+#endif
+
+#if 0
+typedef struct DICTHOLDER {
+ const char *key; // Dictionary key
+ int id; // Id of the item
+ int read; // 1 if molfile plugin read the format
+ int write; // 1 if molfile plugin write in this format
+ struct DICTHOLDER *next; // Next item in the dictionary
+} DICTHOLDER;
+
+struct DICTHOLDER * plugin_find(struct DICTHOLDER *dict, const char *pluginname);
+
+static int plugin_add(struct DICTHOLDER *dict, const char *key, int id);
+
+static int plugin_remove(struct DICTHOLDER *dict, const char *key);
+
+static int has_readsupport(const char *pluginname);
+
+static int has_writesupport(const char *pluginname);
+
+static molfile_plugin_t *get_plugin(const char *pluginname);
+
+static int molfile_register(void *ptr, vmdplugin_t *plugin);
+#endif
+molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no);
+
+molfile_plugin_t** molfile_plugin_list(int maxsize);
+
+int molfile_init(void);
+
+int molfile_finish(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _MOLFILE_H_ */
+
diff --git a/pymolfile/molfile/test.py b/pymolfile/molfile/test.py
new file mode 100644
index 0000000000000000000000000000000000000000..52af65aa65d193c83db4989ec9c3b312189066f1
--- /dev/null
+++ b/pymolfile/molfile/test.py
@@ -0,0 +1,12 @@
+import numpy
+import _libpymolfile
+
+mylib = _libpymolfile
+mylist = mylib.molfile_plugin_list(200)
+numlist = mylib.molfile_init()
+print(numlist)
+for i in range(numlist):
+ testplugin = mylib.molfile_plugin_info(mylist, i)
+ print(i, testplugin)
+
+
diff --git a/pymolfile/vmd_molfile_plugins/LICENSE b/pymolfile/molfile/vmd_molfile_plugins/LICENSE
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/LICENSE
rename to pymolfile/molfile/vmd_molfile_plugins/LICENSE
diff --git a/pymolfile/vmd_molfile_plugins/Make-arch b/pymolfile/molfile/vmd_molfile_plugins/Make-arch
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/Make-arch
rename to pymolfile/molfile/vmd_molfile_plugins/Make-arch
diff --git a/pymolfile/vmd_molfile_plugins/Makefile b/pymolfile/molfile/vmd_molfile_plugins/Makefile
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/Makefile
rename to pymolfile/molfile/vmd_molfile_plugins/Makefile
diff --git a/pymolfile/vmd_molfile_plugins/README b/pymolfile/molfile/vmd_molfile_plugins/README
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/README
rename to pymolfile/molfile/vmd_molfile_plugins/README
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/abinitplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/avsplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/babelplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/basissetplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/bgfplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/binposplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/biomoccaplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/brixplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/carplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/ccp4plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/corplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cpmdplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/crdplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/cubeplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dcdplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dlpolyplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dsn6plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dtrplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/dxplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/edmplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/fs4plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gamessplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/graspplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/grdplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gridplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/gromacsplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/jsplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/lammpsplugin.so
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.a b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.a
new file mode 100644
index 0000000000000000000000000000000000000000..83aeb16c114a05532be1581f2c9953bf8d743c68
Binary files /dev/null and b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.a differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.dylib b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.dylib
new file mode 100755
index 0000000000000000000000000000000000000000..552430c781785a97e23bf1681dcb11e4a3e2bcde
Binary files /dev/null and b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.dylib differ
diff --git a/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.h b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.h
new file mode 100644
index 0000000000000000000000000000000000000000..8c2fbe80bd14b3bc77ee489e1ca54a953e5e973d
--- /dev/null
+++ b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/libmolfile_plugin.h
@@ -0,0 +1,409 @@
+#ifndef LIBMOLFILE_PLUGIN_H
+#define LIBMOLFILE_PLUGIN_H
+#include "vmdplugin.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int molfile_abinitplugin_init(void);
+extern int molfile_abinitplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_abinitplugin_fini(void);
+extern int molfile_avsplugin_init(void);
+extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_avsplugin_fini(void);
+extern int molfile_babelplugin_init(void);
+extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_babelplugin_fini(void);
+extern int molfile_basissetplugin_init(void);
+extern int molfile_basissetplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_basissetplugin_fini(void);
+extern int molfile_bgfplugin_init(void);
+extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_bgfplugin_fini(void);
+extern int molfile_binposplugin_init(void);
+extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_binposplugin_fini(void);
+extern int molfile_biomoccaplugin_init(void);
+extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_biomoccaplugin_fini(void);
+extern int molfile_brixplugin_init(void);
+extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_brixplugin_fini(void);
+extern int molfile_carplugin_init(void);
+extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_carplugin_fini(void);
+extern int molfile_ccp4plugin_init(void);
+extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_ccp4plugin_fini(void);
+extern int molfile_corplugin_init(void);
+extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_corplugin_fini(void);
+extern int molfile_cpmdplugin_init(void);
+extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cpmdplugin_fini(void);
+extern int molfile_crdplugin_init(void);
+extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_crdplugin_fini(void);
+extern int molfile_cubeplugin_init(void);
+extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_cubeplugin_fini(void);
+extern int molfile_dcdplugin_init(void);
+extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dcdplugin_fini(void);
+extern int molfile_dlpolyplugin_init(void);
+extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dlpolyplugin_fini(void);
+extern int molfile_dsn6plugin_init(void);
+extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dsn6plugin_fini(void);
+extern int molfile_dxplugin_init(void);
+extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dxplugin_fini(void);
+extern int molfile_edmplugin_init(void);
+extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_edmplugin_fini(void);
+extern int molfile_fs4plugin_init(void);
+extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_fs4plugin_fini(void);
+extern int molfile_gamessplugin_init(void);
+extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gamessplugin_fini(void);
+extern int molfile_graspplugin_init(void);
+extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_graspplugin_fini(void);
+extern int molfile_grdplugin_init(void);
+extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_grdplugin_fini(void);
+extern int molfile_gridplugin_init(void);
+extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gridplugin_fini(void);
+extern int molfile_gromacsplugin_init(void);
+extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_gromacsplugin_fini(void);
+extern int molfile_jsplugin_init(void);
+extern int molfile_jsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_jsplugin_fini(void);
+extern int molfile_lammpsplugin_init(void);
+extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_lammpsplugin_fini(void);
+extern int molfile_mapplugin_init(void);
+extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mapplugin_fini(void);
+extern int molfile_mdfplugin_init(void);
+extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mdfplugin_fini(void);
+extern int molfile_mol2plugin_init(void);
+extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_mol2plugin_fini(void);
+extern int molfile_moldenplugin_init(void);
+extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_moldenplugin_fini(void);
+extern int molfile_molemeshplugin_init(void);
+extern int molfile_molemeshplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_molemeshplugin_fini(void);
+extern int molfile_msmsplugin_init(void);
+extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_msmsplugin_fini(void);
+extern int molfile_namdbinplugin_init(void);
+extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_namdbinplugin_fini(void);
+extern int molfile_offplugin_init(void);
+extern int molfile_offplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_offplugin_fini(void);
+extern int molfile_parm7plugin_init(void);
+extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parm7plugin_fini(void);
+extern int molfile_parmplugin_init(void);
+extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_parmplugin_fini(void);
+extern int molfile_pbeqplugin_init(void);
+extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pbeqplugin_fini(void);
+extern int molfile_pdbplugin_init(void);
+extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbplugin_fini(void);
+extern int molfile_pdbxplugin_init(void);
+extern int molfile_pdbxplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pdbxplugin_fini(void);
+extern int molfile_phiplugin_init(void);
+extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_phiplugin_fini(void);
+extern int molfile_pltplugin_init(void);
+extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pltplugin_fini(void);
+extern int molfile_plyplugin_init(void);
+extern int molfile_plyplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_plyplugin_fini(void);
+extern int molfile_pqrplugin_init(void);
+extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_pqrplugin_fini(void);
+extern int molfile_psfplugin_init(void);
+extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_psfplugin_fini(void);
+extern int molfile_raster3dplugin_init(void);
+extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_raster3dplugin_fini(void);
+extern int molfile_rst7plugin_init(void);
+extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
+extern int molfile_rst7plugin_fini(void);
+extern int molfile_situsplugin_init(void);
+extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_situsplugin_fini(void);
+extern int molfile_spiderplugin_init(void);
+extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_spiderplugin_fini(void);
+extern int molfile_stlplugin_init(void);
+extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_stlplugin_fini(void);
+extern int molfile_tinkerplugin_init(void);
+extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_tinkerplugin_fini(void);
+extern int molfile_uhbdplugin_init(void);
+extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_uhbdplugin_fini(void);
+extern int molfile_vaspchgcarplugin_init(void);
+extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspchgcarplugin_fini(void);
+extern int molfile_vaspoutcarplugin_init(void);
+extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspoutcarplugin_fini(void);
+extern int molfile_vaspparchgplugin_init(void);
+extern int molfile_vaspparchgplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspparchgplugin_fini(void);
+extern int molfile_vaspposcarplugin_init(void);
+extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspposcarplugin_fini(void);
+extern int molfile_vasp5xdatcarplugin_init(void);
+extern int molfile_vasp5xdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vasp5xdatcarplugin_fini(void);
+extern int molfile_vaspxdatcarplugin_init(void);
+extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxdatcarplugin_fini(void);
+extern int molfile_vaspxmlplugin_init(void);
+extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vaspxmlplugin_fini(void);
+extern int molfile_vtkplugin_init(void);
+extern int molfile_vtkplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_vtkplugin_fini(void);
+extern int molfile_xbgfplugin_init(void);
+extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xbgfplugin_fini(void);
+extern int molfile_xsfplugin_init(void);
+extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xsfplugin_fini(void);
+extern int molfile_xyzplugin_init(void);
+extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_xyzplugin_fini(void);
+extern int molfile_dtrplugin_init(void);
+extern int molfile_dtrplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_dtrplugin_fini(void);
+extern int molfile_maeffplugin_init(void);
+extern int molfile_maeffplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_maeffplugin_fini(void);
+
+#define MOLFILE_INIT_ALL \
+ molfile_abinitplugin_init(); \
+ molfile_avsplugin_init(); \
+ molfile_babelplugin_init(); \
+ molfile_basissetplugin_init(); \
+ molfile_bgfplugin_init(); \
+ molfile_binposplugin_init(); \
+ molfile_biomoccaplugin_init(); \
+ molfile_brixplugin_init(); \
+ molfile_carplugin_init(); \
+ molfile_ccp4plugin_init(); \
+ molfile_corplugin_init(); \
+ molfile_cpmdplugin_init(); \
+ molfile_crdplugin_init(); \
+ molfile_cubeplugin_init(); \
+ molfile_dcdplugin_init(); \
+ molfile_dlpolyplugin_init(); \
+ molfile_dsn6plugin_init(); \
+ molfile_dxplugin_init(); \
+ molfile_edmplugin_init(); \
+ molfile_fs4plugin_init(); \
+ molfile_gamessplugin_init(); \
+ molfile_graspplugin_init(); \
+ molfile_grdplugin_init(); \
+ molfile_gridplugin_init(); \
+ molfile_gromacsplugin_init(); \
+ molfile_jsplugin_init(); \
+ molfile_lammpsplugin_init(); \
+ molfile_mapplugin_init(); \
+ molfile_mdfplugin_init(); \
+ molfile_mol2plugin_init(); \
+ molfile_moldenplugin_init(); \
+ molfile_molemeshplugin_init(); \
+ molfile_msmsplugin_init(); \
+ molfile_namdbinplugin_init(); \
+ molfile_offplugin_init(); \
+ molfile_parm7plugin_init(); \
+ molfile_parmplugin_init(); \
+ molfile_pbeqplugin_init(); \
+ molfile_pdbplugin_init(); \
+ molfile_pdbxplugin_init(); \
+ molfile_phiplugin_init(); \
+ molfile_pltplugin_init(); \
+ molfile_plyplugin_init(); \
+ molfile_pqrplugin_init(); \
+ molfile_psfplugin_init(); \
+ molfile_raster3dplugin_init(); \
+ molfile_rst7plugin_init(); \
+ molfile_situsplugin_init(); \
+ molfile_spiderplugin_init(); \
+ molfile_stlplugin_init(); \
+ molfile_tinkerplugin_init(); \
+ molfile_uhbdplugin_init(); \
+ molfile_vaspchgcarplugin_init(); \
+ molfile_vaspoutcarplugin_init(); \
+ molfile_vaspparchgplugin_init(); \
+ molfile_vaspposcarplugin_init(); \
+ molfile_vasp5xdatcarplugin_init(); \
+ molfile_vaspxdatcarplugin_init(); \
+ molfile_vaspxmlplugin_init(); \
+ molfile_vtkplugin_init(); \
+ molfile_xbgfplugin_init(); \
+ molfile_xsfplugin_init(); \
+ molfile_xyzplugin_init(); \
+ molfile_dtrplugin_init(); \
+ molfile_maeffplugin_init(); \
+
+#define MOLFILE_REGISTER_ALL(v, cb) \
+ molfile_abinitplugin_register(v, cb); \
+ molfile_avsplugin_register(v, cb); \
+ molfile_babelplugin_register(v, cb); \
+ molfile_basissetplugin_register(v, cb); \
+ molfile_bgfplugin_register(v, cb); \
+ molfile_binposplugin_register(v, cb); \
+ molfile_biomoccaplugin_register(v, cb); \
+ molfile_brixplugin_register(v, cb); \
+ molfile_carplugin_register(v, cb); \
+ molfile_ccp4plugin_register(v, cb); \
+ molfile_corplugin_register(v, cb); \
+ molfile_cpmdplugin_register(v, cb); \
+ molfile_crdplugin_register(v, cb); \
+ molfile_cubeplugin_register(v, cb); \
+ molfile_dcdplugin_register(v, cb); \
+ molfile_dlpolyplugin_register(v, cb); \
+ molfile_dsn6plugin_register(v, cb); \
+ molfile_dxplugin_register(v, cb); \
+ molfile_edmplugin_register(v, cb); \
+ molfile_fs4plugin_register(v, cb); \
+ molfile_gamessplugin_register(v, cb); \
+ molfile_graspplugin_register(v, cb); \
+ molfile_grdplugin_register(v, cb); \
+ molfile_gridplugin_register(v, cb); \
+ molfile_gromacsplugin_register(v, cb); \
+ molfile_jsplugin_register(v, cb); \
+ molfile_lammpsplugin_register(v, cb); \
+ molfile_mapplugin_register(v, cb); \
+ molfile_mdfplugin_register(v, cb); \
+ molfile_mol2plugin_register(v, cb); \
+ molfile_moldenplugin_register(v, cb); \
+ molfile_molemeshplugin_register(v, cb); \
+ molfile_msmsplugin_register(v, cb); \
+ molfile_namdbinplugin_register(v, cb); \
+ molfile_offplugin_register(v, cb); \
+ molfile_parm7plugin_register(v, cb); \
+ molfile_parmplugin_register(v, cb); \
+ molfile_pbeqplugin_register(v, cb); \
+ molfile_pdbplugin_register(v, cb); \
+ molfile_pdbxplugin_register(v, cb); \
+ molfile_phiplugin_register(v, cb); \
+ molfile_pltplugin_register(v, cb); \
+ molfile_plyplugin_register(v, cb); \
+ molfile_pqrplugin_register(v, cb); \
+ molfile_psfplugin_register(v, cb); \
+ molfile_raster3dplugin_register(v, cb); \
+ molfile_rst7plugin_register(v, cb); \
+ molfile_situsplugin_register(v, cb); \
+ molfile_spiderplugin_register(v, cb); \
+ molfile_stlplugin_register(v, cb); \
+ molfile_tinkerplugin_register(v, cb); \
+ molfile_uhbdplugin_register(v, cb); \
+ molfile_vaspchgcarplugin_register(v, cb); \
+ molfile_vaspoutcarplugin_register(v, cb); \
+ molfile_vaspparchgplugin_register(v, cb); \
+ molfile_vaspposcarplugin_register(v, cb); \
+ molfile_vasp5xdatcarplugin_register(v, cb); \
+ molfile_vaspxdatcarplugin_register(v, cb); \
+ molfile_vaspxmlplugin_register(v, cb); \
+ molfile_vtkplugin_register(v, cb); \
+ molfile_xbgfplugin_register(v, cb); \
+ molfile_xsfplugin_register(v, cb); \
+ molfile_xyzplugin_register(v, cb); \
+ molfile_dtrplugin_register(v, cb); \
+ molfile_maeffplugin_register(v, cb); \
+
+#define MOLFILE_FINI_ALL \
+ molfile_abinitplugin_fini(); \
+ molfile_avsplugin_fini(); \
+ molfile_babelplugin_fini(); \
+ molfile_basissetplugin_fini(); \
+ molfile_bgfplugin_fini(); \
+ molfile_binposplugin_fini(); \
+ molfile_biomoccaplugin_fini(); \
+ molfile_brixplugin_fini(); \
+ molfile_carplugin_fini(); \
+ molfile_ccp4plugin_fini(); \
+ molfile_corplugin_fini(); \
+ molfile_cpmdplugin_fini(); \
+ molfile_crdplugin_fini(); \
+ molfile_cubeplugin_fini(); \
+ molfile_dcdplugin_fini(); \
+ molfile_dlpolyplugin_fini(); \
+ molfile_dsn6plugin_fini(); \
+ molfile_dxplugin_fini(); \
+ molfile_edmplugin_fini(); \
+ molfile_fs4plugin_fini(); \
+ molfile_gamessplugin_fini(); \
+ molfile_graspplugin_fini(); \
+ molfile_grdplugin_fini(); \
+ molfile_gridplugin_fini(); \
+ molfile_gromacsplugin_fini(); \
+ molfile_jsplugin_fini(); \
+ molfile_lammpsplugin_fini(); \
+ molfile_mapplugin_fini(); \
+ molfile_mdfplugin_fini(); \
+ molfile_mol2plugin_fini(); \
+ molfile_moldenplugin_fini(); \
+ molfile_molemeshplugin_fini(); \
+ molfile_msmsplugin_fini(); \
+ molfile_namdbinplugin_fini(); \
+ molfile_offplugin_fini(); \
+ molfile_parm7plugin_fini(); \
+ molfile_parmplugin_fini(); \
+ molfile_pbeqplugin_fini(); \
+ molfile_pdbplugin_fini(); \
+ molfile_pdbxplugin_fini(); \
+ molfile_phiplugin_fini(); \
+ molfile_pltplugin_fini(); \
+ molfile_plyplugin_fini(); \
+ molfile_pqrplugin_fini(); \
+ molfile_psfplugin_fini(); \
+ molfile_raster3dplugin_fini(); \
+ molfile_rst7plugin_fini(); \
+ molfile_situsplugin_fini(); \
+ molfile_spiderplugin_fini(); \
+ molfile_stlplugin_fini(); \
+ molfile_tinkerplugin_fini(); \
+ molfile_uhbdplugin_fini(); \
+ molfile_vaspchgcarplugin_fini(); \
+ molfile_vaspoutcarplugin_fini(); \
+ molfile_vaspparchgplugin_fini(); \
+ molfile_vaspposcarplugin_fini(); \
+ molfile_vasp5xdatcarplugin_fini(); \
+ molfile_vaspxdatcarplugin_fini(); \
+ molfile_vaspxmlplugin_fini(); \
+ molfile_vtkplugin_fini(); \
+ molfile_xbgfplugin_fini(); \
+ molfile_xsfplugin_fini(); \
+ molfile_xyzplugin_fini(); \
+ molfile_dtrplugin_fini(); \
+ molfile_maeffplugin_fini(); \
+
+#ifdef __cplusplus
+}
+#endif
+#endif
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/maeffplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mapplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mdfplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/mol2plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/moldenplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/molemeshplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/msmsplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/namdbinplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/offplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parm7plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/parmplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pbeqplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pdbxplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/phiplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pltplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/plyplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/pqrplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/psfplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/raster3dplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/rst7plugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/situsplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/spiderplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/stlplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/tinkerplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/uhbdplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vasp5xdatcarplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspchgcarplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspoutcarplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspparchgplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspposcarplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxdatcarplugin.so
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin-s.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin-s.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin-s.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin-s.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.o b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.o
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.o
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.o
diff --git a/pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.so b/pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.so
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.so
rename to pymolfile/molfile/vmd_molfile_plugins/compile/lib_MACOSXX86_64/molfile/vaspxmlplugin.so
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diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/carplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
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rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/carplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ccp4plugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/corplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/corplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cpmdlogplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cpmdplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/crdplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/cubeplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dcdplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dlpolyplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dmsplugin.cxx
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dsn6plugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.cxx
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dtrplugin.hxx
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/dxplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/edmplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/endianswap.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/endianswap.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/fastio.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fastio.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/fastio.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fastio.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/fortread.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fortread.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/fortread.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fortread.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/fs4plugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gamessplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gaussianplugin.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/graspplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/grdplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gridplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/gromacsplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/hash.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hash.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/hash.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hash.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/hash.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hash.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/hash.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hash.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/hoomdplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/inthash.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/inthash.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/inthash.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/inthash.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/inthash.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/inthash.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/inthash.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/inthash.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/jsplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/lammpsplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/largefiles.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/largefiles.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/maeffplugin.cxx
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/main.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/main.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/main.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/main.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mapplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mdfplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/mmcif.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mmcif.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/mol2plugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/moldenplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/molemeshplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/msmsplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/namdbinplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/netcdfplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/offplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/offplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/parm7plugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/parmplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pbeqplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pdbplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pdbxplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/periodic_table.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/phiplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pltplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/plugintest.x b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/plugintest.x
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/ply.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ply.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/ply.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ply.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/ply.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ply.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/ply.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/ply.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/plyplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/pqrplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/psfplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/qmplugin.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/raster3dplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/readpdb.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/readpdb.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/rst7plugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/situsplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/spiderplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/stlplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/tinkerplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/tngplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/uhbdplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/unit_conversion.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vasp5xdatcarplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspchgcarplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspoutcarplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspparchgplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspplugin.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspposcarplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspxdatcarplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vaspxmlplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vmddir.h b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vmddir.h
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vtfplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/vtkplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/webpdbplugin.c
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xbgfplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xsfplugin.C
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c b/pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
similarity index 100%
rename from pymolfile/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
rename to pymolfile/molfile/vmd_molfile_plugins/molfile_plugin/src/xyzplugin.c
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deleted file mode 100644
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--- a/pymolfile/python/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/pymolfile/python/Makefile.in b/pymolfile/python/Makefile.in
deleted file mode 100644
index 1856705397c949ce4289a492ffd2ea45516f16b8..0000000000000000000000000000000000000000
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diff --git a/pymolfile/python/sample.py b/pymolfile/python/sample.py
deleted file mode 100755
index 56b5d4fbf241d354de3193e9e3f17e824c0e8d5a..0000000000000000000000000000000000000000
--- a/pymolfile/python/sample.py
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/python
-# -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
-#
-# $Id$
-#
-# Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
-# Coordinate compression (c) by Frans van Hoesel.
-# Python wrapper (c) by Roland Schulz
-#
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-# BSD license, so you can use it any way you wish, including closed source:
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-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-#
-from xdrfile import *
-import sys
-
-#you have to compile with --enable-shared
-#and have libxdrfile.so in the LD_LIBRARY_PATH
-
-if len(sys.argv)!=2:
- print "Missing file argument\nUsage: sample.py FILE"
- sys.exit()
-
-
-x=xdrfile(sys.argv[1])
-for f in x: #iterates frames
- print "%8s %8s %8s %8s Step: %8d "%("Atom","X","Y","Z",f.step) #print header
- for i,a in enumerate(f.x): #iterate atoms
- print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z
diff --git a/pymolfile/python/xdrfile.py b/pymolfile/python/xdrfile.py
deleted file mode 100644
index ba4d75e1ae3ae527a860635acd06535fe08d54f4..0000000000000000000000000000000000000000
--- a/pymolfile/python/xdrfile.py
+++ /dev/null
@@ -1,147 +0,0 @@
-# -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
-#
-# $Id$
-#
-# Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
-# Coordinate compression (c) by Frans van Hoesel.
-# Python wrapper (c) by Roland Schulz
-#
-# IN contrast to the rest of Gromacs, XDRFILE is distributed under the
-# BSD license, so you can use it any way you wish, including closed source:
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the "Software"),
-# to deal in the Software without restriction, including without limitation
-# the rights to use, copy, modify, merge, publish, distribute, sublicense,
-# and/or sell copies of the Software, and to permit persons to whom the
-# Software is furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-#
-
-from ctypes import *
-import os.path
-
-mTrr,mNumPy=1,2
-try:
- from numpy import *
- from numpy.ctypeslib import ndpointer
- auto_mode=mNumPy
-except:
- auto_mode=0
-
-
-class frame:
- #variables
- #x: rvec*natoms / numpy array if installed
- #box DIM*DIM
- #step
- #time
- #prec
- #lam: lambda
-
- def __init__(self,n,mode):
- #create vector for x
- if mode&mNumPy:
- self.x=empty((n,3),dtype=float32)
- self.box = empty((3,3),float32)
- else:
- self.x=((c_float*3)*n)()
- self.box = (c_float*3*3)()
-
-
-class xdrfile:
- exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE, exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC, exdrNOMEM, exdrENDOFFILE, exdrNR = range(13)
-
- #
- def __init__(self,fn,mode="Auto",ft="Auto"):
- if mode=="NumPy":
- self.mode=mNumPy
- try:
- empty
- except NameError:
- raise IOError("NumPy selected but not correctly installed")
- elif mode=="Std":
- self.mode=0
- elif mode=="Auto":
- self.mode=auto_mode
- else:
- raise IOError("unsupported mode")
-
- if ft=="Auto":
- ft = os.path.splitext(fn)[1][1:]
-
- if ft=="trr":
- self.mode|=mTrr
- elif ft=="xtc":
- pass
- else:
- raise IOError("Only xtc and trr supported")
-
- #load libxdrfil
- try:
- self.xdr=cdll.LoadLibrary("libxdrfile.so")
- except:
- raise IOError("libxdrfile.so can't be loaded")
-
- #open file
- self.xd = self.xdr.xdrfile_open(fn,"r")
- if not self.xd: raise IOError("Cannot open file: '%s'"%fn)
-
- #read natoms
- natoms=c_int()
- if self.mode&mTrr:
- r=self.xdr.read_trr_natoms(fn,byref(natoms))
- else:
- r=self.xdr.read_xtc_natoms(fn,byref(natoms))
- if r!=self.exdrOK: raise IOError("Error reading: '%s'"%fn)
- self.natoms=natoms.value
-
- #for NumPy define argtypes - ndpointer is not automatically converted to POINTER(c_float)
- #alternative of ctypes.data_as(POINTER(c_float)) requires two version for numpy and c_float array
- if self.mode&mNumPy:
- self.xdr.read_xtc.argtypes=[c_int,c_int,POINTER(c_int),POINTER(c_float),
- ndpointer(ndim=2,dtype=float32),ndpointer(ndim=2,dtype=float32),POINTER(c_float)]
- self.xdr.read_trr.argtypes=[c_int,c_int,POINTER(c_int),POINTER(c_float),POINTER(c_float),
- ndpointer(ndim=2,dtype=float32),ndpointer(ndim=2,dtype=float32),
- POINTER(c_float),POINTER(c_float)]
-
-
- def __iter__(self):
- f = frame(self.natoms,self.mode)
- #temporary c_type variables (frame variables are python type)
- step = c_int()
- time = c_float()
- prec = c_float()
- lam = c_float()
- while 1:
- #read next frame
- if not self.mode&mTrr:
- result = self.xdr.read_xtc(self.xd,self.natoms,byref(step),byref(time),f.box,
- f.x,byref(prec))
- f.prec=prec.value
- else:
- result = self.xdr.read_trr(self.xd,self.natoms,byref(step),byref(time),byref(lam),
- f.box,f.x,None,None) #TODO: make v,f possible
- f.lam=lam.value
-
- #check return value
- if result==self.exdrENDOFFILE: break
- if result==self.exdrINT and self.mode&mTrr:
- break #TODO: dirty hack. read_trr return exdrINT not exdrENDOFFILE
- if result!=self.exdrOK: raise IOError("Error reading xdr file")
-
- #convert c_type to python
- f.step=step.value
- f.time=time.value
- yield f
-
diff --git a/pymolfile/python/xdrfile_test.py b/pymolfile/python/xdrfile_test.py
deleted file mode 100755
index d4c6025b23a637d5afa2fa084d40a436bd9692c3..0000000000000000000000000000000000000000
--- a/pymolfile/python/xdrfile_test.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/python
-# -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
-#
-# $Id$
-#
-# Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
-# Coordinate compression (c) by Frans van Hoesel.
-# Python wrapper (c) by Roland Schulz
-#
-# IN contrast to the rest of Gromacs, XDRFILE is distributed under the
-# BSD license, so you can use it any way you wish, including closed source:
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the "Software"),
-# to deal in the Software without restriction, including without limitation
-# the rights to use, copy, modify, merge, publish, distribute, sublicense,
-# and/or sell copies of the Software, and to permit persons to whom the
-# Software is furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-#
-from xdrfile import *
-from math import *
-
-#you have to compile with --enable-shared
-#and have libxdrfile.so in the LD_LIBRARY_PATH
-#it expect the test.xtc/test.trr file generated by xdrfile_c_test
-
-DIM=3
-natoms1 = 173
-step1 = 1993
-prec1 = 1000
-time1 = 1097.23
-lam1 = 0.4
-box1=[[(i+1)*3.7 + (j+1) for j in range(DIM)] for i in range(DIM)]
-toler = 1e-3
-
-def test(fn):
- x=xdrfile(fn)
- if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1
- for k,f in enumerate(x):
- if f.step != step1+k: print "incorrect step",f.step,step1+k,k
- if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
- if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
- if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
- for i in range(DIM):
- for j in range(DIM):
- if fabs(f.box[i][j] - box1[i][j]) > toler: print "box incorrect",f.box[i][j],box1[i][j]
- for i in range(x.natoms):
- for j in range(DIM):
- target = (i+1)*3.7 + (j+1)
- if f.x[i][j] - target > toler : print "x incorrect"
- print fn,"OK"
-
-test("../test.trr")
-test("../test.xtc")
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/f77_molfile.c b/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/f77_molfile.c
deleted file mode 100644
index 1bb6aee33f8e61628d32f88fa160be5f8813234f..0000000000000000000000000000000000000000
--- a/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/f77_molfile.c
+++ /dev/null
@@ -1,363 +0,0 @@
-
-/*
- * molfile fortran interface
- * $Id: f77_molfile.c,v 1.1 2006/03/10 22:48:49 johns Exp $
- * (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <string.h>
-
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
-
-#define F77TESTME 1
-
-/* fortran name mangling */
-#if defined(_F77_NO_UNDERSCORE)
-#define FNAME(n) n
-#elif defined(_F77_F2C_UNDERSCORE)
-#define FNAME(n) n ## __
-#else
-#define FNAME(n) n ## _
-#endif
-
-/* interface typedef magic */
-typedef int int4;
-
-struct molfile_f77_handle
-{
- void *handle;
- const char *fname;
- const char *ftype;
- molfile_plugin_t *plugin;
-};
-typedef struct molfile_f77_handle f77_fd;
-
-/* plugin list */
-#ifndef MAXPLUGINS
-#define MAXPLUGINS 200
-#endif
-static int numplugins=0;
-static molfile_plugin_t *plugin_list[MAXPLUGINS];
-
-/* we maintain a static list of assigned handles */
-#ifndef MAXHADNLES
-#define MAXHANDLES 200
-#endif
-static int4 numhandles=0;
-static f77_fd handle_list[MAXHANDLES];
-
-/* helper functions */
-/* helper function to copy fortran style (a la sun fortran) strings into
- * valid c style strings. just using the string pointers will not work,
- * since the strings are NOT zero terminated.
- *
- * WARNING: do not forget to free(2) them later,
- * or you'll have a memory leak!
- */
-static char *f77strdup(const char *s,const int sz)
-{
- char *r;
-
- r = (char *)malloc(sz + 1);
- r = (char *)memcpy(r, s, sz);
- r[sz] = '\0';
- return r;
-}
-
-/* trim off whitespace at the end of a string */
-static void f77trim(char *s,const int sz)
-{
- int i;
-
- i=1;
- while( (i++ < sz) && isspace(s[sz-i]) ) {
- s[sz-i] ='\0';
- }
-}
-
-/* get the filename extension */
-static const char *f77getfnext(const char *s)
-{
- int i,len;
-
- len = strlen(s);
- for (i=len; i>=0; --i) {
- if(s[i] == '.') {
- return &s[i+1];
- }
- }
- return NULL;
-}
-
-/* check validity of plugins and register them. */
-static int f77register(void *ptr, vmdplugin_t *plugin) {
-
- if (!plugin->type || !plugin->name || !plugin->author) {
- fprintf(stderr," skipping plugin with incomplete header\n");
- return -1;
- }
-
-#if F77TESTME
- fprintf(stderr, " trying to register plugin #%d: %s, type: %s/%d\n"
- " written by: %s\n\n", numplugins+1, plugin->name,
- plugin->type, plugin->abiversion, plugin->author);
-#endif
-
- if (plugin->abiversion != vmdplugin_ABIVERSION) {
- fprintf(stderr, " skipping plugin with incompatible ABI:%d/%d\n",
- plugin->abiversion, vmdplugin_ABIVERSION);
- return -2;
- }
-
- if (0 != strncmp(plugin->type, "mol file", 8)) {
- fprintf(stderr, " skipping plugin of incompatible type:%s\n",
- plugin->type);
- return -3;
- }
-
- if (numplugins < MAXPLUGINS) {
- plugin_list[numplugins] = (molfile_plugin_t *) plugin;
- ++numplugins;
- return 0;
- }
-
- fprintf(stderr, " too many plugins: %d. increase MAXPLUGINS, "
- "recompile, and try again.\n", numplugins);
-
- return -4;
-}
-
-
-/* the official fortran API */
-
-/* register all available plugins and clear handles. */
-void FNAME(f77_molfile_init)(void)
-{
- int i;
-
- MOLFILE_INIT_ALL;
-
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i].handle = NULL;
- }
-
- MOLFILE_REGISTER_ALL(NULL,f77register);
-
- /*
- * FIXME: check all plugins and make
- * sure the babel plugin(s) are last.
- */
-}
-
-/* unregister all available plugins */
-void FNAME(f77_molfile_finish)(void)
-{
-#if 0
- int i;
-
- /* FIXME: add code to close and nullify all open handles */
- for (i=0; i<MAXHANDLES; ++i) {
- handle_list[i] = NULL;
- }
-#endif
-
- MOLFILE_FINI_ALL;
-}
-
-
-/* open a file and provide file descriptor */
-void FNAME(f77_molfile_open_read)(int4 *handle, int4 *natoms,
- const char *infile, const char *intype,
- const int len_if, const int len_it)
-{
- char *fname, *ftype;
- molfile_plugin_t *plugin;
- int i;
-
- if (numhandles >= MAXHANDLES) {
- fprintf(stderr, "too many molfile f77 handles.\n");
- *handle = -666;
- return;
- }
-
- fname = f77strdup(infile, len_if);
- f77trim(fname,len_if);
-
- ftype = f77strdup(intype, len_it);
- f77trim(ftype,len_it);
-
- fprintf(stderr, " %s: trying for: %s/%d, %s/%d\n",
- __FUNCTION__, fname, len_if, ftype, len_it);
-
- plugin = NULL;
- /* determine plugin type automatically */
- if(0 == strncmp(intype, "auto", 4)) {
- const char *fext;
-
- fext = f77getfnext(fname);
- if (fext == NULL) {
- fprintf(stderr, " could not determine file name extension "
- "for automatic plugin guess\n");
- *handle = -111;
- return;
- }
-#if F77TESTME
- fprintf(stderr, " filename extension: %s\n", fext);
-#endif
-
- for (i=0; (i<numplugins) && plugin==NULL; ++i) {
-#if F77TESTME
- fprintf(stderr, " tying filename extension: %s\n",
- plugin_list[i]->filename_extension);
-#endif
- if (0 == strcmp(plugin_list[i]->filename_extension, fext)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
-
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not determine matching plugin type"
- "from file name extension\n");
- *handle = -222;
- return;
- }
- } else {
-
- for (i=0; (i<numplugins) && (plugin==NULL); ++i) {
-#if F77TESTME
- fprintf(stderr, " tying plugin type: %s\n",
- plugin_list[i]->name);
-#endif
- if (0 == strcmp(plugin_list[i]->name, ftype)) {
- fprintf(stderr, " using plugin: %s\n",
- plugin_list[i]->prettyname);
- plugin = plugin_list[i];
- }
- }
- if (plugin == NULL) {
- fprintf(stderr, " could not find plugin for type %s\n",ftype);
- *handle = -333;
- return;
- }
- }
-
- if(plugin == NULL) { /* this should not happen, but... */
- fprintf(stderr, " no plugin found.\n");
- *handle = -444;
- return;
- }
-
- /* build handle */
- ++numhandles;
- for (i=0; i<numhandles; ++i) {
- if(handle_list[i].plugin == NULL) {
- *handle = i;
- handle_list[i].fname=fname;
- handle_list[i].ftype=plugin->name;
- handle_list[i].plugin=plugin;
- }
- }
-
- /* open file for reading and detect number of atoms */
- *natoms=MOLFILE_NUMATOMS_UNKNOWN;
- handle_list[*handle].handle=
- plugin->open_file_read(fname,plugin->name,natoms);
- if(handle_list[*handle].handle == NULL) {
- fprintf(stderr, " open of %s-plugin for file %s failed\n",
- plugin->type, fname);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-777;
- return;
- }
-
- return;
-}
-
-/* read next time step */
-void FNAME(f77_molfile_read_next)(int4 *handle, int4 *natoms, float *xyz,
- float *box, int4 *status)
-{
- molfile_plugin_t *plugin;
- molfile_timestep_t step;
- int retval;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *status = 0;
- return;
- }
-
- /* skip or read the timestep as demanded */
- if(status == 0) {
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, NULL);
- } else {
- step.coords = xyz;
- retval = plugin->read_next_timestep(handle_list[*handle].handle,
- *natoms, &step);
- }
-
- /* copy the box parameters */
- if (retval == MOLFILE_SUCCESS) {
- *status = 1;
- box[0]=step.A;
- box[1]=step.B;
- box[2]=step.C;
- box[3]=step.alpha;
- box[4]=step.beta;
- box[5]=step.gamma;
- } else {
- *status = 0;
- }
-}
-
-/* close a read file descriptor */
-void FNAME(f77_molfile_close_read)(int4 *handle)
-{
- molfile_plugin_t *plugin;
-
- /* do some sanity checks on the handle */
- if((*handle < 0) || (*handle >= MAXHANDLES)) {
- fprintf(stderr, " %s: illegal handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -111;
- return;
- }
-
- plugin = handle_list[*handle].plugin;
- if(plugin==NULL) {
- fprintf(stderr, " %s: inactive handle: %d\n",
- __FUNCTION__, *handle);
- *handle = -222;
- return;
- }
-
-#if F77TESTME
- fprintf(stderr, " %s: trying to close handle %d"
- " for file %s\n", __FUNCTION__, *handle,
- handle_list[*handle].fname);
-#endif
-
- plugin->close_file_read(handle_list[*handle].handle);
- --numhandles;
- handle_list[*handle].plugin=NULL;
- *handle=-1;
-}
diff --git a/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/tester.f b/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/tester.f
deleted file mode 100644
index 40e250bb80cc1ad0d8446dd5d37f2726679b5636..0000000000000000000000000000000000000000
--- a/pymolfile/vmd_molfile_plugins/molfile_plugin/f77/tester.f
+++ /dev/null
@@ -1,110 +0,0 @@
-c testing frontend for the molfile plugin fortran interface
-c $Id: tester.f,v 1.1 2006/03/10 22:48:49 johns Exp $
-c (c) 2006 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
-
- program molfile
- implicit none
-
- integer*4 natom, maxatom, handle(4), status
- parameter (maxatom=3000*3)
- real*4 xyz(maxatom), box(6)
-
- character infile*200, intype*10
- integer i,j
-
- print*,'molfile fortran tester v0.01'
-
-C set some default values
- infile = 'TRAJEC.dcd'
- intype = 'auto'
- natom = -1
- handle(1) = -1
- handle(2) = -1
- handle(3) = -1
- handle(4) = -1
-
- print*,'filename: ', infile
- print*,'type: ', intype
-
-C set up everything and
-C register all static plugins
- call f77_molfile_init
-
- call f77_molfile_open_read(handle(1),natom,infile,intype)
-
- if (handle(1).lt.0) then
- print*,'file type unknown or not registered'
- else
- print*,'file successfully opened:'
- print*,'handle:',handle(1)
- print*,'natom: ',natom
- end if
-
- do i=1,2000
- status = 1 ! status=1 on entry means read
- call f77_molfile_read_next(handle(1),natom,xyz(1),box,status);
- print*,'read ',i,' status:',status
- print*,'atom(1)', (xyz(j),j=1,3)
- print*,'atom(10)',(xyz(j),j=31,33)
- print*,'atom(100)',(xyz(j),j=301,303)
- print*,'box',box
- if(status.eq.0) go to 666
- status = 0 ! status=0 on entry means skip
- call f77_molfile_read_next(handle(1),natom,xyz,box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 666
- end do
- 666 continue
-
- infile='li-nh3_4-end.pdb'
- intype='pdb'
- call f77_molfile_open_read(handle(2),natom,infile,intype)
-
- if (handle(2).lt.0) then
- print*,'file type unknown or not registered'
- else
- print*,'file successfully opened:'
- print*,'handle:',handle(2)
- print*,'natom: ',natom
- end if
-
- do i=1,2000
- status = 1 ! status=1 on entry means read
- call f77_molfile_read_next(handle(2),natom,xyz(1),box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 6666
- print*,'atom(1)', (xyz(j),j=1,3)
- print*,'atom(10)', (xyz(j),j=31,33)
- print*,'atom(100)',(xyz(j),j=301,303)
- print*,'box',box
- status = 0 ! status=0 on entry means skip
- call f77_molfile_read_next(handle(2),natom,xyz,box,status);
- print*,'read ',i,' status:',status
- if(status.eq.0) go to 6666
- end do
- 6666 continue
- call f77_molfile_open_read(handle(3),natom,infile,intype)
- print*,'handle:',handle(3)
-
- call f77_molfile_close_read(handle(1),status)
- print*,'handle:',handle(1)
- call f77_molfile_open_read(handle(1),natom,infile,intype)
- print*,'handle:',handle(1)
- call f77_molfile_open_read(handle(4),natom,infile,intype)
- print*,'handle:',handle(4)
-
-
- call f77_molfile_close_read(handle(2),status)
- print*,'handle:',handle(2)
- call f77_molfile_close_read(handle(1),status)
- print*,'handle:',handle(1)
- call f77_molfile_close_read(handle(3),status)
- print*,'handle:',handle(3)
- call f77_molfile_close_read(handle(2),status)
- print*,'handle:',handle(2)
- call f77_molfile_close_read(handle(4),status)
- print*,'handle:',handle(4)
-
- call f77_molfile_finish
-
- end
diff --git a/setup.py b/setup.py
index 23214208729f17afc63b0fda0746ac1cfdd9e157..0647300cfde420b34e43d9d28dee29deb582f71a 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@ CLASSIFIERS = [
"Development Status :: 1 - Alpha",
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
- "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+ "License :: OSI Approved :: University of Illinois Open Source License (UIUC)",
"Programming Language :: C",
"Programming Language :: Python",
"Programming Language :: Python :: 2",
@@ -82,8 +82,8 @@ def get_numpy_include():
numpy_include = np.get_numpy_include()
return numpy_include
-
-# Needed for large-file seeking under 32bit systems (for xtc/trr indexing and access).
+# from SimpleTraj setup.py (https://github.com/arose/simpletraj)
+# Needed for large-file seeking under 32bit systems (migth need for indexing and access).
largefile_macros = [
( "_LARGEFILE_SOURCE", None ),
( "_LARGEFILE64_SOURCE", None ),
@@ -98,18 +98,25 @@ if __name__ == '__main__':
description = "Python interface for VMD molfile plugins.",
version = VERSION,
classifiers = CLASSIFIERS,
- license = "GPL2",
- url = "https://github.com/berkonat/pymolfile",
+ license = "UIUC",
+ url = "https://gitlab.mpcdf.mpg.de/berko/pymolfile",
zip_safe = False,
packages = find_packages(),
ext_modules = [
NumpyExtension(
- "pymolfile/molfile._libmolfile",
+ "pymolfile/molfile._libpymolfile",
sources = [
- "pymolfile/molfile/libmolfile_wrap.c",
- "pymolfile/molfile/molfile.c",
+ "pymolfile/molfile/libpymolfile_wrap.c",
+ "pymolfile/molfile/pymolfile.c",
+ "pymolfile/molfile/lib/libmolfile_plugin.a",
],
- include_dirs = [ get_numpy_include ],
+ include_dirs = [
+ get_numpy_include,
+ "pymolfile/molfile/",
+ "pymolfile/molfile/vmd_molfile_plugins/include",
+ "pymolfile/molfile/vmd_molfile_plugins/molfile_plugins/src",
+ "pymolfile/molfile/lib",
+ ],
define_macros = largefile_macros
),
],