diff --git a/pymolfile/molfile/1 b/pymolfile/molfile/1
new file mode 100644
index 0000000000000000000000000000000000000000..a20e02af96712d71037c23c3101e1f830c376acc
--- /dev/null
+++ b/pymolfile/molfile/1
@@ -0,0 +1,174 @@
+import numpy
+import ctypes
+import _libpymolfile
+
+class molatom_t(ctypes.Structure):
+ _fields_ = [
+ ('name', ctypes.c_char * 16),
+ ('type', ctypes.c_char * 16),
+ ('resname', ctypes.c_char * 8),
+ ('resid', ctypes.c_uint8),
+ ('segid', ctypes.c_char * 8),
+ ('chain', ctypes.c_char * 2),
+ ('altloc', ctypes.c_char * 2),
+ ('insertion', ctypes.c_char *2),
+ ('occupancy', ctypes.c_float),
+ ('bfactor', ctypes.c_float),
+ ('mass', ctypes.c_float),
+ ('charge', ctypes.c_float),
+ ('radius', ctypes.c_float),
+ ('atomicnumber', ctypes.c_uint8),
+ ('ctnumber', ctypes.c_uint8),
+ ]
+
+class molplugin_t(ctypes.Structure):
+ _fields_ = [
+ ('abiversion', ctypes.c_uint8),
+ ('type', ctypes.c_char_p),
+ ('name', ctypes.c_char_p),
+ ('prettyname', ctypes.c_char_p),
+ ('author', ctypes.c_char_p),
+ ('majorv', ctypes.c_uint8),
+ ('minorv', ctypes.c_uint8),
+ ('is_reentrant', ctypes.c_uint8),
+ ('filename_extension', ctypes.c_char_p),
+ ('open_file_read', ctypes.CFUNCTYPE(ctypes.c_char_p,
+ ctypes.c_char_p, ctypes.POINTER(ctypes.c_uint8))),
+ ('read_structure', ctypes.CFUNCTYPE(ctypes.c_void_p,
+ ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(molatom_t))),
+ ('read_bonds', ctypes.CFUNCTYPE(ctypes.c_void_p,
+ ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
+ ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
+ ctypes.c_char_p)),
+ ('read_next_timestep', ctypes.c_int8),
+ ('close_file_read', ctypes.c_void_p),
+ ('open_file_write', ctypes.c_void_p),
+ ('write_structure', ctypes.c_int8),
+ ('write_timestep', ctypes.c_int8),
+ ('close_file_write', ctypes.c_void_p),
+ ('read_volumetric_metadata', ctypes.c_int8),
+ ('read_volumetric_data', ctypes.c_int8),
+ ('read_volumetric_data_ex', ctypes.c_int8),
+ ('read_rawgraphics', ctypes.c_int8),
+ ('read_molecule_metadata', ctypes.c_int8),
+ ('write_bonds', ctypes.c_int8),
+ ('write_volumetric_data', ctypes.c_int8),
+ ('write_volumetric_data_ex', ctypes.c_int8),
+ ('read_angles', ctypes.c_int8),
+ ('write_angles', ctypes.c_int8),
+ ('read_qm_metadata', ctypes.c_int8),
+ ('read_qm_rundata', ctypes.c_int8),
+ ('read_timestep', ctypes.c_int8),
+ ('read_timestep_metadata', ctypes.c_int8),
+ ('read_qm_timestep_metadata', ctypes.c_int8),
+ ('read_timestep2', ctypes.c_int8),
+ ('read_times', ctypes.c_ssize_t),
+ ('cons_fputs', ctypes.c_uint8)
+ ]
+
+class moltimestep_t(ctypes.Structure):
+ _fields_ = [
+ ('coords', ctypes.POINTER(ctypes.c_float)),
+ ('velocities', ctypes.POINTER(ctypes.c_float)),
+ ('A', ctypes.c_float),
+ ('B', ctypes.c_float),
+ ('C', ctypes.c_float),
+ ('alpha', ctypes.c_float),
+ ('beta', ctypes.c_float),
+ ('gamma', ctypes.c_float),
+ ('physical_time', ctypes.c_double),
+ ('total_energy', ctypes.c_double),
+ ('potential_energy', ctypes.c_double),
+ ('kinetic_energy', ctypes.c_double),
+ ('extended_energy', ctypes.c_double),
+ ('force_energy', ctypes.c_double),
+ ('total_pressure', ctypes.c_double)
+ ]
+
+class molhandle_t(ctypes.Structure):
+ _fields_ = [
+ ('plugin', ctypes.POINTER(molplugin_t)),
+ ('file_handle', ctypes.c_void_p),
+ ('natoms', ctypes.c_int)
+ ]
+
+class molnatoms(ctypes.Structure):
+ _fields_ = [
+ ('natoms', ctypes.c_int)
+ ]
+
+#callback_t = ctypes.CFUNCTYPE(None, ctypes.POINTER(molatom_t))
+
+def get_open_file_read(output):
+ ctypes.open_file_read.restype = ctypes.POINTER(molhandle_t)
+ ctypes.open_file_read.argtypes = [ctypes.POINTER(molplugin_t), ctypes.c_void_p, ctypes.c_uint8]
+ return ctypes.pythonapi.PyCapsule_GetPointer(output, "plugin")
+
+def get_capsule(capsule):
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.c_void_p
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ return ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+
+def get_plugincapsule(capsule):
+ data = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+ return data
+
+def get_plugindata(capsule):
+ data = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+ return data
+
+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)
+
+plugin = mylib.get_plugin(mylist, 81)
+print(plugin)
+natoms=0
+numatoms=molnatoms(natoms)
+fname="../../test/md.gro"
+ftype="gro"
+
+pluginhandle = mylib.open_file_read(plugin, fname, ftype, natoms)
+print("This passed")
+print(pluginhandle)
+print("This passed too")
+print(pluginhandle.natoms)
+print("Here")
+
+x = numpy.array([
+ ('C1','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6),
+ ('C2','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6)
+ ],
+ dtype=[
+ ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
+ ('resid', 'i4'), ('segid', 'S8'), ('chain', 'S2'),
+ ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f8'),
+ ('bfactor', 'f8'), ('mass', 'f8'), ('charge', 'f8'),
+ ('radius', 'f8'), ('atomicnumber', 'i4')
+ ]
+ )
+print(x)
+print(x.__array_interface__)
+print(x.__array_interface__["descr"])
+print(x.__array_struct__)
+#y = mylib.read_fill_structure(pluginhandle, x)
+y = mylib.print_array_struct(x)
+print('Test')
+print(y)
+#outarray = mylib.get_structure(pluginhandle)
+#print(outarray)
+#print(type(outarray))
+#for i in outarray:
+# print(i)
+
+
diff --git a/pymolfile/molfile/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so
index afa3e0a62a50fd7b2efa0c76eae1d2fedf08d253..26d6964a955d12f5da6de48551627239aeb0e3f0 100755
Binary files a/pymolfile/molfile/_libpymolfile.so and b/pymolfile/molfile/_libpymolfile.so differ
diff --git a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so
index d66b822ee7cd1186e842d1ef8fbd9025fe68b6cb..2cf277f2af4c15b5ae011b054defceabfd4abbcc 100644
Binary files a/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so and b/pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Resources/DWARF/_libpymolfile.so differ
diff --git a/pymolfile/molfile/_numpy_swig.so b/pymolfile/molfile/_numpy_swig.so
new file mode 100755
index 0000000000000000000000000000000000000000..e5907947a6fe702d7cf89b0bce5fbfeaa9ae1da5
Binary files /dev/null and b/pymolfile/molfile/_numpy_swig.so differ
diff --git a/pymolfile/molfile/compile-numind.sh b/pymolfile/molfile/compile-numind.sh
new file mode 100644
index 0000000000000000000000000000000000000000..680fa4e374146e23eaab3a4e15e25c120176b42a
--- /dev/null
+++ b/pymolfile/molfile/compile-numind.sh
@@ -0,0 +1,2 @@
+Cython -a numind.pyx --cplus
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ numind.cpp -o numind.so -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/molfile/compile-signedintbuf.sh b/pymolfile/molfile/compile-signedintbuf.sh
new file mode 100644
index 0000000000000000000000000000000000000000..8f50f7763eddada6c420b8db79e195be290d4c4c
--- /dev/null
+++ b/pymolfile/molfile/compile-signedintbuf.sh
@@ -0,0 +1,2 @@
+swig -py3 -Wall -c++ -python numpy_swig.i
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ -I. numpy_swig_wrap.cxx -o _numpy_swig.so -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/molfile/compile.sh b/pymolfile/molfile/compile.sh
index f25b34aa0c231d999945e434aee1d9029f22b487..dd69ffe6f6f83e075e01fc39e101ccd2558e9a7d 100644
--- a/pymolfile/molfile/compile.sh
+++ b/pymolfile/molfile/compile.sh
@@ -1,2 +1,2 @@
swig -py3 -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
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -g -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/molfile/libpymolfile-backup2.i b/pymolfile/molfile/libpymolfile-backup2.i
new file mode 100644
index 0000000000000000000000000000000000000000..52b95f6bdf79a1c87b59f123937173415421c80c
--- /dev/null
+++ b/pymolfile/molfile/libpymolfile-backup2.i
@@ -0,0 +1,576 @@
+/* -*- C -*- (not really, but good for syntax highlighting) */
+/* SWIG interface for libpymolfile of VMD molfile_plugins
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under UIUC LICENSE
+
+ swig -c++ -python -outdir . molfile/libpymolfile.i
+*/
+%define DOCSTRING
+"
+:Author: Berk Onat <b.onat@warwick.ac.uk>
+:Year: 2017
+:Licence: UIUC 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
+#define __STDC_FORMAT_MACROS
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <inttypes.h>
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+#include "pymolfile.h"
+%}
+
+%include "numpy.i"
+
+%init %{
+Py_Initialize();
+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 };
+
+
+/* Definition of molfile_atoms_t from molfile_plugin.h */
+%inline %{
+
+/*
+struct MolAtoms {
+ char name[16];
+ char type[16];
+ char resname[8];
+ int resid;
+ char segid[8];
+ char chain[2];
+ char altloc[2];
+ char insertion[2];
+ float occupancy;
+ float bfactor;
+ float mass;
+ float charge;
+ float radius;
+ float atomicnumber;
+ float ctnumber;
+};
+
+void del_plugin_structure(PyObject* pymolfile_atoms){
+ delete (MolAtoms*)PyCapsule_GetPointer(pymolfile_atoms, "plugin_structure");
+}
+
+static PyObject* alloc_plugin_structure(PyObject *self, PyObject *args) {
+ return PyCapsule_New((void*)new MolAtoms(), "plugin_structure", del_plugin_structure);
+}
+*/
+void del_plugin(PyObject* pymolfile_plugin){
+ delete (MolObject*)PyCapsule_GetPointer(pymolfile_plugin, "plugin");
+}
+
+void del_atoms(PyObject* pymolfile_atoms){
+ delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atoms");
+}
+
+void del_atomname(PyObject* pymolfile_atoms){
+ delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atomname");
+}
+
+
+static PyObject* alloc_plugin(PyObject *self, PyObject *args) {
+ return PyCapsule_New((void*)new MolObject(), "plugin_handle", del_plugin);
+}
+
+%}
+
+
+/* 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") my_open_file_read;
+%rename (open_file_read) my_open_file_read;
+%exception my_open_file_read {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
+ if (PyType_Ready(&MolObjectType) < 0)
+ return NULL;
+ PyTypeObject *type = &MolObjectType;
+ /*plugin_handle = PyCapsule_New((void*)new MolObject(), "plugin", del_plugin); */
+ /*MolObject* plugin_c = new MolObject;*/
+ MolObject *plugin_c;
+ plugin_c = (MolObject *)type->tp_alloc(type, 0);
+ /*PyObject * plugin_c = MolObject_new(&MolObjectType, args, kwds);*/
+ plugin_c->plugin = plugin;
+ plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
+ plugin_c->natoms = natoms;
+ /* PyCapsule_SetPointer(plugin_handle, &plugin_c); */
+ /* PyObject* plugin_handle = PyCapsule_New((void*)plugin_c, "plugin", del_plugin); */
+ PyObject* plugin_handle = (PyObject *)plugin_c;
+ /*if(!plugin_handle) printf("Not assigned\n");*/
+ /*PyObject *tuple = PyTuple_New(2);
+ PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
+ PyTuple_SET_ITEM(tuple, 1, plugin_handle);*/
+ return plugin_handle;
+ }
+%}
+
+/*
+%typemap( argout ) ( char **MolfileAtomT_CharArray )
+{
+ // The result variable is the return value from
+ // c_ephcom_read_constants, the number of actual values that are
+ // defined for cnames/values.
+ npy_intp dims[] = { result };
+ PyArray_Dims newshape_location;
+ PyArray_Dims * newshape = &newshape_location;
+ PyObject * status_check;
+ newshape->len = 1;
+ newshape->ptr = dims;
+
+ // resize array$argnum to actual size needed.
+ // Follow directions at http://www.mail-archive.com/numpy-discussion@scipy.org/msg13013.html
+ status_check = PyArray_Resize( (PyArrayObject *) array$argnum, newshape, 0, NPY_CORDER );
+ if ( !status_check )
+ SWIG_fail;
+ Py_DECREF( status_check );
+ $result = SWIG_Python_AppendOutput( $result, array$argnum );
+}
+%typemap( freearg ) ( char **MolfileAtomT_CharArray )
+{
+ free( $1 );
+}
+*/
+
+/*
+#define DIM 3
+typedef int imatrix[DIM][DIM];
+typedef int ivec[DIM];
+typedef float fmatrix[DIM][DIM];
+typedef float fvec[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)}
+*/
+/*
+%apply (int INPLACE_IARRAY2[ANY][ANY]) {(imatrix intdata)}
+%apply (float INPLACE_FARRAY2[ANY][ANY]) {(fmatrix floatdata)}
+%apply (int DIM1, int* INPLACE_IARRAY2) {(int rnatoms, int* MolAtom_resid)}
+%apply (int DIM1, float* INPLACE_FARRAY2) {(int mnatoms, float* MolAtom_mass),
+ (int anatoms, float* MolAtom_atomicnumber)}
+*/
+/*
+%inline %{
+int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
+ int* natoms, char** MolAtom_name,
+ int* natoms, char** MolAtom_type,
+ int* natoms, char** MolAtom_resname,
+ int* natoms, int** MolAtom_resid,
+ int* natoms, char** MolAtom_segid,
+ int* natoms, char** MolAtom_chain,
+ int* natoms, char** MolAtom_altloc,
+ int* natoms, char** MolAtom_insertion,
+ int* natoms, float** MolAtom_occupancy,
+ int* natoms, float** MolAtom_bfactor,
+ int* natoms, float** MolAtom_mass,
+ int* natoms, float** MolAtom_charge,
+ int* natoms, float** MolAtom_radius,
+ int* natoms, float** MolAtom_atomicnumber,
+ int* natoms, float** MolAtom_ctnumber) {
+ molfile_atom_t* atoms;
+ atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
+ plugin->read_structure(fhandle, options, atoms);
+ MolAtom_name = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_type = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resname = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resid = (int **)malloc(natoms,sizeof(int*));
+%}
+*/
+/*
+%inline %{
+int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
+ int natoms, char** MolAtom_name,
+ int tnatoms, char** MolAtom_type,
+ int rnatoms, int* MolAtom_resid,
+ int mnatoms, float* MolAtom_mass,
+ int anatoms, float* MolAtom_atomicnumber) {
+ int i;
+ molfile_atom_t* atoms;
+ molfile_atom_t atm;
+ atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
+ plugin->read_structure(fhandle, options, atoms);
+ if(atoms == NULL) { free(atoms); return 1; }
+ if(atoms->type == NULL || atoms->name == NULL){ free(atoms); return 1; }
+ MolAtom_name = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_type = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resid = (int *)malloc(natoms,sizeof(int));
+ MolAtom_mass = (float *)malloc(natoms,sizeof(float));
+ MolAtom_atomicnumber = (float *)malloc(natoms,sizeof(float));
+ for (i=0;i<natoms;i++){
+ atm = atoms[i];
+ MolAtom_name[i] = atm.name;
+ MolAtom_type[i] = atm.type;
+ MolAtom_resid[i] = atm.resid;
+ MolAtom_mass[i] = atm.mass;
+ MolAtom_atomicnumber[i] = atm.atomicnumber;
+ }
+ return 0;
+ }
+%}
+*/
+
+%feature("autodoc", "0") my_read_structure;
+%rename (read_structure) my_read_structure;
+extern PyObject * my_read_structure(PyObject* molpack);
+
+%feature("autodoc", "0") get_structure;
+extern PyObject * get_structure(PyObject* molpack);
+
+/*
+%feature("autodoc", "0") my_read_structure;
+%rename (read_structure) my_read_structure;
+%exception my_read_structure {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * my_read_structure(PyObject* molpack) {
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* atoms;
+ int numatoms, status;
+ char** atom_names;
+ char** atom_types;
+ PyObject *npatoms = NULL; */
+ /*MolObject* plugin_handle = (MolObject*)PyCapsule_GetPointer(molpack, "plugin");*/
+/* MolObject* plugin_handle = (MolObject*)molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ printf("Test1\n");
+ status = plugin->read_structure(file_handle, &options, atoms);
+ printf("Test2 %d\n",status);
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
+ return NULL;
+ }
+ printf("Test3\n");
+ npy_intp natoms[1] = { numatoms };
+
+ PyArrayObject* oresid;
+ int64_t* cresid;
+
+ int typenum;
+ int nd = 1;
+ npy_intp dims[1] = { numatoms }; */
+ /*dims[0] = numatoms;*/
+/* oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
+ npy_intp* n = PyArray_DIMS(oresid);
+ printf("dimensions %ld\n", n[0]);
+ cresid = (int64_t*) PyArray_DATA(oresid);
+
+ PyObject* npatomresid = NULL;
+ char** MolAtom_name = (char **)malloc(numatoms*sizeof(char*));
+ char** MolAtom_type = (char **)malloc(numatoms*sizeof(char*));
+ int64_t* MolAtom_resid = NULL; */
+ /*int64_t* MolAtom_resid = (int64_t *)malloc(numatoms*sizeof(int64_t));*/
+/* float* MolAtom_mass = (float *)malloc(numatoms*sizeof(float));
+ float* MolAtom_atomicnumber = (float *)malloc(numatoms*sizeof(float));
+ for (i=0;i<numatoms;i++){
+ MolAtom_name[i] = atoms[i].name;
+ MolAtom_type[i] = atoms[i].type;
+ cresid[i] = (int64_t) atoms[i].resid;
+ MolAtom_mass[i] = atoms[i].mass;
+ MolAtom_atomicnumber[i] = atoms[i].atomicnumber;
+ } */
+ /*Py_DECREF( obj );*/
+ /*npy_intp dims[3];*/ /* PyArray_AsCArray is for ndim <= 3 */
+/* PyArray_Descr *descr;
+ npatoms = PyArray_SimpleNewFromData(1, natoms, NPY_USERDEF, atoms);
+ printf("Test4 numatoms=%d\n", numatoms);
+ PyObject* npatomname = NULL;
+ npatomname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_name[0]);
+ PyObject* npatomtype = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_type); */
+ /*PyObject* npatomresname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->resname);*/
+ /*PyObject* npatomsegid = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->segid);*/
+ /*PyObject* npatomchain = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->chain);*/
+ /*PyObject* npatomaltloc = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->altloc);*/
+ /*PyObject* npatominsert = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->insertion);*/
+ /*PyObject* npatomoccup = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->occupancy);*/
+ /*PyObject* npatombfact = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->bfactor);*/
+/* PyObject* npatommass = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, MolAtom_mass); */
+ /*PyObject* npatomcharge = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->charge);*/
+ /*PyObject* npatomradius = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->radius);*/
+/* PyObject* npatomicnumber = PyArray_SimpleNewFromData(1, natoms, NPY_INT64, MolAtom_atomicnumber); */
+ /*if (npatomname==NULL || npatomtype==NULL || npatomresname==NULL ||
+ npatomresid==NULL || npatomsegid==NULL || npatomchain==NULL )
+ {
+ free(atoms);
+ Py_XDECREF(npatomname); Py_XDECREF(npatomtype);
+ Py_XDECREF(npatomresname); Py_XDECREF(npatomresid); Py_XDECREF(npatomsegid);
+ Py_XDECREF(npatomchain); Py_XDECREF(npatomaltloc); Py_XDECREF(npatominsert);
+ Py_XDECREF(npatomoccup); Py_XDECREF(npatombfact); Py_XDECREF(npatommass);
+ Py_XDECREF(npatomcharge); Py_XDECREF(npatomradius); Py_XDECREF(npatomicnumber);
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
+ return 0;
+ }
+ PyArray_BASE(npatomname) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomtype) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomresname) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomresid) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomsegid) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomchain) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomaltloc) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatominsert) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomoccup) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatombfact) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatommass) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomcharge) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomradius) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomicnumber) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatoms) = PyCObject_FromVoidPtr(atoms, free);
+ PyArray_BASE((PyArrayObject *)npatoms) = PyCapsule_New(atoms, "atoms", del_atoms);*/
+ /*PyArray_BASE((PyArrayObject *)npatoms); */
+/* printf("Test4-2\n"); */
+ /*PyObject* Py_MolAtom_name = PyCapsule_New((void*)MolAtom_name, "atomname", del_atomname);*/
+ /*PyObject* Py_MolAtom_name;
+ Py_INCREF(Py_MolAtom_name);*/
+/* printf("Test4-3\n"); */
+ /*PyArray_SetBaseObject((PyArrayObject *)npatomname, Py_MolAtom_name);*/
+ /*PyArray_SetBaseObject((PyArrayObject *)npatomtype, MolAtom_type);
+ PyArray_SetBaseObject((PyArrayObject *)npatomresid, MolAtom_resid);
+ PyArray_SetBaseObject((PyArrayObject *)npatommass, MolAtom_mass);
+ PyArray_SetBaseObject((PyArrayObject *)npatomicnumber, MolAtom_atomicnumber); */
+/* printf("Test5\n");
+ PyObject *tuple = PyTuple_New(2);
+ PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
+ printf("Test6\n");
+ PyTuple_SET_ITEM(tuple, 1, npatomname); */
+ /*PyTuple_SET_ITEM(tuple, 2, npatomtype);
+ PyTuple_SET_ITEM(tuple, 3, npatomresid);
+ PyTuple_SET_ITEM(tuple, 4, npatommass);
+ PyTuple_SET_ITEM(tuple, 5, npatomicnumber);
+ PyObject* vars = PyDict_New();
+ printf("Test7\n");
+ PyDict_SetItemString( vars, "name", npatomname ); */
+/* printf("Test8\n"); */
+ /*PyDict_SetItemString( vars, "resid", npatomresid ); */
+ /*return Py_BuildValue("O", oresid); */
+ /*return PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);*/
+/* return 0;
+ }
+%}
+*/
+
+
+/*
+ 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 */
+
+/*
+%feature("autodoc", "0") molfile_open_file_read;
+%rename (open_file_read) molfile_open_file_read;
+%exception molfile_open_file_read {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * molfile_open_file_read(molfile_plugin_t* plugin, char *fname, int natoms) {
+ int *plugno = &plugin_no;
+ return plugin;
+ }
+%}
+*/
+/*
+ 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-new.i b/pymolfile/molfile/libpymolfile-new.i
new file mode 100644
index 0000000000000000000000000000000000000000..65670f340a9e40ea61838eea0bb61888aac567bf
--- /dev/null
+++ b/pymolfile/molfile/libpymolfile-new.i
@@ -0,0 +1,578 @@
+/* -*- C -*- (not really, but good for syntax highlighting) */
+/* SWIG interface for libpymolfile of VMD molfile_plugins
+ Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
+ Published under UIUC LICENSE
+
+ swig -c++ -python -outdir . molfile/libpymolfile.i
+*/
+%define DOCSTRING
+"
+:Author: Berk Onat <b.onat@warwick.ac.uk>
+:Year: 2017
+:Licence: UIUC 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
+#define __STDC_FORMAT_MACROS
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <inttypes.h>
+#include "molfile_plugin.h"
+#include "libmolfile_plugin.h"
+#include "vmdplugin.h"
+#include "pymolfile.h"
+%}
+
+%include "numpy.i"
+
+%init %{
+Py_Initialize();
+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 };
+
+
+/* Definition of molfile_atoms_t from molfile_plugin.h */
+%inline %{
+
+/*
+struct MolAtoms {
+ char name[16];
+ char type[16];
+ char resname[8];
+ int resid;
+ char segid[8];
+ char chain[2];
+ char altloc[2];
+ char insertion[2];
+ float occupancy;
+ float bfactor;
+ float mass;
+ float charge;
+ float radius;
+ float atomicnumber;
+ float ctnumber;
+};
+
+void del_plugin_structure(PyObject* pymolfile_atoms){
+ delete (MolAtoms*)PyCapsule_GetPointer(pymolfile_atoms, "plugin_structure");
+}
+
+static PyObject* alloc_plugin_structure(PyObject *self, PyObject *args) {
+ return PyCapsule_New((void*)new MolAtoms(), "plugin_structure", del_plugin_structure);
+}
+*/
+void del_plugin(PyObject* pymolfile_plugin){
+ delete (MolObject*)PyCapsule_GetPointer(pymolfile_plugin, "plugin");
+}
+
+void del_atoms(PyObject* pymolfile_atoms){
+ delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atoms");
+}
+
+void del_atomname(PyObject* pymolfile_atoms){
+ delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atomname");
+}
+
+
+static PyObject* alloc_plugin(PyObject *self, PyObject *args) {
+ return PyCapsule_New((void*)new MolObject(), "plugin_handle", del_plugin);
+}
+
+%}
+
+
+/* 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") my_open_file_read;
+%rename (open_file_read) my_open_file_read;
+%exception my_open_file_read {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
+ if (PyType_Ready(&MolObjectType) < 0)
+ return NULL;
+ PyTypeObject *type = &MolObjectType;
+ /*plugin_handle = PyCapsule_New((void*)new MolObject(), "plugin", del_plugin); */
+ /*MolObject* plugin_c = new MolObject;*/
+ MolObject *plugin_c;
+ plugin_c = (MolObject *)type->tp_alloc(type, 0);
+ /*PyObject * plugin_c = MolObject_new(&MolObjectType, args, kwds);*/
+ plugin_c->plugin = plugin;
+ plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
+ plugin_c->natoms = natoms;
+ /* PyCapsule_SetPointer(plugin_handle, &plugin_c); */
+ /* PyObject* plugin_handle = PyCapsule_New((void*)plugin_c, "plugin", del_plugin); */
+ PyObject* plugin_handle = (PyObject *)plugin_c;
+ /*if(!plugin_handle) printf("Not assigned\n");*/
+ /*PyObject *tuple = PyTuple_New(2);
+ PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
+ PyTuple_SET_ITEM(tuple, 1, plugin_handle);*/
+ return plugin_handle;
+ }
+%}
+
+/*
+%typemap( argout ) ( char **MolfileAtomT_CharArray )
+{
+ // The result variable is the return value from
+ // c_ephcom_read_constants, the number of actual values that are
+ // defined for cnames/values.
+ npy_intp dims[] = { result };
+ PyArray_Dims newshape_location;
+ PyArray_Dims * newshape = &newshape_location;
+ PyObject * status_check;
+ newshape->len = 1;
+ newshape->ptr = dims;
+
+ // resize array$argnum to actual size needed.
+ // Follow directions at http://www.mail-archive.com/numpy-discussion@scipy.org/msg13013.html
+ status_check = PyArray_Resize( (PyArrayObject *) array$argnum, newshape, 0, NPY_CORDER );
+ if ( !status_check )
+ SWIG_fail;
+ Py_DECREF( status_check );
+ $result = SWIG_Python_AppendOutput( $result, array$argnum );
+}
+%typemap( freearg ) ( char **MolfileAtomT_CharArray )
+{
+ free( $1 );
+}
+*/
+
+/*
+#define DIM 3
+typedef int imatrix[DIM][DIM];
+typedef int ivec[DIM];
+typedef float fmatrix[DIM][DIM];
+typedef float fvec[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)}
+*/
+/*
+%apply (int INPLACE_IARRAY2[ANY][ANY]) {(imatrix intdata)}
+%apply (float INPLACE_FARRAY2[ANY][ANY]) {(fmatrix floatdata)}
+%apply (int DIM1, int* INPLACE_IARRAY2) {(int rnatoms, int* MolAtom_resid)}
+%apply (int DIM1, float* INPLACE_FARRAY2) {(int mnatoms, float* MolAtom_mass),
+ (int anatoms, float* MolAtom_atomicnumber)}
+*/
+/*
+%inline %{
+int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
+ int* natoms, char** MolAtom_name,
+ int* natoms, char** MolAtom_type,
+ int* natoms, char** MolAtom_resname,
+ int* natoms, int** MolAtom_resid,
+ int* natoms, char** MolAtom_segid,
+ int* natoms, char** MolAtom_chain,
+ int* natoms, char** MolAtom_altloc,
+ int* natoms, char** MolAtom_insertion,
+ int* natoms, float** MolAtom_occupancy,
+ int* natoms, float** MolAtom_bfactor,
+ int* natoms, float** MolAtom_mass,
+ int* natoms, float** MolAtom_charge,
+ int* natoms, float** MolAtom_radius,
+ int* natoms, float** MolAtom_atomicnumber,
+ int* natoms, float** MolAtom_ctnumber) {
+ molfile_atom_t* atoms;
+ atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
+ plugin->read_structure(fhandle, options, atoms);
+ MolAtom_name = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_type = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resname = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resid = (int **)malloc(natoms,sizeof(int*));
+%}
+*/
+/*
+%inline %{
+int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
+ int natoms, char** MolAtom_name,
+ int tnatoms, char** MolAtom_type,
+ int rnatoms, int* MolAtom_resid,
+ int mnatoms, float* MolAtom_mass,
+ int anatoms, float* MolAtom_atomicnumber) {
+ int i;
+ molfile_atom_t* atoms;
+ molfile_atom_t atm;
+ atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
+ plugin->read_structure(fhandle, options, atoms);
+ if(atoms == NULL) { free(atoms); return 1; }
+ if(atoms->type == NULL || atoms->name == NULL){ free(atoms); return 1; }
+ MolAtom_name = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_type = (char **)malloc(natoms,sizeof(char*));
+ MolAtom_resid = (int *)malloc(natoms,sizeof(int));
+ MolAtom_mass = (float *)malloc(natoms,sizeof(float));
+ MolAtom_atomicnumber = (float *)malloc(natoms,sizeof(float));
+ for (i=0;i<natoms;i++){
+ atm = atoms[i];
+ MolAtom_name[i] = atm.name;
+ MolAtom_type[i] = atm.type;
+ MolAtom_resid[i] = atm.resid;
+ MolAtom_mass[i] = atm.mass;
+ MolAtom_atomicnumber[i] = atm.atomicnumber;
+ }
+ return 0;
+ }
+%}
+*/
+
+%feature("autodoc", "0") my_read_structure;
+%rename (read_structure) my_read_structure;
+extern PyObject * my_read_structure(PyObject* molpack);
+
+%feature("autodoc", "0") get_structure;
+extern PyObject * get_structure(PyObject* molpack);
+
+%feature("autodoc", "0") read_fill_structure;
+extern PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
+/*
+%feature("autodoc", "0") my_read_structure;
+%rename (read_structure) my_read_structure;
+%exception my_read_structure {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * my_read_structure(PyObject* molpack) {
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* atoms;
+ int numatoms, status;
+ char** atom_names;
+ char** atom_types;
+ PyObject *npatoms = NULL; */
+ /*MolObject* plugin_handle = (MolObject*)PyCapsule_GetPointer(molpack, "plugin");*/
+/* MolObject* plugin_handle = (MolObject*)molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ printf("Test1\n");
+ status = plugin->read_structure(file_handle, &options, atoms);
+ printf("Test2 %d\n",status);
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
+ return NULL;
+ }
+ printf("Test3\n");
+ npy_intp natoms[1] = { numatoms };
+
+ PyArrayObject* oresid;
+ int64_t* cresid;
+
+ int typenum;
+ int nd = 1;
+ npy_intp dims[1] = { numatoms }; */
+ /*dims[0] = numatoms;*/
+/* oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
+ npy_intp* n = PyArray_DIMS(oresid);
+ printf("dimensions %ld\n", n[0]);
+ cresid = (int64_t*) PyArray_DATA(oresid);
+
+ PyObject* npatomresid = NULL;
+ char** MolAtom_name = (char **)malloc(numatoms*sizeof(char*));
+ char** MolAtom_type = (char **)malloc(numatoms*sizeof(char*));
+ int64_t* MolAtom_resid = NULL; */
+ /*int64_t* MolAtom_resid = (int64_t *)malloc(numatoms*sizeof(int64_t));*/
+/* float* MolAtom_mass = (float *)malloc(numatoms*sizeof(float));
+ float* MolAtom_atomicnumber = (float *)malloc(numatoms*sizeof(float));
+ for (i=0;i<numatoms;i++){
+ MolAtom_name[i] = atoms[i].name;
+ MolAtom_type[i] = atoms[i].type;
+ cresid[i] = (int64_t) atoms[i].resid;
+ MolAtom_mass[i] = atoms[i].mass;
+ MolAtom_atomicnumber[i] = atoms[i].atomicnumber;
+ } */
+ /*Py_DECREF( obj );*/
+ /*npy_intp dims[3];*/ /* PyArray_AsCArray is for ndim <= 3 */
+/* PyArray_Descr *descr;
+ npatoms = PyArray_SimpleNewFromData(1, natoms, NPY_USERDEF, atoms);
+ printf("Test4 numatoms=%d\n", numatoms);
+ PyObject* npatomname = NULL;
+ npatomname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_name[0]);
+ PyObject* npatomtype = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_type); */
+ /*PyObject* npatomresname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->resname);*/
+ /*PyObject* npatomsegid = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->segid);*/
+ /*PyObject* npatomchain = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->chain);*/
+ /*PyObject* npatomaltloc = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->altloc);*/
+ /*PyObject* npatominsert = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->insertion);*/
+ /*PyObject* npatomoccup = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->occupancy);*/
+ /*PyObject* npatombfact = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->bfactor);*/
+/* PyObject* npatommass = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, MolAtom_mass); */
+ /*PyObject* npatomcharge = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->charge);*/
+ /*PyObject* npatomradius = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->radius);*/
+/* PyObject* npatomicnumber = PyArray_SimpleNewFromData(1, natoms, NPY_INT64, MolAtom_atomicnumber); */
+ /*if (npatomname==NULL || npatomtype==NULL || npatomresname==NULL ||
+ npatomresid==NULL || npatomsegid==NULL || npatomchain==NULL )
+ {
+ free(atoms);
+ Py_XDECREF(npatomname); Py_XDECREF(npatomtype);
+ Py_XDECREF(npatomresname); Py_XDECREF(npatomresid); Py_XDECREF(npatomsegid);
+ Py_XDECREF(npatomchain); Py_XDECREF(npatomaltloc); Py_XDECREF(npatominsert);
+ Py_XDECREF(npatomoccup); Py_XDECREF(npatombfact); Py_XDECREF(npatommass);
+ Py_XDECREF(npatomcharge); Py_XDECREF(npatomradius); Py_XDECREF(npatomicnumber);
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
+ return 0;
+ }
+ PyArray_BASE(npatomname) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomtype) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomresname) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomresid) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomsegid) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomchain) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomaltloc) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatominsert) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomoccup) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatombfact) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatommass) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomcharge) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomradius) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatomicnumber) = PyCObject_FromVoidPtr(*atoms, free);
+ PyArray_BASE(npatoms) = PyCObject_FromVoidPtr(atoms, free);
+ PyArray_BASE((PyArrayObject *)npatoms) = PyCapsule_New(atoms, "atoms", del_atoms);*/
+ /*PyArray_BASE((PyArrayObject *)npatoms); */
+/* printf("Test4-2\n"); */
+ /*PyObject* Py_MolAtom_name = PyCapsule_New((void*)MolAtom_name, "atomname", del_atomname);*/
+ /*PyObject* Py_MolAtom_name;
+ Py_INCREF(Py_MolAtom_name);*/
+/* printf("Test4-3\n"); */
+ /*PyArray_SetBaseObject((PyArrayObject *)npatomname, Py_MolAtom_name);*/
+ /*PyArray_SetBaseObject((PyArrayObject *)npatomtype, MolAtom_type);
+ PyArray_SetBaseObject((PyArrayObject *)npatomresid, MolAtom_resid);
+ PyArray_SetBaseObject((PyArrayObject *)npatommass, MolAtom_mass);
+ PyArray_SetBaseObject((PyArrayObject *)npatomicnumber, MolAtom_atomicnumber); */
+/* printf("Test5\n");
+ PyObject *tuple = PyTuple_New(2);
+ PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
+ printf("Test6\n");
+ PyTuple_SET_ITEM(tuple, 1, npatomname); */
+ /*PyTuple_SET_ITEM(tuple, 2, npatomtype);
+ PyTuple_SET_ITEM(tuple, 3, npatomresid);
+ PyTuple_SET_ITEM(tuple, 4, npatommass);
+ PyTuple_SET_ITEM(tuple, 5, npatomicnumber);
+ PyObject* vars = PyDict_New();
+ printf("Test7\n");
+ PyDict_SetItemString( vars, "name", npatomname ); */
+/* printf("Test8\n"); */
+ /*PyDict_SetItemString( vars, "resid", npatomresid ); */
+ /*return Py_BuildValue("O", oresid); */
+ /*return PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);*/
+/* return 0;
+ }
+%}
+*/
+
+
+/*
+ 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 */
+
+/*
+%feature("autodoc", "0") molfile_open_file_read;
+%rename (open_file_read) molfile_open_file_read;
+%exception molfile_open_file_read {
+ $action
+ if (PyErr_Occurred()) SWIG_fail;
+}
+%inline %{
+PyObject * molfile_open_file_read(molfile_plugin_t* plugin, char *fname, int natoms) {
+ int *plugno = &plugin_no;
+ return plugin;
+ }
+%}
+*/
+/*
+ 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.i b/pymolfile/molfile/libpymolfile.i
index b5027679e0b522b8f8a74398d4db4172ff9c30da..417756e0adc2b2b743d8f00a9b9253cf4c69ebf8 100644
--- a/pymolfile/molfile/libpymolfile.i
+++ b/pymolfile/molfile/libpymolfile.i
@@ -324,6 +324,15 @@ int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
%rename (read_structure) my_read_structure;
extern PyObject * my_read_structure(PyObject* molpack);
+%feature("autodoc", "0") get_structure;
+extern PyObject * get_structure(PyObject* molpack);
+
+%feature("autodoc", "0") read_fill_structure;
+extern PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
+
+%feature("autodoc", "0") print_array_struct;
+extern PyObject* print_array_struct(PyObject* prototype);
+
/*
%feature("autodoc", "0") my_read_structure;
%rename (read_structure) my_read_structure;
diff --git a/pymolfile/molfile/libpymolfile.py b/pymolfile/molfile/libpymolfile.py
index 504cde21c682b39139f1be654c5966b33f6d28d0..2d4dae89db09e9402dd5f6be677ff2960501bb90 100644
--- a/pymolfile/molfile/libpymolfile.py
+++ b/pymolfile/molfile/libpymolfile.py
@@ -113,92 +113,6 @@ pluginNOMEM = _libpymolfile.pluginNOMEM
pluginENDOFFILE = _libpymolfile.pluginENDOFFILE
pluginFILENOTFOUND = _libpymolfile.pluginFILENOTFOUND
pluginFORMATERROR = _libpymolfile.pluginFORMATERROR
-class MolAtoms(_object):
- __swig_setmethods__ = {}
- __setattr__ = lambda self, name, value: _swig_setattr(self, MolAtoms, name, value)
- __swig_getmethods__ = {}
- __getattr__ = lambda self, name: _swig_getattr(self, MolAtoms, name)
- __repr__ = _swig_repr
- __swig_setmethods__["name"] = _libpymolfile.MolAtoms_name_set
- __swig_getmethods__["name"] = _libpymolfile.MolAtoms_name_get
- if _newclass:
- name = _swig_property(_libpymolfile.MolAtoms_name_get, _libpymolfile.MolAtoms_name_set)
- __swig_setmethods__["type"] = _libpymolfile.MolAtoms_type_set
- __swig_getmethods__["type"] = _libpymolfile.MolAtoms_type_get
- if _newclass:
- type = _swig_property(_libpymolfile.MolAtoms_type_get, _libpymolfile.MolAtoms_type_set)
- __swig_setmethods__["resname"] = _libpymolfile.MolAtoms_resname_set
- __swig_getmethods__["resname"] = _libpymolfile.MolAtoms_resname_get
- if _newclass:
- resname = _swig_property(_libpymolfile.MolAtoms_resname_get, _libpymolfile.MolAtoms_resname_set)
- __swig_setmethods__["resid"] = _libpymolfile.MolAtoms_resid_set
- __swig_getmethods__["resid"] = _libpymolfile.MolAtoms_resid_get
- if _newclass:
- resid = _swig_property(_libpymolfile.MolAtoms_resid_get, _libpymolfile.MolAtoms_resid_set)
- __swig_setmethods__["segid"] = _libpymolfile.MolAtoms_segid_set
- __swig_getmethods__["segid"] = _libpymolfile.MolAtoms_segid_get
- if _newclass:
- segid = _swig_property(_libpymolfile.MolAtoms_segid_get, _libpymolfile.MolAtoms_segid_set)
- __swig_setmethods__["chain"] = _libpymolfile.MolAtoms_chain_set
- __swig_getmethods__["chain"] = _libpymolfile.MolAtoms_chain_get
- if _newclass:
- chain = _swig_property(_libpymolfile.MolAtoms_chain_get, _libpymolfile.MolAtoms_chain_set)
- __swig_setmethods__["altloc"] = _libpymolfile.MolAtoms_altloc_set
- __swig_getmethods__["altloc"] = _libpymolfile.MolAtoms_altloc_get
- if _newclass:
- altloc = _swig_property(_libpymolfile.MolAtoms_altloc_get, _libpymolfile.MolAtoms_altloc_set)
- __swig_setmethods__["insertion"] = _libpymolfile.MolAtoms_insertion_set
- __swig_getmethods__["insertion"] = _libpymolfile.MolAtoms_insertion_get
- if _newclass:
- insertion = _swig_property(_libpymolfile.MolAtoms_insertion_get, _libpymolfile.MolAtoms_insertion_set)
- __swig_setmethods__["occupancy"] = _libpymolfile.MolAtoms_occupancy_set
- __swig_getmethods__["occupancy"] = _libpymolfile.MolAtoms_occupancy_get
- if _newclass:
- occupancy = _swig_property(_libpymolfile.MolAtoms_occupancy_get, _libpymolfile.MolAtoms_occupancy_set)
- __swig_setmethods__["bfactor"] = _libpymolfile.MolAtoms_bfactor_set
- __swig_getmethods__["bfactor"] = _libpymolfile.MolAtoms_bfactor_get
- if _newclass:
- bfactor = _swig_property(_libpymolfile.MolAtoms_bfactor_get, _libpymolfile.MolAtoms_bfactor_set)
- __swig_setmethods__["mass"] = _libpymolfile.MolAtoms_mass_set
- __swig_getmethods__["mass"] = _libpymolfile.MolAtoms_mass_get
- if _newclass:
- mass = _swig_property(_libpymolfile.MolAtoms_mass_get, _libpymolfile.MolAtoms_mass_set)
- __swig_setmethods__["charge"] = _libpymolfile.MolAtoms_charge_set
- __swig_getmethods__["charge"] = _libpymolfile.MolAtoms_charge_get
- if _newclass:
- charge = _swig_property(_libpymolfile.MolAtoms_charge_get, _libpymolfile.MolAtoms_charge_set)
- __swig_setmethods__["radius"] = _libpymolfile.MolAtoms_radius_set
- __swig_getmethods__["radius"] = _libpymolfile.MolAtoms_radius_get
- if _newclass:
- radius = _swig_property(_libpymolfile.MolAtoms_radius_get, _libpymolfile.MolAtoms_radius_set)
- __swig_setmethods__["atomicnumber"] = _libpymolfile.MolAtoms_atomicnumber_set
- __swig_getmethods__["atomicnumber"] = _libpymolfile.MolAtoms_atomicnumber_get
- if _newclass:
- atomicnumber = _swig_property(_libpymolfile.MolAtoms_atomicnumber_get, _libpymolfile.MolAtoms_atomicnumber_set)
- __swig_setmethods__["ctnumber"] = _libpymolfile.MolAtoms_ctnumber_set
- __swig_getmethods__["ctnumber"] = _libpymolfile.MolAtoms_ctnumber_get
- if _newclass:
- ctnumber = _swig_property(_libpymolfile.MolAtoms_ctnumber_get, _libpymolfile.MolAtoms_ctnumber_set)
-
- def __init__(self):
- this = _libpymolfile.new_MolAtoms()
- try:
- self.this.append(this)
- except __builtin__.Exception:
- self.this = this
- __swig_destroy__ = _libpymolfile.delete_MolAtoms
- __del__ = lambda self: None
-MolAtoms_swigregister = _libpymolfile.MolAtoms_swigregister
-MolAtoms_swigregister(MolAtoms)
-
-
-def del_plugin_structure(pymolfile_atoms: 'PyObject *') -> "void":
- return _libpymolfile.del_plugin_structure(pymolfile_atoms)
-del_plugin_structure = _libpymolfile.del_plugin_structure
-
-def alloc_plugin_structure(arg1: 'PyObject *', args: 'PyObject *') -> "PyObject *":
- return _libpymolfile.alloc_plugin_structure(arg1, args)
-alloc_plugin_structure = _libpymolfile.alloc_plugin_structure
def del_plugin(pymolfile_plugin: 'PyObject *') -> "void":
return _libpymolfile.del_plugin(pymolfile_plugin)
@@ -243,6 +157,18 @@ def open_file_read(plugin: 'molfile_plugin_t *', fname: 'char *', ftype: 'char *
def read_structure(molpack: 'PyObject *') -> "PyObject *":
"""read_structure(molpack) -> PyObject *"""
return _libpymolfile.read_structure(molpack)
+
+def get_structure(molpack: 'PyObject *') -> "PyObject *":
+ """get_structure(molpack) -> PyObject *"""
+ return _libpymolfile.get_structure(molpack)
+
+def read_fill_structure(molpack: 'PyObject *', prototype: 'PyObject *') -> "PyObject *":
+ """read_fill_structure(molpack, prototype) -> PyObject *"""
+ return _libpymolfile.read_fill_structure(molpack, prototype)
+
+def print_array_struct(prototype: 'PyObject *') -> "PyObject *":
+ """print_array_struct(prototype) -> PyObject *"""
+ return _libpymolfile.print_array_struct(prototype)
# This file is compatible with both classic and new-style classes.
diff --git a/pymolfile/molfile/libpymolfile_wrap.cxx b/pymolfile/molfile/libpymolfile_wrap.cxx
index 95bdb95e9932318e5292506992be9aab7f63405f..561451bb9d9bcd393089c34e8d421b6cd05f3279 100644
--- a/pymolfile/molfile/libpymolfile_wrap.cxx
+++ b/pymolfile/molfile/libpymolfile_wrap.cxx
@@ -3003,12 +3003,11 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
/* -------- TYPES TABLE (BEGIN) -------- */
-#define SWIGTYPE_p_MolAtoms swig_types[0]
-#define SWIGTYPE_p_char swig_types[1]
-#define SWIGTYPE_p_molfile_plugin_t swig_types[2]
-#define SWIGTYPE_p_p_molfile_plugin_t 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_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)
@@ -3149,7 +3148,7 @@ SWIGINTERNINLINE PyObject*
-
+/*
struct MolAtoms {
char name[16];
char type[16];
@@ -3175,7 +3174,7 @@ void del_plugin_structure(PyObject* pymolfile_atoms){
static PyObject* alloc_plugin_structure(PyObject *self, PyObject *args) {
return PyCapsule_New((void*)new MolAtoms(), "plugin_structure", del_plugin_structure);
}
-
+*/
void del_plugin(PyObject* pymolfile_plugin){
delete (MolObject*)PyCapsule_GetPointer(pymolfile_plugin, "plugin");
}
@@ -3195,196 +3194,6 @@ static PyObject* alloc_plugin(PyObject *self, PyObject *args) {
-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;
- }
- return info;
-}
-
-
-SWIGINTERN int
-SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc)
-{
-#if PY_VERSION_HEX>=0x03000000
-#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
- if (PyBytes_Check(obj))
-#else
- if (PyUnicode_Check(obj))
-#endif
-#else
- if (PyString_Check(obj))
-#endif
- {
- char *cstr; Py_ssize_t len;
-#if PY_VERSION_HEX>=0x03000000
-#if !defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
- 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;
- }
- obj = PyUnicode_AsUTF8String(obj);
- if(alloc) *alloc = SWIG_NEWOBJ;
-#endif
- PyBytes_AsStringAndSize(obj, &cstr, &len);
-#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 = reinterpret_cast< char* >(memcpy(new char[len + 1], cstr, sizeof(char)*(len + 1)));
- *alloc = SWIG_NEWOBJ;
- } else {
- *cptr = cstr;
- *alloc = SWIG_OLDOBJ;
- }
- } else {
-#if PY_VERSION_HEX>=0x03000000
-#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
- *cptr = PyBytes_AsString(obj);
-#else
- assert(0); /* Should never reach here with Unicode strings in Python 3 */
-#endif
-#else
- *cptr = SWIG_Python_str_AsChar(obj);
-#endif
- }
- }
- if (psize) *psize = len + 1;
-#if PY_VERSION_HEX>=0x03000000 && !defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
- Py_XDECREF(obj);
-#endif
- return SWIG_OK;
- } else {
-#if defined(SWIG_PYTHON_2_UNICODE)
-#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
-#error "Cannot use both SWIG_PYTHON_2_UNICODE and SWIG_PYTHON_STRICT_BYTE_CHAR at once"
-#endif
-#if PY_VERSION_HEX<0x03000000
- if (PyUnicode_Check(obj)) {
- char *cstr; Py_ssize_t len;
- if (!alloc && cptr) {
- return SWIG_RuntimeError;
- }
- obj = PyUnicode_AsUTF8String(obj);
- if (PyString_AsStringAndSize(obj, &cstr, &len) != -1) {
- if (cptr) {
- if (alloc) *alloc = SWIG_NEWOBJ;
- *cptr = reinterpret_cast< char* >(memcpy(new char[len + 1], cstr, sizeof(char)*(len + 1)));
- }
- if (psize) *psize = len + 1;
-
- Py_XDECREF(obj);
- return SWIG_OK;
- } else {
- Py_XDECREF(obj);
- }
- }
-#endif
-#endif
-
- 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;
- }
- }
- }
- return SWIG_TypeError;
-}
-
-
-SWIGINTERN int
-SWIG_AsCharArray(PyObject * obj, char *val, size_t size)
-{
- char* cptr = 0; size_t csize = 0; int alloc = SWIG_OLDOBJ;
- int res = SWIG_AsCharPtrAndSize(obj, &cptr, &csize, &alloc);
- if (SWIG_IsOK(res)) {
- /* special case of single char conversion when we don't need space for NUL */
- if (size == 1 && csize == 2 && cptr && !cptr[1]) --csize;
- if (csize <= size) {
- if (val) {
- if (csize) memcpy(val, cptr, csize*sizeof(char));
- if (csize < size) memset(val + csize, 0, (size - csize)*sizeof(char));
- }
- if (alloc == SWIG_NEWOBJ) {
- delete[] cptr;
- res = SWIG_DelNewMask(res);
- }
- return res;
- }
- if (alloc == SWIG_NEWOBJ) delete[] cptr;
- }
- return SWIG_TypeError;
-}
-
-
-SWIGINTERNINLINE PyObject *
-SWIG_FromCharPtrAndSize(const char* carray, size_t size)
-{
- if (carray) {
- if (size > INT_MAX) {
- swig_type_info* pchar_descriptor = SWIG_pchar_descriptor();
- return pchar_descriptor ?
- SWIG_InternalNewPointerObj(const_cast< char * >(carray), pchar_descriptor, 0) : SWIG_Py_Void();
- } else {
-#if PY_VERSION_HEX >= 0x03000000
-#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
- return PyBytes_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
-#else
-#if PY_VERSION_HEX >= 0x03010000
- return PyUnicode_DecodeUTF8(carray, static_cast< Py_ssize_t >(size), "surrogateescape");
-#else
- return PyUnicode_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
-#endif
-#endif
-#else
- return PyString_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
-#endif
- }
- } else {
- return SWIG_Py_Void();
- }
-}
-
-
-SWIGINTERN size_t
-SWIG_strnlen(const char* s, size_t maxlen)
-{
- const char *p;
- for (p = s; maxlen-- && *p; p++)
- ;
- return p - s;
-}
-
-
#include <limits.h>
#if !defined(SWIG_NO_LLONG_MAX)
# if !defined(LLONG_MAX) && defined(__GNUC__) && defined (__LONG_LONG_MAX__)
@@ -3536,70 +3345,6 @@ SWIG_AsVal_int (PyObject * obj, int *val)
}
-/* Getting isfinite working pre C99 across multiple platforms is non-trivial. Users can provide SWIG_isfinite on older platforms. */
-#ifndef SWIG_isfinite
-/* isfinite() is a macro for C99 */
-# if defined(isfinite)
-# define SWIG_isfinite(X) (isfinite(X))
-# elif defined __cplusplus && __cplusplus >= 201103L
-/* Use a template so that this works whether isfinite() is std::isfinite() or
- * in the global namespace. The reality seems to vary between compiler
- * versions.
- *
- * Make sure namespace std exists to avoid compiler warnings.
- *
- * extern "C++" is required as this fragment can end up inside an extern "C" { } block
- */
-namespace std { }
-extern "C++" template<typename T>
-inline int SWIG_isfinite_func(T x) {
- using namespace std;
- return isfinite(x);
-}
-# define SWIG_isfinite(X) (SWIG_isfinite_func(X))
-# elif defined(_MSC_VER)
-# define SWIG_isfinite(X) (_finite(X))
-# elif defined(__sun) && defined(__SVR4)
-# include <ieeefp.h>
-# define SWIG_isfinite(X) (finite(X))
-# endif
-#endif
-
-
-/* Accept infinite as a valid float value unless we are unable to check if a value is finite */
-#ifdef SWIG_isfinite
-# define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX) && SWIG_isfinite(X))
-#else
-# define SWIG_Float_Overflow_Check(X) ((X < -FLT_MAX || X > FLT_MAX))
-#endif
-
-
-SWIGINTERN int
-SWIG_AsVal_float (PyObject * obj, float *val)
-{
- double v;
- int res = SWIG_AsVal_double (obj, &v);
- if (SWIG_IsOK(res)) {
- if (SWIG_Float_Overflow_Check(v)) {
- return SWIG_OverflowError;
- } else {
- if (val) *val = static_cast< float >(v);
- }
- }
- return res;
-}
-
-
- #define SWIG_From_double PyFloat_FromDouble
-
-
-SWIGINTERNINLINE PyObject *
-SWIG_From_float (float value)
-{
- return SWIG_From_double (value);
-}
-
-
PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
molfile_plugin_t *plugin;
int *plugno = &plugin_no;
@@ -3674,915 +3419,137 @@ PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype,
}
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-SWIGINTERN PyObject *_wrap_MolAtoms_name_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[16] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_name_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_name_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 16);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_name_set" "', argument " "2"" of type '" "char [16]""'");
+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;
}
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->name,arg2,16*sizeof(char));
- else memset(arg1->name,0,16*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
+ return info;
}
-SWIGINTERN PyObject *_wrap_MolAtoms_name_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_name_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_name_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->name);
+SWIGINTERN int
+SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc)
+{
+#if PY_VERSION_HEX>=0x03000000
+#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+ if (PyBytes_Check(obj))
+#else
+ if (PyUnicode_Check(obj))
+#endif
+#else
+ if (PyString_Check(obj))
+#endif
{
- size_t size = SWIG_strnlen(result, 16);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_type_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[16] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_type_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_type_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 16);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_type_set" "', argument " "2"" of type '" "char [16]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->type,arg2,16*sizeof(char));
- else memset(arg1->type,0,16*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_type_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_type_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_type_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->type);
- {
- size_t size = SWIG_strnlen(result, 16);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_resname_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[8] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_resname_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_resname_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 8);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_resname_set" "', argument " "2"" of type '" "char [8]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->resname,arg2,8*sizeof(char));
- else memset(arg1->resname,0,8*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_resname_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_resname_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_resname_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->resname);
- {
- size_t size = SWIG_strnlen(result, 8);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_resid_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- int arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- int val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_resid_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_resid_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_int(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_resid_set" "', argument " "2"" of type '" "int""'");
- }
- arg2 = static_cast< int >(val2);
- if (arg1) (arg1)->resid = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_resid_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- int result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_resid_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_resid_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (int) ((arg1)->resid);
- resultobj = SWIG_From_int(static_cast< int >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_segid_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[8] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_segid_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_segid_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 8);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_segid_set" "', argument " "2"" of type '" "char [8]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->segid,arg2,8*sizeof(char));
- else memset(arg1->segid,0,8*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_segid_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_segid_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_segid_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->segid);
- {
- size_t size = SWIG_strnlen(result, 8);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_chain_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[2] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_chain_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_chain_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 2);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_chain_set" "', argument " "2"" of type '" "char [2]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->chain,arg2,2*sizeof(char));
- else memset(arg1->chain,0,2*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_chain_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_chain_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_chain_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->chain);
- {
- size_t size = SWIG_strnlen(result, 2);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_altloc_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[2] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_altloc_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_altloc_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 2);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_altloc_set" "', argument " "2"" of type '" "char [2]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->altloc,arg2,2*sizeof(char));
- else memset(arg1->altloc,0,2*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_altloc_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_altloc_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_altloc_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->altloc);
- {
- size_t size = SWIG_strnlen(result, 2);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_insertion_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- char *arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- char temp2[2] ;
- int res2 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_insertion_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_insertion_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- res2 = SWIG_AsCharArray(obj1, temp2, 2);
- if (!SWIG_IsOK(res2)) {
- SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "MolAtoms_insertion_set" "', argument " "2"" of type '" "char [2]""'");
- }
- arg2 = reinterpret_cast< char * >(temp2);
- if (arg2) memcpy(arg1->insertion,arg2,2*sizeof(char));
- else memset(arg1->insertion,0,2*sizeof(char));
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_insertion_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- char *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_insertion_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_insertion_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (char *)(char *) ((arg1)->insertion);
- {
- size_t size = SWIG_strnlen(result, 2);
-
-
-
- resultobj = SWIG_FromCharPtrAndSize(result, size);
- }
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_occupancy_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_occupancy_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_occupancy_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_occupancy_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->occupancy = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_occupancy_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_occupancy_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_occupancy_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->occupancy);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_bfactor_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_bfactor_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_bfactor_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_bfactor_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->bfactor = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_bfactor_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_bfactor_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_bfactor_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->bfactor);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_mass_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_mass_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_mass_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_mass_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->mass = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_mass_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_mass_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_mass_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->mass);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_charge_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_charge_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_charge_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_charge_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->charge = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_charge_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_charge_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_charge_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->charge);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_radius_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_radius_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_radius_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_radius_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->radius = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_radius_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_radius_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_radius_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->radius);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_atomicnumber_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_atomicnumber_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_atomicnumber_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_atomicnumber_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->atomicnumber = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_atomicnumber_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_atomicnumber_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_atomicnumber_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->atomicnumber);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_ctnumber_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- float arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- float val2 ;
- int ecode2 = 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:MolAtoms_ctnumber_set",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_ctnumber_set" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- ecode2 = SWIG_AsVal_float(obj1, &val2);
- if (!SWIG_IsOK(ecode2)) {
- SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "MolAtoms_ctnumber_set" "', argument " "2"" of type '" "float""'");
- }
- arg2 = static_cast< float >(val2);
- if (arg1) (arg1)->ctnumber = arg2;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *_wrap_MolAtoms_ctnumber_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
- float result;
-
- if (!PyArg_ParseTuple(args,(char *)"O:MolAtoms_ctnumber_get",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "MolAtoms_ctnumber_get" "', argument " "1"" of type '" "MolAtoms *""'");
- }
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- result = (float) ((arg1)->ctnumber);
- resultobj = SWIG_From_float(static_cast< float >(result));
- return resultobj;
-fail:
- return NULL;
-}
-
+ char *cstr; Py_ssize_t len;
+#if PY_VERSION_HEX>=0x03000000
+#if !defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+ 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;
+ }
+ obj = PyUnicode_AsUTF8String(obj);
+ if(alloc) *alloc = SWIG_NEWOBJ;
+#endif
+ PyBytes_AsStringAndSize(obj, &cstr, &len);
+#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.
-SWIGINTERN PyObject *_wrap_new_MolAtoms(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)":new_MolAtoms")) SWIG_fail;
- result = (MolAtoms *)new MolAtoms();
- resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_MolAtoms, SWIG_POINTER_NEW | 0 );
- return resultobj;
-fail:
- return NULL;
-}
+ 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 = reinterpret_cast< char* >(memcpy(new char[len + 1], cstr, sizeof(char)*(len + 1)));
+ *alloc = SWIG_NEWOBJ;
+ } else {
+ *cptr = cstr;
+ *alloc = SWIG_OLDOBJ;
+ }
+ } else {
+#if PY_VERSION_HEX>=0x03000000
+#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+ *cptr = PyBytes_AsString(obj);
+#else
+ assert(0); /* Should never reach here with Unicode strings in Python 3 */
+#endif
+#else
+ *cptr = SWIG_Python_str_AsChar(obj);
+#endif
+ }
+ }
+ if (psize) *psize = len + 1;
+#if PY_VERSION_HEX>=0x03000000 && !defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+ Py_XDECREF(obj);
+#endif
+ return SWIG_OK;
+ } else {
+#if defined(SWIG_PYTHON_2_UNICODE)
+#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+#error "Cannot use both SWIG_PYTHON_2_UNICODE and SWIG_PYTHON_STRICT_BYTE_CHAR at once"
+#endif
+#if PY_VERSION_HEX<0x03000000
+ if (PyUnicode_Check(obj)) {
+ char *cstr; Py_ssize_t len;
+ if (!alloc && cptr) {
+ return SWIG_RuntimeError;
+ }
+ obj = PyUnicode_AsUTF8String(obj);
+ if (PyString_AsStringAndSize(obj, &cstr, &len) != -1) {
+ if (cptr) {
+ if (alloc) *alloc = SWIG_NEWOBJ;
+ *cptr = reinterpret_cast< char* >(memcpy(new char[len + 1], cstr, sizeof(char)*(len + 1)));
+ }
+ if (psize) *psize = len + 1;
+ Py_XDECREF(obj);
+ return SWIG_OK;
+ } else {
+ Py_XDECREF(obj);
+ }
+ }
+#endif
+#endif
-SWIGINTERN PyObject *_wrap_delete_MolAtoms(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- MolAtoms *arg1 = (MolAtoms *) 0 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
- PyObject * obj0 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:delete_MolAtoms",&obj0)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_MolAtoms, SWIG_POINTER_DISOWN | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_MolAtoms" "', argument " "1"" of type '" "MolAtoms *""'");
+ 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;
+ }
+ }
}
- arg1 = reinterpret_cast< MolAtoms * >(argp1);
- delete arg1;
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
-}
-
-
-SWIGINTERN PyObject *MolAtoms_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *obj;
- if (!PyArg_ParseTuple(args,(char *)"O:swigregister", &obj)) return NULL;
- SWIG_TypeNewClientData(SWIGTYPE_p_MolAtoms, SWIG_NewClientData(obj));
- return SWIG_Py_Void();
-}
-
-SWIGINTERN PyObject *_wrap_del_plugin_structure(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- PyObject *arg1 = (PyObject *) 0 ;
- PyObject * obj0 = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"O:del_plugin_structure",&obj0)) SWIG_fail;
- arg1 = obj0;
- del_plugin_structure(arg1);
- resultobj = SWIG_Py_Void();
- return resultobj;
-fail:
- return NULL;
+ return SWIG_TypeError;
}
-SWIGINTERN PyObject *_wrap_alloc_plugin_structure(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
- PyObject *resultobj = 0;
- PyObject *arg1 = (PyObject *) 0 ;
- PyObject *arg2 = (PyObject *) 0 ;
- PyObject * obj0 = 0 ;
- PyObject * obj1 = 0 ;
- PyObject *result = 0 ;
-
- if (!PyArg_ParseTuple(args,(char *)"OO:alloc_plugin_structure",&obj0,&obj1)) SWIG_fail;
- arg1 = obj0;
- arg2 = obj1;
- result = (PyObject *)alloc_plugin_structure(arg1,arg2);
- resultobj = result;
- return resultobj;
-fail:
- return NULL;
-}
+#ifdef __cplusplus
+extern "C" {
+#endif
SWIGINTERN PyObject *_wrap_del_plugin(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
PyObject *arg1 = (PyObject *) 0 ;
@@ -4834,43 +3801,59 @@ fail:
}
+SWIGINTERN PyObject *_wrap_get_structure(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ PyObject *arg1 = (PyObject *) 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:get_structure",&obj0)) SWIG_fail;
+ arg1 = obj0;
+ result = (PyObject *)get_structure(arg1);
+ resultobj = result;
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_read_fill_structure(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ PyObject *arg1 = (PyObject *) 0 ;
+ PyObject *arg2 = (PyObject *) 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:read_fill_structure",&obj0,&obj1)) SWIG_fail;
+ arg1 = obj0;
+ arg2 = obj1;
+ result = (PyObject *)read_fill_structure(arg1,arg2);
+ resultobj = result;
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_print_array_struct(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ PyObject *arg1 = (PyObject *) 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:print_array_struct",&obj0)) SWIG_fail;
+ arg1 = obj0;
+ result = (PyObject *)print_array_struct(arg1);
+ resultobj = result;
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
static PyMethodDef SwigMethods[] = {
{ (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL},
- { (char *)"MolAtoms_name_set", _wrap_MolAtoms_name_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_name_get", _wrap_MolAtoms_name_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_type_set", _wrap_MolAtoms_type_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_type_get", _wrap_MolAtoms_type_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_resname_set", _wrap_MolAtoms_resname_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_resname_get", _wrap_MolAtoms_resname_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_resid_set", _wrap_MolAtoms_resid_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_resid_get", _wrap_MolAtoms_resid_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_segid_set", _wrap_MolAtoms_segid_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_segid_get", _wrap_MolAtoms_segid_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_chain_set", _wrap_MolAtoms_chain_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_chain_get", _wrap_MolAtoms_chain_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_altloc_set", _wrap_MolAtoms_altloc_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_altloc_get", _wrap_MolAtoms_altloc_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_insertion_set", _wrap_MolAtoms_insertion_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_insertion_get", _wrap_MolAtoms_insertion_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_occupancy_set", _wrap_MolAtoms_occupancy_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_occupancy_get", _wrap_MolAtoms_occupancy_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_bfactor_set", _wrap_MolAtoms_bfactor_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_bfactor_get", _wrap_MolAtoms_bfactor_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_mass_set", _wrap_MolAtoms_mass_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_mass_get", _wrap_MolAtoms_mass_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_charge_set", _wrap_MolAtoms_charge_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_charge_get", _wrap_MolAtoms_charge_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_radius_set", _wrap_MolAtoms_radius_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_radius_get", _wrap_MolAtoms_radius_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_atomicnumber_set", _wrap_MolAtoms_atomicnumber_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_atomicnumber_get", _wrap_MolAtoms_atomicnumber_get, METH_VARARGS, NULL},
- { (char *)"MolAtoms_ctnumber_set", _wrap_MolAtoms_ctnumber_set, METH_VARARGS, NULL},
- { (char *)"MolAtoms_ctnumber_get", _wrap_MolAtoms_ctnumber_get, METH_VARARGS, NULL},
- { (char *)"new_MolAtoms", _wrap_new_MolAtoms, METH_VARARGS, NULL},
- { (char *)"delete_MolAtoms", _wrap_delete_MolAtoms, METH_VARARGS, NULL},
- { (char *)"MolAtoms_swigregister", MolAtoms_swigregister, METH_VARARGS, NULL},
- { (char *)"del_plugin_structure", _wrap_del_plugin_structure, METH_VARARGS, NULL},
- { (char *)"alloc_plugin_structure", _wrap_alloc_plugin_structure, METH_VARARGS, NULL},
{ (char *)"del_plugin", _wrap_del_plugin, METH_VARARGS, NULL},
{ (char *)"del_atoms", _wrap_del_atoms, METH_VARARGS, NULL},
{ (char *)"del_atomname", _wrap_del_atomname, METH_VARARGS, NULL},
@@ -4882,31 +3865,30 @@ static PyMethodDef SwigMethods[] = {
{ (char *)"molfile_plugin_info", _wrap_molfile_plugin_info, METH_VARARGS, (char *)"molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"},
{ (char *)"open_file_read", _wrap_open_file_read, METH_VARARGS, (char *)"open_file_read(plugin, fname, ftype, natoms) -> PyObject *"},
{ (char *)"read_structure", _wrap_read_structure, METH_VARARGS, (char *)"read_structure(molpack) -> PyObject *"},
+ { (char *)"get_structure", _wrap_get_structure, METH_VARARGS, (char *)"get_structure(molpack) -> PyObject *"},
+ { (char *)"read_fill_structure", _wrap_read_fill_structure, METH_VARARGS, (char *)"read_fill_structure(molpack, prototype) -> PyObject *"},
+ { (char *)"print_array_struct", _wrap_print_array_struct, METH_VARARGS, (char *)"print_array_struct(prototype) -> PyObject *"},
{ NULL, NULL, 0, NULL }
};
/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
-static swig_type_info _swigt__p_MolAtoms = {"_p_MolAtoms", "MolAtoms *", 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_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_MolAtoms,
&_swigt__p_char,
&_swigt__p_molfile_plugin_t,
&_swigt__p_p_molfile_plugin_t,
};
-static swig_cast_info _swigc__p_MolAtoms[] = { {&_swigt__p_MolAtoms, 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_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_MolAtoms,
_swigc__p_char,
_swigc__p_molfile_plugin_t,
_swigc__p_p_molfile_plugin_t,
diff --git a/pymolfile/molfile/numind-cython/compile-numind.sh b/pymolfile/molfile/numind-cython/compile-numind.sh
new file mode 100644
index 0000000000000000000000000000000000000000..680fa4e374146e23eaab3a4e15e25c120176b42a
--- /dev/null
+++ b/pymolfile/molfile/numind-cython/compile-numind.sh
@@ -0,0 +1,2 @@
+Cython -a numind.pyx --cplus
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ numind.cpp -o numind.so -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/molfile/numind-cython/numind.cpp b/pymolfile/molfile/numind-cython/numind.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..3313212c090a1abf3bc94bc3ec7a6dca11b62667
--- /dev/null
+++ b/pymolfile/molfile/numind-cython/numind.cpp
@@ -0,0 +1,5454 @@
+/* Generated by Cython 0.26.1 */
+
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+#ifndef Py_PYTHON_H
+ #error Python headers needed to compile C extensions, please install development version of Python.
+#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
+ #error Cython requires Python 2.6+ or Python 3.2+.
+#else
+#define CYTHON_ABI "0_26_1"
+#include <stddef.h>
+#ifndef offsetof
+ #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
+#endif
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+ #ifndef __fastcall
+ #define __fastcall
+ #endif
+#endif
+#ifndef DL_IMPORT
+ #define DL_IMPORT(t) t
+#endif
+#ifndef DL_EXPORT
+ #define DL_EXPORT(t) t
+#endif
+#define __PYX_COMMA ,
+#ifndef HAVE_LONG_LONG
+ #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000)
+ #define HAVE_LONG_LONG
+ #endif
+#endif
+#ifndef PY_LONG_LONG
+ #define PY_LONG_LONG LONG_LONG
+#endif
+#ifndef Py_HUGE_VAL
+ #define Py_HUGE_VAL HUGE_VAL
+#endif
+#ifdef PYPY_VERSION
+ #define CYTHON_COMPILING_IN_PYPY 1
+ #define CYTHON_COMPILING_IN_PYSTON 0
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #undef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 0
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #undef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 1
+ #undef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 0
+ #undef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 0
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+#elif defined(PYSTON_VERSION)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 1
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+#else
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
+ #define CYTHON_COMPILING_IN_CPYTHON 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #if PY_VERSION_HEX < 0x02070000
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #elif !defined(CYTHON_USE_PYTYPE_LOOKUP)
+ #define CYTHON_USE_PYTYPE_LOOKUP 1
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #elif !defined(CYTHON_USE_ASYNC_SLOTS)
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #if PY_VERSION_HEX < 0x02070000
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
+ #define CYTHON_USE_PYLONG_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #if PY_VERSION_HEX < 0x030300F0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #elif !defined(CYTHON_USE_UNICODE_WRITER)
+ #define CYTHON_USE_UNICODE_WRITER 1
+ #endif
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #ifndef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 1
+ #endif
+ #ifndef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 1
+ #endif
+#endif
+#if !defined(CYTHON_FAST_PYCCALL)
+#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
+#endif
+#if CYTHON_USE_PYLONG_INTERNALS
+ #include "longintrepr.h"
+ #undef SHIFT
+ #undef BASE
+ #undef MASK
+#endif
+#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
+ #define Py_OptimizeFlag 0
+#endif
+#define __PYX_BUILD_PY_SSIZE_T "n"
+#define CYTHON_FORMAT_SSIZE_T "z"
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
+ PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyClass_Type
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyType_Type
+#endif
+#ifndef Py_TPFLAGS_CHECKTYPES
+ #define Py_TPFLAGS_CHECKTYPES 0
+#endif
+#ifndef Py_TPFLAGS_HAVE_INDEX
+ #define Py_TPFLAGS_HAVE_INDEX 0
+#endif
+#ifndef Py_TPFLAGS_HAVE_NEWBUFFER
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
+#endif
+#ifndef Py_TPFLAGS_HAVE_FINALIZE
+ #define Py_TPFLAGS_HAVE_FINALIZE 0
+#endif
+#if PY_VERSION_HEX < 0x030700A0 || !defined(METH_FASTCALL)
+ #ifndef METH_FASTCALL
+ #define METH_FASTCALL 0x80
+ #endif
+ typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, Py_ssize_t nargs);
+ typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject **args,
+ Py_ssize_t nargs, PyObject *kwnames);
+#else
+ #define __Pyx_PyCFunctionFast _PyCFunctionFast
+ #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
+#endif
+#if CYTHON_FAST_PYCCALL
+#define __Pyx_PyFastCFunction_Check(func)\
+ ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS)))))
+#else
+#define __Pyx_PyFastCFunction_Check(func) 0
+#endif
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
+ #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
+ #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch)
+ #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define PyUnicode_1BYTE_KIND 1
+ #define PyUnicode_2BYTE_KIND 2
+ #define PyUnicode_4BYTE_KIND 4
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
+ #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
+ #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
+ #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
+#endif
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
+#else
+ #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
+ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
+ #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
+ #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
+ #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
+ #define PyObject_Malloc(s) PyMem_Malloc(s)
+ #define PyObject_Free(p) PyMem_Free(p)
+ #define PyObject_Realloc(p) PyMem_Realloc(p)
+#endif
+#if CYTHON_COMPILING_IN_PYSTON
+ #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
+#else
+ #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
+#endif
+#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
+#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
+#else
+ #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
+#endif
+#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
+ #define PyObject_ASCII(o) PyObject_Repr(o)
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyStringObject PyUnicodeObject
+ #define PyString_Type PyUnicode_Type
+ #define PyString_Check PyUnicode_Check
+ #define PyString_CheckExact PyUnicode_CheckExact
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
+ #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
+#else
+ #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
+ #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
+#endif
+#ifndef PySet_CheckExact
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
+#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+ #define PyNumber_Int PyNumber_Long
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyBoolObject PyLongObject
+#endif
+#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
+ #ifndef PyUnicode_InternFromString
+ #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
+ #endif
+#endif
+#if PY_VERSION_HEX < 0x030200A4
+ typedef long Py_hash_t;
+ #define __Pyx_PyInt_FromHash_t PyInt_FromLong
+ #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+#else
+ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
+ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#else
+ #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
+#endif
+#ifndef __has_attribute
+ #define __has_attribute(x) 0
+#endif
+#ifndef __has_cpp_attribute
+ #define __has_cpp_attribute(x) 0
+#endif
+#if CYTHON_USE_ASYNC_SLOTS
+ #if PY_VERSION_HEX >= 0x030500B1
+ #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
+ #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
+ #else
+ typedef struct {
+ unaryfunc am_await;
+ unaryfunc am_aiter;
+ unaryfunc am_anext;
+ } __Pyx_PyAsyncMethodsStruct;
+ #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
+ #endif
+#else
+ #define __Pyx_PyType_AsAsync(obj) NULL
+#endif
+#ifndef CYTHON_RESTRICT
+ #if defined(__GNUC__)
+ #define CYTHON_RESTRICT __restrict__
+ #elif defined(_MSC_VER) && _MSC_VER >= 1400
+ #define CYTHON_RESTRICT __restrict
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_RESTRICT restrict
+ #else
+ #define CYTHON_RESTRICT
+ #endif
+#endif
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+#ifndef CYTHON_MAYBE_UNUSED_VAR
+# if defined(__cplusplus)
+ template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
+# else
+# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
+# endif
+#endif
+#ifndef CYTHON_NCP_UNUSED
+# if CYTHON_COMPILING_IN_CPYTHON
+# define CYTHON_NCP_UNUSED
+# else
+# define CYTHON_NCP_UNUSED CYTHON_UNUSED
+# endif
+#endif
+#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
+#ifdef _MSC_VER
+ #ifndef _MSC_STDINT_H_
+ #if _MSC_VER < 1300
+ typedef unsigned char uint8_t;
+ typedef unsigned int uint32_t;
+ #else
+ typedef unsigned __int8 uint8_t;
+ typedef unsigned __int32 uint32_t;
+ #endif
+ #endif
+#else
+ #include <stdint.h>
+#endif
+#ifndef CYTHON_FALLTHROUGH
+ #ifdef __cplusplus
+ #if __has_cpp_attribute(fallthrough)
+ #define CYTHON_FALLTHROUGH [[fallthrough]]
+ #elif __has_cpp_attribute(clang::fallthrough)
+ #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
+ #endif
+ #endif
+ #ifndef CYTHON_FALLTHROUGH
+ #if __has_attribute(fallthrough) || (defined(__GNUC__) && defined(__attribute__))
+ #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
+ #else
+ #define CYTHON_FALLTHROUGH
+ #endif
+ #endif
+#endif
+
+#ifndef __cplusplus
+ #error "Cython files generated with the C++ option must be compiled with a C++ compiler."
+#endif
+#ifndef CYTHON_INLINE
+ #if defined(__clang__)
+ #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
+ #else
+ #define CYTHON_INLINE inline
+ #endif
+#endif
+template<typename T>
+void __Pyx_call_destructor(T& x) {
+ x.~T();
+}
+template<typename T>
+class __Pyx_FakeReference {
+ public:
+ __Pyx_FakeReference() : ptr(NULL) { }
+ __Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { }
+ T *operator->() { return ptr; }
+ T *operator&() { return ptr; }
+ operator T&() { return *ptr; }
+ template<typename U> bool operator ==(U other) { return *ptr == other; }
+ template<typename U> bool operator !=(U other) { return *ptr != other; }
+ private:
+ T *ptr;
+};
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+ #define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+#ifdef NAN
+#define __PYX_NAN() ((float) NAN)
+#else
+static CYTHON_INLINE float __PYX_NAN() {
+ float value;
+ memset(&value, 0xFF, sizeof(value));
+ return value;
+}
+#endif
+#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
+#define __Pyx_truncl trunc
+#else
+#define __Pyx_truncl truncl
+#endif
+
+
+#define __PYX_ERR(f_index, lineno, Ln_error) \
+{ \
+ __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \
+}
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
+#ifndef __PYX_EXTERN_C
+ #ifdef __cplusplus
+ #define __PYX_EXTERN_C extern "C"
+ #else
+ #define __PYX_EXTERN_C extern
+ #endif
+#endif
+
+#define __PYX_HAVE__numind
+#define __PYX_HAVE_API__numind
+#include "stdlib.h"
+#include "numind.h"
+#ifdef _OPENMP
+#include <omp.h>
+#endif /* _OPENMP */
+
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
+ const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
+
+#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
+#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
+#define __PYX_DEFAULT_STRING_ENCODING ""
+#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
+#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#define __Pyx_uchar_cast(c) ((unsigned char)c)
+#define __Pyx_long_cast(x) ((long)x)
+#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
+ (sizeof(type) < sizeof(Py_ssize_t)) ||\
+ (sizeof(type) > sizeof(Py_ssize_t) &&\
+ likely(v < (type)PY_SSIZE_T_MAX ||\
+ v == (type)PY_SSIZE_T_MAX) &&\
+ (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
+ v == (type)PY_SSIZE_T_MIN))) ||\
+ (sizeof(type) == sizeof(Py_ssize_t) &&\
+ (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
+ v == (type)PY_SSIZE_T_MAX))) )
+#if defined (__cplusplus) && __cplusplus >= 201103L
+ #include <cstdlib>
+ #define __Pyx_sst_abs(value) std::abs(value)
+#elif SIZEOF_INT >= SIZEOF_SIZE_T
+ #define __Pyx_sst_abs(value) abs(value)
+#elif SIZEOF_LONG >= SIZEOF_SIZE_T
+ #define __Pyx_sst_abs(value) labs(value)
+#elif defined (_MSC_VER) && defined (_M_X64)
+ #define __Pyx_sst_abs(value) _abs64(value)
+#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define __Pyx_sst_abs(value) llabs(value)
+#elif defined (__GNUC__)
+ #define __Pyx_sst_abs(value) __builtin_llabs(value)
+#else
+ #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
+#endif
+static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
+static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
+#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
+#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
+#define __Pyx_PyBytes_FromString PyBytes_FromString
+#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#else
+ #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
+#endif
+#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
+#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
+#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
+#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
+#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
+#if PY_MAJOR_VERSION < 3
+static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
+{
+ const Py_UNICODE *u_end = u;
+ while (*u_end++) ;
+ return (size_t)(u_end - u - 1);
+}
+#else
+#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
+#endif
+#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
+#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
+#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
+#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
+#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+#if CYTHON_ASSUME_SAFE_MACROS
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
+#else
+#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
+#endif
+#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+static int __Pyx_sys_getdefaultencoding_not_ascii;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ PyObject* ascii_chars_u = NULL;
+ PyObject* ascii_chars_b = NULL;
+ const char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ if (strcmp(default_encoding_c, "ascii") == 0) {
+ __Pyx_sys_getdefaultencoding_not_ascii = 0;
+ } else {
+ char ascii_chars[128];
+ int c;
+ for (c = 0; c < 128; c++) {
+ ascii_chars[c] = c;
+ }
+ __Pyx_sys_getdefaultencoding_not_ascii = 1;
+ ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
+ if (!ascii_chars_u) goto bad;
+ ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
+ if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
+ PyErr_Format(
+ PyExc_ValueError,
+ "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
+ default_encoding_c);
+ goto bad;
+ }
+ Py_DECREF(ascii_chars_u);
+ Py_DECREF(ascii_chars_b);
+ }
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ Py_XDECREF(ascii_chars_u);
+ Py_XDECREF(ascii_chars_b);
+ return -1;
+}
+#endif
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
+#else
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+static char* __PYX_DEFAULT_STRING_ENCODING;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
+ if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
+ strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ return -1;
+}
+#endif
+#endif
+
+
+/* Test for GCC > 2.95 */
+#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* !__GNUC__ or GCC < 2.95 */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+#endif /* __GNUC__ */
+static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_d;
+static PyObject *__pyx_b;
+static PyObject *__pyx_cython_runtime;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static PyObject *__pyx_empty_unicode;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+
+static const char *__pyx_f[] = {
+ "numind.pyx",
+ "stringsource",
+};
+
+/*--- Type declarations ---*/
+struct __pyx_obj_6numind_NumInd;
+struct __pyx_t_6numind_PyArrayInterface;
+typedef struct __pyx_t_6numind_PyArrayInterface __pyx_t_6numind_PyArrayInterface;
+
+/* "numind.pyx":42
+ * byteorder = {'<':'little', '>':'big'}
+ *
+ * ctypedef struct PyArrayInterface: # <<<<<<<<<<<<<<
+ * int version # contains the integer 2 as a sanity check
+ * int nd # number of dimensions
+ */
+struct __pyx_t_6numind_PyArrayInterface {
+ int version;
+ int nd;
+ char typekind;
+ int itemsize;
+ int flags;
+ Py_intptr_t *shape;
+ Py_intptr_t *strides;
+ void *data;
+};
+
+/* "numind.pyx":56
+ *
+ *
+ * cdef class NumInd: # <<<<<<<<<<<<<<
+ * cdef void *data
+ * cdef int _nd
+ */
+struct __pyx_obj_6numind_NumInd {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_6numind_NumInd *__pyx_vtab;
+ void *data;
+ int _nd;
+ Py_intptr_t *_shape;
+ Py_intptr_t *_strides;
+ __pyx_t_6numind_PyArrayInterface *inter;
+ PyObject *_t_shape;
+ PyObject *_t_strides;
+ PyObject *_undarray;
+};
+
+
+
+struct __pyx_vtabstruct_6numind_NumInd {
+ __pyx_t_6numind_PyArrayInterface *(*_get_array_interface)(struct __pyx_obj_6numind_NumInd *);
+};
+static struct __pyx_vtabstruct_6numind_NumInd *__pyx_vtabptr_6numind_NumInd;
+
+/* --- Runtime support code (head) --- */
+/* Refnanny.proto */
+#ifndef CYTHON_REFNANNY
+ #define CYTHON_REFNANNY 0
+#endif
+#if CYTHON_REFNANNY
+ typedef struct {
+ void (*INCREF)(void*, PyObject*, int);
+ void (*DECREF)(void*, PyObject*, int);
+ void (*GOTREF)(void*, PyObject*, int);
+ void (*GIVEREF)(void*, PyObject*, int);
+ void* (*SetupContext)(const char*, int, const char*);
+ void (*FinishContext)(void**);
+ } __Pyx_RefNannyAPIStruct;
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
+ #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
+#ifdef WITH_THREAD
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)\
+ if (acquire_gil) {\
+ PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
+ PyGILState_Release(__pyx_gilstate_save);\
+ } else {\
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
+ }
+#else
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)\
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+#endif
+ #define __Pyx_RefNannyFinishContext()\
+ __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+ #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
+ #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
+ #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
+ #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
+#else
+ #define __Pyx_RefNannyDeclarations
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)
+ #define __Pyx_RefNannyFinishContext()
+ #define __Pyx_INCREF(r) Py_INCREF(r)
+ #define __Pyx_DECREF(r) Py_DECREF(r)
+ #define __Pyx_GOTREF(r)
+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XINCREF(r) Py_XINCREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
+ #define __Pyx_XGOTREF(r)
+ #define __Pyx_XGIVEREF(r)
+#endif
+#define __Pyx_XDECREF_SET(r, v) do {\
+ PyObject *tmp = (PyObject *) r;\
+ r = v; __Pyx_XDECREF(tmp);\
+ } while (0)
+#define __Pyx_DECREF_SET(r, v) do {\
+ PyObject *tmp = (PyObject *) r;\
+ r = v; __Pyx_DECREF(tmp);\
+ } while (0)
+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
+
+/* PyObjectGetAttrStr.proto */
+#if CYTHON_USE_TYPE_SLOTS
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
+ PyTypeObject* tp = Py_TYPE(obj);
+ if (likely(tp->tp_getattro))
+ return tp->tp_getattro(obj, attr_name);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_getattr))
+ return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
+#endif
+ return PyObject_GetAttr(obj, attr_name);
+}
+#else
+#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
+#endif
+
+/* GetBuiltinName.proto */
+static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+
+/* RaiseDoubleKeywords.proto */
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
+
+/* ParseKeywords.proto */
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
+ const char* function_name);
+
+/* RaiseArgTupleInvalid.proto */
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
+
+/* GetItemInt.proto */
+#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
+ __Pyx_GetItemInt_Generic(o, to_py_func(i))))
+#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
+ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
+ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck);
+
+/* SliceObject.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
+ PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
+ PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
+ int has_cstart, int has_cstop, int wraparound);
+
+/* SetItemInt.proto */
+#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\
+ __Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
+ int is_list, int wraparound, int boundscheck);
+
+/* PyObjectCall.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
+#else
+#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
+#endif
+
+/* GetAttr.proto */
+static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *);
+
+/* HasAttr.proto */
+static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *);
+
+/* UnicodeAsUCS4.proto */
+static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject*);
+
+/* object_ord.proto */
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyObject_Ord(c)\
+ (likely(PyUnicode_Check(c)) ? (long)__Pyx_PyUnicode_AsPy_UCS4(c) : __Pyx__PyObject_Ord(c))
+#else
+#define __Pyx_PyObject_Ord(c) __Pyx__PyObject_Ord(c)
+#endif
+static long __Pyx__PyObject_Ord(PyObject* c);
+
+/* IncludeStringH.proto */
+#include <string.h>
+
+/* BytesEquals.proto */
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);
+
+/* UnicodeEquals.proto */
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);
+
+/* StrEquals.proto */
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
+/* GetModuleGlobalName.proto */
+static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
+
+/* PyThreadStateGet.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
+#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET();
+#else
+#define __Pyx_PyThreadState_declare
+#define __Pyx_PyThreadState_assign
+#endif
+
+/* PyErrFetchRestore.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
+#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
+#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
+#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
+static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#else
+#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb)
+#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb)
+#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb)
+#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb)
+#endif
+
+/* WriteUnraisableException.proto */
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename,
+ int full_traceback, int nogil);
+
+/* RaiseException.proto */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
+
+/* SetVTable.proto */
+static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+
+/* SetupReduce.proto */
+static int __Pyx_setup_reduce(PyObject* type_obj);
+
+/* Import.proto */
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
+/* CLineInTraceback.proto */
+static int __Pyx_CLineForTraceback(int c_line);
+
+/* CodeObjectCache.proto */
+typedef struct {
+ PyCodeObject* code_object;
+ int code_line;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+/* AddTraceback.proto */
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+
+/* CheckBinaryVersion.proto */
+static int __Pyx_check_binary_version(void);
+
+/* InitStrings.proto */
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+
+static __pyx_t_6numind_PyArrayInterface *__pyx_f_6numind_6NumInd__get_array_interface(struct __pyx_obj_6numind_NumInd *__pyx_v_self); /* proto*/
+
+/* Module declarations from 'cpython.pycapsule' */
+
+/* Module declarations from 'numind' */
+static PyTypeObject *__pyx_ptype_6numind_NumInd = 0;
+static void *__pyx_f_6numind_free_array_interface(PyObject *); /*proto*/
+#define __Pyx_MODULE_NAME "numind"
+int __pyx_module_is_main_numind = 0;
+
+/* Implementation of 'numind' */
+static PyObject *__pyx_builtin_chr;
+static PyObject *__pyx_builtin_MemoryError;
+static PyObject *__pyx_builtin_TypeError;
+static const char __pyx_k_f[] = "f";
+static const char __pyx_k_i[] = "i";
+static const char __pyx_k__3[] = "|";
+static const char __pyx_k__6[] = "<";
+static const char __pyx_k__7[] = ">";
+static const char __pyx_k_big[] = "big";
+static const char __pyx_k_chr[] = "chr";
+static const char __pyx_k_sys[] = "sys";
+static const char __pyx_k_data[] = "data";
+static const char __pyx_k_main[] = "__main__";
+static const char __pyx_k_name[] = "__name__";
+static const char __pyx_k_test[] = "__test__";
+static const char __pyx_k_shape[] = "shape";
+static const char __pyx_k_import[] = "__import__";
+static const char __pyx_k_little[] = "little";
+static const char __pyx_k_reduce[] = "__reduce__";
+static const char __pyx_k_ALIGNED[] = "ALIGNED";
+static const char __pyx_k_FORTRAN[] = "FORTRAN";
+static const char __pyx_k_strides[] = "strides";
+static const char __pyx_k_typestr[] = "typestr";
+static const char __pyx_k_getstate[] = "__getstate__";
+static const char __pyx_k_readonly[] = "readonly";
+static const char __pyx_k_setstate[] = "__setstate__";
+static const char __pyx_k_undarray[] = "undarray";
+static const char __pyx_k_TypeError[] = "TypeError";
+static const char __pyx_k_WRITEABLE[] = "WRITEABLE";
+static const char __pyx_k_byteorder[] = "byteorder";
+static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
+static const char __pyx_k_CONTIGUOUS[] = "CONTIGUOUS";
+static const char __pyx_k_NOTSWAPPED[] = "NOTSWAPPED";
+static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
+static const char __pyx_k_MemoryError[] = "MemoryError";
+static const char __pyx_k_array_struct[] = "__array_struct__";
+static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
+static const char __pyx_k_array_interface[] = "__array_interface__";
+static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
+static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
+static const char __pyx_k_self__shape_self__strides_self_d[] = "self._shape,self._strides,self.data,self.inter cannot be converted to a Python object for pickling";
+static PyObject *__pyx_n_s_ALIGNED;
+static PyObject *__pyx_n_s_CONTIGUOUS;
+static PyObject *__pyx_n_s_FORTRAN;
+static PyObject *__pyx_n_s_MemoryError;
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+ if (*name) {
+ values[name-argnames] = value;
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
+ }
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
+ }
+ }
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%.200s() got an unexpected keyword argument '%.200s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
+/* RaiseArgTupleInvalid */
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *more_or_less;
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ func_name, more_or_less, num_expected,
+ (num_expected == 1) ? "" : "s", num_found);
+}
+
+/* GetItemInt */
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ CYTHON_NCP_UNUSED int wraparound,
+ CYTHON_NCP_UNUSED int boundscheck) {
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
+ Py_ssize_t wrapped_i = i;
+ if (wraparound & unlikely(i < 0)) {
+ wrapped_i += PyList_GET_SIZE(o);
+ }
+ if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, wrapped_i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ CYTHON_NCP_UNUSED int wraparound,
+ CYTHON_NCP_UNUSED int boundscheck) {
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
+ Py_ssize_t wrapped_i = i;
+ if (wraparound & unlikely(i < 0)) {
+ wrapped_i += PyTuple_GET_SIZE(o);
+ }
+ if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
+ CYTHON_NCP_UNUSED int wraparound,
+ CYTHON_NCP_UNUSED int boundscheck) {
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
+ if (is_list || PyList_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (likely(l >= 0)) {
+ i += l;
+ } else {
+ if (!PyErr_ExceptionMatches(PyExc_OverflowError))
+ return NULL;
+ PyErr_Clear();
+ }
+ }
+ return m->sq_item(o, i);
+ }
+ }
+#else
+ if (is_list || PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+/* SliceObject */
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj,
+ Py_ssize_t cstart, Py_ssize_t cstop,
+ PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
+ int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
+#if CYTHON_USE_TYPE_SLOTS
+ PyMappingMethods* mp;
+#if PY_MAJOR_VERSION < 3
+ PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
+ if (likely(ms && ms->sq_slice)) {
+ if (!has_cstart) {
+ if (_py_start && (*_py_start != Py_None)) {
+ cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
+ if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
+ } else
+ cstart = 0;
+ }
+ if (!has_cstop) {
+ if (_py_stop && (*_py_stop != Py_None)) {
+ cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
+ if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
+ } else
+ cstop = PY_SSIZE_T_MAX;
+ }
+ if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
+ Py_ssize_t l = ms->sq_length(obj);
+ if (likely(l >= 0)) {
+ if (cstop < 0) {
+ cstop += l;
+ if (cstop < 0) cstop = 0;
+ }
+ if (cstart < 0) {
+ cstart += l;
+ if (cstart < 0) cstart = 0;
+ }
+ } else {
+ if (!PyErr_ExceptionMatches(PyExc_OverflowError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ return ms->sq_slice(obj, cstart, cstop);
+ }
+#endif
+ mp = Py_TYPE(obj)->tp_as_mapping;
+ if (likely(mp && mp->mp_subscript))
+#endif
+ {
+ PyObject* result;
+ PyObject *py_slice, *py_start, *py_stop;
+ if (_py_slice) {
+ py_slice = *_py_slice;
+ } else {
+ PyObject* owned_start = NULL;
+ PyObject* owned_stop = NULL;
+ if (_py_start) {
+ py_start = *_py_start;
+ } else {
+ if (has_cstart) {
+ owned_start = py_start = PyInt_FromSsize_t(cstart);
+ if (unlikely(!py_start)) goto bad;
+ } else
+ py_start = Py_None;
+ }
+ if (_py_stop) {
+ py_stop = *_py_stop;
+ } else {
+ if (has_cstop) {
+ owned_stop = py_stop = PyInt_FromSsize_t(cstop);
+ if (unlikely(!py_stop)) {
+ Py_XDECREF(owned_start);
+ goto bad;
+ }
+ } else
+ py_stop = Py_None;
+ }
+ py_slice = PySlice_New(py_start, py_stop, Py_None);
+ Py_XDECREF(owned_start);
+ Py_XDECREF(owned_stop);
+ if (unlikely(!py_slice)) goto bad;
+ }
+#if CYTHON_USE_TYPE_SLOTS
+ result = mp->mp_subscript(obj, py_slice);
+#else
+ result = PyObject_GetItem(obj, py_slice);
+#endif
+ if (!_py_slice) {
+ Py_DECREF(py_slice);
+ }
+ return result;
+ }
+ PyErr_Format(PyExc_TypeError,
+ "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
+bad:
+ return NULL;
+}
+
+/* SetItemInt */
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
+ int r;
+ if (!j) return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list,
+ CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) {
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
+ if (is_list || PyList_CheckExact(o)) {
+ Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
+ if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject* old = PyList_GET_ITEM(o, n);
+ Py_INCREF(v);
+ PyList_SET_ITEM(o, n, v);
+ Py_DECREF(old);
+ return 1;
+ }
+ } else {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_ass_item)) {
+ if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (likely(l >= 0)) {
+ i += l;
+ } else {
+ if (!PyErr_ExceptionMatches(PyExc_OverflowError))
+ return -1;
+ PyErr_Clear();
+ }
+ }
+ return m->sq_ass_item(o, i, v);
+ }
+ }
+#else
+#if CYTHON_COMPILING_IN_PYPY
+ if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) {
+#else
+ if (is_list || PySequence_Check(o)) {
+#endif
+ return PySequence_SetItem(o, i, v);
+ }
+#endif
+ return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
+}
+
+/* PyObjectCall */
+ #if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyObject *result;
+ ternaryfunc call = func->ob_type->tp_call;
+ if (unlikely(!call))
+ return PyObject_Call(func, arg, kw);
+ if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
+ return NULL;
+ result = (*call)(func, arg, kw);
+ Py_LeaveRecursiveCall();
+ if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
+ PyErr_SetString(
+ PyExc_SystemError,
+ "NULL result without error in PyObject_Call");
+ }
+ return result;
+}
+#endif
+
+/* GetAttr */
+ static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) {
+#if CYTHON_COMPILING_IN_CPYTHON
+#if PY_MAJOR_VERSION >= 3
+ if (likely(PyUnicode_Check(n)))
+#else
+ if (likely(PyString_Check(n)))
+#endif
+ return __Pyx_PyObject_GetAttrStr(o, n);
+#endif
+ return PyObject_GetAttr(o, n);
+}
+
+/* HasAttr */
+ static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) {
+ PyObject *r;
+ if (unlikely(!__Pyx_PyBaseString_Check(n))) {
+ PyErr_SetString(PyExc_TypeError,
+ "hasattr(): attribute name must be string");
+ return -1;
+ }
+ r = __Pyx_GetAttr(o, n);
+ if (unlikely(!r)) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ Py_DECREF(r);
+ return 1;
+ }
+}
+
+/* UnicodeAsUCS4 */
+ static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject* x) {
+ Py_ssize_t length;
+ #if CYTHON_PEP393_ENABLED
+ length = PyUnicode_GET_LENGTH(x);
+ if (likely(length == 1)) {
+ return PyUnicode_READ_CHAR(x, 0);
+ }
+ #else
+ length = PyUnicode_GET_SIZE(x);
+ if (likely(length == 1)) {
+ return PyUnicode_AS_UNICODE(x)[0];
+ }
+ #if Py_UNICODE_SIZE == 2
+ else if (PyUnicode_GET_SIZE(x) == 2) {
+ Py_UCS4 high_val = PyUnicode_AS_UNICODE(x)[0];
+ if (high_val >= 0xD800 && high_val <= 0xDBFF) {
+ Py_UCS4 low_val = PyUnicode_AS_UNICODE(x)[1];
+ if (low_val >= 0xDC00 && low_val <= 0xDFFF) {
+ return 0x10000 + (((high_val & ((1<<10)-1)) << 10) | (low_val & ((1<<10)-1)));
+ }
+ }
+ }
+ #endif
+ #endif
+ PyErr_Format(PyExc_ValueError,
+ "only single character unicode strings can be converted to Py_UCS4, "
+ "got length %" CYTHON_FORMAT_SSIZE_T "d", length);
+ return (Py_UCS4)-1;
+}
+
+/* object_ord */
+ static long __Pyx__PyObject_Ord(PyObject* c) {
+ Py_ssize_t size;
+ if (PyBytes_Check(c)) {
+ size = PyBytes_GET_SIZE(c);
+ if (likely(size == 1)) {
+ return (unsigned char) PyBytes_AS_STRING(c)[0];
+ }
+#if PY_MAJOR_VERSION < 3
+ } else if (PyUnicode_Check(c)) {
+ return (long)__Pyx_PyUnicode_AsPy_UCS4(c);
+#endif
+#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
+ } else if (PyByteArray_Check(c)) {
+ size = PyByteArray_GET_SIZE(c);
+ if (likely(size == 1)) {
+ return (unsigned char) PyByteArray_AS_STRING(c)[0];
+ }
+#endif
+ } else {
+ PyErr_Format(PyExc_TypeError,
+ "ord() expected string of length 1, but %.200s found", c->ob_type->tp_name);
+ return (long)(Py_UCS4)-1;
+ }
+ PyErr_Format(PyExc_TypeError,
+ "ord() expected a character, but string of length %zd found", size);
+ return (long)(Py_UCS4)-1;
+}
+
+/* BytesEquals */
+ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+#if CYTHON_COMPILING_IN_PYPY
+ return PyObject_RichCompareBool(s1, s2, equals);
+#else
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ const char *ps1, *ps2;
+ Py_ssize_t length = PyBytes_GET_SIZE(s1);
+ if (length != PyBytes_GET_SIZE(s2))
+ return (equals == Py_NE);
+ ps1 = PyBytes_AS_STRING(s1);
+ ps2 = PyBytes_AS_STRING(s2);
+ if (ps1[0] != ps2[0]) {
+ return (equals == Py_NE);
+ } else if (length == 1) {
+ return (equals == Py_EQ);
+ } else {
+ int result;
+#if CYTHON_USE_UNICODE_INTERNALS
+ Py_hash_t hash1, hash2;
+ hash1 = ((PyBytesObject*)s1)->ob_shash;
+ hash2 = ((PyBytesObject*)s2)->ob_shash;
+ if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
+ return (equals == Py_NE);
+ }
+#endif
+ result = memcmp(ps1, ps2, (size_t)length);
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+#endif
+}
+
+/* UnicodeEquals */
+ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+#if CYTHON_COMPILING_IN_PYPY
+ return PyObject_RichCompareBool(s1, s2, equals);
+#else
+#if PY_MAJOR_VERSION < 3
+ PyObject* owned_ref = NULL;
+#endif
+ int s1_is_unicode, s2_is_unicode;
+ if (s1 == s2) {
+ goto return_eq;
+ }
+ s1_is_unicode = PyUnicode_CheckExact(s1);
+ s2_is_unicode = PyUnicode_CheckExact(s2);
+#if PY_MAJOR_VERSION < 3
+ if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
+ owned_ref = PyUnicode_FromObject(s2);
+ if (unlikely(!owned_ref))
+ return -1;
+ s2 = owned_ref;
+ s2_is_unicode = 1;
+ } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
+ owned_ref = PyUnicode_FromObject(s1);
+ if (unlikely(!owned_ref))
+ return -1;
+ s1 = owned_ref;
+ s1_is_unicode = 1;
+ } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
+ return __Pyx_PyBytes_Equals(s1, s2, equals);
+ }
+#endif
+ if (s1_is_unicode & s2_is_unicode) {
+ Py_ssize_t length;
+ int kind;
+ void *data1, *data2;
+ if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
+ return -1;
+ length = __Pyx_PyUnicode_GET_LENGTH(s1);
+ if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
+ goto return_ne;
+ }
+#if CYTHON_USE_UNICODE_INTERNALS
+ {
+ Py_hash_t hash1, hash2;
+ #if CYTHON_PEP393_ENABLED
+ hash1 = ((PyASCIIObject*)s1)->hash;
+ hash2 = ((PyASCIIObject*)s2)->hash;
+ #else
+ hash1 = ((PyUnicodeObject*)s1)->hash;
+ hash2 = ((PyUnicodeObject*)s2)->hash;
+ #endif
+ if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
+ goto return_ne;
+ }
+ }
+#endif
+ kind = __Pyx_PyUnicode_KIND(s1);
+ if (kind != __Pyx_PyUnicode_KIND(s2)) {
+ goto return_ne;
+ }
+ data1 = __Pyx_PyUnicode_DATA(s1);
+ data2 = __Pyx_PyUnicode_DATA(s2);
+ if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
+ goto return_ne;
+ } else if (length == 1) {
+ goto return_eq;
+ } else {
+ int result = memcmp(data1, data2, (size_t)(length * kind));
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & s2_is_unicode) {
+ goto return_ne;
+ } else if ((s2 == Py_None) & s1_is_unicode) {
+ goto return_ne;
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+return_eq:
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_EQ);
+return_ne:
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_NE);
+#endif
+}
+
+/* GetModuleGlobalName */
+ static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
+ PyObject *result;
+#if !CYTHON_AVOID_BORROWED_REFS
+ result = PyDict_GetItem(__pyx_d, name);
+ if (likely(result)) {
+ Py_INCREF(result);
+ } else {
+#else
+ result = PyObject_GetItem(__pyx_d, name);
+ if (!result) {
+ PyErr_Clear();
+#endif
+ result = __Pyx_GetBuiltinName(name);
+ }
+ return result;
+}
+
+/* PyErrFetchRestore */
+ #if CYTHON_FAST_THREAD_STATE
+static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+#endif
+
+/* WriteUnraisableException */
+ static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
+ CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
+ int full_traceback, CYTHON_UNUSED int nogil) {
+ PyObject *old_exc, *old_val, *old_tb;
+ PyObject *ctx;
+ __Pyx_PyThreadState_declare
+#ifdef WITH_THREAD
+ PyGILState_STATE state;
+ if (nogil)
+ state = PyGILState_Ensure();
+#ifdef _MSC_VER
+ else state = (PyGILState_STATE)-1;
+#endif
+#endif
+ __Pyx_PyThreadState_assign
+ __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
+ if (full_traceback) {
+ Py_XINCREF(old_exc);
+ Py_XINCREF(old_val);
+ Py_XINCREF(old_tb);
+ __Pyx_ErrRestore(old_exc, old_val, old_tb);
+ PyErr_PrintEx(1);
+ }
+ #if PY_MAJOR_VERSION < 3
+ ctx = PyString_FromString(name);
+ #else
+ ctx = PyUnicode_FromString(name);
+ #endif
+ __Pyx_ErrRestore(old_exc, old_val, old_tb);
+ if (!ctx) {
+ PyErr_WriteUnraisable(Py_None);
+ } else {
+ PyErr_WriteUnraisable(ctx);
+ Py_DECREF(ctx);
+ }
+#ifdef WITH_THREAD
+ if (nogil)
+ PyGILState_Release(state);
+#endif
+}
+
+/* RaiseException */
+ #if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
+ __Pyx_PyThreadState_declare
+ Py_XINCREF(type);
+ if (!value || value == Py_None)
+ value = NULL;
+ else
+ Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ }
+ if (PyType_Check(type)) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ }
+ __Pyx_PyThreadState_assign
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+#else
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *instance_class = NULL;
+ if (value && PyExceptionInstance_Check(value)) {
+ instance_class = (PyObject*) Py_TYPE(value);
+ if (instance_class != type) {
+ int is_subclass = PyObject_IsSubclass(instance_class, type);
+ if (!is_subclass) {
+ instance_class = NULL;
+ } else if (unlikely(is_subclass == -1)) {
+ goto bad;
+ } else {
+ type = instance_class;
+ }
+ }
+ }
+ if (!instance_class) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ } else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyObject_Call(type, args, NULL);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ }
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+#if PY_VERSION_HEX >= 0x03030000
+ if (cause) {
+#else
+ if (cause && cause != Py_None) {
+#endif
+ PyObject *fixed_cause;
+ if (cause == Py_None) {
+ fixed_cause = NULL;
+ } else if (PyExceptionClass_Check(cause)) {
+ fixed_cause = PyObject_CallObject(cause, NULL);
+ if (fixed_cause == NULL)
+ goto bad;
+ } else if (PyExceptionInstance_Check(cause)) {
+ fixed_cause = cause;
+ Py_INCREF(fixed_cause);
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "exception causes must derive from "
+ "BaseException");
+ goto bad;
+ }
+ PyException_SetCause(value, fixed_cause);
+ }
+ PyErr_SetObject(type, value);
+ if (tb) {
+#if CYTHON_COMPILING_IN_PYPY
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
+ Py_INCREF(tb);
+ PyErr_Restore(tmp_type, tmp_value, tb);
+ Py_XDECREF(tmp_tb);
+#else
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+#endif
+ }
+bad:
+ Py_XDECREF(owned_instance);
+ return;
+}
+#endif
+
+/* SetVTable */
+ static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+/* SetupReduce */
+ static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
+ int ret;
+ PyObject *name_attr;
+ name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name);
+ if (likely(name_attr)) {
+ ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
+ } else {
+ ret = -1;
+ }
+ if (unlikely(ret < 0)) {
+ PyErr_Clear();
+ ret = 0;
+ }
+ Py_XDECREF(name_attr);
+ return ret;
+}
+static int __Pyx_setup_reduce(PyObject* type_obj) {
+ int ret = 0;
+ PyObject *object_reduce = NULL;
+ PyObject *object_reduce_ex = NULL;
+ PyObject *reduce = NULL;
+ PyObject *reduce_ex = NULL;
+ PyObject *reduce_cython = NULL;
+ PyObject *setstate = NULL;
+ PyObject *setstate_cython = NULL;
+#if CYTHON_USE_PYTYPE_LOOKUP
+ if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD;
+#else
+ if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD;
+#endif
+#if CYTHON_USE_PYTYPE_LOOKUP
+ object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
+#else
+ object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
+#endif
+ reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD;
+ if (reduce_ex == object_reduce_ex) {
+#if CYTHON_USE_PYTYPE_LOOKUP
+ object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD;
+#else
+ object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD;
+#endif
+ reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD;
+ if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
+ reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD;
+ ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD;
+ ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD;
+ setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate);
+ if (!setstate) PyErr_Clear();
+ if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
+ setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD;
+ ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD;
+ ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD;
+ }
+ PyType_Modified((PyTypeObject*)type_obj);
+ }
+ }
+ goto GOOD;
+BAD:
+ if (!PyErr_Occurred())
+ PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name);
+ ret = -1;
+GOOD:
+#if !CYTHON_COMPILING_IN_CPYTHON
+ Py_XDECREF(object_reduce);
+ Py_XDECREF(object_reduce_ex);
+#endif
+ Py_XDECREF(reduce);
+ Py_XDECREF(reduce_ex);
+ Py_XDECREF(reduce_cython);
+ Py_XDECREF(setstate);
+ Py_XDECREF(setstate_cython);
+ return ret;
+}
+
+/* Import */
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ {
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0;
+ }
+ #endif
+ if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
+ }
+ }
+bad:
+ #if PY_VERSION_HEX < 0x03030000
+ Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+/* CLineInTraceback */
+ static int __Pyx_CLineForTraceback(int c_line) {
+#ifdef CYTHON_CLINE_IN_TRACEBACK
+ return ((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0;
+#else
+ PyObject *use_cline;
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject **cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
+ if (likely(cython_runtime_dict)) {
+ use_cline = PyDict_GetItem(*cython_runtime_dict, __pyx_n_s_cline_in_traceback);
+ } else
+#endif
+ {
+ PyObject *ptype, *pvalue, *ptraceback;
+ PyObject *use_cline_obj;
+ PyErr_Fetch(&ptype, &pvalue, &ptraceback);
+ use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
+ if (use_cline_obj) {
+ use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
+ Py_DECREF(use_cline_obj);
+ } else {
+ use_cline = NULL;
+ }
+ PyErr_Restore(ptype, pvalue, ptraceback);
+ }
+ if (!use_cline) {
+ c_line = 0;
+ PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
+ }
+ else if (PyObject_Not(use_cline) != 0) {
+ c_line = 0;
+ }
+ return c_line;
+#endif
+}
+
+/* CodeObjectCache */
+ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = start + (end - start) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
+/* AddTraceback */
+ #include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(filename);
+ #else
+ py_srcfile = PyUnicode_FromString(filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (c_line) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_code = __Pyx_PyCode_New(
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ py_line,
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+ if (c_line) {
+ c_line = __Pyx_CLineForTraceback(c_line);
+ }
+ py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
+ }
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ __pyx_d, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+/* CIntToPy */
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
+ const int neg_one = (int) -1, const_zero = (int) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(int) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(int) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
+ }
+ } else {
+ if (sizeof(int) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(int),
+ little, !is_unsigned);
+ }
+}
+
+/* CIntFromPyVerify */
+ #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
+ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
+#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
+ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
+#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
+ {\
+ func_type value = func_value;\
+ if (sizeof(target_type) < sizeof(func_type)) {\
+ if (unlikely(value != (func_type) (target_type) value)) {\
+ func_type zero = 0;\
+ if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
+ return (target_type) -1;\
+ if (is_unsigned && unlikely(value < zero))\
+ goto raise_neg_overflow;\
+ else\
+ goto raise_overflow;\
+ }\
+ }\
+ return (target_type) value;\
+ }
+
+/* CIntToPy */
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value) {
+ const char neg_one = (char) -1, const_zero = (char) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(char) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(char) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
+ }
+ } else {
+ if (sizeof(char) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(char),
+ little, !is_unsigned);
+ }
+}
+
+/* CIntToPy */
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
+ const long neg_one = (long) -1, const_zero = (long) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(long) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(long) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
+ }
+ } else {
+ if (sizeof(long) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(long),
+ little, !is_unsigned);
+ }
+}
+
+/* CIntFromPy */
+ static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) {
+ const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(Py_intptr_t) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (Py_intptr_t) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (Py_intptr_t) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, digits[0])
+ case 2:
+ if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) >= 2 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) >= 3 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) >= 4 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0]));
+ }
+ }
+ break;
+ }
+#endif
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+#else
+ {
+ int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
+ if (unlikely(result < 0))
+ return (Py_intptr_t) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
+ if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
+ }
+ } else {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (Py_intptr_t) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, sdigit, (sdigit) (-(sdigit)digits[0]))
+ case 1: __PYX_VERIFY_RETURN_INT(Py_intptr_t, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(Py_intptr_t) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((Py_intptr_t)-1)*(((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(Py_intptr_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) {
+ return (Py_intptr_t) ((((((Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(Py_intptr_t) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(Py_intptr_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) {
+ return (Py_intptr_t) ((((((((Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(Py_intptr_t) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) {
+ return (Py_intptr_t) (((Py_intptr_t)-1)*(((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(Py_intptr_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(Py_intptr_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(Py_intptr_t) - 1 > 4 * PyLong_SHIFT) {
+ return (Py_intptr_t) ((((((((((Py_intptr_t)digits[3]) << PyLong_SHIFT) | (Py_intptr_t)digits[2]) << PyLong_SHIFT) | (Py_intptr_t)digits[1]) << PyLong_SHIFT) | (Py_intptr_t)digits[0])));
+ }
+ }
+ break;
+ }
+#endif
+ if (sizeof(Py_intptr_t) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(Py_intptr_t, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ Py_intptr_t val;
+ PyObject *v = __Pyx_PyNumber_IntOrLong(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (Py_intptr_t) -1;
+ }
+ } else {
+ Py_intptr_t val;
+ PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
+ if (!tmp) return (Py_intptr_t) -1;
+ val = __Pyx_PyInt_As_Py_intptr_t(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to Py_intptr_t");
+ return (Py_intptr_t) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to Py_intptr_t");
+ return (Py_intptr_t) -1;
+}
+
+/* CIntFromPy */
+ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
+ const int neg_one = (int) -1, const_zero = (int) 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(int) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (int) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (int) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0])
+ case 2:
+ if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) {
+ return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) {
+ return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) {
+ return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
+ }
+ }
+ break;
+ }
+#endif
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+#else
+ {
+ int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
+ if (unlikely(result < 0))
+ return (int) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
+ if (sizeof(int) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
+ }
+ } else {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (int) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0]))
+ case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
+ return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
+ return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
+ return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
+ return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
+ return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
+ return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
+ }
+ }
+ break;
+ }
+#endif
+ if (sizeof(int) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ int val;
+ PyObject *v = __Pyx_PyNumber_IntOrLong(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (int) -1;
+ }
+ } else {
+ int val;
+ PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
+ if (!tmp) return (int) -1;
+ val = __Pyx_PyInt_As_int(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to int");
+ return (int) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to int");
+ return (int) -1;
+}
+
+/* CIntFromPy */
+ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
+ const long neg_one = (long) -1, const_zero = (long) 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(long) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (long) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (long) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0])
+ case 2:
+ if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) {
+ return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) {
+ return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) {
+ return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
+ }
+ }
+ break;
+ }
+#endif
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+#else
+ {
+ int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
+ if (unlikely(result < 0))
+ return (long) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
+ if (sizeof(long) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
+ }
+ } else {
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
+ switch (Py_SIZE(x)) {
+ case 0: return (long) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0]))
+ case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
+ return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
+ return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
+ return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
+ return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
+ return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
+ return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
+ }
+ }
+ break;
+ }
+#endif
+ if (sizeof(long) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ long val;
+ PyObject *v = __Pyx_PyNumber_IntOrLong(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (long) -1;
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
+ if (!tmp) return (long) -1;
+ val = __Pyx_PyInt_As_long(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to long");
+ return (long) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long) -1;
+}
+
+/* CheckBinaryVersion */
+ static int __Pyx_check_binary_version(void) {
+ char ctversion[4], rtversion[4];
+ PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
+ if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char message[200];
+ PyOS_snprintf(message, sizeof(message),
+ "compiletime version %s of module '%.100s' "
+ "does not match runtime version %s",
+ ctversion, __Pyx_MODULE_NAME, rtversion);
+ return PyErr_WarnEx(NULL, message, 1);
+ }
+ return 0;
+}
+
+/* InitStrings */
+ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else
+ if (t->is_unicode | t->is_str) {
+ if (t->intern) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->encoding) {
+ *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+ } else {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ }
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ if (PyObject_Hash(*t->p) == -1)
+ PyErr_Clear();
+ ++t;
+ }
+ return 0;
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
+ return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
+}
+static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
+ Py_ssize_t ignore;
+ return __Pyx_PyObject_AsStringAndSize(o, &ignore);
+}
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+#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
+ if (
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ __Pyx_sys_getdefaultencoding_not_ascii &&
+#endif
+ PyUnicode_Check(o)) {
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+ char* defenc_c;
+ PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
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+ {
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+ char* c;
+ for (c = defenc_c; c < end; c++) {
+ if ((unsigned char) (*c) >= 128) {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+ }
+ }
+#endif
+ *length = PyBytes_GET_SIZE(defenc);
+ return defenc_c;
+#else
+ if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ if (PyUnicode_IS_ASCII(o)) {
+ *length = PyUnicode_GET_LENGTH(o);
+ return PyUnicode_AsUTF8(o);
+ } else {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+#else
+ return PyUnicode_AsUTF8AndSize(o, length);
+#endif
+#endif
+ } else
+#endif
+#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
+ if (PyByteArray_Check(o)) {
+ *length = PyByteArray_GET_SIZE(o);
+ return PyByteArray_AS_STRING(o);
+ } else
+#endif
+ {
+ char* result;
+ int r = PyBytes_AsStringAndSize(o, &result, length);
+ if (unlikely(r < 0)) {
+ return NULL;
+ } else {
+ return result;
+ }
+ }
+}
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ int is_true = x == Py_True;
+ if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
+ else return PyObject_IsTrue(x);
+}
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
+#if CYTHON_USE_TYPE_SLOTS
+ PyNumberMethods *m;
+#endif
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_MAJOR_VERSION < 3
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return __Pyx_NewRef(x);
+#if CYTHON_USE_TYPE_SLOTS
+ m = Py_TYPE(x)->tp_as_number;
+ #if PY_MAJOR_VERSION < 3
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+ #else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+ #endif
+#else
+ res = PyNumber_Int(x);
+#endif
+ if (res) {
+#if PY_MAJOR_VERSION < 3
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%.4s__ returned non-%.4s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
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+}
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject *x;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_CheckExact(b))) {
+ if (sizeof(Py_ssize_t) >= sizeof(long))
+ return PyInt_AS_LONG(b);
+ else
+ return PyInt_AsSsize_t(x);
+ }
+#endif
+ if (likely(PyLong_CheckExact(b))) {
+ #if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)b)->ob_digit;
+ const Py_ssize_t size = Py_SIZE(b);
+ if (likely(__Pyx_sst_abs(size) <= 1)) {
+ ival = likely(size) ? digits[0] : 0;
+ if (size == -1) ival = -ival;
+ return ival;
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+ if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
+ return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ case -2:
+ if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
+ return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ case 3:
+ if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
+ return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ case -3:
+ if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
+ return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ case 4:
+ if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
+ return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ case -4:
+ if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
+ return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
+ }
+ break;
+ }
+ }
+ #endif
+ return PyLong_AsSsize_t(b);
+ }
+ x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+ return PyInt_FromSize_t(ival);
+}
+
+
+#endif /* Py_PYTHON_H */
diff --git a/pymolfile/molfile/numind-cython/numind.h b/pymolfile/molfile/numind-cython/numind.h
new file mode 100644
index 0000000000000000000000000000000000000000..988c2c80604711a3067cf39a3976896c48867526
--- /dev/null
+++ b/pymolfile/molfile/numind-cython/numind.h
@@ -0,0 +1,12 @@
+#ifndef NUMIND_H
+#define NUMIND_H
+
+typedef struct SignedIntBuf
+{
+ int* data;
+ int shape[2];
+ int strides[2];
+} SignedIntBuf;
+
+#endif
+
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new file mode 100644
index 0000000000000000000000000000000000000000..96768d145b96058d800f53ece01d88f4c34cb278
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+ <script>
+ function toggleDiv(id) {
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+<p><span style="border-bottom: solid 1px grey;">Generated by Cython 0.26.1</span></p>
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+<div class="cython"><pre class="cython line score-0"> <span class="">001</span>: # This Pyrex extension class can take a numpy/numarray/Numeric object</pre>
+<pre class="cython line score-0"> <span class="">002</span>: # as a parameter and wrap it so that its information can be accessed</pre>
+<pre class="cython line score-0"> <span class="">003</span>: # in a standard way, both in Python space and C space.</pre>
+<pre class="cython line score-0"> <span class="">004</span>: #</pre>
+<pre class="cython line score-0"> <span class="">005</span>: # Heavily based on an idea of Andrew Straw. See</pre>
+<pre class="cython line score-0"> <span class="">006</span>: # http://www.scipy.org/Cookbook/ArrayStruct_and_Pyrex</pre>
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+<pre class='cython code score-0 '>struct __pyx_t_6numind_PyArrayInterface {
+ int version;
+ int nd;
+ char typekind;
+ int itemsize;
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+ PyObject *_t_shape;
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+ __pyx_t_1 = 0;
+ __pyx_t_1 = <span class='pyx_c_api'>__Pyx_PyObject_Call</span>(__pyx_builtin_chr, __pyx_t_2, NULL);<span class='error_goto'> if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 180, __pyx_L1_error)</span>
+ <span class='refnanny'>__Pyx_GOTREF</span>(__pyx_t_1);
+ <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = (<span class='pyx_c_api'>__Pyx_PyString_Equals</span>(__pyx_t_1, __pyx_n_s_i, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) <span class='error_goto'>__PYX_ERR(0, 180, __pyx_L1_error)</span>
+ <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_3) {
+/* … */
+ goto __pyx_L3;
+ }
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">181</span>: ldata = <long *>self.inter.data</pre>
+<pre class='cython code score-0 '> __pyx_v_ldata = ((long *)__pyx_v_self->inter->data);
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">182</span>: for i from 0 <= i < self.inter.shape[self.inter.nd-1]:</pre>
+<pre class='cython code score-0 '> __pyx_t_4 = (__pyx_v_self->inter->shape[(__pyx_v_self->inter->nd - 1)]);
+ for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">183</span>: ldata[i] = ldata[i] + 1</pre>
+<pre class='cython code score-0 '> (__pyx_v_ldata[__pyx_v_i]) = ((__pyx_v_ldata[__pyx_v_i]) + 1);
+ }
+</pre><pre class="cython line score-14" onclick='toggleDiv(this)'>+<span class="">184</span>: elif chr(self.inter.typekind) == 'f':</pre>
+<pre class='cython code score-14 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_PyInt_From_char</span>(__pyx_v_self->inter->typekind);<span class='error_goto'> if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 184, __pyx_L1_error)</span>
+ <span class='refnanny'>__Pyx_GOTREF</span>(__pyx_t_1);
+ __pyx_t_2 = <span class='py_c_api'>PyTuple_New</span>(1);<span class='error_goto'> if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 184, __pyx_L1_error)</span>
+ <span class='refnanny'>__Pyx_GOTREF</span>(__pyx_t_2);
+ <span class='refnanny'>__Pyx_GIVEREF</span>(__pyx_t_1);
+ <span class='py_macro_api'>PyTuple_SET_ITEM</span>(__pyx_t_2, 0, __pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = <span class='pyx_c_api'>__Pyx_PyObject_Call</span>(__pyx_builtin_chr, __pyx_t_2, NULL);<span class='error_goto'> if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 184, __pyx_L1_error)</span>
+ <span class='refnanny'>__Pyx_GOTREF</span>(__pyx_t_1);
+ <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = (<span class='pyx_c_api'>__Pyx_PyString_Equals</span>(__pyx_t_1, __pyx_n_s_f, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) <span class='error_goto'>__PYX_ERR(0, 184, __pyx_L1_error)</span>
+ <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_3) {
+/* … */
+ }
+ __pyx_L3:;
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">185</span>: fdata = <double *>self.inter.data</pre>
+<pre class='cython code score-0 '> __pyx_v_fdata = ((double *)__pyx_v_self->inter->data);
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">186</span>: for i from 0 <= i < self.inter.shape[self.inter.nd-1]:</pre>
+<pre class='cython code score-0 '> __pyx_t_4 = (__pyx_v_self->inter->shape[(__pyx_v_self->inter->nd - 1)]);
+ for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">187</span>: fdata[i] = fdata[i] + 1</pre>
+<pre class='cython code score-0 '> (__pyx_v_fdata[__pyx_v_i]) = ((__pyx_v_fdata[__pyx_v_i]) + 1.0);
+ }
+</pre><pre class="cython line score-0"> <span class="">188</span>: </pre>
+<pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">189</span>: def __dealloc__(self):</pre>
+<pre class='cython code score-0 '>/* Python wrapper */
+static void __pyx_pw_6numind_6NumInd_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_6numind_6NumInd_5__dealloc__(PyObject *__pyx_v_self) {
+ <span class='refnanny'>__Pyx_RefNannyDeclarations</span>
+ <span class='refnanny'>__Pyx_RefNannySetupContext</span>("__dealloc__ (wrapper)", 0);
+ __pyx_pf_6numind_6NumInd_4__dealloc__(((struct __pyx_obj_6numind_NumInd *)__pyx_v_self));
+
+ /* function exit code */
+ <span class='refnanny'>__Pyx_RefNannyFinishContext</span>();
+}
+
+static void __pyx_pf_6numind_6NumInd_4__dealloc__(struct __pyx_obj_6numind_NumInd *__pyx_v_self) {
+ <span class='refnanny'>__Pyx_RefNannyDeclarations</span>
+ <span class='refnanny'>__Pyx_RefNannySetupContext</span>("__dealloc__", 0);
+/* … */
+ /* function exit code */
+ <span class='refnanny'>__Pyx_RefNannyFinishContext</span>();
+}
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">190</span>: free(self._shape)</pre>
+<pre class='cython code score-0 '> free(__pyx_v_self->_shape);
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">191</span>: free(self._strides)</pre>
+<pre class='cython code score-0 '> free(__pyx_v_self->_strides);
+</pre><pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">192</span>: free(self.inter)</pre>
+<pre class='cython code score-0 '> free(__pyx_v_self->inter);
+</pre></div></body></html>
diff --git a/pymolfile/molfile/numind-cython/numind.pyx b/pymolfile/molfile/numind-cython/numind.pyx
new file mode 100644
index 0000000000000000000000000000000000000000..d959b2b65e14304cb21eb72b71e4d1f004451772
--- /dev/null
+++ b/pymolfile/molfile/numind-cython/numind.pyx
@@ -0,0 +1,192 @@
+# This Pyrex extension class can take a numpy/numarray/Numeric object
+# as a parameter and wrap it so that its information can be accessed
+# in a standard way, both in Python space and C space.
+#
+# Heavily based on an idea of Andrew Straw. See
+# http://www.scipy.org/Cookbook/ArrayStruct_and_Pyrex
+# Very inspiring! :-)
+#
+# First version: 2006-03-25
+# Last update: 2006-03-25
+# Author: Francesc Altet
+
+import sys
+from cpython.pycapsule cimport *
+
+cdef extern from "Python.h":
+ ctypedef int Py_intptr_t
+ ctypedef object PyObject
+ long PyInt_AsLong(object)
+ void Py_INCREF(object)
+ void Py_DECREF(object)
+
+cdef extern from "stdlib.h":
+ ctypedef long size_t
+ ctypedef long intptr_t
+ void *malloc(size_t size)
+ void free(void* ptr)
+
+cdef extern from "numind.h":
+ ctypedef struct SignedIntBuf
+
+# for PyArrayInterface:
+CONTIGUOUS=0x01
+FORTRAN=0x02
+ALIGNED=0x100
+NOTSWAPPED=0x200
+WRITEABLE=0x400
+
+# byteorder dictionary
+byteorder = {'<':'little', '>':'big'}
+
+ctypedef struct PyArrayInterface:
+ int version # contains the integer 2 as a sanity check
+ int nd # number of dimensions
+ char typekind # kind in array --- character code of typestr
+ int itemsize # size of each element
+ int flags # flags indicating how the data should be interpreted
+ Py_intptr_t *shape # A length-nd array of shape information
+ Py_intptr_t *strides # A length-nd array of stride information
+ void *data # A pointer to the first element of the array
+
+cdef void* free_array_interface(object arr):
+ Py_DECREF(arr)
+
+
+cdef class NumInd:
+ cdef void *data
+ cdef int _nd
+ cdef Py_intptr_t *_shape
+ cdef Py_intptr_t *_strides
+ cdef PyArrayInterface *inter
+ cdef object _t_shape, _t_strides, _undarray
+
+ def __init__(self, object undarray):
+ cdef int i, stride
+ cdef object array_shape, array_strides
+
+ # Keep a reference to the underlying object
+ self._undarray = undarray
+ # Get the shape and strides C arrays
+ array_shape = undarray.__array_interface__["shape"]
+ self._t_shape = array_shape
+ # The number of dimensions
+ self._nd = len(array_shape)
+ # The shape
+ self._shape = <Py_intptr_t *>malloc(self._nd*sizeof(Py_intptr_t))
+ for i from 0 <= i < self._nd:
+ self._shape[i] = self._t_shape[i]
+ # The strides (compute them if needed)
+ array_strides = undarray.__array_interface__["strides"]
+ self._t_strides = array_strides
+ self._strides = <Py_intptr_t *>malloc(self._nd*sizeof(Py_intptr_t))
+ if array_strides:
+ for i from 0 <= i < self._nd:
+ self._strides[i] = array_strides[i]
+ else:
+ # strides is None. Compute them explicitely.
+ self._t_strides = [0] * self._nd
+ stride = int(self.typestr[2:])
+ for i from self._nd > i >= 0:
+ self._strides[i] = stride
+ self._t_strides[i] = stride
+ stride = stride * array_shape[i]
+ self._t_strides = tuple(self._t_strides)
+ # Populate the C array interface
+ self.inter = self._get_array_interface()
+
+ # Properties. This are visible from Python space.
+ # Add as many as you want.
+
+ property undarray: # Returns the underlying array
+ def __get__(self):
+ return self._undarray
+
+ property shape:
+ def __get__(self):
+ return self._t_shape
+
+ property strides:
+ def __get__(self):
+ return self._t_strides
+
+ property typestr:
+ def __get__(self):
+ return self._undarray.__array_interface__["typestr"]
+
+ property typekind:
+ def __get__(self):
+ return chr(self.inter.typekind)
+
+ property readonly:
+ def __get__(self):
+ return self._undarray.__array_interface__["data"][1]
+
+ property __array_struct__:
+ "Allows other numerical packages to obtain a new object."
+ def __get__(self):
+ if hasattr(self._undarray, "__array_struct__"):
+ return self._undarray.__array_struct__
+ else:
+ # No an underlying array with __array_struct__
+ # Deliver an equivalent PyCObject.
+ Py_INCREF(self)
+ return PyCapsule_New(<void*>self.inter,
+ "struct array",
+ <PyCapsule_Destructor>free_array_interface)
+
+ cdef PyArrayInterface *_get_array_interface(self):
+ "Populates the array interface"
+ cdef PyArrayInterface *inter
+ cdef object undarray, data_address, typestr
+ cdef object obj
+
+ undarray = self._undarray
+ typestr = self.typestr
+ inter = <PyArrayInterface *>malloc(sizeof(PyArrayInterface))
+ if inter is NULL:
+ raise MemoryError()
+
+ inter.version = 2
+ inter.nd = self._nd
+ inter.typekind = ord(typestr[1])
+ inter.itemsize = int(typestr[2:])
+ inter.flags = 0 # initialize flags
+ if typestr[0] == '|':
+ inter.flags = inter.flags | NOTSWAPPED
+ elif byteorder[typestr[0]] == sys.byteorder:
+ inter.flags = inter.flags | NOTSWAPPED
+ if not self.readonly:
+ inter.flags = inter.flags | WRITEABLE
+ # XXX how to determine the ALIGNED flag?
+ inter.strides = self._strides
+ inter.shape = self._shape
+ # Get the data address
+ obj = undarray.__array_interface__["data"]
+ data_address = obj[0]
+ inter.data = <void*>PyInt_AsLong(data_address)
+ return inter
+
+
+ # This is just an example on how to modify the data in C space
+ # (and at C speed! :-)
+ def modify(self):
+ "Modify the values of the underlying array"
+ cdef long *ldata
+ cdef double *fdata
+ cdef int i
+
+ # Modify just the first row
+ if chr(self.inter.typekind) == 'i':
+ ldata = <long *>self.inter.data
+ for i from 0 <= i < self.inter.shape[self.inter.nd-1]:
+ ldata[i] = ldata[i] + 1
+ elif chr(self.inter.typekind) == 'f':
+ fdata = <double *>self.inter.data
+ for i from 0 <= i < self.inter.shape[self.inter.nd-1]:
+ fdata[i] = fdata[i] + 1
+
+ def __dealloc__(self):
+ free(self._shape)
+ free(self._strides)
+ free(self.inter)
diff --git a/pymolfile/molfile/numind-cython/numind.so b/pymolfile/molfile/numind-cython/numind.so
new file mode 100755
index 0000000000000000000000000000000000000000..f8b762476eb1d362018f305fce67cf22ec134e2f
Binary files /dev/null and b/pymolfile/molfile/numind-cython/numind.so differ
diff --git a/pymolfile/molfile/numind-cython/test_numpy_swig.py b/pymolfile/molfile/numind-cython/test_numpy_swig.py
new file mode 100644
index 0000000000000000000000000000000000000000..d53a1b1d2874a0a7592975989918f36a5e0be95d
--- /dev/null
+++ b/pymolfile/molfile/numind-cython/test_numpy_swig.py
@@ -0,0 +1,42 @@
+import numpy
+import ctypes
+import numind
+
+# Create an arbitrary object for each package
+np=numpy.arange(12, dtype=numpy.float)
+#np=numpy.arange(12)
+np.shape = (4,3)
+
+#ns = _numpy_swig(2,2)
+#print(ns)
+
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+##for obj in [np]:
+# ni = _numpy_swig
+# print("original object type-->", type(ni.inter))
+# # Print some values
+# #print("typestr --> {0}", ni.typestr)
+# #print("shape --> {0}", ni.shape)
+# #print("strides --> {0}", ni.strides)
+# npa = numpy.asarray(ni)
+# print("object after a numpy re-wrapping --> " , npa)
+# #ni.modify()
+# #print("object after modification in C space --> {0}", npa)
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+for obj in [np]:
+ ni = numind.NumInd(obj)
+ print("original object type-->", type(ni.undarray))
+ # Print some values
+ print("typestr -->", ni.typestr)
+ print("typekind -->", ni.typekind)
+ print("shape -->", ni.shape)
+ print("strides -->", ni.strides)
+ npa = numpy.asarray(ni)
+ print("object after a numpy re-wrapping -->", npa)
+ ni.modify()
+ print("object after modification in C space -->", npa)
+
diff --git a/pymolfile/molfile/numpy_swig.h b/pymolfile/molfile/numpy_swig.h
new file mode 100644
index 0000000000000000000000000000000000000000..f884368cfc15478b8389f61abe8bbc9cb26da68e
--- /dev/null
+++ b/pymolfile/molfile/numpy_swig.h
@@ -0,0 +1,12 @@
+#ifndef NUMPY_SWIG
+#define NUMPY_SWIG
+
+typedef struct SignedIntBuf
+{
+ int* data;
+ int shape[2];
+ int strides[2];
+} SignedIntBuf;
+
+#endif
+
diff --git a/pymolfile/molfile/numpy_swig.i b/pymolfile/molfile/numpy_swig.i
new file mode 100644
index 0000000000000000000000000000000000000000..7adc4f2ccbdc8d09e814778c4c15d74c44e837da
--- /dev/null
+++ b/pymolfile/molfile/numpy_swig.i
@@ -0,0 +1,178 @@
+%{
+#define SWIG_FILE_WITH_INIT
+%}
+%include "numpy.i"
+%init %{
+import_array();
+%}
+
+%module (docstring="This is a Python SWIG-wrapped module") numpy_swig
+
+%{
+#include "numpy_swig.h"
+#include <numpy/arrayobject.h>
+
+#if PY_VERSION_HEX >= 0x03000000
+NPY_NO_EXPORT void
+gentype_struct_free(PyObject *ptr)
+{
+ PyArrayInterface *arrif;
+ PyObject *context;
+
+ arrif = (PyArrayInterface*)PyCapsule_GetPointer(ptr, NULL);
+ context = (PyObject *)PyCapsule_GetContext(ptr);
+ Py_DECREF(context);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtr(void *ptr, void (*dtor)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, dtor);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context, void (*dtor)(PyObject *))
+{
+ PyObject *ret = NpyCapsule_FromVoidPtr(ptr, dtor);
+ if (ret != NULL && PyCapsule_SetContext(ret, context) != 0) {
+ PyErr_Clear();
+ Py_DECREF(ret);
+ ret = NULL;
+ }
+ return ret;
+}
+#else
+NPY_NO_EXPORT void
+gentype_struct_free(void *ptr, void *arg)
+{
+ PyArrayInterface *arrif = (PyArrayInterface *)ptr;
+ Py_DECREF((PyObject *)arg);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context,
+ void (*dtor)(void *, void *))
+{
+ return PyCObject_FromVoidPtrAndDesc(ptr, context, dtor);
+}
+#endif
+
+#ifndef Py_CAPSULE_H
+typedef void(*PyCapsule_Destructor)(void *, void *);
+#endif
+
+void delete_SignedIntBuf(SignedIntBuf* buffer)
+{
+ free(buffer->data);
+ free(buffer);
+}
+
+void free_array_interface( void* ptr, void *arr )
+{
+ PyArrayInterface* inter;
+ PyObject* arrpy;
+
+ inter = (PyArrayInterface*)ptr;
+ arrpy = (PyObject*)arr;
+ Py_DECREF(arrpy);
+ free(inter);
+}
+void free_capsule(PyObject* arr)
+{
+ PyArrayInterface* inter;
+ inter = (PyArrayInterface*) PyCapsule_GetPointer(arr, "struct SignedIntBuf");
+ Py_DECREF(arr);
+ free(inter);
+}
+%}
+
+%inline %{PyObject* get__array_struct__(PyObject* self)
+{
+ PyArrayInterface *inter;
+ PyObject *obj;
+ int nd;
+ nd = 2;
+ Py_intptr_t *shape, *strides;
+ void *data = NULL;
+
+ shape = (Py_intptr_t *)malloc(nd*sizeof(Py_intptr_t));
+ strides = (Py_intptr_t *)malloc(nd*sizeof(Py_intptr_t));
+
+ inter = (PyArrayInterface*)malloc(sizeof(PyArrayInterface));
+ if (inter==NULL)
+ return PyErr_NoMemory();
+
+ inter->two = 2;
+ inter->nd = nd;
+ inter->typekind = 'i';
+ inter->itemsize = sizeof(int);
+ inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE;
+ inter->strides = strides;
+ inter->shape = shape;
+ inter->data = (void*) data;
+ Py_INCREF(self);
+ obj = NpyCapsule_FromVoidPtrAndDesc(inter, self, gentype_struct_free);
+/*
+#ifdef Py_CAPSULE_H
+ obj = PyCapsule_New((void*)inter, "struct SignedIntBuf", free_capsule);
+#else
+ obj = PyCObject_FromVoidPtrAndDesc((void*)inter, (void*)self, free_array_interface);
+#endif
+*/
+ return obj;
+}
+%}
+
+%include numpy_swig.h
+
+%extend SignedIntBuf{
+ %feature("autodoc", "The comment docstring")SignedIntBuf;
+ SignedIntBuf(int width, int height)
+ {
+ SignedIntBuf* buffer = (SignedIntBuf*) malloc(sizeof(SignedIntBuf));
+ int shape[2] = { height, width };
+ int strides[2] = { width * sizeof(int), sizeof(int) };
+ buffer->shape[0] = shape[0];
+ buffer->shape[1] = shape[1];
+ buffer->strides[0] = strides[0];
+ buffer->strides[1] = strides[1];
+ buffer->data = (int*) malloc(width*height*sizeof(int));
+ return buffer;
+ }
+
+ ~SignedIntBuf();
+
+ char *__str__()
+ {
+ static char tmp[1024];
+ int i, j;
+ int used = 0;
+ used += sprintf(tmp, "Array:\n");
+ for(i=0; i < $self->shape[0]; i++)
+ {
+ for(j=0; j < $self->shape[1]; j++)
+ used += sprintf(tmp + used, "%d\t", $self->data[j + i*$self->shape[1]]);
+ used += sprintf(tmp + used, "\n");
+ }
+ return tmp;
+ }
+
+ %pythoncode
+ {
+ def __array_struct__get(self):
+ return get__array_struct__(self)
+
+ property __array_struct__:
+ "Allows other numerical packages to obtain a new object."
+ def __get__(self):
+ return __array_struct__get(self)
+ }
+};
+
+
diff --git a/pymolfile/molfile/numpy_swig.py b/pymolfile/molfile/numpy_swig.py
new file mode 100644
index 0000000000000000000000000000000000000000..32b6df758c6c317243639454f4e4122bc1841c16
--- /dev/null
+++ b/pymolfile/molfile/numpy_swig.py
@@ -0,0 +1,150 @@
+# 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.
+
+"""This is a Python SWIG-wrapped module"""
+
+
+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, '_numpy_swig')).lstrip('.')
+ try:
+ return importlib.import_module(mname)
+ except ImportError:
+ return importlib.import_module('_numpy_swig')
+ _numpy_swig = 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('_numpy_swig', [dirname(__file__)])
+ except ImportError:
+ import _numpy_swig
+ return _numpy_swig
+ try:
+ _mod = imp.load_module('_numpy_swig', fp, pathname, description)
+ finally:
+ if fp is not None:
+ fp.close()
+ return _mod
+ _numpy_swig = swig_import_helper()
+ del swig_import_helper
+else:
+ import _numpy_swig
+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
+
+
+def get__array_struct__(arg1: 'PyObject *') -> "PyObject *":
+ return _numpy_swig.get__array_struct__(arg1)
+get__array_struct__ = _numpy_swig.get__array_struct__
+class SignedIntBuf(_object):
+ __swig_setmethods__ = {}
+ __setattr__ = lambda self, name, value: _swig_setattr(self, SignedIntBuf, name, value)
+ __swig_getmethods__ = {}
+ __getattr__ = lambda self, name: _swig_getattr(self, SignedIntBuf, name)
+ __repr__ = _swig_repr
+ __swig_setmethods__["data"] = _numpy_swig.SignedIntBuf_data_set
+ __swig_getmethods__["data"] = _numpy_swig.SignedIntBuf_data_get
+ if _newclass:
+ data = _swig_property(_numpy_swig.SignedIntBuf_data_get, _numpy_swig.SignedIntBuf_data_set)
+ __swig_setmethods__["shape"] = _numpy_swig.SignedIntBuf_shape_set
+ __swig_getmethods__["shape"] = _numpy_swig.SignedIntBuf_shape_get
+ if _newclass:
+ shape = _swig_property(_numpy_swig.SignedIntBuf_shape_get, _numpy_swig.SignedIntBuf_shape_set)
+ __swig_setmethods__["strides"] = _numpy_swig.SignedIntBuf_strides_set
+ __swig_getmethods__["strides"] = _numpy_swig.SignedIntBuf_strides_get
+ if _newclass:
+ strides = _swig_property(_numpy_swig.SignedIntBuf_strides_get, _numpy_swig.SignedIntBuf_strides_set)
+
+ def __init__(self, width: 'int', height: 'int'):
+ """The comment docstring"""
+ this = _numpy_swig.new_SignedIntBuf(width, height)
+ try:
+ self.this.append(this)
+ except __builtin__.Exception:
+ self.this = this
+ __swig_destroy__ = _numpy_swig.delete_SignedIntBuf
+ __del__ = lambda self: None
+
+ def __str__(self) -> "char *":
+ return _numpy_swig.SignedIntBuf___str__(self)
+
+ def __array_struct__get(self):
+ return get__array_struct__(self)
+
+ property __array_struct__:
+ "Allows other numerical packages to obtain a new object."
+ def __get__(self):
+ return __array_struct__get(self)
+
+SignedIntBuf_swigregister = _numpy_swig.SignedIntBuf_swigregister
+SignedIntBuf_swigregister(SignedIntBuf)
+
+# This file is compatible with both classic and new-style classes.
+
+
diff --git a/pymolfile/molfile/numpy_swig_wrap.cxx b/pymolfile/molfile/numpy_swig_wrap.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..c2224d3c08a808e30b9fbeb2e894613c4eaadb3a
--- /dev/null
+++ b/pymolfile/molfile/numpy_swig_wrap.cxx
@@ -0,0 +1,4477 @@
+/* ----------------------------------------------------------------------------
+ * 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_SignedIntBuf swig_types[0]
+#define SWIGTYPE_p_char swig_types[1]
+#define SWIGTYPE_p_int 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):= _numpy_swig.so
+ ------------------------------------------------*/
+#if PY_VERSION_HEX >= 0x03000000
+# define SWIG_init PyInit__numpy_swig
+
+#else
+# define SWIG_init init_numpy_swig
+
+#endif
+#define SWIG_name "_numpy_swig"
+
+#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;
+ }
+ };
+}
+
+
+#define SWIG_FILE_WITH_INIT
+
+
+#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>
+
+
+#include "numpy_swig.h"
+#include <numpy/arrayobject.h>
+
+#if PY_VERSION_HEX >= 0x03000000
+NPY_NO_EXPORT void
+gentype_struct_free(PyObject *ptr)
+{
+ PyArrayInterface *arrif;
+ PyObject *context;
+
+ arrif = (PyArrayInterface*)PyCapsule_GetPointer(ptr, NULL);
+ context = (PyObject *)PyCapsule_GetContext(ptr);
+ Py_DECREF(context);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtr(void *ptr, void (*dtor)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, dtor);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context, void (*dtor)(PyObject *))
+{
+ PyObject *ret = NpyCapsule_FromVoidPtr(ptr, dtor);
+ if (ret != NULL && PyCapsule_SetContext(ret, context) != 0) {
+ PyErr_Clear();
+ Py_DECREF(ret);
+ ret = NULL;
+ }
+ return ret;
+}
+#else
+NPY_NO_EXPORT void
+gentype_struct_free(void *ptr, void *arg)
+{
+ PyArrayInterface *arrif = (PyArrayInterface *)ptr;
+ Py_DECREF((PyObject *)arg);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context,
+ void (*dtor)(void *, void *))
+{
+ return PyCObject_FromVoidPtrAndDesc(ptr, context, dtor);
+}
+#endif
+
+#ifndef Py_CAPSULE_H
+typedef void(*PyCapsule_Destructor)(void *, void *);
+#endif
+
+void delete_SignedIntBuf(SignedIntBuf* buffer)
+{
+ free(buffer->data);
+ free(buffer);
+}
+
+void free_array_interface( void* ptr, void *arr )
+{
+ PyArrayInterface* inter;
+ PyObject* arrpy;
+
+ inter = (PyArrayInterface*)ptr;
+ arrpy = (PyObject*)arr;
+ Py_DECREF(arrpy);
+ free(inter);
+}
+void free_capsule(PyObject* arr)
+{
+ PyArrayInterface* inter;
+ inter = (PyArrayInterface*) PyCapsule_GetPointer(arr, "struct SignedIntBuf");
+ Py_DECREF(arr);
+ free(inter);
+}
+
+PyObject* get__array_struct__(PyObject* self)
+{
+ PyArrayInterface *inter;
+ PyObject *obj;
+ int nd;
+ nd = 2;
+ Py_intptr_t *shape, *strides;
+ void *data = NULL;
+
+ shape = (Py_intptr_t *)malloc(nd*sizeof(Py_intptr_t));
+ strides = (Py_intptr_t *)malloc(nd*sizeof(Py_intptr_t));
+
+ inter = (PyArrayInterface*)malloc(sizeof(PyArrayInterface));
+ if (inter==NULL)
+ return PyErr_NoMemory();
+
+ inter->two = 2;
+ inter->nd = nd;
+ inter->typekind = 'i';
+ inter->itemsize = sizeof(int);
+ inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE;
+ inter->strides = strides;
+ inter->shape = shape;
+ inter->data = (void*) data;
+ Py_INCREF(self);
+ obj = NpyCapsule_FromVoidPtrAndDesc(inter, self, gentype_struct_free);
+/*
+#ifdef Py_CAPSULE_H
+ obj = PyCapsule_New((void*)inter, "struct SignedIntBuf", free_capsule);
+#else
+ obj = PyCObject_FromVoidPtrAndDesc((void*)inter, (void*)self, free_array_interface);
+#endif
+*/
+ return obj;
+}
+
+
+#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;
+}
+
+SWIGINTERN SignedIntBuf *new_SignedIntBuf(int width,int height){
+ SignedIntBuf* buffer = (SignedIntBuf*) malloc(sizeof(SignedIntBuf));
+ int shape[2] = { height, width };
+ int strides[2] = { width * sizeof(int), sizeof(int) };
+ buffer->shape[0] = shape[0];
+ buffer->shape[1] = shape[1];
+ buffer->strides[0] = strides[0];
+ buffer->strides[1] = strides[1];
+ buffer->data = (int*) malloc(width*height*sizeof(int));
+ return buffer;
+ }
+SWIGINTERN char *SignedIntBuf___str__(SignedIntBuf *self){
+ static char tmp[1024];
+ int i, j;
+ int used = 0;
+ used += sprintf(tmp, "Array:\n");
+ for(i=0; i < self->shape[0]; i++)
+ {
+ for(j=0; j < self->shape[1]; j++)
+ used += sprintf(tmp + used, "%d\t", self->data[j + i*self->shape[1]]);
+ used += sprintf(tmp + used, "\n");
+ }
+ return tmp;
+ }
+
+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;
+ }
+ return info;
+}
+
+
+SWIGINTERNINLINE PyObject *
+SWIG_FromCharPtrAndSize(const char* carray, size_t size)
+{
+ if (carray) {
+ if (size > INT_MAX) {
+ swig_type_info* pchar_descriptor = SWIG_pchar_descriptor();
+ return pchar_descriptor ?
+ SWIG_InternalNewPointerObj(const_cast< char * >(carray), pchar_descriptor, 0) : SWIG_Py_Void();
+ } else {
+#if PY_VERSION_HEX >= 0x03000000
+#if defined(SWIG_PYTHON_STRICT_BYTE_CHAR)
+ return PyBytes_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
+#else
+#if PY_VERSION_HEX >= 0x03010000
+ return PyUnicode_DecodeUTF8(carray, static_cast< Py_ssize_t >(size), "surrogateescape");
+#else
+ return PyUnicode_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
+#endif
+#endif
+#else
+ return PyString_FromStringAndSize(carray, static_cast< Py_ssize_t >(size));
+#endif
+ }
+ } else {
+ return SWIG_Py_Void();
+ }
+}
+
+
+SWIGINTERNINLINE PyObject *
+SWIG_FromCharPtr(const char *cptr)
+{
+ return SWIG_FromCharPtrAndSize(cptr, (cptr ? strlen(cptr) : 0));
+}
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+SWIGINTERN PyObject *_wrap_get__array_struct__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ PyObject *arg1 = (PyObject *) 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:get__array_struct__",&obj0)) SWIG_fail;
+ arg1 = obj0;
+ result = (PyObject *)get__array_struct__(arg1);
+ resultobj = result;
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_data_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ int *arg2 = (int *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ void *argp2 = 0 ;
+ int res2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:SignedIntBuf_data_set",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_data_set" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_int, SWIG_POINTER_DISOWN | 0 );
+ if (!SWIG_IsOK(res2)) {
+ SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "SignedIntBuf_data_set" "', argument " "2"" of type '" "int *""'");
+ }
+ arg2 = reinterpret_cast< int * >(argp2);
+ if (arg1) (arg1)->data = arg2;
+ resultobj = SWIG_Py_Void();
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_data_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject * obj0 = 0 ;
+ int *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:SignedIntBuf_data_get",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_data_get" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ result = (int *) ((arg1)->data);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_shape_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ int *arg2 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ void *argp2 = 0 ;
+ int res2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:SignedIntBuf_shape_set",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_shape_set" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_int, 0 | 0 );
+ if (!SWIG_IsOK(res2)) {
+ SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "SignedIntBuf_shape_set" "', argument " "2"" of type '" "int [2]""'");
+ }
+ arg2 = reinterpret_cast< int * >(argp2);
+ {
+ if (arg2) {
+ size_t ii = 0;
+ for (; ii < (size_t)2; ++ii) *(int *)&arg1->shape[ii] = *((int *)arg2 + ii);
+ } else {
+ SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""shape""' of type '""int [2]""'");
+ }
+ }
+ resultobj = SWIG_Py_Void();
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_shape_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject * obj0 = 0 ;
+ int *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:SignedIntBuf_shape_get",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_shape_get" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ result = (int *)(int *) ((arg1)->shape);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_strides_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ int *arg2 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ void *argp2 = 0 ;
+ int res2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:SignedIntBuf_strides_set",&obj0,&obj1)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_strides_set" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_int, 0 | 0 );
+ if (!SWIG_IsOK(res2)) {
+ SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "SignedIntBuf_strides_set" "', argument " "2"" of type '" "int [2]""'");
+ }
+ arg2 = reinterpret_cast< int * >(argp2);
+ {
+ if (arg2) {
+ size_t ii = 0;
+ for (; ii < (size_t)2; ++ii) *(int *)&arg1->strides[ii] = *((int *)arg2 + ii);
+ } else {
+ SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in variable '""strides""' of type '""int [2]""'");
+ }
+ }
+ resultobj = SWIG_Py_Void();
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf_strides_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject * obj0 = 0 ;
+ int *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:SignedIntBuf_strides_get",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf_strides_get" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ result = (int *)(int *) ((arg1)->strides);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_int, 0 | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_new_SignedIntBuf(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ int arg1 ;
+ int arg2 ;
+ int val1 ;
+ int ecode1 = 0 ;
+ int val2 ;
+ int ecode2 = 0 ;
+ PyObject * obj0 = 0 ;
+ PyObject * obj1 = 0 ;
+ SignedIntBuf *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"OO:new_SignedIntBuf",&obj0,&obj1)) SWIG_fail;
+ ecode1 = SWIG_AsVal_int(obj0, &val1);
+ if (!SWIG_IsOK(ecode1)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_SignedIntBuf" "', argument " "1"" of type '" "int""'");
+ }
+ arg1 = static_cast< int >(val1);
+ ecode2 = SWIG_AsVal_int(obj1, &val2);
+ if (!SWIG_IsOK(ecode2)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "new_SignedIntBuf" "', argument " "2"" of type '" "int""'");
+ }
+ arg2 = static_cast< int >(val2);
+ result = (SignedIntBuf *)new_SignedIntBuf(arg1,arg2);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SignedIntBuf, SWIG_POINTER_NEW | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_delete_SignedIntBuf(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject * obj0 = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:delete_SignedIntBuf",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, SWIG_POINTER_DISOWN | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_SignedIntBuf" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ delete_SignedIntBuf(arg1);
+ resultobj = SWIG_Py_Void();
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_SignedIntBuf___str__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ SignedIntBuf *arg1 = (SignedIntBuf *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject * obj0 = 0 ;
+ char *result = 0 ;
+
+ if (!PyArg_ParseTuple(args,(char *)"O:SignedIntBuf___str__",&obj0)) SWIG_fail;
+ res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_SignedIntBuf, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SignedIntBuf___str__" "', argument " "1"" of type '" "SignedIntBuf *""'");
+ }
+ arg1 = reinterpret_cast< SignedIntBuf * >(argp1);
+ result = (char *)SignedIntBuf___str__(arg1);
+ resultobj = SWIG_FromCharPtr((const char *)result);
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *SignedIntBuf_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *obj;
+ if (!PyArg_ParseTuple(args,(char *)"O:swigregister", &obj)) return NULL;
+ SWIG_TypeNewClientData(SWIGTYPE_p_SignedIntBuf, SWIG_NewClientData(obj));
+ return SWIG_Py_Void();
+}
+
+static PyMethodDef SwigMethods[] = {
+ { (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL},
+ { (char *)"get__array_struct__", _wrap_get__array_struct__, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_data_set", _wrap_SignedIntBuf_data_set, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_data_get", _wrap_SignedIntBuf_data_get, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_shape_set", _wrap_SignedIntBuf_shape_set, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_shape_get", _wrap_SignedIntBuf_shape_get, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_strides_set", _wrap_SignedIntBuf_strides_set, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_strides_get", _wrap_SignedIntBuf_strides_get, METH_VARARGS, NULL},
+ { (char *)"new_SignedIntBuf", _wrap_new_SignedIntBuf, METH_VARARGS, (char *)"The comment docstring"},
+ { (char *)"delete_SignedIntBuf", _wrap_delete_SignedIntBuf, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf___str__", _wrap_SignedIntBuf___str__, METH_VARARGS, NULL},
+ { (char *)"SignedIntBuf_swigregister", SignedIntBuf_swigregister, METH_VARARGS, NULL},
+ { NULL, NULL, 0, NULL }
+};
+
+
+/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
+
+static swig_type_info _swigt__p_SignedIntBuf = {"_p_SignedIntBuf", "SignedIntBuf *", 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 *swig_type_initial[] = {
+ &_swigt__p_SignedIntBuf,
+ &_swigt__p_char,
+ &_swigt__p_int,
+};
+
+static swig_cast_info _swigc__p_SignedIntBuf[] = { {&_swigt__p_SignedIntBuf, 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 *swig_cast_initial[] = {
+ _swigc__p_SignedIntBuf,
+ _swigc__p_char,
+ _swigc__p_int,
+};
+
+
+/* -------- 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();
+
+#if PY_VERSION_HEX >= 0x03000000
+ return m;
+#else
+ return;
+#endif
+}
+
diff --git a/pymolfile/molfile/pymolfile-backup.c b/pymolfile/molfile/pymolfile-backup.c
new file mode 100644
index 0000000000000000000000000000000000000000..9e58ed6b0ddee6cd175455dd65178720aed106a7
--- /dev/null
+++ b/pymolfile/molfile/pymolfile-backup.c
@@ -0,0 +1,329 @@
+/* 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"
+
+//for PyArrayInterface:
+#define CONTIGUOUS=0x01
+#define FORTRAN=0x02
+#define ALIGNED=0x100
+#define NOTSWAPPED=0x200
+#define WRITEABLE=0x400
+
+//byteorder dictionary
+char* byteorder = {"<", "little", ">", "big"}
+
+int numplugins=0;
+molfile_plugin_t** plugin_list;
+
+
+typedef struct PyArrayInterface{
+ int version; //contains the integer 2 as a sanity check
+ int nd; //number of dimensions
+ char typekind; //kind in array --- character code of typestr
+ int itemsize; //size of each element
+ int flags; //flags indicating how the data should be interpreted
+ Py_intptr_t *shape; //A length-nd array of shape information
+ Py_intptr_t *strides; //A length-nd array of stride information
+ void *data; //A pointer to the first element of the array
+};
+
+
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Helper functions to set and store plugins *
+ * * * * * * * * * * * * * * * * * * * * * * */
+
+void* free_array_interface(PyObject *arr){
+ Py_DECREF(arr);
+}
+
+#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)
+{
+ molfile_plugin_t* plugin;
+ if(plug_no < 0){
+ plugin = NULL;
+ } else {
+ plugin = plug_list[plug_no];
+ }
+ return plugin;
+}
+
+#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 */
+
+PyObject * my_read_structure(PyObject* molpack) {
+ Py_Initialize();
+ import_array();
+
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* atoms;
+ int numatoms, status;
+ PyArray_Descr *descr;
+ PyObject p*;
+ if (PyType_Ready(&MolAtomType) < 0)
+ return NULL;
+ PyTypeObject *atype = &MolAtomType;
+ MolAtom *atom_t;
+ atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
+ p = (PyObject*) atom_t;
+ descr = PyArray_DescrFromObject(p, NULL)
+ MolObject* plugin_handle = (MolObject*) molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ status = plugin->read_structure(file_handle, &options, atoms);
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ PyArrayObject* oresid;
+ PyObject* array;
+ int64_t* cresid;
+ int nd = 1;
+ npy_intp dims[1] = { numatoms };
+ oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
+ Py_DECREF(p);
+ array = (PyArrayObject*) PyArray_SimpleNewFromDescr(1, dims, descr);
+ PyObject_Print(array, stdout, 0);
+ if (!oresid){
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into numpy array.");
+ return NULL;
+ }
+ npy_intp* n = PyArray_DIMS(oresid);
+ cresid = (int64_t*) PyArray_DATA(oresid);
+
+// for (i=0;i<numatoms;i++){
+// cresid[i] = (int64_t) atoms[i].resid;
+// }
+ return (PyObject*) PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);
+}
+
+
diff --git a/pymolfile/molfile/pymolfile-backup2.c b/pymolfile/molfile/pymolfile-backup2.c
new file mode 100644
index 0000000000000000000000000000000000000000..3411b394b87105aad96f3903b0311e4acd61899c
--- /dev/null
+++ b/pymolfile/molfile/pymolfile-backup2.c
@@ -0,0 +1,565 @@
+/* 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"
+
+//for PyArrayInterface:
+/*
+#define CONTIGUOUS 0x01
+#define FORTRAN 0x02
+#define ALIGNED 0x100
+#define NOTSWAPPED 0x200
+#define WRITEABLE 0x400
+#define ARR_HAS_DESCR 0x800
+*/
+//byteorder dictionary
+//char** byteorder = {"<", "little", ">", "big"};
+
+int numplugins=0;
+molfile_plugin_t** plugin_list;
+
+/*
+typedef struct PyArrayInterface{
+ int version; //contains the integer 2 as a sanity check
+ int nd; //number of dimensions
+ char typekind; //kind in array --- character code of typestr
+ int itemsize; //size of each element
+ int flags; //flags indicating how the data should be interpreted
+ Py_intptr_t *shape; //A length-nd array of shape information
+ Py_intptr_t *strides; //A length-nd array of stride information
+ void *data; //A pointer to the first element of the array
+};
+*/
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Helper functions to set and store plugins *
+ * * * * * * * * * * * * * * * * * * * * * * */
+
+#if PY_VERSION_HEX >= 0x03000000
+#define PyString_FromString PyBytes_FromString
+NPY_NO_EXPORT void
+gentype_struct_free(PyObject *ptr)
+{
+ PyArrayInterface *arrif;
+ PyObject *context;
+
+ arrif = (PyArrayInterface*)PyCapsule_GetPointer(ptr, NULL);
+ context = (PyObject *)PyCapsule_GetContext(ptr);
+ Py_DECREF(context);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtr(void *ptr, void (*dtor)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, dtor);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context, void (*dtor)(PyObject *))
+{
+ PyObject *ret = NpyCapsule_FromVoidPtr(ptr, dtor);
+ if (ret != NULL && PyCapsule_SetContext(ret, context) != 0) {
+ PyErr_Clear();
+ Py_DECREF(ret);
+ ret = NULL;
+ }
+ return ret;
+}
+#else
+#define PyBytes_FromString PyString_FromString
+NPY_NO_EXPORT void
+gentype_struct_free(void *ptr, void *arg)
+{
+ PyArrayInterface *arrif = (PyArrayInterface *)ptr;
+ Py_DECREF((PyObject *)arg);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context,
+ void (*dtor)(void *, void *))
+{
+ return PyCObject_FromVoidPtrAndDesc(ptr, context, dtor);
+}
+#endif
+
+
+#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)
+{
+ molfile_plugin_t* plugin;
+ if(plug_no < 0){
+ plugin = NULL;
+ } else {
+ plugin = plug_list[plug_no];
+ }
+ return plugin;
+}
+
+#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 */
+
+PyObject * my_read_structure(PyObject* molpack) {
+ Py_Initialize();
+ import_array();
+
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* atoms;
+ int numatoms, status;
+ PyArray_Descr *descr;
+ PyObject *p = NULL;
+ //if (PyType_Ready(&MolAtomType) < 0)
+ // return NULL;
+ //PyTypeObject *atype = &MolAtomType;
+ //MolAtom *atom_t;
+ //atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
+ //p = (PyObject*) atom_t;
+ descr = PyArray_DescrFromObject(p, NULL);
+ MolObject* plugin_handle = (MolObject*) molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ status = plugin->read_structure(file_handle, &options, atoms);
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ PyArrayObject* oresid;
+ PyObject* array;
+ int64_t* cresid;
+ int nd = 1;
+ npy_intp dims[1] = { numatoms };
+ oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
+ Py_DECREF(p);
+ //array = (PyArrayObject*) PyArray_SimpleNewFromDescr(1, dims, descr);
+ //PyObject_Print(array, stdout, 0);
+ if (!oresid){
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into numpy array.");
+ return NULL;
+ }
+ npy_intp* n = PyArray_DIMS(oresid);
+ cresid = (int64_t*) PyArray_DATA(oresid);
+
+// for (i=0;i<numatoms;i++){
+// cresid[i] = (int64_t) atoms[i].resid;
+// }
+ return (PyObject*) PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);
+}
+
+
+PyObject* get_structure(PyObject* self)
+{
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* data;
+ int numatoms, status;
+ int nd;
+ PyArrayInterface *inter;
+ PyArrayObject *ret;
+ char endian = NPY_NATBYTE;
+ // Access plugin_handle values
+ MolObject* plugin_handle = (MolObject*) self;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ // Allocate memory for array of molfile_atom_t struct
+ data = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ // Get array values in molfile_atom_t
+ status = plugin->read_structure(file_handle, &options, data);
+ // Check if the plugin returns the results
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ // Now, we need to allocate a PyArray with PyArrayInterface
+ // and assign the allocated memory block to the data.
+ // To do this, we will build a numpy array from scratch.
+ // First, allocate a PyObject of PyArrayInterface and
+ // assign relevant information such as typestr, descr for C-side
+ // struct and second we will assign molfile_atom_t array as a block
+ // of data. Last, hope this works.
+ nd = 1;
+ npy_intp dims[1] = { 1 };
+ // We would allocate a numpy array with
+ // but will not look clever to copy all the data into the new array.
+ // Instead, we allocate a numpy array with one element and change
+ // the definition of array. I know I said that it will be from scratch
+ // but let's accept nobody wants to define everything in numpy again.
+ //oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT);
+ // NPY_INT? Don't worry, we will change it.
+ //Py_intptr_t *shape, *strides;
+ //void *data = NULL;
+
+ inter = (PyArrayInterface*)malloc(sizeof(PyArrayInterface));
+ if (inter==NULL)
+ return PyErr_NoMemory();
+
+ // __array_interface__ descr for C side of __array_struct__
+ // Could not find a better way to generate the list of tuples for
+ // Python side. May need to change this later.
+ PyObject *tuple = PyTuple_New(13);
+ // One tuple to bind them
+ PyObject *py_list_name = PyList_New(2);
+ PyList_SET_ITEM(py_list_name, 0, PyString_FromString("name"));
+ PyList_SET_ITEM(py_list_name, 0, PyString_FromString("|S16"));
+ PyTuple_SET_ITEM(tuple, 0, py_list_name);
+ PyObject *py_list_type = PyList_New(2);
+ PyList_SET_ITEM(py_list_type, 0, PyString_FromString("type"));
+ PyList_SET_ITEM(py_list_type, 0, PyString_FromString("|S16"));
+ PyTuple_SET_ITEM(tuple, 1, py_list_type);
+ PyObject *py_list_resname = PyList_New(2);
+ PyList_SET_ITEM(py_list_resname, 0, PyString_FromString("resname"));
+ PyList_SET_ITEM(py_list_resname, 0, PyString_FromString("|S8"));
+ PyTuple_SET_ITEM(tuple, 2, py_list_resname);
+ PyObject *py_list_resid = PyList_New(2);
+ PyList_SET_ITEM(py_list_resid, 0, PyString_FromString("resid"));
+ PyList_SET_ITEM(py_list_resid, 0, PyString_FromString("<i4"));
+ PyTuple_SET_ITEM(tuple, 3, py_list_resid);
+ PyObject *py_list_segid = PyList_New(2);
+ PyList_SET_ITEM(py_list_segid, 0, PyString_FromString("segid"));
+ PyList_SET_ITEM(py_list_segid, 0, PyString_FromString("|S8"));
+ PyTuple_SET_ITEM(tuple, 4, py_list_segid);
+ PyObject *py_list_chain = PyList_New(2);
+ PyList_SET_ITEM(py_list_chain, 0, PyString_FromString("chain"));
+ PyList_SET_ITEM(py_list_chain, 0, PyString_FromString("|S2"));
+ PyTuple_SET_ITEM(tuple, 5, py_list_chain);
+ PyObject *py_list_altloc = PyList_New(2);
+ PyList_SET_ITEM(py_list_altloc, 0, PyString_FromString("altloc"));
+ PyList_SET_ITEM(py_list_altloc, 0, PyString_FromString("|S2"));
+ PyTuple_SET_ITEM(tuple, 6, py_list_altloc);
+ PyObject *py_list_insertion = PyList_New(2);
+ PyList_SET_ITEM(py_list_insertion, 0, PyString_FromString("insertion"));
+ PyList_SET_ITEM(py_list_insertion, 0, PyString_FromString("|S2"));
+ PyTuple_SET_ITEM(tuple, 7, py_list_insertion);
+ PyObject *py_list_occupancy = PyList_New(2);
+ PyList_SET_ITEM(py_list_occupancy, 0, PyString_FromString("occupancy"));
+ PyList_SET_ITEM(py_list_occupancy, 0, PyString_FromString("|f4"));
+ PyTuple_SET_ITEM(tuple, 8, py_list_occupancy);
+ PyObject *py_list_bfactor = PyList_New(2);
+ PyList_SET_ITEM(py_list_bfactor, 0, PyString_FromString("bfactor"));
+ PyList_SET_ITEM(py_list_bfactor, 0, PyString_FromString("|f4"));
+ PyTuple_SET_ITEM(tuple, 9, py_list_bfactor);
+ PyObject *py_list_mass = PyList_New(2);
+ PyList_SET_ITEM(py_list_mass, 0, PyString_FromString("mass"));
+ PyList_SET_ITEM(py_list_mass, 0, PyString_FromString("|f4"));
+ PyTuple_SET_ITEM(tuple, 10, py_list_mass);
+ PyObject *py_list_charge = PyList_New(2);
+ PyList_SET_ITEM(py_list_charge, 0, PyString_FromString("charge"));
+ PyList_SET_ITEM(py_list_charge, 0, PyString_FromString("|f4"));
+ PyTuple_SET_ITEM(tuple, 11, py_list_charge);
+ PyObject *py_list_radius = PyList_New(2);
+ PyList_SET_ITEM(py_list_radius, 0, PyString_FromString("radius"));
+ PyList_SET_ITEM(py_list_radius, 0, PyString_FromString("|f4"));
+ PyTuple_SET_ITEM(tuple, 12, py_list_radius);
+ PyObject *py_list_atomicnumber = PyList_New(2);
+ PyList_SET_ITEM(py_list_atomicnumber, 0, PyString_FromString("atomicnumber"));
+ PyList_SET_ITEM(py_list_atomicnumber, 0, PyString_FromString("|i4"));
+ PyTuple_SET_ITEM(tuple, 13, py_list_atomicnumber);
+ //PyArray_Descr *descr = (PyObject*) tuple;
+ PyArray_Descr *descr = NULL;
+ // Here we define the size and stride parameters
+ npy_intp shape[1] = { numatoms };
+ npy_intp strides[1] = { 54*sizeof(char) + 8*sizeof(int) + 20*sizeof(float) };
+
+ inter->two = 2;
+ inter->nd = nd;
+ inter->typekind = 'V';
+ inter->itemsize = 82*sizeof(char);
+ inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE | NPY_ARR_HAS_DESCR;
+ inter->strides = (Py_intptr_t *)strides;
+ inter->shape = (Py_intptr_t *)shape;
+ inter->data = (void*) data;
+ // inter->descr = (PyObject*) tuple;
+ if ((inter->flags & NPY_ARRAY_NOTSWAPPED) != NPY_ARRAY_NOTSWAPPED) {
+ endian = NPY_OPPBYTE;
+ inter->flags &= ~NPY_ARRAY_NOTSWAPPED;
+ }
+ // typestr is relatively easy to assign to __array_interface__
+ printf("TEST1\n");
+ if (inter->flags & NPY_ARR_HAS_DESCR) {
+ printf("TEST1-1\n");
+ if (PyArray_DescrConverter(inter->descr, &descr) == NPY_FAIL) {
+ descr = NULL;
+ PyErr_Clear();
+ }
+ }
+ printf("TEST1-2\n");
+ char buf[40];
+ PyOS_snprintf(buf, sizeof(buf),
+ "%c%c%d", endian,
+ inter->typekind,
+ inter->itemsize);
+ printf("TEST2\n");
+ PyObject *stringobj = PyString_FromString(buf);
+ if (stringobj == NULL) {
+ return NULL;
+ }
+ printf("TEST2-2\n");
+ if (PyArray_DescrConverter(stringobj, &descr) != NPY_SUCCEED) {
+ Py_DECREF(stringobj);
+ return NULL;
+ }
+ printf("TEST2-3\n");
+ Py_DECREF(stringobj);
+
+ printf("TEST3\n");
+ ret = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, descr,
+ inter->nd, inter->shape,
+ inter->strides, inter->data,
+ inter->flags, NULL);
+ printf("TEST4\n");
+ Py_INCREF(inter);
+ if (PyArray_SetBaseObject(ret, (PyObject *)inter) < 0) {
+ Py_DECREF(ret);
+ return NULL;
+ }
+ printf("TEST5\n");
+// Py_DECREF(attr);
+ PyArray_UpdateFlags(ret, NPY_ARRAY_UPDATE_ALL);
+ printf("TEST6\n");
+ return (PyObject *)ret;
+}
+// obj = NpyCapsule_FromVoidPtrAndDesc(inter, self, gentype_struct_free);
+/*
+#ifdef Py_CAPSULE_H
+ obj = PyCapsule_New((void*)inter, "struct SignedIntBuf", free_capsule);
+#else
+ obj = PyCObject_FromVoidPtrAndDesc((void*)inter, (void*)self, free_array_interface);
+#endif
+*/
+ // Cross fingers here.
+// return obj;
+
diff --git a/pymolfile/molfile/pymolfile-backup2.h b/pymolfile/molfile/pymolfile-backup2.h
new file mode 100644
index 0000000000000000000000000000000000000000..a97de9efecb0b8ab79e791abb2a68a3013957c2b
--- /dev/null
+++ b/pymolfile/molfile/pymolfile-backup2.h
@@ -0,0 +1,354 @@
+/* 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"
+#include "Python.h"
+#include "structmember.h"
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#include <numpy/arrayobject.h>
+
+enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
+ pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
+
+#ifndef MAXPLUGINS
+#define MAXPLUGINS 200
+#endif
+
+struct MolObject {
+ PyObject_HEAD
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ int natoms;
+ MolObject(void) {}
+};
+
+static void MolObject_dealloc(MolObject* self)
+{
+ Py_XDECREF(self->plugin);
+ Py_XDECREF(self->file_handle);
+ Py_TYPE(self)->tp_free((PyObject*)self);
+}
+
+static PyObject * MolObject_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
+{
+ MolObject *self;
+
+ self = (MolObject *)type->tp_alloc(type, 0);
+ if (self != NULL) {
+ self->plugin = NULL;
+ self->file_handle = NULL;
+ self->natoms = 0;
+ }
+
+ return (PyObject *)self;
+}
+
+static int MolObject_init(MolObject *self, PyObject *args, PyObject *kwds)
+{
+ molfile_plugin_t *plugin = NULL;
+ void *file_handle = NULL;
+ molfile_plugin_t *tmp1 = NULL;
+ void *tmp2 = NULL;
+
+ static char *kwlist[] = {"plugin", "file_handle", "natoms", NULL};
+
+ if (! PyArg_ParseTupleAndKeywords(args, kwds, "|OOi", kwlist,
+ &plugin, &file_handle,
+ &self->natoms))
+ return -1;
+
+ if (plugin) {
+ tmp1 = self->plugin;
+ Py_INCREF(plugin);
+ self->plugin = plugin;
+ Py_XDECREF(tmp1);
+ }
+
+ if (file_handle) {
+ tmp2 = self->file_handle;
+ Py_INCREF(file_handle);
+ self->file_handle = file_handle;
+ Py_XDECREF(tmp2);
+ }
+
+ return 0;
+}
+
+static molfile_plugin_t* MolObject_plugin(MolObject* self)
+{
+ return self->plugin;
+}
+
+static void* MolObject_file_handle(MolObject* self)
+{
+ return self->file_handle;
+}
+
+static PyObject* MolObject_natoms(MolObject* self)
+{
+ return PyLong_FromLong((long)self->natoms);
+}
+
+static PyMemberDef MolObject_members[] = {
+ {"plugin", T_OBJECT_EX, offsetof(MolObject, plugin), 0,
+ "molfile_plugin_t type plugin"},
+ {"file_handle", T_OBJECT_EX, offsetof(MolObject, file_handle), 0,
+ "file handle for plugin"},
+ {"natoms", T_INT, offsetof(MolObject, natoms), 0,
+ "number of atoms"},
+ {NULL} /* Sentinel */
+};
+
+static PyMethodDef MolObject_methods[] = {
+ {"get_plugin", (PyCFunction)MolObject_plugin, METH_NOARGS,
+ "Return the plugin"
+ },
+ {"get_file_handle", (PyCFunction)MolObject_file_handle, METH_NOARGS,
+ "Return the plugin"
+ },
+ {"get_natoms", (PyCFunction)MolObject_natoms, METH_NOARGS,
+ "Return the number of atoms"
+ },
+ {NULL} /* Sentinel */
+};
+
+
+#ifndef PyVarObject_HEAD_INIT
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+#endif
+
+static PyTypeObject MolObjectType = {
+ PyVarObject_HEAD_INIT(NULL, 0)
+ "molobject", /*tp_name*/
+ sizeof(MolObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)MolObject_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_reserved*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT |
+ Py_TPFLAGS_BASETYPE, /* tp_flags */
+ "molobject objects", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ MolObject_methods, /* tp_methods */
+ MolObject_members, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ (initproc)MolObject_init, /* tp_init */
+ 0, /* tp_alloc */
+ MolObject_new, /* tp_new */
+};
+
+#if 0
+struct MolAtom {
+ PyObject_HEAD
+ char* name;
+ char* type;
+ char* resname;
+ int* resid;
+ char* segid;
+ char* chain;
+ char* altloc;
+ char* insertion;
+ float* occupancy;
+ float* bfactor;
+ float* mass;
+ float* charge;
+ float* radius;
+ float* atomicnumber;
+ float* ctnumber;
+ MolAtom(void) {}
+};
+
+static void MolAtom_dealloc(MolAtom* self)
+{
+ Py_XDECREF(self->name);
+ Py_XDECREF(self->type);
+ Py_XDECREF(self->resname);
+ Py_XDECREF(self->resid);
+ Py_XDECREF(self->segid);
+ Py_XDECREF(self->chain);
+ Py_XDECREF(self->altloc);
+ Py_XDECREF(self->insertion);
+ Py_XDECREF(self->occupancy);
+ Py_XDECREF(self->bfactor);
+ Py_XDECREF(self->mass);
+ Py_XDECREF(self->charge);
+ Py_XDECREF(self->radius);
+ Py_XDECREF(self->atomicnumber);
+ Py_XDECREF(self->ctnumber);
+ Py_TYPE(self)->tp_free((PyObject*)self);
+}
+
+static PyObject * MolAtom_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
+{
+ MolAtom *self;
+
+ self = (MolAtom *)type->tp_alloc(type, 0);
+ if (self != NULL) {
+ self->name = NULL;
+ self->type = NULL;
+ self->resname = NULL;
+ self->resid = NULL;
+ self->segid = NULL;
+ self->chain = NULL;
+ self->altloc = NULL;
+ self->insertion = NULL;
+ self->occupancy = NULL;
+ self->bfactor = NULL;
+ self->mass = NULL;
+ self->charge = NULL;
+ self->radius = NULL;
+ self->atomicnumber = NULL;
+ self->ctnumber = NULL;
+ }
+
+ return (PyObject *)self;
+}
+
+static PyMemberDef MolAtom_members[] = {
+ {"name", T_STRING, offsetof(MolAtom, name), 0,""},
+ {"type", T_STRING, offsetof(MolAtom, type), 0,""},
+ {"resname", T_STRING, offsetof(MolAtom, resname), 0,""},
+ {"resid", T_INT, offsetof(MolAtom, resid), 0,""},
+ {"segid", T_STRING, offsetof(MolAtom, segid), 0,""},
+ {"chain", T_STRING, offsetof(MolAtom, chain), 0,""},
+ {"altloc", T_STRING, offsetof(MolAtom, altloc), 0,""},
+ {"insertion", T_STRING, offsetof(MolAtom, insertion), 0,""},
+ {"occupancy", T_FLOAT, offsetof(MolAtom, occupancy), 0,""},
+ {"bfactor", T_FLOAT, offsetof(MolAtom, bfactor), 0,""},
+ {"mass", T_FLOAT, offsetof(MolAtom, mass), 0,""},
+ {"charge", T_FLOAT, offsetof(MolAtom, charge), 0,""},
+ {"radius", T_FLOAT, offsetof(MolAtom, radius), 0,""},
+ {"atomicnumber", T_INT, offsetof(MolAtom, atomicnumber), 0,""},
+ {"ctnumber", T_INT, offsetof(MolAtom, ctnumber), 0,""},
+ {NULL, NULL, 0, NULL} /* Sentinel */
+};
+
+static PyTypeObject MolAtomType = {
+ PyVarObject_HEAD_INIT(NULL, 0)
+ "molobject", /*tp_name*/
+ sizeof(MolAtom), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)MolAtom_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_reserved*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT |
+ Py_TPFLAGS_BASETYPE, /* tp_flags */
+ "molatom objects", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ MolAtom_members, /* 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 */
+ MolAtom_new, /* tp_new */
+};
+#endif
+PyObject * my_read_structure(PyObject* molpack);
+PyObject * get_structure(PyObject* molpack);
+
+#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/pymolfile-new.c b/pymolfile/molfile/pymolfile-new.c
new file mode 100644
index 0000000000000000000000000000000000000000..21b1c00209ce30e6994149cfa8ee242034c3545e
--- /dev/null
+++ b/pymolfile/molfile/pymolfile-new.c
@@ -0,0 +1,1522 @@
+/* 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"
+
+
+//for PyArrayInterface:
+/*
+#define CONTIGUOUS 0x01
+#define FORTRAN 0x02
+#define ALIGNED 0x100
+#define NOTSWAPPED 0x200
+#define WRITEABLE 0x400
+#define ARR_HAS_DESCR 0x800
+*/
+//byteorder dictionary
+//char** byteorder = {"<", "little", ">", "big"};
+
+int numplugins=0;
+molfile_plugin_t** plugin_list;
+
+/*
+typedef struct PyArrayInterface{
+ int version; //contains the integer 2 as a sanity check
+ int nd; //number of dimensions
+ char typekind; //kind in array --- character code of typestr
+ int itemsize; //size of each element
+ int flags; //flags indicating how the data should be interpreted
+ Py_intptr_t *shape; //A length-nd array of shape information
+ Py_intptr_t *strides; //A length-nd array of stride information
+ void *data; //A pointer to the first element of the array
+};
+*/
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Helper functions to set and store plugins *
+ * * * * * * * * * * * * * * * * * * * * * * */
+
+#define PyInt_AsSsize_t PyLong_AsSsize_t
+#define PyArray_Check(op) PyObject_TypeCheck(op, &PyArray_Type)
+
+#if PY_VERSION_HEX >= 0x03000000
+#define PyString_FromString PyBytes_FromString
+NPY_NO_EXPORT void
+gentype_struct_free(PyObject *ptr)
+{
+ PyArrayInterface *arrif;
+ PyObject *context;
+
+ arrif = (PyArrayInterface*)PyCapsule_GetPointer(ptr, NULL);
+ context = (PyObject *)PyCapsule_GetContext(ptr);
+ Py_DECREF(context);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+static NPY_INLINE void *
+NpyCapsule_AsVoidPtr(PyObject *obj)
+{
+ void *ret = PyCapsule_GetPointer(obj, NULL);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtr(void *ptr, void (*dtor)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, dtor);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context, void (*dtor)(PyObject *))
+{
+ PyObject *ret = NpyCapsule_FromVoidPtr(ptr, dtor);
+ if (ret != NULL && PyCapsule_SetContext(ret, context) != 0) {
+ PyErr_Clear();
+ Py_DECREF(ret);
+ ret = NULL;
+ }
+ return ret;
+}
+#else
+#define PyBytes_FromString PyString_FromString
+NPY_NO_EXPORT void
+gentype_struct_free(void *ptr, void *arg)
+{
+ PyArrayInterface *arrif = (PyArrayInterface *)ptr;
+ Py_DECREF((PyObject *)arg);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context,
+ void (*dtor)(void *, void *))
+{
+ return PyCObject_FromVoidPtrAndDesc(ptr, context, dtor);
+}
+#endif
+static PyObject *typeDict = NULL; /* Must be explicitly loaded */
+
+#define PyUString_Check PyUnicode_Check
+#define PyUString_GET_SIZE PyUnicode_GET_SIZE
+#define PyUString_FromFormat PyUnicode_FromFormat
+#define PyInt_FromLong PyLong_FromLong
+#define PyString_Type PyBytes_Type
+#define PyInt_Type PyLong_Type
+
+#define NPY_NEXT_ALIGNED_OFFSET(offset, alignment) \
+ (((offset) + (alignment) - 1) & (-(alignment)))
+
+static PyArray_Descr *
+_convert_from_array_descr(PyObject *obj, int align)
+{
+ int n, i, totalsize;
+ int ret;
+ PyObject *fields, *item, *newobj;
+ PyObject *name, *tup, *title;
+ PyObject *nameslist;
+ PyArray_Descr *newea;
+ PyArray_Descr *conv;
+ /* Types with fields need the Python C API for field access */
+ char dtypeflags = NPY_NEEDS_PYAPI;
+ int maxalign = 0;
+
+ printf("Test1\n");
+ n = PyList_GET_SIZE(obj);
+ nameslist = PyTuple_New(n);
+ if (!nameslist) {
+ return NULL;
+ }
+ totalsize = 0;
+ fields = PyDict_New();
+ for (i = 0; i < n; i++) {
+ item = PyList_GET_ITEM(obj, i);
+ if (!PyTuple_Check(item) || (PyTuple_GET_SIZE(item) < 2)) {
+ goto fail;
+ }
+ name = PyTuple_GET_ITEM(item, 0);
+ if (PyUString_Check(name)) {
+ title = NULL;
+ }
+ else if (PyTuple_Check(name)) {
+ if (PyTuple_GET_SIZE(name) != 2) {
+ goto fail;
+ }
+ title = PyTuple_GET_ITEM(name, 0);
+ name = PyTuple_GET_ITEM(name, 1);
+ if (!PyUString_Check(name)) {
+ goto fail;
+ }
+ }
+ else {
+ goto fail;
+ }
+
+ /* Insert name into nameslist */
+ Py_INCREF(name);
+
+ if (PyUString_GET_SIZE(name) == 0) {
+ Py_DECREF(name);
+ if (title == NULL) {
+ name = PyUString_FromFormat("f%d", i);
+ }
+#if PY_VERSION_HEX >= 0x03000000
+ /* On Py3, allow only non-empty Unicode strings as field names */
+ else if (PyUString_Check(title) && PyUString_GET_SIZE(title) > 0) {
+ name = title;
+ Py_INCREF(name);
+ }
+ else {
+ goto fail;
+ }
+#else
+ else {
+ name = title;
+ Py_INCREF(name);
+ }
+#endif
+ }
+ PyTuple_SET_ITEM(nameslist, i, name);
+
+ /* Process rest */
+
+ printf("Test2\n");
+ if (PyTuple_GET_SIZE(item) == 2) {
+ if (align) {
+ printf("Test3\n");
+ ret = PyArray_DescrAlignConverter(PyTuple_GET_ITEM(item, 1),
+ &conv);
+ }
+ else {
+ printf("Test4\n");
+ ret = PyArray_DescrConverter(PyTuple_GET_ITEM(item, 1), &conv);
+ }
+ if (ret == NPY_FAIL) {
+ PyObject_Print(PyTuple_GET_ITEM(item, 1), stderr, 0);
+ }
+ }
+ else if (PyTuple_GET_SIZE(item) == 3) {
+ newobj = PyTuple_GetSlice(item, 1, 3);
+ if (align) {
+ printf("Test5\n");
+ ret = PyArray_DescrAlignConverter(newobj, &conv);
+ }
+ else {
+ printf("Test6\n");
+ ret = PyArray_DescrConverter(newobj, &conv);
+ }
+ Py_DECREF(newobj);
+ }
+ else {
+ goto fail;
+ }
+ if (ret == NPY_FAIL) {
+ goto fail;
+ }
+ if ((PyDict_GetItem(fields, name) != NULL)
+ || (title
+#if PY_VERSION_HEX >= 0x03000000
+ && PyUString_Check(title)
+#else
+ && (PyUString_Check(title) || PyUnicode_Check(title))
+#endif
+ && (PyDict_GetItem(fields, title) != NULL))) {
+#if PY_VERSION_HEX >= 0x03000000
+ name = PyUnicode_AsUTF8String(name);
+#endif
+ PyErr_Format(PyExc_ValueError,
+ "field '%s' occurs more than once", PyBytes_AsString(name));
+#if PY_VERSION_HEX >= 0x03000000
+ Py_DECREF(name);
+#endif
+ goto fail;
+ }
+ dtypeflags |= (conv->flags & NPY_FROM_FIELDS);
+ if (align) {
+ int _align;
+
+ _align = conv->alignment;
+ if (_align > 1) {
+ totalsize = NPY_NEXT_ALIGNED_OFFSET(totalsize, _align);
+ }
+ maxalign = PyArray_MAX(maxalign, _align);
+ }
+ tup = PyTuple_New((title == NULL ? 2 : 3));
+ PyTuple_SET_ITEM(tup, 0, (PyObject *)conv);
+ PyTuple_SET_ITEM(tup, 1, PyInt_FromLong((long) totalsize));
+
+ /*
+ * Title can be "meta-data". Only insert it
+ * into the fields dictionary if it is a string
+ * and if it is not the same as the name.
+ */
+ if (title != NULL) {
+ Py_INCREF(title);
+ PyTuple_SET_ITEM(tup, 2, title);
+ PyDict_SetItem(fields, name, tup);
+#if PY_VERSION_HEX >= 0x03000000
+ if (PyUString_Check(title)) {
+#else
+ if (PyUString_Check(title) || PyUnicode_Check(title)) {
+#endif
+ if (PyDict_GetItem(fields, title) != NULL) {
+ PyErr_SetString(PyExc_ValueError,
+ "title already used as a name or title.");
+ Py_DECREF(tup);
+ goto fail;
+ }
+ PyDict_SetItem(fields, title, tup);
+ }
+ }
+ else {
+ PyDict_SetItem(fields, name, tup);
+ }
+
+ totalsize += conv->elsize;
+ Py_DECREF(tup);
+ }
+
+ if (maxalign > 1) {
+ totalsize = NPY_NEXT_ALIGNED_OFFSET(totalsize, maxalign);
+ }
+
+ newea = PyArray_DescrNewFromType(NPY_VOID);
+ if (newea == NULL) {
+ Py_XDECREF(fields);
+ Py_XDECREF(nameslist);
+ return NULL;
+ }
+ newea->fields = fields;
+ newea->names = nameslist;
+ newea->elsize = totalsize;
+ newea->flags = dtypeflags;
+
+ /* Structured arrays get a sticky aligned bit */
+ if (align) {
+ newea->flags |= NPY_ALIGNED_STRUCT;
+ newea->alignment = maxalign;
+ }
+ return newea;
+
+ fail:
+ Py_DECREF(fields);
+ Py_DECREF(nameslist);
+ return NULL;
+
+}
+
+static NPY_INLINE npy_bool
+_is_basic_python_type(PyTypeObject *tp)
+{
+ return (
+ /* Basic number types */
+ tp == &PyBool_Type ||
+#if PY_VERSION_HEX >= 0x03000000
+ tp == &PyInt_Type ||
+#endif
+ tp == &PyLong_Type ||
+ tp == &PyFloat_Type ||
+ tp == &PyComplex_Type ||
+
+ /* Basic sequence types */
+ tp == &PyList_Type ||
+ tp == &PyTuple_Type ||
+ tp == &PyDict_Type ||
+ tp == &PySet_Type ||
+ tp == &PyFrozenSet_Type ||
+ tp == &PyUnicode_Type ||
+ tp == &PyBytes_Type ||
+#if PY_VERSION_HEX >= 0x03000000
+ tp == &PyString_Type ||
+#endif
+
+ /* other builtins */
+ tp == &PySlice_Type ||
+ tp == Py_TYPE(Py_None) ||
+ tp == Py_TYPE(Py_Ellipsis) ||
+ tp == Py_TYPE(Py_NotImplemented) ||
+
+ /* TODO: ndarray, but we can't see PyArray_Type here */
+
+ /* sentinel to swallow trailing || */
+ NPY_FALSE
+ );
+}
+
+static NPY_INLINE PyObject *
+maybe_get_attr(PyObject *obj, char *name)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ PyObject *res = (PyObject *)NULL;
+
+ /* Attribute referenced by (char *)name */
+ if (tp->tp_getattr != NULL) {
+ res = (*tp->tp_getattr)(obj, name);
+ if (res == NULL) {
+ PyErr_Clear();
+ }
+ }
+ /* Attribute referenced by (PyObject *)name */
+ else if (tp->tp_getattro != NULL) {
+#if PY_VERSION_HEX >= 0x03000000
+ PyObject *w = PyUnicode_InternFromString(name);
+#else
+ PyObject *w = PyString_InternFromString(name);
+#endif
+ if (w == NULL) {
+ return (PyObject *)NULL;
+ }
+ res = (*tp->tp_getattro)(obj, w);
+ Py_DECREF(w);
+ if (res == NULL) {
+ PyErr_Clear();
+ }
+ }
+ return res;
+}
+
+static int
+maybe_set_attr(PyObject *obj, char *name, PyObject *attr)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ int status;
+
+ /* Attribute referenced by (char *)name */
+ if (tp->tp_setattr != NULL) {
+ status = (*tp->tp_setattr)(obj, name, attr);
+ if (status < 0) {
+ PyErr_Clear();
+ return -1;
+ }
+ }
+ /* Attribute referenced by (PyObject *)name */
+ else if (tp->tp_setattro != NULL) {
+#if PY_VERSION_HEX >= 0x03000000
+ PyObject *w = PyUnicode_InternFromString(name);
+#else
+ PyObject *w = PyString_InternFromString(name);
+#endif
+ if (w == NULL) {
+ return -1;
+ }
+ status = (*tp->tp_setattro)(obj, w, attr);
+ Py_DECREF(w);
+ if (status < 0) {
+ PyErr_Clear();
+ return -1;
+ }
+ }
+ return 0;
+}
+
+static int get_array_struct(PyObject* obj, int *maxndim, npy_intp *d_shape, PyArrayInterface* inter)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ PyObject* ret;
+ char* str;
+ int i;
+ str = "__array_struct__";
+ /* We do not need to check for special attributes on trivial types */
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_struct__ interface */
+ ret = maybe_get_attr(obj, str);
+ if (ret != NULL) {
+ int nd = -1;
+ if (PyCapsule_CheckExact(ret)) {
+ PyArrayInterface *inter;
+ inter = (PyArrayInterface *)NpyCapsule_AsVoidPtr(ret);
+ if (inter->two == 2) {
+ nd = inter->nd;
+ if (nd >= 0) {
+ if (nd < *maxndim) {
+ *maxndim = nd;
+ }
+ for (i=0; i<*maxndim; i++) {
+ d_shape[i] = inter->shape[i];
+ }
+ }
+ }
+ }
+ if(nd >= 0){
+ return 0;
+ } else {
+ return -1;
+ }
+ } else {
+ return -1;
+ }
+}
+
+static int my_get_array_attr_interface(PyObject* obj, PyObject* newi){
+ newi = obj;
+// Py_INCREF(obj);
+// Py_DECREF(obj);
+ return 0;
+}
+
+static int get_array_attr_interface(PyObject* obj, char* str, int *maxndim, npy_intp *d_shape, PyObject* newi){
+ PyTypeObject *tp = Py_TYPE(obj);
+ char* dictstr;
+ int i;
+ dictstr = "__array_interface__";
+ PyObject* ret;
+ PyObject* objj;
+ newi = obj;
+ return 0;
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_interface__ interface */
+ printf("T1\n");
+ ret = maybe_get_attr(obj, dictstr);
+ printf("T2\n");
+ if (ret != NULL) {
+ int nd = -1;
+ if (PyDict_Check(ret)) {
+ objj = PyDict_GetItemString(ret, "shape");
+ //newi = PyDict_GetItemString(ret, str);
+ printf("T3\n");
+ if (objj && PyTuple_Check(objj)) {
+ nd = PyTuple_GET_SIZE(objj);
+ printf("T4\n");
+ if (nd >= 0) {
+ *maxndim = nd;
+ for (i=0; i<nd; i++) {
+ d_shape[i] = PyInt_AsSsize_t(PyTuple_GET_ITEM(objj, i));
+ if (d_shape[i] < 0) {
+ PyErr_SetString(PyExc_RuntimeError,
+ "Invalid shape in __array_interface__");
+ return -1;
+ }
+ }
+ }
+ }
+ }
+ if (nd >= 0) {
+ printf("T5\n");
+ //newi = (PyArrayObject*) objj;
+ PyObject* tuple = PyTuple_New(1);
+ PyTuple_SET_ITEM(tuple, 0, objj);
+ newi = (PyObject*) tuple;
+ return 0;
+ } else {
+ return -1;
+ }
+ } else {
+ return -1;
+ }
+}
+
+static int set_array_attr_interface(PyObject* obj, PyObject* attr, int *nd, npy_intp *d_shape, void* data)
+{
+ int i, status;
+/* obj has the __array_interface__ interface */
+ if (obj != NULL || attr !=NULL) {
+ if (PyDict_Check(attr)) {
+ PyObject *new_shape = PyTuple_New(*nd);
+ for (i=0; i<*nd; i++) {
+ PyTuple_SET_ITEM(new_shape, i, PyInt_FromLong((int)d_shape[i]));
+ }
+ status = PyDict_SetItemString(attr, "shape", new_shape);
+ if (status<0){
+ Py_DECREF(new_shape);
+ PyErr_Clear();
+ return -1;
+ }
+ PyObject *new_data = PyTuple_New(*nd);
+ PyTuple_SET_ITEM(new_data, 0, PyLong_FromVoidPtr(data));
+ PyTuple_SET_ITEM(new_data, 1, PyInt_FromLong((long)1));
+ status = PyDict_SetItemString(attr, "data", new_data);
+ if (status<0){
+ Py_DECREF(new_data);
+ PyErr_Clear();
+ return -1;
+ }
+ status = maybe_set_attr(obj, "__array_interface__", attr);
+ if (status<0){
+ Py_DECREF(new_data);
+ Py_DECREF(new_shape);
+ PyErr_Clear();
+ return -1;
+ }
+ return 0;
+ } else {
+ return -1;
+ }
+ } else {
+ return -1;
+ }
+}
+
+
+
+
+#if 0
+NPY_NO_EXPORT int
+MyArray_DescrConverter(PyObject *obj, PyArray_Descr **at)
+{
+ int check_num = NPY_NOTYPE + 10;
+ PyObject *item;
+ int elsize = 0;
+ char endian = '=';
+
+ *at = NULL;
+
+ printf("Test0\n");
+ /* default */
+ if (obj == Py_None) {
+ *at = PyArray_DescrFromType(NPY_DEFAULT_TYPE);
+ return NPY_SUCCEED;
+ }
+
+ printf("Test1\n");
+ if (PyArray_DescrCheck(obj)) {
+ *at = (PyArray_Descr *)obj;
+ Py_INCREF(*at);
+ return NPY_SUCCEED;
+ }
+
+ printf("Test2\n");
+ if (PyType_Check(obj)) {
+ if (PyType_IsSubtype((PyTypeObject *)obj, &PyGenericArrType_Type)) {
+ *at = PyArray_DescrFromTypeObject(obj);
+ return (*at) ? NPY_SUCCEED : NPY_FAIL;
+ }
+ check_num = NPY_OBJECT;
+#if !defined(NPY_PY3K)
+ if (obj == (PyObject *)(&PyInt_Type)) {
+ check_num = NPY_LONG;
+ }
+ else if (obj == (PyObject *)(&PyLong_Type)) {
+ check_num = NPY_LONGLONG;
+ }
+#else
+ if (obj == (PyObject *)(&PyLong_Type)) {
+ check_num = NPY_LONG;
+ }
+#endif
+ else if (obj == (PyObject *)(&PyFloat_Type)) {
+ check_num = NPY_DOUBLE;
+ }
+ else if (obj == (PyObject *)(&PyComplex_Type)) {
+ check_num = NPY_CDOUBLE;
+ }
+ else if (obj == (PyObject *)(&PyBool_Type)) {
+ check_num = NPY_BOOL;
+ }
+ else if (obj == (PyObject *)(&PyBytes_Type)) {
+ check_num = NPY_STRING;
+ }
+ else if (obj == (PyObject *)(&PyUnicode_Type)) {
+ check_num = NPY_UNICODE;
+ }
+#if defined(NPY_PY3K)
+ else if (obj == (PyObject *)(&PyMemoryView_Type)) {
+#else
+ else if (obj == (PyObject *)(&PyBuffer_Type)) {
+#endif
+ check_num = NPY_VOID;
+ }
+ else {
+ *at = _arraydescr_fromobj(obj);
+ if (*at) {
+ return NPY_SUCCEED;
+ }
+ }
+ goto finish;
+ }
+ printf("Test3\n");
+
+ /* or a typecode string */
+
+ if (PyUnicode_Check(obj)) {
+ /* Allow unicode format strings: convert to bytes */
+ int retval;
+ PyObject *obj2;
+ obj2 = PyUnicode_AsASCIIString(obj);
+ if (obj2 == NULL) {
+ return NPY_FAIL;
+ }
+ retval = PyArray_DescrConverter(obj2, at);
+ Py_DECREF(obj2);
+ return retval;
+ }
+
+ printf("Test4\n");
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+
+ /* Check for a string typecode. */
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+
+ /* Empty string is invalid */
+ if (len == 0) {
+ goto fail;
+ }
+
+ /* check for commas present or first (or second) element a digit */
+ if (_check_for_commastring(type, len)) {
+ *at = _convert_from_commastring(obj, 0);
+ return (*at) ? NPY_SUCCEED : NPY_FAIL;
+ }
+
+ /* Process the endian character. '|' is replaced by '='*/
+ switch (type[0]) {
+ case '>':
+ case '<':
+ case '=':
+ endian = type[0];
+ ++type;
+ --len;
+ break;
+
+ case '|':
+ endian = '=';
+ ++type;
+ --len;
+ break;
+ }
+
+ /* Just an endian character is invalid */
+ if (len == 0) {
+ goto fail;
+ }
+
+ /* Check for datetime format */
+ if (is_datetime_typestr(type, len)) {
+ *at = parse_dtype_from_datetime_typestr(type, len);
+ if (*at == NULL) {
+ return NPY_FAIL;
+ }
+ /* *at has byte order '=' at this point */
+ if (!PyArray_ISNBO(endian)) {
+ (*at)->byteorder = endian;
+ }
+ return NPY_SUCCEED;
+ }
+
+ /* A typecode like 'd' */
+ if (len == 1) {
+ check_num = type[0];
+ }
+ /* A kind + size like 'f8' */
+ else {
+ char *typeend = NULL;
+ int kind;
+
+ /* Parse the integer, make sure it's the rest of the string */
+ elsize = (int)strtol(type + 1, &typeend, 10);
+ if (typeend - type == len) {
+
+ kind = type[0];
+ switch (kind) {
+ case NPY_STRINGLTR:
+ case NPY_STRINGLTR2:
+ check_num = NPY_STRING;
+ break;
+
+ /*
+ * When specifying length of UNICODE
+ * the number of characters is given to match
+ * the STRING interface. Each character can be
+ * more than one byte and itemsize must be
+ * the number of bytes.
+ */
+ case NPY_UNICODELTR:
+ check_num = NPY_UNICODE;
+ elsize <<= 2;
+ break;
+
+ case NPY_VOIDLTR:
+ check_num = NPY_VOID;
+ break;
+
+ default:
+ if (elsize == 0) {
+ check_num = NPY_NOTYPE+10;
+ }
+ /* Support for generic processing c8, i4, f8, etc...*/
+ else {
+ check_num = PyArray_TypestrConvert(elsize, kind);
+ if (check_num == NPY_NOTYPE) {
+ check_num += 10;
+ }
+ elsize = 0;
+ }
+ }
+ }
+ }
+ }
+ else if (PyTuple_Check(obj)) {
+ /* or a tuple */
+ *at = _convert_from_tuple(obj);
+ if (*at == NULL){
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyList_Check(obj)) {
+ /* or a list */
+ *at = _convert_from_array_descr(obj,0);
+ if (*at == NULL) {
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyDict_Check(obj) || PyDictProxy_Check(obj)) {
+ /* or a dictionary */
+ *at = _convert_from_dict(obj,0);
+ if (*at == NULL) {
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyArray_Check(obj)) {
+ goto fail;
+ }
+ else {
+ *at = _arraydescr_fromobj(obj);
+ if (*at) {
+ return NPY_SUCCEED;
+ }
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ if (PyErr_Occurred()) {
+ goto fail;
+ }
+
+finish:
+ printf("Test5\n");
+ if ((check_num == NPY_NOTYPE + 10) ||
+ (*at = PyArray_DescrFromType(check_num)) == NULL) {
+ PyErr_Clear();
+ /* Now check to see if the object is registered in typeDict */
+ if (typeDict != NULL) {
+ item = PyDict_GetItem(typeDict, obj);
+#if defined(NPY_PY3K)
+ if (!item && PyBytes_Check(obj)) {
+ PyObject *tmp;
+ tmp = PyUnicode_FromEncodedObject(obj, "ascii", "strict");
+ if (tmp != NULL) {
+ item = PyDict_GetItem(typeDict, tmp);
+ Py_DECREF(tmp);
+ }
+ }
+#endif
+ if (item) {
+ /* Check for a deprecated Numeric-style typecode */
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+ char *dep_tps[] = {"Bool", "Complex", "Float", "Int",
+ "Object0", "String0", "Timedelta64",
+ "Unicode0", "UInt", "Void0"};
+ int ndep_tps = sizeof(dep_tps) / sizeof(dep_tps[0]);
+ int i;
+
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+ for (i = 0; i < ndep_tps; ++i) {
+ char *dep_tp = dep_tps[i];
+
+ if (strncmp(type, dep_tp, strlen(dep_tp)) == 0) {
+ if (DEPRECATE("Numeric-style type codes are "
+ "deprecated and will result in "
+ "an error in the future.") < 0) {
+ goto fail;
+ }
+ }
+ }
+ }
+ return PyArray_DescrConverter(item, at);
+ }
+ }
+ goto fail;
+ }
+
+ if (((*at)->elsize == 0) && (elsize != 0)) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->elsize = elsize;
+ }
+ if (endian != '=' && PyArray_ISNBO(endian)) {
+ endian = '=';
+ }
+ if (endian != '=' && (*at)->byteorder != '|'
+ && (*at)->byteorder != endian) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->byteorder = endian;
+ }
+ return NPY_SUCCEED;
+
+fail:
+ if (PyBytes_Check(obj)) {
+ PyErr_Format(PyExc_TypeError,
+ "data type \"%s\" not understood", PyBytes_AS_STRING(obj));
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "data type not understood");
+ }
+
+error:
+ *at = NULL;
+ return NPY_FAIL;
+}
+#endif
+
+
+NPY_NO_EXPORT int
+MyPyArray_DescrConverter(PyObject *obj, PyArray_Descr **at)
+{
+ int check_num = NPY_NOTYPE + 10;
+ PyObject *item;
+ int elsize = 0;
+ char endian = '=';
+
+ printf("Test -1\n");
+ *at = NULL;
+
+ check_num = NPY_VOID;
+ printf("Test0\n");
+ if (check_num != NPY_VOID) {
+ PyErr_Clear();
+ /* Now check to see if the object is registered in typeDict */
+ printf("Test1\n");
+ if (typeDict != NULL) {
+ item = PyDict_GetItem(typeDict, obj);
+#if defined(NPY_PY3K)
+ if (!item && PyBytes_Check(obj)) {
+ PyObject *tmp;
+ tmp = PyUnicode_FromEncodedObject(obj, "ascii", "strict");
+ if (tmp != NULL) {
+ item = PyDict_GetItem(typeDict, tmp);
+ Py_DECREF(tmp);
+ }
+ }
+#endif
+ if (item) {
+ /* Check for a deprecated Numeric-style typecode */
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+ char *dep_tps[] = {"Bool", "Complex", "Float", "Int",
+ "Object0", "String0", "Timedelta64",
+ "Unicode0", "UInt", "Void0"};
+ int ndep_tps = sizeof(dep_tps) / sizeof(dep_tps[0]);
+ int i;
+
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+ for (i = 0; i < ndep_tps; ++i) {
+ char *dep_tp = dep_tps[i];
+
+ if (strncmp(type, dep_tp, strlen(dep_tp)) == 0) {
+ if (DEPRECATE("Numeric-style type codes are "
+ "deprecated and will result in "
+ "an error in the future.") < 0) {
+ goto fail;
+ }
+ }
+ }
+ }
+ return PyArray_DescrConverter(item, at);
+ }
+ }
+ printf("Test2\n");
+ goto fail;
+ }
+
+ printf("Test3\n");
+ if (((*at)->elsize == 0) && (elsize != 0)) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->elsize = elsize;
+ printf("Test4\n");
+ }
+ if (endian != '=' && PyArray_ISNBO(endian)) {
+ endian = '=';
+ printf("Test5\n");
+ }
+ if (endian != '=' && (*at)->byteorder != '|'
+ && (*at)->byteorder != endian) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->byteorder = endian;
+ printf("Test6\n");
+ }
+ return NPY_SUCCEED;
+
+fail:
+ if (PyBytes_Check(obj)) {
+ PyErr_Format(PyExc_TypeError,
+ "data type \"%s\" not understood", PyBytes_AS_STRING(obj));
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "data type not understood");
+ }
+
+error:
+ *at = NULL;
+ return NPY_FAIL;
+}
+
+
+
+#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)
+{
+ molfile_plugin_t* plugin;
+ if(plug_no < 0){
+ plugin = NULL;
+ } else {
+ plugin = plug_list[plug_no];
+ }
+ return plugin;
+}
+
+#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 */
+
+PyObject * my_read_structure(PyObject* molpack) {
+ Py_Initialize();
+ import_array();
+
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* atoms;
+ int numatoms, status;
+ PyArray_Descr *descr;
+ PyObject *p = NULL;
+ //if (PyType_Ready(&MolAtomType) < 0)
+ // return NULL;
+ //PyTypeObject *atype = &MolAtomType;
+ //MolAtom *atom_t;
+ //atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
+ //p = (PyObject*) atom_t;
+ descr = PyArray_DescrFromObject(p, NULL);
+ MolObject* plugin_handle = (MolObject*) molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ status = plugin->read_structure(file_handle, &options, atoms);
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ PyArrayObject* oresid;
+ PyObject* array;
+ int64_t* cresid;
+ int nd = 1;
+ npy_intp dims[1] = { numatoms };
+ oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
+ Py_DECREF(p);
+ //array = (PyArrayObject*) PyArray_SimpleNewFromDescr(1, dims, descr);
+ //PyObject_Print(array, stdout, 0);
+ if (!oresid){
+ PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into numpy array.");
+ return NULL;
+ }
+ npy_intp* n = PyArray_DIMS(oresid);
+ cresid = (int64_t*) PyArray_DATA(oresid);
+
+// for (i=0;i<numatoms;i++){
+// cresid[i] = (int64_t) atoms[i].resid;
+// }
+ return (PyObject*) PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);
+}
+
+PyObject* read_fill_structure(PyObject* molpack, PyObject* prototype)
+{
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* data;
+ int numatoms, status;
+ int nd;
+ PyArrayInterface *inter;
+ //PyArrayObject *ret;
+ PyObject *ret;
+ char endian = NPY_NATBYTE;
+ nd = 1;
+ npy_intp dims[1] = { 1 };
+ PyArrayObject *obj;
+ printf("Test1\n");
+ obj = (PyArrayObject *)prototype;
+ if(obj == NULL){
+ PyErr_Format(PyExc_IOError, "Error: Given PyObject does not include numpy array.");
+ return NULL;
+ }
+ // Access plugin_handle values
+ MolObject* plugin_handle = (MolObject*) molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ printf("Test2-1\n");
+ // Allocate memory for array of molfile_atom_t struct
+ data = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ // Get array values in molfile_atom_t
+ printf("Test2-2\n");
+ status = plugin->read_structure(file_handle, &options, data);
+ printf("Test2-3\n");
+ // Check if the plugin returns the results
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ printf("Test3\n");
+ int *maxndim;
+ npy_intp *d_shape;
+ //status = my_get_array_attr_interface((PyObject*)obj, "descr", maxndim, d_shape, ret);
+ status = my_get_array_attr_interface(prototype, ret);
+ printf("Test4 Status:%d nd:%d\n",status,*maxndim);
+ if (status<0){
+ Py_DECREF(obj);
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+ return NULL;
+ }
+ printf("Test5\n");
+ //return (PyObject*) PyArray_FromArray((PyArrayObject*)ret, PyArray_DESCR((PyArrayObject*)ret), 0);
+ return (PyObject*) ret;
+}
+
+PyObject* get_structure(PyObject* self)
+{
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* data;
+ int numatoms, status;
+ int nd;
+ PyArrayInterface *inter;
+ PyArrayObject *ret;
+ char endian = NPY_NATBYTE;
+ // Access plugin_handle values
+ MolObject* plugin_handle = (MolObject*) self;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ // Allocate memory for array of molfile_atom_t struct
+ data = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ // Get array values in molfile_atom_t
+ status = plugin->read_structure(file_handle, &options, data);
+ // Check if the plugin returns the results
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ // Now, we need to allocate a PyArray with PyArrayInterface
+ // and assign the allocated memory block to the data.
+ // To do this, we will build a numpy array from scratch.
+ // First, allocate a PyObject of PyArrayInterface and
+ // assign relevant information such as typestr, descr for C-side
+ // struct and second we will assign molfile_atom_t array as a block
+ // of data. Last, hope this works.
+ nd = 1;
+ npy_intp dims[1] = { 1 };
+ // We would allocate a numpy array with
+ // but will not look clever to copy all the data into the new array.
+ // Instead, we allocate a numpy array with one element and change
+ // the definition of array. I know I said that it will be from scratch
+ // but let's accept nobody wants to define everything in numpy again.
+ //oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT);
+ // NPY_INT? Don't worry, we will change it.
+ //Py_intptr_t *shape, *strides;
+ //void *data = NULL;
+
+ inter = (PyArrayInterface*)malloc(sizeof(PyArrayInterface));
+ if (inter==NULL)
+ return PyErr_NoMemory();
+
+ // __array_interface__ descr for C side of __array_struct__
+ // Could not find a better way to generate the list of tuples for
+ // Python side. May need to change this later.
+ PyObject *descrlist = PyList_New(13);
+ // One tuple to bind them
+ PyObject *py_tuple_name = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_name, 0, PyUnicode_FromString("name"));
+ PyTuple_SET_ITEM(py_tuple_name, 1, PyUnicode_FromString("|S16"));
+ PyList_SET_ITEM(descrlist, 0, py_tuple_name);
+ PyObject *py_tuple_type = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_type, 0, PyUnicode_FromString("type"));
+ PyTuple_SET_ITEM(py_tuple_type, 1, PyUnicode_FromString("|S16"));
+ PyList_SET_ITEM(descrlist, 1, py_tuple_type);
+ PyObject *py_tuple_resname = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_resname, 0, PyUnicode_FromString("resname"));
+ PyTuple_SET_ITEM(py_tuple_resname, 1, PyUnicode_FromString("|S8"));
+ PyList_SET_ITEM(descrlist, 2, py_tuple_resname);
+ PyObject *py_tuple_resid = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_resid, 0, PyUnicode_FromString("resid"));
+ PyTuple_SET_ITEM(py_tuple_resid, 1, PyUnicode_FromString("<i4"));
+ PyList_SET_ITEM(descrlist, 3, py_tuple_resid);
+ PyObject *py_tuple_segid = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_segid, 0, PyUnicode_FromString("segid"));
+ PyTuple_SET_ITEM(py_tuple_segid, 1, PyUnicode_FromString("|S8"));
+ PyList_SET_ITEM(descrlist, 4, py_tuple_segid);
+ PyObject *py_tuple_chain = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_chain, 0, PyUnicode_FromString("chain"));
+ PyTuple_SET_ITEM(py_tuple_chain, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 5, py_tuple_chain);
+ PyObject *py_tuple_altloc = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_altloc, 0, PyUnicode_FromString("altloc"));
+ PyTuple_SET_ITEM(py_tuple_altloc, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 6, py_tuple_altloc);
+ PyObject *py_tuple_insertion = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_insertion, 0, PyUnicode_FromString("insertion"));
+ PyTuple_SET_ITEM(py_tuple_insertion, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 7, py_tuple_insertion);
+ PyObject *py_tuple_occupancy = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_occupancy, 0, PyUnicode_FromString("occupancy"));
+ PyTuple_SET_ITEM(py_tuple_occupancy, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 8, py_tuple_occupancy);
+ PyObject *py_tuple_bfactor = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_bfactor, 0, PyUnicode_FromString("bfactor"));
+ PyTuple_SET_ITEM(py_tuple_bfactor, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 9, py_tuple_bfactor);
+ PyObject *py_tuple_mass = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_mass, 0, PyUnicode_FromString("mass"));
+ PyTuple_SET_ITEM(py_tuple_mass, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 10, py_tuple_mass);
+ PyObject *py_tuple_charge = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_charge, 0, PyUnicode_FromString("charge"));
+ PyTuple_SET_ITEM(py_tuple_charge, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 11, py_tuple_charge);
+ PyObject *py_tuple_radius = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_radius, 0, PyUnicode_FromString("radius"));
+ PyTuple_SET_ITEM(py_tuple_radius, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 12, py_tuple_radius);
+ PyObject *py_tuple_atomicnumber = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_atomicnumber, 0, PyUnicode_FromString("atomicnumber"));
+ PyTuple_SET_ITEM(py_tuple_atomicnumber, 1, PyUnicode_FromString("<i4"));
+ PyList_SET_ITEM(descrlist, 13, py_tuple_atomicnumber);
+ //PyArray_Descr *descr = (PyObject*) tuple;
+ PyArray_Descr *thetype = NULL;
+ // Here we define the size and stride parameters
+ npy_intp shape[1] = { numatoms };
+ npy_intp strides[1] = { 54*sizeof(char) + 8*sizeof(int) + 20*sizeof(float) };
+
+ inter->two = 2;
+ inter->nd = nd;
+ inter->typekind = 'V';
+ inter->itemsize = 82*sizeof(char);
+ //inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE;
+ inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE | NPY_ARR_HAS_DESCR;
+ inter->strides = (Py_intptr_t *)strides;
+ inter->shape = (Py_intptr_t *)shape;
+ inter->data = (void*) data;
+ // inter->descr = (PyObject*) tuple;
+ if ((inter->flags & NPY_ARRAY_NOTSWAPPED) != NPY_ARRAY_NOTSWAPPED) {
+ endian = NPY_OPPBYTE;
+ inter->flags &= ~NPY_ARRAY_NOTSWAPPED;
+ }
+ // typestr is relatively easy to assign to __array_interface__
+ printf("TEST1\n");
+ //thetype = (PyArray_Descr*) tuple;
+ if (inter->flags & NPY_ARR_HAS_DESCR) {
+ printf("TEST1-1\n");
+ thetype = _convert_from_array_descr(descrlist,0);
+ //thetype = PyArray_DescrFromTypeObject(descrlist);
+ printf("TEST1-2\n");
+ //if (PyArray_DescrConverter(inter->descr, &thetype) == NPY_FAIL) {
+ // thetype = NULL;
+ // PyErr_Clear();
+ // }
+ }
+ printf("TEST1-3\n");
+#if 0
+ char buf[40];
+ PyOS_snprintf(buf, sizeof(buf),
+ "%c%c%d", endian,
+ inter->typekind,
+ inter->itemsize);
+ printf("TEST2 String:%s\n",buf);
+ PyObject *stringobj = PyUnicode_FromString(buf);
+ if (stringobj == NULL) {
+ return NULL;
+ }
+ printf("TEST2-2\n");
+ if (MyPyArray_DescrConverter(stringobj, &thetype) != NPY_SUCCEED) {
+ Py_DECREF(stringobj);
+ return NULL;
+ }
+ printf("TEST2-3\n");
+ Py_DECREF(stringobj);
+#endif
+ printf("TEST3\n");
+ ret = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, thetype,
+ inter->nd, inter->shape,
+ inter->strides, inter->data,
+ inter->flags, NULL);
+ printf("TEST4\n");
+ Py_INCREF(inter);
+ if (PyArray_SetBaseObject(ret, (PyObject *)inter) < 0) {
+ Py_DECREF(ret);
+ return NULL;
+ }
+ printf("TEST5\n");
+// Py_DECREF(attr);
+ PyArray_UpdateFlags(ret, NPY_ARRAY_UPDATE_ALL);
+ printf("TEST6\n");
+ return (PyObject *)ret;
+}
+// obj = NpyCapsule_FromVoidPtrAndDesc(inter, self, gentype_struct_free);
+/*
+#ifdef Py_CAPSULE_H
+ obj = PyCapsule_New((void*)inter, "struct SignedIntBuf", free_capsule);
+#else
+ obj = PyCObject_FromVoidPtrAndDesc((void*)inter, (void*)self, free_array_interface);
+#endif
+*/
+ // Cross fingers here.
+// return obj;
+
diff --git a/pymolfile/molfile/pymolfile-new.h b/pymolfile/molfile/pymolfile-new.h
new file mode 100644
index 0000000000000000000000000000000000000000..5bf304ee461b11bb8d04b3d03caad856252fb4a6
--- /dev/null
+++ b/pymolfile/molfile/pymolfile-new.h
@@ -0,0 +1,356 @@
+/* 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"
+#include "Python.h"
+#include "structmember.h"
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#include <numpy/arrayobject.h>
+
+
+enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
+ pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
+
+#ifndef MAXPLUGINS
+#define MAXPLUGINS 200
+#endif
+
+struct MolObject {
+ PyObject_HEAD
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ int natoms;
+ MolObject(void) {}
+};
+
+static void MolObject_dealloc(MolObject* self)
+{
+ Py_XDECREF(self->plugin);
+ Py_XDECREF(self->file_handle);
+ Py_TYPE(self)->tp_free((PyObject*)self);
+}
+
+static PyObject * MolObject_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
+{
+ MolObject *self;
+
+ self = (MolObject *)type->tp_alloc(type, 0);
+ if (self != NULL) {
+ self->plugin = NULL;
+ self->file_handle = NULL;
+ self->natoms = 0;
+ }
+
+ return (PyObject *)self;
+}
+
+static int MolObject_init(MolObject *self, PyObject *args, PyObject *kwds)
+{
+ molfile_plugin_t *plugin = NULL;
+ void *file_handle = NULL;
+ molfile_plugin_t *tmp1 = NULL;
+ void *tmp2 = NULL;
+
+ static char *kwlist[] = {"plugin", "file_handle", "natoms", NULL};
+
+ if (! PyArg_ParseTupleAndKeywords(args, kwds, "|OOi", kwlist,
+ &plugin, &file_handle,
+ &self->natoms))
+ return -1;
+
+ if (plugin) {
+ tmp1 = self->plugin;
+ Py_INCREF(plugin);
+ self->plugin = plugin;
+ Py_XDECREF(tmp1);
+ }
+
+ if (file_handle) {
+ tmp2 = self->file_handle;
+ Py_INCREF(file_handle);
+ self->file_handle = file_handle;
+ Py_XDECREF(tmp2);
+ }
+
+ return 0;
+}
+
+static molfile_plugin_t* MolObject_plugin(MolObject* self)
+{
+ return self->plugin;
+}
+
+static void* MolObject_file_handle(MolObject* self)
+{
+ return self->file_handle;
+}
+
+static PyObject* MolObject_natoms(MolObject* self)
+{
+ return PyLong_FromLong((long)self->natoms);
+}
+
+static PyMemberDef MolObject_members[] = {
+ {"plugin", T_OBJECT_EX, offsetof(MolObject, plugin), 0,
+ "molfile_plugin_t type plugin"},
+ {"file_handle", T_OBJECT_EX, offsetof(MolObject, file_handle), 0,
+ "file handle for plugin"},
+ {"natoms", T_INT, offsetof(MolObject, natoms), 0,
+ "number of atoms"},
+ {NULL} /* Sentinel */
+};
+
+static PyMethodDef MolObject_methods[] = {
+ {"get_plugin", (PyCFunction)MolObject_plugin, METH_NOARGS,
+ "Return the plugin"
+ },
+ {"get_file_handle", (PyCFunction)MolObject_file_handle, METH_NOARGS,
+ "Return the plugin"
+ },
+ {"get_natoms", (PyCFunction)MolObject_natoms, METH_NOARGS,
+ "Return the number of atoms"
+ },
+ {NULL} /* Sentinel */
+};
+
+
+#ifndef PyVarObject_HEAD_INIT
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+#endif
+
+static PyTypeObject MolObjectType = {
+ PyVarObject_HEAD_INIT(NULL, 0)
+ "molobject", /*tp_name*/
+ sizeof(MolObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)MolObject_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_reserved*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT |
+ Py_TPFLAGS_BASETYPE, /* tp_flags */
+ "molobject objects", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ MolObject_methods, /* tp_methods */
+ MolObject_members, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ (initproc)MolObject_init, /* tp_init */
+ 0, /* tp_alloc */
+ MolObject_new, /* tp_new */
+};
+
+#if 0
+struct MolAtom {
+ PyObject_HEAD
+ char* name;
+ char* type;
+ char* resname;
+ int* resid;
+ char* segid;
+ char* chain;
+ char* altloc;
+ char* insertion;
+ float* occupancy;
+ float* bfactor;
+ float* mass;
+ float* charge;
+ float* radius;
+ float* atomicnumber;
+ float* ctnumber;
+ MolAtom(void) {}
+};
+
+static void MolAtom_dealloc(MolAtom* self)
+{
+ Py_XDECREF(self->name);
+ Py_XDECREF(self->type);
+ Py_XDECREF(self->resname);
+ Py_XDECREF(self->resid);
+ Py_XDECREF(self->segid);
+ Py_XDECREF(self->chain);
+ Py_XDECREF(self->altloc);
+ Py_XDECREF(self->insertion);
+ Py_XDECREF(self->occupancy);
+ Py_XDECREF(self->bfactor);
+ Py_XDECREF(self->mass);
+ Py_XDECREF(self->charge);
+ Py_XDECREF(self->radius);
+ Py_XDECREF(self->atomicnumber);
+ Py_XDECREF(self->ctnumber);
+ Py_TYPE(self)->tp_free((PyObject*)self);
+}
+
+static PyObject * MolAtom_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
+{
+ MolAtom *self;
+
+ self = (MolAtom *)type->tp_alloc(type, 0);
+ if (self != NULL) {
+ self->name = NULL;
+ self->type = NULL;
+ self->resname = NULL;
+ self->resid = NULL;
+ self->segid = NULL;
+ self->chain = NULL;
+ self->altloc = NULL;
+ self->insertion = NULL;
+ self->occupancy = NULL;
+ self->bfactor = NULL;
+ self->mass = NULL;
+ self->charge = NULL;
+ self->radius = NULL;
+ self->atomicnumber = NULL;
+ self->ctnumber = NULL;
+ }
+
+ return (PyObject *)self;
+}
+
+static PyMemberDef MolAtom_members[] = {
+ {"name", T_STRING, offsetof(MolAtom, name), 0,""},
+ {"type", T_STRING, offsetof(MolAtom, type), 0,""},
+ {"resname", T_STRING, offsetof(MolAtom, resname), 0,""},
+ {"resid", T_INT, offsetof(MolAtom, resid), 0,""},
+ {"segid", T_STRING, offsetof(MolAtom, segid), 0,""},
+ {"chain", T_STRING, offsetof(MolAtom, chain), 0,""},
+ {"altloc", T_STRING, offsetof(MolAtom, altloc), 0,""},
+ {"insertion", T_STRING, offsetof(MolAtom, insertion), 0,""},
+ {"occupancy", T_FLOAT, offsetof(MolAtom, occupancy), 0,""},
+ {"bfactor", T_FLOAT, offsetof(MolAtom, bfactor), 0,""},
+ {"mass", T_FLOAT, offsetof(MolAtom, mass), 0,""},
+ {"charge", T_FLOAT, offsetof(MolAtom, charge), 0,""},
+ {"radius", T_FLOAT, offsetof(MolAtom, radius), 0,""},
+ {"atomicnumber", T_INT, offsetof(MolAtom, atomicnumber), 0,""},
+ {"ctnumber", T_INT, offsetof(MolAtom, ctnumber), 0,""},
+ {NULL, NULL, 0, NULL} /* Sentinel */
+};
+
+static PyTypeObject MolAtomType = {
+ PyVarObject_HEAD_INIT(NULL, 0)
+ "molobject", /*tp_name*/
+ sizeof(MolAtom), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)MolAtom_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_reserved*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT |
+ Py_TPFLAGS_BASETYPE, /* tp_flags */
+ "molatom objects", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ MolAtom_members, /* 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 */
+ MolAtom_new, /* tp_new */
+};
+#endif
+PyObject * my_read_structure(PyObject* molpack);
+PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
+PyObject * get_structure(PyObject* molpack);
+
+#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/pymolfile.c b/pymolfile/molfile/pymolfile.c
index b3033e97440a13dc50ef4c006f9ebb4ecdb35fe4..1b813044c1b4d938eec536e5617cc721a1bc22df 100644
--- a/pymolfile/molfile/pymolfile.c
+++ b/pymolfile/molfile/pymolfile.c
@@ -33,15 +33,1099 @@
#include "pymolfile.h"
-int numplugins=0;
-molfile_plugin_t** plugin_list;
-
+//for PyArrayInterface:
+/*
+#define CONTIGUOUS 0x01
+#define FORTRAN 0x02
+#define ALIGNED 0x100
+#define NOTSWAPPED 0x200
+#define WRITEABLE 0x400
+#define ARR_HAS_DESCR 0x800
+*/
+//byteorder dictionary
+//char** byteorder = {"<", "little", ">", "big"};
+int numplugins=0;
+molfile_plugin_t** plugin_list;
+/*
+typedef struct PyArrayInterface{
+ int version; //contains the integer 2 as a sanity check
+ int nd; //number of dimensions
+ char typekind; //kind in array --- character code of typestr
+ int itemsize; //size of each element
+ int flags; //flags indicating how the data should be interpreted
+ Py_intptr_t *shape; //A length-nd array of shape information
+ Py_intptr_t *strides; //A length-nd array of stride information
+ void *data; //A pointer to the first element of the array
+};
+*/
/* * * * * * * * * * * * * * * * * * * * * * *
* Helper functions to set and store plugins *
* * * * * * * * * * * * * * * * * * * * * * */
+
+
+#if PY_VERSION_HEX >= 0x03000000
+#define PyInt_AsSsize_t PyLong_AsSsize_t
+#define PyInt_AsLong PyLong_AsLong
+#define PyArray_Check(op) PyObject_TypeCheck(op, &PyArray_Type)
+#define PyString_FromString PyBytes_FromString
+#define PyUString_Check PyUnicode_Check
+#define PyUString_GET_SIZE PyUnicode_GET_SIZE
+#define PyUString_FromFormat PyUnicode_FromFormat
+#define PyInt_FromLong PyLong_FromLong
+#define PyString_Type PyBytes_Type
+#define PyInt_Type PyLong_Type
+
+NPY_NO_EXPORT void
+gentype_struct_free(PyObject *ptr)
+{
+ PyArrayInterface *arrif;
+ PyObject *context;
+
+ arrif = (PyArrayInterface*)PyCapsule_GetPointer(ptr, NULL);
+ context = (PyObject *)PyCapsule_GetContext(ptr);
+ Py_DECREF(context);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+static NPY_INLINE void *
+NpyCapsule_AsVoidPtr(PyObject *obj)
+{
+ void *ret = PyCapsule_GetPointer(obj, NULL);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtr(void *ptr, void (*dtor)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, dtor);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+static NPY_INLINE PyObject *
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context, void (*dtor)(PyObject *))
+{
+ PyObject *ret = NpyCapsule_FromVoidPtr(ptr, dtor);
+ if (ret != NULL && PyCapsule_SetContext(ret, context) != 0) {
+ PyErr_Clear();
+ Py_DECREF(ret);
+ ret = NULL;
+ }
+ return ret;
+}
+#else
+#define PyBytes_FromString PyString_FromString
+NPY_NO_EXPORT void
+gentype_struct_free(void *ptr, void *arg)
+{
+ PyArrayInterface *arrif = (PyArrayInterface *)ptr;
+ Py_DECREF((PyObject *)arg);
+ Py_XDECREF(arrif->descr);
+ PyArray_free(arrif->shape);
+ PyArray_free(arrif);
+}
+NpyCapsule_FromVoidPtrAndDesc(void *ptr, void* context,
+ void (*dtor)(void *, void *))
+{
+ return PyCObject_FromVoidPtrAndDesc(ptr, context, dtor);
+}
+#endif
+static PyObject *typeDict = NULL; /* Must be explicitly loaded */
+
+
+#define NPY_NEXT_ALIGNED_OFFSET(offset, alignment) \
+ (((offset) + (alignment) - 1) & (-(alignment)))
+
+static PyArray_Descr *
+_convert_from_array_descr(PyObject *obj, int align)
+{
+ int n, i, totalsize;
+ int ret;
+ PyObject *fields, *item, *newobj;
+ PyObject *name, *tup, *title;
+ PyObject *nameslist;
+ PyArray_Descr *newea;
+ PyArray_Descr *conv;
+ /* Types with fields need the Python C API for field access */
+ char dtypeflags = NPY_NEEDS_PYAPI;
+ int maxalign = 0;
+
+ printf("Test1\n");
+ n = PyList_GET_SIZE(obj);
+ nameslist = PyTuple_New(n);
+ if (!nameslist) {
+ return NULL;
+ }
+ totalsize = 0;
+ fields = PyDict_New();
+ for (i = 0; i < n; i++) {
+ item = PyList_GET_ITEM(obj, i);
+ if (!PyTuple_Check(item) || (PyTuple_GET_SIZE(item) < 2)) {
+ goto fail;
+ }
+ name = PyTuple_GET_ITEM(item, 0);
+ if (PyUString_Check(name)) {
+ title = NULL;
+ }
+ else if (PyTuple_Check(name)) {
+ if (PyTuple_GET_SIZE(name) != 2) {
+ goto fail;
+ }
+ title = PyTuple_GET_ITEM(name, 0);
+ name = PyTuple_GET_ITEM(name, 1);
+ if (!PyUString_Check(name)) {
+ goto fail;
+ }
+ }
+ else {
+ goto fail;
+ }
+
+ /* Insert name into nameslist */
+ Py_INCREF(name);
+
+ if (PyUString_GET_SIZE(name) == 0) {
+ Py_DECREF(name);
+ if (title == NULL) {
+ name = PyUString_FromFormat("f%d", i);
+ }
+#if PY_VERSION_HEX >= 0x03000000
+ /* On Py3, allow only non-empty Unicode strings as field names */
+ else if (PyUString_Check(title) && PyUString_GET_SIZE(title) > 0) {
+ name = title;
+ Py_INCREF(name);
+ }
+ else {
+ goto fail;
+ }
+#else
+ else {
+ name = title;
+ Py_INCREF(name);
+ }
+#endif
+ }
+ PyTuple_SET_ITEM(nameslist, i, name);
+
+ /* Process rest */
+
+ printf("Test2\n");
+ if (PyTuple_GET_SIZE(item) == 2) {
+ if (align) {
+ printf("Test3\n");
+ ret = PyArray_DescrAlignConverter(PyTuple_GET_ITEM(item, 1),
+ &conv);
+ }
+ else {
+ printf("Test4\n");
+ ret = PyArray_DescrConverter(PyTuple_GET_ITEM(item, 1), &conv);
+ }
+ if (ret == NPY_FAIL) {
+ PyObject_Print(PyTuple_GET_ITEM(item, 1), stderr, 0);
+ }
+ }
+ else if (PyTuple_GET_SIZE(item) == 3) {
+ newobj = PyTuple_GetSlice(item, 1, 3);
+ if (align) {
+ printf("Test5\n");
+ ret = PyArray_DescrAlignConverter(newobj, &conv);
+ }
+ else {
+ printf("Test6\n");
+ ret = PyArray_DescrConverter(newobj, &conv);
+ }
+ Py_DECREF(newobj);
+ }
+ else {
+ goto fail;
+ }
+ if (ret == NPY_FAIL) {
+ goto fail;
+ }
+ if ((PyDict_GetItem(fields, name) != NULL)
+ || (title
+#if PY_VERSION_HEX >= 0x03000000
+ && PyUString_Check(title)
+#else
+ && (PyUString_Check(title) || PyUnicode_Check(title))
+#endif
+ && (PyDict_GetItem(fields, title) != NULL))) {
+#if PY_VERSION_HEX >= 0x03000000
+ name = PyUnicode_AsUTF8String(name);
+#endif
+ PyErr_Format(PyExc_ValueError,
+ "field '%s' occurs more than once", PyBytes_AsString(name));
+#if PY_VERSION_HEX >= 0x03000000
+ Py_DECREF(name);
+#endif
+ goto fail;
+ }
+ dtypeflags |= (conv->flags & NPY_FROM_FIELDS);
+ if (align) {
+ int _align;
+
+ _align = conv->alignment;
+ if (_align > 1) {
+ totalsize = NPY_NEXT_ALIGNED_OFFSET(totalsize, _align);
+ }
+ maxalign = PyArray_MAX(maxalign, _align);
+ }
+ tup = PyTuple_New((title == NULL ? 2 : 3));
+ PyTuple_SET_ITEM(tup, 0, (PyObject *)conv);
+ PyTuple_SET_ITEM(tup, 1, PyInt_FromLong((long) totalsize));
+
+ /*
+ * Title can be "meta-data". Only insert it
+ * into the fields dictionary if it is a string
+ * and if it is not the same as the name.
+ */
+ if (title != NULL) {
+ Py_INCREF(title);
+ PyTuple_SET_ITEM(tup, 2, title);
+ PyDict_SetItem(fields, name, tup);
+#if PY_VERSION_HEX >= 0x03000000
+ if (PyUString_Check(title)) {
+#else
+ if (PyUString_Check(title) || PyUnicode_Check(title)) {
+#endif
+ if (PyDict_GetItem(fields, title) != NULL) {
+ PyErr_SetString(PyExc_ValueError,
+ "title already used as a name or title.");
+ Py_DECREF(tup);
+ goto fail;
+ }
+ PyDict_SetItem(fields, title, tup);
+ }
+ }
+ else {
+ PyDict_SetItem(fields, name, tup);
+ }
+
+ totalsize += conv->elsize;
+ Py_DECREF(tup);
+ }
+
+ if (maxalign > 1) {
+ totalsize = NPY_NEXT_ALIGNED_OFFSET(totalsize, maxalign);
+ }
+
+ newea = PyArray_DescrNewFromType(NPY_VOID);
+ if (newea == NULL) {
+ Py_XDECREF(fields);
+ Py_XDECREF(nameslist);
+ return NULL;
+ }
+ newea->fields = fields;
+ newea->names = nameslist;
+ newea->elsize = totalsize;
+ newea->flags = dtypeflags;
+
+ /* Structured arrays get a sticky aligned bit */
+ if (align) {
+ newea->flags |= NPY_ALIGNED_STRUCT;
+ newea->alignment = maxalign;
+ }
+ return newea;
+
+ fail:
+ Py_DECREF(fields);
+ Py_DECREF(nameslist);
+ return NULL;
+
+}
+
+static NPY_INLINE npy_bool
+_is_basic_python_type(PyTypeObject *tp)
+{
+ return (
+ /* Basic number types */
+ tp == &PyBool_Type ||
+#if PY_VERSION_HEX >= 0x03000000
+ tp == &PyInt_Type ||
+#endif
+ tp == &PyLong_Type ||
+ tp == &PyFloat_Type ||
+ tp == &PyComplex_Type ||
+
+ /* Basic sequence types */
+ tp == &PyList_Type ||
+ tp == &PyTuple_Type ||
+ tp == &PyDict_Type ||
+ tp == &PySet_Type ||
+ tp == &PyFrozenSet_Type ||
+ tp == &PyUnicode_Type ||
+ tp == &PyBytes_Type ||
+#if PY_VERSION_HEX >= 0x03000000
+ tp == &PyString_Type ||
+#endif
+
+ /* other builtins */
+ tp == &PySlice_Type ||
+ tp == Py_TYPE(Py_None) ||
+ tp == Py_TYPE(Py_Ellipsis) ||
+ tp == Py_TYPE(Py_NotImplemented) ||
+
+ /* TODO: ndarray, but we can't see PyArray_Type here */
+
+ /* sentinel to swallow trailing || */
+ NPY_FALSE
+ );
+}
+
+static NPY_INLINE PyObject *
+maybe_get_attr(PyObject *obj, char *name)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ PyObject *res = (PyObject *)NULL;
+
+ /* Attribute referenced by (char *)name */
+ if (tp->tp_getattr != NULL) {
+ res = (*tp->tp_getattr)(obj, name);
+ if (res == NULL) {
+ PyErr_Clear();
+ }
+ }
+ /* Attribute referenced by (PyObject *)name */
+ else if (tp->tp_getattro != NULL) {
+#if PY_VERSION_HEX >= 0x03000000
+ PyObject *w = PyUnicode_InternFromString(name);
+#else
+ PyObject *w = PyString_InternFromString(name);
+#endif
+ if (w == NULL) {
+ return (PyObject *)NULL;
+ }
+ res = (*tp->tp_getattro)(obj, w);
+ Py_DECREF(w);
+ if (res == NULL) {
+ PyErr_Clear();
+ }
+ }
+ return res;
+}
+
+static NPY_INLINE PyObject *
+maybe_set_attr(PyObject *obj, char *name, PyObject *attr)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ int status;
+
+ /* Attribute referenced by (char *)name */
+ if (tp->tp_setattr != NULL) {
+ printf("tp_setattr not null\n");
+ status = (*tp->tp_setattr)(obj, name, attr);
+ if (status < 0) {
+ printf("No tp_setattr\n");
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: no __array_interface__ attribute in object.");
+ return NULL;
+ }
+ }
+ /* Attribute referenced by (PyObject *)name */
+ else if (tp->tp_setattro != NULL) {
+ printf("tp_setattr null but tp_setattro is not null\n");
+#if PY_VERSION_HEX >= 0x03000000
+ PyObject *w = PyUnicode_InternFromString(name);
+ printf("PyUnicode_InternFromString name\n");
+#else
+ PyObject *w = PyString_InternFromString(name);
+ printf("PyString_InternFromString name\n");
+#endif
+ if (w == NULL) {
+ printf("Name is NULL\n");
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: no __array_interface__ attribute in object.");
+ return NULL;
+ }
+ //status = (*tp->tp_setattro)(obj, w, attr);
+ //status = PyObject_GenericSetAttr(obj, w, attr);
+ status = PyObject_SetAttrString(obj, name, attr);
+ if (status < 0) {
+ printf("can not use tp_setattro status:%d\n", status);
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not set interface attribute.");
+ return NULL;
+ }
+ }
+ return obj;
+}
+
+static int get_array_struct(PyObject* obj, int *maxndim, npy_intp *d_shape, PyArrayInterface* inter)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ PyObject* ret;
+ char* str;
+ int i;
+ str = "__array_struct__";
+ /* We do not need to check for special attributes on trivial types */
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_struct__ interface */
+ ret = maybe_get_attr(obj, str);
+ if (ret != NULL) {
+ int nd = -1;
+ if (PyCapsule_CheckExact(ret)) {
+ PyArrayInterface *inter;
+ inter = (PyArrayInterface *)NpyCapsule_AsVoidPtr(ret);
+ if (inter->two == 2) {
+ nd = inter->nd;
+ if (nd >= 0) {
+ if (nd < *maxndim) {
+ *maxndim = nd;
+ }
+ for (i=0; i<*maxndim; i++) {
+ d_shape[i] = inter->shape[i];
+ }
+ }
+ }
+ }
+ if(nd >= 0){
+ return 0;
+ } else {
+ return -1;
+ }
+ } else {
+ return -1;
+ }
+}
+
+PyObject* my_get_array_attr_interface(PyObject* obj){
+ printf("Check-in my_get_array_attr_interface\n");
+ printf("Check-out my_get_array_attr_interface\n");
+ return obj;
+}
+
+PyObject* get_array_attr_interface(PyObject* obj, char* str, int *maxndim, npy_intp *d_shape){
+ PyTypeObject *tp = Py_TYPE(obj);
+ char* dictstr;
+ int i, failflag=0;
+ dictstr = "__array_interface__";
+ PyObject* ret;
+ PyObject* retuni = NULL;
+ PyObject* newi = NULL;
+ PyObject* objj = NULL;
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_interface__ interface */
+ ret = maybe_get_attr(obj, dictstr);
+ if (ret != NULL) {
+ int nd = -1;
+ if (PyDict_Check(ret)) {
+ printf("I- %s\n",str);
+ objj = PyDict_GetItemString(ret, str);
+ printf("O- %s\n",str);
+ //newi = PyDict_GetItemString(ret, str);
+ if (str == "shape"){
+ if (objj && PyTuple_Check(objj)) {
+ nd = PyTuple_GET_SIZE(objj);
+ if (nd >= 0) {
+ maxndim = &nd;
+ printf("nd:%d\n",*maxndim);
+ for (i=0; i<nd; i++) {
+ //Py_INCREF(objj);
+ retuni = PyTuple_GET_ITEM(objj, i);
+ printf("step:%d\n",i);
+ //d_shape[i] = (npy_intp) PyInt_AsSsize_t(retuni);
+ //d_shape[i] = PyInt_AsSsize_t(PyTuple_GET_ITEM(objj, i));
+ //Py_DECREF(objj);
+ printf("T- %d\n",i);
+ //if (d_shape[i] < 0) {
+ // PyErr_SetString(PyExc_RuntimeError,
+ // "Invalid shape in __array_interface__");
+ // failflag = 1;
+ //}
+ }
+ }
+ }
+ } else {
+ printf("T5\n");
+ PyObject* tuple = PyTuple_New(1);
+ PyTuple_SET_ITEM(tuple, 0, objj);
+ printf("T6\n");
+ return (PyObject*) tuple;
+ }
+ }
+ if (nd >= 0) {
+ printf("T5\n");
+ //newi = (PyArrayObject*) objj;
+ PyObject* tuple = PyTuple_New(1);
+ PyTuple_SET_ITEM(tuple, 0, objj);
+ printf("T6\n");
+ return (PyObject*) tuple;
+ } else {
+ failflag = 1;
+ }
+ } else {
+ failflag = 1;
+ }
+ if (failflag){
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+ return NULL;
+ }
+}
+
+PyObject* get_descr_array_interface(PyObject* obj){
+ PyTypeObject *tp = Py_TYPE(obj);
+ char* dictstr;
+ char* descrstr;
+ int i, failflag=0;
+ dictstr = "__array_interface__";
+ descrstr = "descr";
+ PyObject* ret;
+ PyObject* retuni = NULL;
+ PyObject* newi = NULL;
+ PyObject* objj = NULL;
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_interface__ interface */
+ ret = maybe_get_attr(obj, dictstr);
+ if (ret != NULL) {
+ if (PyDict_Check(ret)) {
+ objj = PyDict_GetItemString(ret, descrstr);
+ return (PyObject*) objj;
+ } else {
+ failflag = 1;
+ }
+ } else {
+ failflag = 1;
+ }
+ if (failflag){
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+ return NULL;
+ }
+}
+
+PyObject* set_array_attr_interface(PyObject* obj, int nsize, void* data)
+{
+ PyTypeObject *tp = Py_TYPE(obj);
+ char* dictstr;
+ char* shapestr;
+ char* datastr;
+ int i, failflag=0;
+ dictstr = "__array_interface__";
+ shapestr= "shape";
+ datastr= "data";
+ PyObject* ret;
+ //PyObject* retuni = NULL;
+ //PyObject* newi = NULL;
+ PyObject* shapeobj = NULL;
+ PyObject* dataobj = NULL;
+ PyObject* new_shape = NULL;
+ int status;
+ if (_is_basic_python_type(tp)) {
+ ret = NULL;
+ }
+ /* obj has the __array_interface__ interface */
+ ret = maybe_get_attr(obj, dictstr);
+ printf("AA0\n");
+ if (ret != NULL) {
+ int nd = -1;
+ if (PyDict_Check(ret)) {
+ shapeobj = PyDict_GetItemString(ret, shapestr);
+ printf("AA1\n");
+ if (shapeobj && PyTuple_Check(shapeobj)) {
+ nd = PyTuple_GET_SIZE(shapeobj);
+ printf("AA1-1\n");
+ if (nd >= 0) {
+ new_shape = PyTuple_New(nd);
+ for (i=0; i<nd; i++) {
+ PyTuple_SET_ITEM(new_shape, i, PyInt_FromLong((int)nsize));
+ }
+ status = PyDict_SetItemString(ret, shapestr, new_shape);
+ if (status<0){
+ printf("AA1-2\n");
+ Py_DECREF(new_shape);
+ PyErr_Clear();
+ failflag = 1;
+ }
+ } else {
+ printf("AA1-3\n");
+ failflag = 1;
+ }
+ }
+ printf("AA2\n");
+ if(!failflag){
+ dataobj = PyDict_GetItemString(ret, datastr);
+ printf("AA2-1\n");
+ if (dataobj && PyTuple_Check(dataobj)) {
+ PyTuple_SET_ITEM(dataobj, 0, PyLong_FromVoidPtr(data));
+ status = PyDict_SetItemString(ret, datastr, dataobj);
+ if (status<0){
+ printf("AA2-2\n");
+ failflag = 1;
+ }
+ }
+ }
+ printf("AA3\n");
+ if(!failflag){
+ printf("AA3-1\n");
+ obj = maybe_set_attr(obj, dictstr, ret);
+ if (!obj){
+ printf("AA3-2\n");
+ failflag = 1;
+ }
+ }
+ printf("AA4\n");
+ } else {
+ printf("AA1-0\n");
+ failflag = 1;
+ }
+ } else {
+ printf("AA0-1\n");
+ failflag = 1;
+ }
+ if (failflag){
+ Py_DECREF(new_shape);
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+ printf("AA Fail\n");
+ return NULL;
+ } else {
+ printf("AA Return\n");
+ return obj;
+ }
+}
+
+
+#if 0
+NPY_NO_EXPORT int
+MyArray_DescrConverter(PyObject *obj, PyArray_Descr **at)
+{
+ int check_num = NPY_NOTYPE + 10;
+ PyObject *item;
+ int elsize = 0;
+ char endian = '=';
+
+ *at = NULL;
+
+ printf("Test0\n");
+ /* default */
+ if (obj == Py_None) {
+ *at = PyArray_DescrFromType(NPY_DEFAULT_TYPE);
+ return NPY_SUCCEED;
+ }
+
+ printf("Test1\n");
+ if (PyArray_DescrCheck(obj)) {
+ *at = (PyArray_Descr *)obj;
+ Py_INCREF(*at);
+ return NPY_SUCCEED;
+ }
+
+ printf("Test2\n");
+ if (PyType_Check(obj)) {
+ if (PyType_IsSubtype((PyTypeObject *)obj, &PyGenericArrType_Type)) {
+ *at = PyArray_DescrFromTypeObject(obj);
+ return (*at) ? NPY_SUCCEED : NPY_FAIL;
+ }
+ check_num = NPY_OBJECT;
+#if !defined(NPY_PY3K)
+ if (obj == (PyObject *)(&PyInt_Type)) {
+ check_num = NPY_LONG;
+ }
+ else if (obj == (PyObject *)(&PyLong_Type)) {
+ check_num = NPY_LONGLONG;
+ }
+#else
+ if (obj == (PyObject *)(&PyLong_Type)) {
+ check_num = NPY_LONG;
+ }
+#endif
+ else if (obj == (PyObject *)(&PyFloat_Type)) {
+ check_num = NPY_DOUBLE;
+ }
+ else if (obj == (PyObject *)(&PyComplex_Type)) {
+ check_num = NPY_CDOUBLE;
+ }
+ else if (obj == (PyObject *)(&PyBool_Type)) {
+ check_num = NPY_BOOL;
+ }
+ else if (obj == (PyObject *)(&PyBytes_Type)) {
+ check_num = NPY_STRING;
+ }
+ else if (obj == (PyObject *)(&PyUnicode_Type)) {
+ check_num = NPY_UNICODE;
+ }
+#if defined(NPY_PY3K)
+ else if (obj == (PyObject *)(&PyMemoryView_Type)) {
+#else
+ else if (obj == (PyObject *)(&PyBuffer_Type)) {
+#endif
+ check_num = NPY_VOID;
+ }
+ else {
+ *at = _arraydescr_fromobj(obj);
+ if (*at) {
+ return NPY_SUCCEED;
+ }
+ }
+ goto finish;
+ }
+ printf("Test3\n");
+
+ /* or a typecode string */
+
+ if (PyUnicode_Check(obj)) {
+ /* Allow unicode format strings: convert to bytes */
+ int retval;
+ PyObject *obj2;
+ obj2 = PyUnicode_AsASCIIString(obj);
+ if (obj2 == NULL) {
+ return NPY_FAIL;
+ }
+ retval = PyArray_DescrConverter(obj2, at);
+ Py_DECREF(obj2);
+ return retval;
+ }
+
+ printf("Test4\n");
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+
+ /* Check for a string typecode. */
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+
+ /* Empty string is invalid */
+ if (len == 0) {
+ goto fail;
+ }
+
+ /* check for commas present or first (or second) element a digit */
+ if (_check_for_commastring(type, len)) {
+ *at = _convert_from_commastring(obj, 0);
+ return (*at) ? NPY_SUCCEED : NPY_FAIL;
+ }
+
+ /* Process the endian character. '|' is replaced by '='*/
+ switch (type[0]) {
+ case '>':
+ case '<':
+ case '=':
+ endian = type[0];
+ ++type;
+ --len;
+ break;
+
+ case '|':
+ endian = '=';
+ ++type;
+ --len;
+ break;
+ }
+
+ /* Just an endian character is invalid */
+ if (len == 0) {
+ goto fail;
+ }
+
+ /* Check for datetime format */
+ if (is_datetime_typestr(type, len)) {
+ *at = parse_dtype_from_datetime_typestr(type, len);
+ if (*at == NULL) {
+ return NPY_FAIL;
+ }
+ /* *at has byte order '=' at this point */
+ if (!PyArray_ISNBO(endian)) {
+ (*at)->byteorder = endian;
+ }
+ return NPY_SUCCEED;
+ }
+
+ /* A typecode like 'd' */
+ if (len == 1) {
+ check_num = type[0];
+ }
+ /* A kind + size like 'f8' */
+ else {
+ char *typeend = NULL;
+ int kind;
+
+ /* Parse the integer, make sure it's the rest of the string */
+ elsize = (int)strtol(type + 1, &typeend, 10);
+ if (typeend - type == len) {
+
+ kind = type[0];
+ switch (kind) {
+ case NPY_STRINGLTR:
+ case NPY_STRINGLTR2:
+ check_num = NPY_STRING;
+ break;
+
+ /*
+ * When specifying length of UNICODE
+ * the number of characters is given to match
+ * the STRING interface. Each character can be
+ * more than one byte and itemsize must be
+ * the number of bytes.
+ */
+ case NPY_UNICODELTR:
+ check_num = NPY_UNICODE;
+ elsize <<= 2;
+ break;
+
+ case NPY_VOIDLTR:
+ check_num = NPY_VOID;
+ break;
+
+ default:
+ if (elsize == 0) {
+ check_num = NPY_NOTYPE+10;
+ }
+ /* Support for generic processing c8, i4, f8, etc...*/
+ else {
+ check_num = PyArray_TypestrConvert(elsize, kind);
+ if (check_num == NPY_NOTYPE) {
+ check_num += 10;
+ }
+ elsize = 0;
+ }
+ }
+ }
+ }
+ }
+ else if (PyTuple_Check(obj)) {
+ /* or a tuple */
+ *at = _convert_from_tuple(obj);
+ if (*at == NULL){
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyList_Check(obj)) {
+ /* or a list */
+ *at = _convert_from_array_descr(obj,0);
+ if (*at == NULL) {
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyDict_Check(obj) || PyDictProxy_Check(obj)) {
+ /* or a dictionary */
+ *at = _convert_from_dict(obj,0);
+ if (*at == NULL) {
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ return NPY_SUCCEED;
+ }
+ else if (PyArray_Check(obj)) {
+ goto fail;
+ }
+ else {
+ *at = _arraydescr_fromobj(obj);
+ if (*at) {
+ return NPY_SUCCEED;
+ }
+ if (PyErr_Occurred()) {
+ return NPY_FAIL;
+ }
+ goto fail;
+ }
+ if (PyErr_Occurred()) {
+ goto fail;
+ }
+
+finish:
+ printf("Test5\n");
+ if ((check_num == NPY_NOTYPE + 10) ||
+ (*at = PyArray_DescrFromType(check_num)) == NULL) {
+ PyErr_Clear();
+ /* Now check to see if the object is registered in typeDict */
+ if (typeDict != NULL) {
+ item = PyDict_GetItem(typeDict, obj);
+#if defined(NPY_PY3K)
+ if (!item && PyBytes_Check(obj)) {
+ PyObject *tmp;
+ tmp = PyUnicode_FromEncodedObject(obj, "ascii", "strict");
+ if (tmp != NULL) {
+ item = PyDict_GetItem(typeDict, tmp);
+ Py_DECREF(tmp);
+ }
+ }
+#endif
+ if (item) {
+ /* Check for a deprecated Numeric-style typecode */
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+ char *dep_tps[] = {"Bool", "Complex", "Float", "Int",
+ "Object0", "String0", "Timedelta64",
+ "Unicode0", "UInt", "Void0"};
+ int ndep_tps = sizeof(dep_tps) / sizeof(dep_tps[0]);
+ int i;
+
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+ for (i = 0; i < ndep_tps; ++i) {
+ char *dep_tp = dep_tps[i];
+
+ if (strncmp(type, dep_tp, strlen(dep_tp)) == 0) {
+ if (DEPRECATE("Numeric-style type codes are "
+ "deprecated and will result in "
+ "an error in the future.") < 0) {
+ goto fail;
+ }
+ }
+ }
+ }
+ return PyArray_DescrConverter(item, at);
+ }
+ }
+ goto fail;
+ }
+
+ if (((*at)->elsize == 0) && (elsize != 0)) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->elsize = elsize;
+ }
+ if (endian != '=' && PyArray_ISNBO(endian)) {
+ endian = '=';
+ }
+ if (endian != '=' && (*at)->byteorder != '|'
+ && (*at)->byteorder != endian) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->byteorder = endian;
+ }
+ return NPY_SUCCEED;
+
+fail:
+ if (PyBytes_Check(obj)) {
+ PyErr_Format(PyExc_TypeError,
+ "data type \"%s\" not understood", PyBytes_AS_STRING(obj));
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "data type not understood");
+ }
+
+error:
+ *at = NULL;
+ return NPY_FAIL;
+}
+#endif
+
+
+NPY_NO_EXPORT int
+MyPyArray_DescrConverter(PyObject *obj, PyArray_Descr **at)
+{
+ int check_num = NPY_NOTYPE + 10;
+ PyObject *item;
+ int elsize = 0;
+ char endian = '=';
+
+ printf("Test -1\n");
+ *at = NULL;
+
+ check_num = NPY_VOID;
+ printf("Test0\n");
+ if (check_num != NPY_VOID) {
+ PyErr_Clear();
+ /* Now check to see if the object is registered in typeDict */
+ printf("Test1\n");
+ if (typeDict != NULL) {
+ item = PyDict_GetItem(typeDict, obj);
+#if defined(NPY_PY3K)
+ if (!item && PyBytes_Check(obj)) {
+ PyObject *tmp;
+ tmp = PyUnicode_FromEncodedObject(obj, "ascii", "strict");
+ if (tmp != NULL) {
+ item = PyDict_GetItem(typeDict, tmp);
+ Py_DECREF(tmp);
+ }
+ }
+#endif
+ if (item) {
+ /* Check for a deprecated Numeric-style typecode */
+ if (PyBytes_Check(obj)) {
+ char *type = NULL;
+ Py_ssize_t len = 0;
+ char *dep_tps[] = {"Bool", "Complex", "Float", "Int",
+ "Object0", "String0", "Timedelta64",
+ "Unicode0", "UInt", "Void0"};
+ int ndep_tps = sizeof(dep_tps) / sizeof(dep_tps[0]);
+ int i;
+
+ if (PyBytes_AsStringAndSize(obj, &type, &len) < 0) {
+ goto error;
+ }
+ for (i = 0; i < ndep_tps; ++i) {
+ char *dep_tp = dep_tps[i];
+
+ if (strncmp(type, dep_tp, strlen(dep_tp)) == 0) {
+ if (DEPRECATE("Numeric-style type codes are "
+ "deprecated and will result in "
+ "an error in the future.") < 0) {
+ goto fail;
+ }
+ }
+ }
+ }
+ return PyArray_DescrConverter(item, at);
+ }
+ }
+ printf("Test2\n");
+ goto fail;
+ }
+
+ printf("Test3\n");
+ if (((*at)->elsize == 0) && (elsize != 0)) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->elsize = elsize;
+ printf("Test4\n");
+ }
+ if (endian != '=' && PyArray_ISNBO(endian)) {
+ endian = '=';
+ printf("Test5\n");
+ }
+ if (endian != '=' && (*at)->byteorder != '|'
+ && (*at)->byteorder != endian) {
+ PyArray_DESCR_REPLACE(*at);
+ (*at)->byteorder = endian;
+ printf("Test6\n");
+ }
+ return NPY_SUCCEED;
+
+fail:
+ if (PyBytes_Check(obj)) {
+ PyErr_Format(PyExc_TypeError,
+ "data type \"%s\" not understood", PyBytes_AS_STRING(obj));
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "data type not understood");
+ }
+
+error:
+ *at = NULL;
+ return NPY_FAIL;
+}
+
+
+
#if 0
void init_readwriteaccess(struct DICTHOLDER *dict);
@@ -261,14 +1345,14 @@ PyObject * my_read_structure(PyObject* molpack) {
molfile_atom_t* atoms;
int numatoms, status;
PyArray_Descr *descr;
- PyObject p*;
- if (PyType_Ready(&MolAtomType) < 0)
- return NULL;
- PyTypeObject *atype = &MolAtomType;
- MolAtom *atom_t;
- atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
- p = (PyObject*) atom_t;
- descr = PyArray_DescrFromObject(p, NULL)
+ PyObject *p = NULL;
+ //if (PyType_Ready(&MolAtomType) < 0)
+ // return NULL;
+ //PyTypeObject *atype = &MolAtomType;
+ //MolAtom *atom_t;
+ //atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
+ //p = (PyObject*) atom_t;
+ descr = PyArray_DescrFromObject(p, NULL);
MolObject* plugin_handle = (MolObject*) molpack;
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
@@ -286,8 +1370,8 @@ PyObject * my_read_structure(PyObject* molpack) {
npy_intp dims[1] = { numatoms };
oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
Py_DECREF(p);
- array = (PyArrayObject*) PyArray_SimpleNewFromDescr(1, dims, descr);
- PyObject_Print(array, stdout, 0);
+ //array = (PyArrayObject*) PyArray_SimpleNewFromDescr(1, dims, descr);
+ //PyObject_Print(array, stdout, 0);
if (!oresid){
PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into numpy array.");
return NULL;
@@ -301,4 +1385,296 @@ PyObject * my_read_structure(PyObject* molpack) {
return (PyObject*) PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);
}
+PyObject* print_array_struct(PyObject* prototype)
+{
+ Py_Initialize();
+ import_array();
+ int status = -10;
+ PyObject *ret = NULL;
+ int *maxndim = NULL;
+ npy_intp *d_shape = NULL;
+ printf("Check-in print_array_struct\n");
+ Py_INCREF(prototype);
+ ret = get_array_attr_interface(prototype, "descr", maxndim, d_shape);
+ printf("Returned\n");
+ //printf("Returned nd:%d\n", *maxndim);
+ Py_DECREF(prototype);
+ if (!ret){
+ PyErr_Clear();
+ PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+ Py_XDECREF(ret);
+ return NULL;
+ }
+ printf("Check-out print_array_struct\n");
+ return ret;
+}
+
+PyObject* read_fill_structure(PyObject* molpack, PyObject* prototype)
+{
+ Py_Initialize();
+ import_array();
+ int options = 0;
+// int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* data;
+ int numatoms, status;
+ int nd;
+ PyArray_Descr *descr;
+// PyArrayInterface *inter;
+ //PyArrayObject *ret = NULL;
+ PyObject *ret = NULL;
+ PyObject *descr_obj = NULL;
+// char endian = NPY_NATBYTE;
+// PyArrayObject *obj;
+// printf("Test1\n");
+// obj = (PyArrayObject *)prototype;
+// if(obj == NULL){
+// PyErr_Format(PyExc_IOError, "Error: Given PyObject does not include numpy array.");
+// return NULL;
+// }
+ // Access plugin_handle values
+ MolObject* plugin_handle = (MolObject*) molpack;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ printf("Test2-1\n");
+ // Allocate memory for array of molfile_atom_t struct
+ data = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ // Get array values in molfile_atom_t
+ printf("Test2-2\n");
+ status = plugin->read_structure(file_handle, &options, data);
+ printf("Test2-3\n");
+ // Check if the plugin returns the results
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ nd = 1;
+ npy_intp dims[1] = { numatoms };
+ npy_intp strides[1] = { sizeof(molfile_atom_t) };
+ printf("Test3\n");
+ Py_INCREF(prototype);
+ //ret = set_array_attr_interface(prototype, numatoms, data);
+ descr_obj = get_descr_array_interface(prototype);
+ descr = (PyArray_Descr*) descr_obj;
+ //ret = set_array_attr_struct(ret, numatoms, data);
+ printf("Returned 1\n");
+ Py_DECREF(prototype);
+ printf("Set\n");
+ Py_INCREF(prototype);
+ ret = PyArray_NewFromDescr(Py_TYPE(prototype), PyArray_DESCR((PyArrayObject*)prototype),
+ nd, dims,
+ strides, data,
+ PyArray_FLAGS((PyArrayObject*)prototype), prototype);
+ //PyArray_STRIDES((PyArrayObject*)prototype), data,
+ Py_DECREF(prototype);
+ printf("Returned 2\n");
+ //status = my_get_array_attr_interface((PyObject*)obj, "descr", maxndim, d_shape, ret);
+ //status = my_get_array_attr_interface(prototype, ret);
+ //printf("Test4 Status:%d nd:%d\n",status,*maxndim);
+ //printf("Test4 Status:%d\n",status);
+// if (status<0){
+// Py_DECREF(obj);
+// PyErr_Clear();
+// PyErr_Format(PyExc_IOError, "Error: can not get attribute of given numpy array.");
+// return NULL;
+// }
+// printf("Test5\n");
+// Py_INCREF(prototype);
+// Py_DECREF(ret);
+ //return (PyObject*) PyArray_FromArray((PyArrayObject*)ret, PyArray_DESCR((PyArrayObject*)ret), 0);
+ return (PyObject*) ret;
+}
+
+PyObject* get_structure(PyObject* self)
+{
+ int options = 0;
+ int i;
+ molfile_plugin_t* plugin;
+ void* file_handle;
+ molfile_atom_t* data;
+ int numatoms, status;
+ int nd;
+ PyArrayInterface *inter;
+ PyArrayObject *ret;
+ char endian = NPY_NATBYTE;
+ // Access plugin_handle values
+ MolObject* plugin_handle = (MolObject*) self;
+ plugin = plugin_handle->plugin;
+ file_handle = plugin_handle->file_handle;
+ numatoms = plugin_handle->natoms;
+ // Allocate memory for array of molfile_atom_t struct
+ data = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
+ // Get array values in molfile_atom_t
+ status = plugin->read_structure(file_handle, &options, data);
+ // Check if the plugin returns the results
+ if (status!=0){
+ PyErr_Format(PyExc_IOError, "Error accessing molfile_atom_t in read_structure function of plugin.");
+ return NULL;
+ }
+ // Now, we need to allocate a PyArray with PyArrayInterface
+ // and assign the allocated memory block to the data.
+ // To do this, we will build a numpy array from scratch.
+ // First, allocate a PyObject of PyArrayInterface and
+ // assign relevant information such as typestr, descr for C-side
+ // struct and second we will assign molfile_atom_t array as a block
+ // of data. Last, hope this works.
+ nd = 1;
+ npy_intp dims[1] = { 1 };
+ // We would allocate a numpy array with
+ // but will not look clever to copy all the data into the new array.
+ // Instead, we allocate a numpy array with one element and change
+ // the definition of array. I know I said that it will be from scratch
+ // but let's accept nobody wants to define everything in numpy again.
+ //oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT);
+ // NPY_INT? Don't worry, we will change it.
+ //Py_intptr_t *shape, *strides;
+ //void *data = NULL;
+
+ inter = (PyArrayInterface*)malloc(sizeof(PyArrayInterface));
+ if (inter==NULL)
+ return PyErr_NoMemory();
+
+ // __array_interface__ descr for C side of __array_struct__
+ // Could not find a better way to generate the list of tuples for
+ // Python side. May need to change this later.
+ PyObject *descrlist = PyList_New(13);
+ // One tuple to bind them
+ PyObject *py_tuple_name = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_name, 0, PyUnicode_FromString("name"));
+ PyTuple_SET_ITEM(py_tuple_name, 1, PyUnicode_FromString("|S16"));
+ PyList_SET_ITEM(descrlist, 0, py_tuple_name);
+ PyObject *py_tuple_type = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_type, 0, PyUnicode_FromString("type"));
+ PyTuple_SET_ITEM(py_tuple_type, 1, PyUnicode_FromString("|S16"));
+ PyList_SET_ITEM(descrlist, 1, py_tuple_type);
+ PyObject *py_tuple_resname = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_resname, 0, PyUnicode_FromString("resname"));
+ PyTuple_SET_ITEM(py_tuple_resname, 1, PyUnicode_FromString("|S8"));
+ PyList_SET_ITEM(descrlist, 2, py_tuple_resname);
+ PyObject *py_tuple_resid = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_resid, 0, PyUnicode_FromString("resid"));
+ PyTuple_SET_ITEM(py_tuple_resid, 1, PyUnicode_FromString("<i4"));
+ PyList_SET_ITEM(descrlist, 3, py_tuple_resid);
+ PyObject *py_tuple_segid = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_segid, 0, PyUnicode_FromString("segid"));
+ PyTuple_SET_ITEM(py_tuple_segid, 1, PyUnicode_FromString("|S8"));
+ PyList_SET_ITEM(descrlist, 4, py_tuple_segid);
+ PyObject *py_tuple_chain = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_chain, 0, PyUnicode_FromString("chain"));
+ PyTuple_SET_ITEM(py_tuple_chain, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 5, py_tuple_chain);
+ PyObject *py_tuple_altloc = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_altloc, 0, PyUnicode_FromString("altloc"));
+ PyTuple_SET_ITEM(py_tuple_altloc, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 6, py_tuple_altloc);
+ PyObject *py_tuple_insertion = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_insertion, 0, PyUnicode_FromString("insertion"));
+ PyTuple_SET_ITEM(py_tuple_insertion, 1, PyUnicode_FromString("|S2"));
+ PyList_SET_ITEM(descrlist, 7, py_tuple_insertion);
+ PyObject *py_tuple_occupancy = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_occupancy, 0, PyUnicode_FromString("occupancy"));
+ PyTuple_SET_ITEM(py_tuple_occupancy, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 8, py_tuple_occupancy);
+ PyObject *py_tuple_bfactor = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_bfactor, 0, PyUnicode_FromString("bfactor"));
+ PyTuple_SET_ITEM(py_tuple_bfactor, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 9, py_tuple_bfactor);
+ PyObject *py_tuple_mass = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_mass, 0, PyUnicode_FromString("mass"));
+ PyTuple_SET_ITEM(py_tuple_mass, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 10, py_tuple_mass);
+ PyObject *py_tuple_charge = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_charge, 0, PyUnicode_FromString("charge"));
+ PyTuple_SET_ITEM(py_tuple_charge, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 11, py_tuple_charge);
+ PyObject *py_tuple_radius = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_radius, 0, PyUnicode_FromString("radius"));
+ PyTuple_SET_ITEM(py_tuple_radius, 1, PyUnicode_FromString("<f4"));
+ PyList_SET_ITEM(descrlist, 12, py_tuple_radius);
+ PyObject *py_tuple_atomicnumber = PyTuple_New(2);
+ PyTuple_SET_ITEM(py_tuple_atomicnumber, 0, PyUnicode_FromString("atomicnumber"));
+ PyTuple_SET_ITEM(py_tuple_atomicnumber, 1, PyUnicode_FromString("<i4"));
+ PyList_SET_ITEM(descrlist, 13, py_tuple_atomicnumber);
+ //PyArray_Descr *descr = (PyObject*) tuple;
+ PyArray_Descr *thetype = NULL;
+ // Here we define the size and stride parameters
+ npy_intp shape[1] = { numatoms };
+ npy_intp strides[1] = { 54*sizeof(char) + 8*sizeof(int) + 20*sizeof(float) };
+
+ inter->two = 2;
+ inter->nd = nd;
+ inter->typekind = 'V';
+ inter->itemsize = 82*sizeof(char);
+ //inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE;
+ inter->flags = NPY_ARRAY_NOTSWAPPED | NPY_ARRAY_ALIGNED | NPY_ARRAY_WRITEABLE | NPY_ARR_HAS_DESCR;
+ inter->strides = (Py_intptr_t *)strides;
+ inter->shape = (Py_intptr_t *)shape;
+ inter->data = (void*) data;
+ // inter->descr = (PyObject*) tuple;
+ if ((inter->flags & NPY_ARRAY_NOTSWAPPED) != NPY_ARRAY_NOTSWAPPED) {
+ endian = NPY_OPPBYTE;
+ inter->flags &= ~NPY_ARRAY_NOTSWAPPED;
+ }
+ // typestr is relatively easy to assign to __array_interface__
+ printf("TEST1\n");
+ //thetype = (PyArray_Descr*) tuple;
+ if (inter->flags & NPY_ARR_HAS_DESCR) {
+ printf("TEST1-1\n");
+ thetype = _convert_from_array_descr(descrlist,0);
+ //thetype = PyArray_DescrFromTypeObject(descrlist);
+ printf("TEST1-2\n");
+ //if (PyArray_DescrConverter(inter->descr, &thetype) == NPY_FAIL) {
+ // thetype = NULL;
+ // PyErr_Clear();
+ // }
+ }
+ printf("TEST1-3\n");
+#if 0
+ char buf[40];
+ PyOS_snprintf(buf, sizeof(buf),
+ "%c%c%d", endian,
+ inter->typekind,
+ inter->itemsize);
+ printf("TEST2 String:%s\n",buf);
+ PyObject *stringobj = PyUnicode_FromString(buf);
+ if (stringobj == NULL) {
+ return NULL;
+ }
+ printf("TEST2-2\n");
+ if (MyPyArray_DescrConverter(stringobj, &thetype) != NPY_SUCCEED) {
+ Py_DECREF(stringobj);
+ return NULL;
+ }
+ printf("TEST2-3\n");
+ Py_DECREF(stringobj);
+#endif
+ printf("TEST3\n");
+ ret = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, thetype,
+ inter->nd, inter->shape,
+ inter->strides, inter->data,
+ inter->flags, NULL);
+ printf("TEST4\n");
+ Py_INCREF(inter);
+ if (PyArray_SetBaseObject(ret, (PyObject *)inter) < 0) {
+ Py_DECREF(ret);
+ return NULL;
+ }
+ printf("TEST5\n");
+// Py_DECREF(attr);
+ PyArray_UpdateFlags(ret, NPY_ARRAY_UPDATE_ALL);
+ printf("TEST6\n");
+ return (PyObject *)ret;
+}
+// obj = NpyCapsule_FromVoidPtrAndDesc(inter, self, gentype_struct_free);
+/*
+#ifdef Py_CAPSULE_H
+ obj = PyCapsule_New((void*)inter, "struct SignedIntBuf", free_capsule);
+#else
+ obj = PyCObject_FromVoidPtrAndDesc((void*)inter, (void*)self, free_array_interface);
+#endif
+*/
+ // Cross fingers here.
+// return obj;
diff --git a/pymolfile/molfile/pymolfile.h b/pymolfile/molfile/pymolfile.h
index 5d37f5d2dc12ed010c2baa45c4edb26cbe77ae75..6a0c1b5161f6bd1bc19178bcf644e7d0ffc5cb22 100644
--- a/pymolfile/molfile/pymolfile.h
+++ b/pymolfile/molfile/pymolfile.h
@@ -30,6 +30,7 @@ extern "C"
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
+
enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
@@ -119,7 +120,7 @@ static PyMemberDef MolObject_members[] = {
"file handle for plugin"},
{"natoms", T_INT, offsetof(MolObject, natoms), 0,
"number of atoms"},
- {NULL, NULL, 0, NULL} /* Sentinel */
+ {NULL} /* Sentinel */
};
static PyMethodDef MolObject_methods[] = {
@@ -132,7 +133,7 @@ static PyMethodDef MolObject_methods[] = {
{"get_natoms", (PyCFunction)MolObject_natoms, METH_NOARGS,
"Return the number of atoms"
},
- {NULL, NULL, 0, NULL} /* Sentinel */
+ {NULL} /* Sentinel */
};
@@ -183,6 +184,7 @@ static PyTypeObject MolObjectType = {
MolObject_new, /* tp_new */
};
+#if 0
struct MolAtom {
PyObject_HEAD
char* name;
@@ -257,8 +259,8 @@ static PyMemberDef MolAtom_members[] = {
{"segid", T_STRING, offsetof(MolAtom, segid), 0,""},
{"chain", T_STRING, offsetof(MolAtom, chain), 0,""},
{"altloc", T_STRING, offsetof(MolAtom, altloc), 0,""},
- {"insertion", T_STRING, offsetof(MolAtom, occupancy), 0,""},
- {"occupancy", T_FLOAT, offsetof(MolAtom, ), 0,""},
+ {"insertion", T_STRING, offsetof(MolAtom, insertion), 0,""},
+ {"occupancy", T_FLOAT, offsetof(MolAtom, occupancy), 0,""},
{"bfactor", T_FLOAT, offsetof(MolAtom, bfactor), 0,""},
{"mass", T_FLOAT, offsetof(MolAtom, mass), 0,""},
{"charge", T_FLOAT, offsetof(MolAtom, charge), 0,""},
@@ -309,8 +311,11 @@ static PyTypeObject MolAtomType = {
0, /* tp_alloc */
MolAtom_new, /* tp_new */
};
-
+#endif
PyObject * my_read_structure(PyObject* molpack);
+PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
+PyObject * get_structure(PyObject* molpack);
+PyObject * print_array_struct(PyObject* prototype);
#if 0
typedef struct DICTHOLDER {
diff --git a/pymolfile/molfile/signedintbuf-cython/compile-numind.sh b/pymolfile/molfile/signedintbuf-cython/compile-numind.sh
new file mode 100644
index 0000000000000000000000000000000000000000..680fa4e374146e23eaab3a4e15e25c120176b42a
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/compile-numind.sh
@@ -0,0 +1,2 @@
+Cython -a numind.pyx --cplus
+g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ numind.cpp -o numind.so -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/molfile/signedintbuf-cython/numind.cpp b/pymolfile/molfile/signedintbuf-cython/numind.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..06f2230dd7ee03c887290f5a40d14c053ceb556d
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/numind.cpp
@@ -0,0 +1 @@
+#error Do not use this file, it is the result of a failed Cython compilation.
diff --git a/pymolfile/molfile/signedintbuf-cython/numind.h b/pymolfile/molfile/signedintbuf-cython/numind.h
new file mode 100644
index 0000000000000000000000000000000000000000..988c2c80604711a3067cf39a3976896c48867526
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/numind.h
@@ -0,0 +1,12 @@
+#ifndef NUMIND_H
+#define NUMIND_H
+
+typedef struct SignedIntBuf
+{
+ int* data;
+ int shape[2];
+ int strides[2];
+} SignedIntBuf;
+
+#endif
+
diff --git a/pymolfile/molfile/signedintbuf-cython/numind.html b/pymolfile/molfile/signedintbuf-cython/numind.html
new file mode 100644
index 0000000000000000000000000000000000000000..96768d145b96058d800f53ece01d88f4c34cb278
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/numind.html
@@ -0,0 +1,1243 @@
+<!DOCTYPE html>
+<!-- Generated by Cython 0.26.1 -->
+<html>
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Cython: numind.pyx</title>
+ <style type="text/css">
+
+body.cython { font-family: courier; font-size: 12; }
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+.cython.score-253 {background-color: #FFFF09;}
+.cython.score-254 {background-color: #FFFF09;}
+ </style>
+ <script>
+ function toggleDiv(id) {
+ theDiv = id.nextElementSibling
+ if (theDiv.style.display != 'block') theDiv.style.display = 'block';
+ else theDiv.style.display = 'none';
+ }
+ </script>
+</head>
+<body class="cython">
+<p><span style="border-bottom: solid 1px grey;">Generated by Cython 0.26.1</span></p>
+<p>
+ <span style="background-color: #FFFF00">Yellow lines</span> hint at Python interaction.<br />
+ Click on a line that starts with a "<code>+</code>" to see the C code that Cython generated for it.
+</p>
+<p>Raw output: <a href="numind.cpp">numind.cpp</a></p>
+<div class="cython"><pre class="cython line score-0"> <span class="">001</span>: # This Pyrex extension class can take a numpy/numarray/Numeric object</pre>
+<pre class="cython line score-0"> <span class="">002</span>: # as a parameter and wrap it so that its information can be accessed</pre>
+<pre class="cython line score-0"> <span class="">003</span>: # in a standard way, both in Python space and C space.</pre>
+<pre class="cython line score-0"> <span class="">004</span>: #</pre>
+<pre class="cython line score-0"> <span class="">005</span>: # Heavily based on an idea of Andrew Straw. See</pre>
+<pre class="cython line score-0"> <span class="">006</span>: # http://www.scipy.org/Cookbook/ArrayStruct_and_Pyrex</pre>
+<pre class="cython line score-0"> <span class="">007</span>: # Very inspiring! :-)</pre>
+<pre class="cython line score-0"> <span class="">008</span>: #</pre>
+<pre class="cython line score-0"> <span class="">009</span>: # First version: 2006-03-25</pre>
+<pre class="cython line score-0"> <span class="">010</span>: # Last update: 2006-03-25</pre>
+<pre class="cython line score-0"> <span class="">011</span>: # Author: Francesc Altet</pre>
+<pre class="cython line score-0"> <span class="">012</span>: </pre>
+<pre class="cython line score-8" onclick='toggleDiv(this)'>+<span class="">013</span>: import sys</pre>
+<pre class='cython code score-8 '> __pyx_t_1 = <span class='pyx_c_api'>__Pyx_Import</span>(__pyx_n_s_sys, 0, -1);<span class='error_goto'> if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 13, __pyx_L1_error)</span>
+ <span class='refnanny'>__Pyx_GOTREF</span>(__pyx_t_1);
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+ <span class='pyx_macro_api'>__Pyx_DECREF</span>(__pyx_t_1); __pyx_t_1 = 0;
+</pre><pre class="cython line score-0"> <span class="">014</span>: from cpython.pycapsule cimport *</pre>
+<pre class="cython line score-0"> <span class="">015</span>: </pre>
+<pre class="cython line score-0"> <span class="">016</span>: cdef extern from "Python.h":</pre>
+<pre class="cython line score-0"> <span class="">017</span>: ctypedef int Py_intptr_t</pre>
+<pre class="cython line score-0"> <span class="">018</span>: ctypedef object PyObject</pre>
+<pre class="cython line score-0"> <span class="">019</span>: long PyInt_AsLong(object)</pre>
+<pre class="cython line score-0"> <span class="">020</span>: void Py_INCREF(object)</pre>
+<pre class="cython line score-0"> <span class="">021</span>: void Py_DECREF(object)</pre>
+<pre class="cython line score-0"> <span class="">022</span>: </pre>
+<pre class="cython line score-0"> <span class="">023</span>: cdef extern from "stdlib.h":</pre>
+<pre class="cython line score-0"> <span class="">024</span>: ctypedef long size_t</pre>
+<pre class="cython line score-0"> <span class="">025</span>: ctypedef long intptr_t</pre>
+<pre class="cython line score-0"> <span class="">026</span>: void *malloc(size_t size)</pre>
+<pre class="cython line score-0"> <span class="">027</span>: void free(void* ptr)</pre>
+<pre class="cython line score-0"> <span class="">028</span>: </pre>
+<pre class="cython line score-0"> <span class="">029</span>: cdef extern from "numind.h":</pre>
+<pre class="cython line score-0"> <span class="">030</span>: ctypedef struct SignedIntBuf</pre>
+<pre class="cython line score-0"> <span class="">031</span>: </pre>
+<pre class="cython line score-0"> <span class="">032</span>: # for PyArrayInterface:</pre>
+<pre class="cython line score-5" onclick='toggleDiv(this)'>+<span class="">033</span>: CONTIGUOUS=0x01</pre>
+<pre class='cython code score-5 '> if (<span class='py_c_api'>PyDict_SetItem</span>(__pyx_d, __pyx_n_s_CONTIGUOUS, __pyx_int_1) < 0) <span class='error_goto'>__PYX_ERR(0, 33, __pyx_L1_error)</span>
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+</pre><pre class="cython line score-0"> <span class="">038</span>: </pre>
+<pre class="cython line score-0"> <span class="">039</span>: # byteorder dictionary</pre>
+<pre class="cython line score-21" onclick='toggleDiv(this)'>+<span class="">040</span>: byteorder = {'<':'little', '>':'big'}</pre>
+<pre class='cython code score-21 '> __pyx_t_1 = <span class='py_c_api'>PyDict_New</span>();<span class='error_goto'> if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 40, __pyx_L1_error)</span>
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+<pre class="cython line score-0" onclick='toggleDiv(this)'>+<span class="">042</span>: ctypedef struct PyArrayInterface:</pre>
+<pre class='cython code score-0 '>struct __pyx_t_6numind_PyArrayInterface {
+ int version;
+ int nd;
+ char typekind;
+ int itemsize;
+ int flags;
+ Py_intptr_t *shape;
+ Py_intptr_t *strides;
+ void *data;
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diff --git a/pymolfile/molfile/signedintbuf-cython/numind.pyx b/pymolfile/molfile/signedintbuf-cython/numind.pyx
new file mode 100644
index 0000000000000000000000000000000000000000..4e9aa817ab369c7bd8baf27906d9d17a0bd04df8
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/numind.pyx
@@ -0,0 +1,268 @@
+# This Pyrex extension class can take a numpy/numarray/Numeric object
+# as a parameter and wrap it so that its information can be accessed
+# in a standard way, both in Python space and C space.
+#
+# Heavily based on an idea of Andrew Straw. See
+# http://www.scipy.org/Cookbook/ArrayStruct_and_Pyrex
+# Very inspiring! :-)
+#
+# First version: 2006-03-25
+# Last update: 2006-03-25
+# Author: Francesc Altet
+
+import sys
+from cpython.pycapsule cimport *
+
+cdef extern from "Python.h":
+ ctypedef int Py_intptr_t
+ ctypedef object PyObject
+ long PyInt_AsLong(object)
+ void Py_INCREF(object)
+ void Py_DECREF(object)
+
+cdef extern from "stdlib.h":
+ ctypedef long size_t
+ ctypedef long intptr_t
+ void *malloc(size_t size)
+ void free(void* ptr)
+
+cdef extern from "string.h":
+ int strncmp(const char *str1, const char *str2, size_t n)
+
+cdef extern from "vmdplugin.h":
+ ctypedef struct vmdplugin_t
+ ctypedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
+
+cdef extern from "molfile_plugin.h":
+ ctypedef struct molfile_atom_t
+ ctypedef struct molfile_timestep_t
+ ctypedef struct molfile_plugin_t
+
+cdef extern from "libmolfile_plugin.h":
+ MOLFILE_INIT_ALL()
+ MOLFILE_REGISTER_ALL(void* , vmdplugin_register_cb)
+ MOLFILE_FINI_ALL()
+
+# for PyArrayInterface:
+CONTIGUOUS=0x01
+FORTRAN=0x02
+ALIGNED=0x100
+NOTSWAPPED=0x200
+WRITEABLE=0x400
+
+# for VMDPLUGIN
+VMDPLUGIN_SUCCESS=0
+VMDPLUGIN_ERROR=-1
+vmdplugin_ABIVERSION=17
+MAXPLUGINS=200
+
+# byteorder dictionary
+byteorder = {'<':'little', '>':'big'}
+
+cdef int numplugins = 0
+cdef (molfile_plugin_t*) plugin_list = NULL
+
+ctypedef struct PyArrayInterface:
+ int version # contains the integer 2 as a sanity check
+ int nd # number of dimensions
+ char typekind # kind in array --- character code of typestr
+ int itemsize # size of each element
+ int flags # flags indicating how the data should be interpreted
+ Py_intptr_t *shape # A length-nd array of shape information
+ Py_intptr_t *strides # A length-nd array of stride information
+ void *data # A pointer to the first element of the array
+
+ctypedef struct MolObject:
+ molfile_plugin_t* plugin
+ void* file_handle
+ int natoms
+
+cdef void* free_array_interface(object arr):
+ Py_DECREF(arr)
+
+cdef molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no):
+ cdef molfile_plugin_t* plugin;
+ if(plug_no < 0):
+ plugin = NULL
+ else:
+ plugin = plug_list[plug_no]
+ return plugin
+
+cdef int molfile_register(void* ptr, vmdplugin_t *plugin):
+ global numplugins, plugin_list
+ if (plugin.type is NULL or
+ plugin.name is NULL or
+ plugin.author is NULL):
+ return VMDPLUGIN_ERROR
+ elif plugin.abiversion != vmdplugin_ABIVERSION:
+ return VMDPLUGIN_ERROR
+ elif 0 != strncmp(plugin.type, "mol file", 8):
+ return VMDPLUGIN_ERROR
+ elif numplugins >= MAXPLUGINS:
+ return VMDPLUGIN_ERROR
+
+ plugin_list[numplugins] = <molfile_plugin_t *> plugin
+ numplugins = numplugins + 1
+ return VMDPLUGIN_SUCCESS
+
+cdef molfile_plugin_t** molfile_plugin_list(int maxsize):
+ global numplugins, plugin_list
+ if maxsize < MAXPLUGINS:
+ maxsize = MAXPLUGINS
+ plugin_list = <molfile_plugin_t**>malloc(sizeof(molfile_plugin_t*)*maxsize)
+ return plugin_list
+
+cdef int molfile_init(void):
+ global numplugins, plugin_list
+ MOLFILE_INIT_ALL
+ MOLFILE_REGISTER_ALL(NULL,molfile_register)
+ return numplugins
+
+cdef int molfile_finish(void):
+ MOLFILE_FINI_ALL
+ return 0
+
+cdef class NumCy:
+ cdef void *data
+ cdef int _nd
+ cdef Py_intptr_t *_shape
+ cdef Py_intptr_t *_strides
+ cdef PyArrayInterface *inter
+ cdef MolObject *plugin_handle
+ cdef object _t_shape, _t_strides, _undarray
+
+ def __init__(self):
+ cdef int i, stride
+ cdef object array_shape, array_strides
+ cdef molfile_plugin_t *plugin;
+ cdef void *file_handle;
+
+ # Initialize available VMD molfile plugins
+
+
+ # Keep a reference to the underlying object
+ self.plugin_handle = molpack;
+ self._undarray = undarray
+ # Get the shape and strides C arrays
+ array_shape = undarray.__array_interface__["shape"]
+ self._t_shape = array_shape
+ # The number of dimensions
+ self._nd = len(array_shape)
+ # The shape
+ self._shape = <Py_intptr_t *>malloc(self._nd*sizeof(Py_intptr_t))
+ for i from 0 <= i < self._nd:
+ self._shape[i] = self._t_shape[i]
+ # The strides (compute them if needed)
+ array_strides = undarray.__array_interface__["strides"]
+ self._t_strides = array_strides
+ self._strides = <Py_intptr_t *>malloc(self._nd*sizeof(Py_intptr_t))
+ if array_strides:
+ for i from 0 <= i < self._nd:
+ self._strides[i] = array_strides[i]
+ else:
+ # strides is None. Compute them explicitely.
+ self._t_strides = [0] * self._nd
+ stride = int(self.typestr[2:])
+ for i from self._nd > i >= 0:
+ self._strides[i] = stride
+ self._t_strides[i] = stride
+ stride = stride * array_shape[i]
+ self._t_strides = tuple(self._t_strides)
+ # Populate the C array interface
+ self.inter = self._get_array_interface()
+
+ # Properties. This are visible from Python space.
+ # Add as many as you want.
+
+ property undarray: # Returns the underlying array
+ def __get__(self):
+ return self._undarray
+
+ property shape:
+ def __get__(self):
+ return self._t_shape
+
+ property strides:
+ def __get__(self):
+ return self._t_strides
+
+ property typestr:
+ def __get__(self):
+ return self._undarray.__array_interface__["typestr"]
+
+ property typekind:
+ def __get__(self):
+ return chr(self.inter.typekind)
+
+ property readonly:
+ def __get__(self):
+ return self._undarray.__array_interface__["data"][1]
+
+ property __array_struct__:
+ "Allows other numerical packages to obtain a new object."
+ def __get__(self):
+ if hasattr(self._undarray, "__array_struct__"):
+ return self._undarray.__array_struct__
+ else:
+ # No an underlying array with __array_struct__
+ # Deliver an equivalent PyCObject.
+ Py_INCREF(self)
+ return PyCapsule_New(<void*>self.inter,
+ "struct array",
+ <PyCapsule_Destructor>free_array_interface)
+
+ cdef PyArrayInterface *_get_array_interface(self):
+ "Populates the array interface"
+ cdef PyArrayInterface *inter
+ cdef object undarray, data_address, typestr
+ cdef object obj
+
+ undarray = self._undarray
+ typestr = self.typestr
+ inter = <PyArrayInterface *>malloc(sizeof(PyArrayInterface))
+ if inter is NULL:
+ raise MemoryError()
+
+ inter.version = 2
+ inter.nd = self._nd
+ inter.typekind = ord(typestr[1])
+ inter.itemsize = int(typestr[2:])
+ inter.flags = 0 # initialize flags
+ if typestr[0] == '|':
+ inter.flags = inter.flags | NOTSWAPPED
+ elif byteorder[typestr[0]] == sys.byteorder:
+ inter.flags = inter.flags | NOTSWAPPED
+ if not self.readonly:
+ inter.flags = inter.flags | WRITEABLE
+ # XXX how to determine the ALIGNED flag?
+ inter.strides = self._strides
+ inter.shape = self._shape
+ # Get the data address
+ obj = undarray.__array_interface__["data"]
+ data_address = obj[0]
+ inter.data = <void*>PyInt_AsLong(data_address)
+ return inter
+
+
+ # This is just an example on how to modify the data in C space
+ # (and at C speed! :-)
+ def modify(self):
+ "Modify the values of the underlying array"
+ cdef long *ldata
+ cdef double *fdata
+ cdef int i
+
+ # Modify just the first row
+ if chr(self.inter.typekind) == 'i':
+ ldata = <long *>self.inter.data
+ for i from 0 <= i < self.inter.shape[self.inter.nd-1]:
+ ldata[i] = ldata[i] + 1
+ elif chr(self.inter.typekind) == 'f':
+ fdata = <double *>self.inter.data
+ for i from 0 <= i < self.inter.shape[self.inter.nd-1]:
+ fdata[i] = fdata[i] + 1
+
+ def __dealloc__(self):
+ free(self._shape)
+ free(self._strides)
+ free(self.inter)
diff --git a/pymolfile/molfile/signedintbuf-cython/numind.so b/pymolfile/molfile/signedintbuf-cython/numind.so
new file mode 100755
index 0000000000000000000000000000000000000000..f8b762476eb1d362018f305fce67cf22ec134e2f
Binary files /dev/null and b/pymolfile/molfile/signedintbuf-cython/numind.so differ
diff --git a/pymolfile/molfile/signedintbuf-cython/test_numpy_swig.py b/pymolfile/molfile/signedintbuf-cython/test_numpy_swig.py
new file mode 100644
index 0000000000000000000000000000000000000000..d53a1b1d2874a0a7592975989918f36a5e0be95d
--- /dev/null
+++ b/pymolfile/molfile/signedintbuf-cython/test_numpy_swig.py
@@ -0,0 +1,42 @@
+import numpy
+import ctypes
+import numind
+
+# Create an arbitrary object for each package
+np=numpy.arange(12, dtype=numpy.float)
+#np=numpy.arange(12)
+np.shape = (4,3)
+
+#ns = _numpy_swig(2,2)
+#print(ns)
+
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+##for obj in [np]:
+# ni = _numpy_swig
+# print("original object type-->", type(ni.inter))
+# # Print some values
+# #print("typestr --> {0}", ni.typestr)
+# #print("shape --> {0}", ni.shape)
+# #print("strides --> {0}", ni.strides)
+# npa = numpy.asarray(ni)
+# print("object after a numpy re-wrapping --> " , npa)
+# #ni.modify()
+# #print("object after modification in C space --> {0}", npa)
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+for obj in [np]:
+ ni = numind.NumInd(obj)
+ print("original object type-->", type(ni.undarray))
+ # Print some values
+ print("typestr -->", ni.typestr)
+ print("typekind -->", ni.typekind)
+ print("shape -->", ni.shape)
+ print("strides -->", ni.strides)
+ npa = numpy.asarray(ni)
+ print("object after a numpy re-wrapping -->", npa)
+ ni.modify()
+ print("object after modification in C space -->", npa)
+
diff --git a/pymolfile/molfile/test-backup.py b/pymolfile/molfile/test-backup.py
new file mode 100644
index 0000000000000000000000000000000000000000..5490a0527f0962ff0c1a8f03b48acdb476bf437c
--- /dev/null
+++ b/pymolfile/molfile/test-backup.py
@@ -0,0 +1,153 @@
+import numpy
+import ctypes
+import _libpymolfile
+
+class molatom_t(ctypes.Structure):
+ _fields_ = [
+ ('name', ctypes.c_char * 16),
+ ('type', ctypes.c_char * 16),
+ ('resname', ctypes.c_char * 8),
+ ('resid', ctypes.c_uint8),
+ ('segid', ctypes.c_char * 8),
+ ('chain', ctypes.c_char * 2),
+ ('altloc', ctypes.c_char * 2),
+ ('insertion', ctypes.c_char *2),
+ ('occupancy', ctypes.c_float),
+ ('bfactor', ctypes.c_float),
+ ('mass', ctypes.c_float),
+ ('charge', ctypes.c_float),
+ ('radius', ctypes.c_float),
+ ('atomicnumber', ctypes.c_uint8),
+ ('ctnumber', ctypes.c_uint8),
+ ]
+
+class molplugin_t(ctypes.Structure):
+ _fields_ = [
+ ('abiversion', ctypes.c_uint8),
+ ('type', ctypes.c_char_p),
+ ('name', ctypes.c_char_p),
+ ('prettyname', ctypes.c_char_p),
+ ('author', ctypes.c_char_p),
+ ('majorv', ctypes.c_uint8),
+ ('minorv', ctypes.c_uint8),
+ ('is_reentrant', ctypes.c_uint8),
+ ('filename_extension', ctypes.c_char_p),
+ ('open_file_read', ctypes.CFUNCTYPE(ctypes.c_char_p,
+ ctypes.c_char_p, ctypes.POINTER(ctypes.c_uint8))),
+ ('read_structure', ctypes.CFUNCTYPE(ctypes.c_void_p,
+ ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(molatom_t))),
+ ('read_bonds', ctypes.CFUNCTYPE(ctypes.c_void_p,
+ ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
+ ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
+ ctypes.c_char_p)),
+ ('read_next_timestep', ctypes.c_int8),
+ ('close_file_read', ctypes.c_void_p),
+ ('open_file_write', ctypes.c_void_p),
+ ('write_structure', ctypes.c_int8),
+ ('write_timestep', ctypes.c_int8),
+ ('close_file_write', ctypes.c_void_p),
+ ('read_volumetric_metadata', ctypes.c_int8),
+ ('read_volumetric_data', ctypes.c_int8),
+ ('read_volumetric_data_ex', ctypes.c_int8),
+ ('read_rawgraphics', ctypes.c_int8),
+ ('read_molecule_metadata', ctypes.c_int8),
+ ('write_bonds', ctypes.c_int8),
+ ('write_volumetric_data', ctypes.c_int8),
+ ('write_volumetric_data_ex', ctypes.c_int8),
+ ('read_angles', ctypes.c_int8),
+ ('write_angles', ctypes.c_int8),
+ ('read_qm_metadata', ctypes.c_int8),
+ ('read_qm_rundata', ctypes.c_int8),
+ ('read_timestep', ctypes.c_int8),
+ ('read_timestep_metadata', ctypes.c_int8),
+ ('read_qm_timestep_metadata', ctypes.c_int8),
+ ('read_timestep2', ctypes.c_int8),
+ ('read_times', ctypes.c_ssize_t),
+ ('cons_fputs', ctypes.c_uint8)
+ ]
+
+class moltimestep_t(ctypes.Structure):
+ _fields_ = [
+ ('coords', ctypes.POINTER(ctypes.c_float)),
+ ('velocities', ctypes.POINTER(ctypes.c_float)),
+ ('A', ctypes.c_float),
+ ('B', ctypes.c_float),
+ ('C', ctypes.c_float),
+ ('alpha', ctypes.c_float),
+ ('beta', ctypes.c_float),
+ ('gamma', ctypes.c_float),
+ ('physical_time', ctypes.c_double),
+ ('total_energy', ctypes.c_double),
+ ('potential_energy', ctypes.c_double),
+ ('kinetic_energy', ctypes.c_double),
+ ('extended_energy', ctypes.c_double),
+ ('force_energy', ctypes.c_double),
+ ('total_pressure', ctypes.c_double)
+ ]
+
+class molhandle_t(ctypes.Structure):
+ _fields_ = [
+ ('plugin', ctypes.POINTER(molplugin_t)),
+ ('file_handle', ctypes.c_void_p),
+ ('natoms', ctypes.c_int)
+ ]
+
+class molnatoms(ctypes.Structure):
+ _fields_ = [
+ ('natoms', ctypes.c_int)
+ ]
+
+#callback_t = ctypes.CFUNCTYPE(None, ctypes.POINTER(molatom_t))
+
+def get_open_file_read(output):
+ ctypes.open_file_read.restype = ctypes.POINTER(molhandle_t)
+ ctypes.open_file_read.argtypes = [ctypes.POINTER(molplugin_t), ctypes.c_void_p, ctypes.c_uint8]
+ return ctypes.pythonapi.PyCapsule_GetPointer(output, "plugin")
+
+def get_capsule(capsule):
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.c_void_p
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ return ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+
+def get_plugincapsule(capsule):
+ data = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+ return data
+
+def get_plugindata(capsule):
+ data = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
+ ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
+ data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
+ return data
+
+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)
+
+plugin = mylib.get_plugin(mylist, 81)
+print(plugin)
+natoms=0
+numatoms=molnatoms(natoms)
+fname="../../test/md.gro"
+ftype="gro"
+
+pluginhandle = mylib.open_file_read(plugin, fname, ftype, natoms)
+print("This passed")
+print(pluginhandle)
+print("This passed too")
+print(pluginhandle.natoms)
+print("Here")
+outarray = mylib.get_structure(pluginhandle)
+print(outarray)
+#print(type(outarray))
+#for i in outarray:
+# print(i)
+
+
diff --git a/pymolfile/molfile/test.py b/pymolfile/molfile/test.py
index afca74ed4fb9117e100c586e16cbb94e359dd340..65c178d3dce637aede004256e4efa638ba39d4a1 100644
--- a/pymolfile/molfile/test.py
+++ b/pymolfile/molfile/test.py
@@ -131,12 +131,29 @@ for i in range(numlist):
testplugin = mylib.molfile_plugin_info(mylist, i)
print(i, testplugin)
-plugin = mylib.get_plugin(mylist, 81)
+#plugin = mylib.get_plugin(mylist, 99) #pdb
+#plugin = mylib.get_plugin(mylist, 83) #trr
+#plugin = mylib.get_plugin(mylist, 85) #xtc
+plugin = mylib.get_plugin(mylist, 105) #psf
+#plugin = mylib.get_plugin(mylist, 81) #gro
+#plugin = mylib.get_plugin(mylist, 69) #dcd
print(plugin)
natoms=0
numatoms=molnatoms(natoms)
-fname="../../test/md.gro"
-ftype="gro"
+#fname="../../test/DPDP.pdb"
+#fname="../../test/md.gro"
+#fname="../../test/ala3.dcd"
+#fname="../../test/ala3.pdb"
+fname="../../test/ala3.psf"
+#fname="../../test/md.trr"
+#fname="../../test/md.xtc"
+#fname="../../test/md_1u19.xtc"
+#ftype="pdb"
+#ftype="trr"
+#ftype="xtc"
+ftype="psf"
+#ftype="gro"
+#ftype="dcd"
pluginhandle = mylib.open_file_read(plugin, fname, ftype, natoms)
print("This passed")
@@ -144,8 +161,31 @@ print(pluginhandle)
print("This passed too")
print(pluginhandle.natoms)
print("Here")
-outarray = mylib.read_structure(pluginhandle)
-print(outarray)
+
+x = numpy.array([
+ ('C1','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6),
+ ('C2','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6)
+ ],
+ dtype=[
+ ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
+ ('resid', 'i4'), ('segid', 'S8'), ('chain', 'S2'),
+ ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f8'),
+ ('bfactor', 'f8'), ('mass', 'f8'), ('charge', 'f8'),
+ ('radius', 'f8'), ('atomicnumber', 'i4')
+ ]
+ )
+print(x)
+print(x.__array_interface__)
+print(x.__array_interface__["descr"])
+print(x.__array_struct__)
+y = mylib.read_fill_structure(pluginhandle, x)
+#y = mylib.print_array_struct(x)
+print(y)
+print(len(y))
+print(y.__array_interface__)
+print(y.__array_interface__["descr"])
+#outarray = mylib.get_structure(pluginhandle)
+#print(outarray)
#print(type(outarray))
#for i in outarray:
# print(i)
diff --git a/pymolfile/molfile/test_numpy_swig.py b/pymolfile/molfile/test_numpy_swig.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ea2632148e309ae10dbfdb8f95b862366a106c3
--- /dev/null
+++ b/pymolfile/molfile/test_numpy_swig.py
@@ -0,0 +1,46 @@
+import numpy
+import ctypes
+import _numpy_swig
+#import numind
+
+ns = _numpy_swig
+
+# Create an arbitrary object for each package
+np=numpy.arange(12)
+np.shape = (4,3)
+
+newSIB = ns.new_SignedIntBuf(np.shape[0], np.shape[1])
+print(newSIB)
+struct = ns.get__array_struct__(np)
+print(struct)
+ns.delete_SignedIntBuf(newSIB)
+
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+#for obj in [np]:
+# ni = _numpy_swig
+# print("original object type-->", ni)
+# # Print some values
+# #print("typestr --> {0}", ni.typestr)
+# #print("shape --> {0}", ni.shape)
+# print("strides --> {0}", ni)
+# npa = numpy.asarray(ni)
+# print("object after a numpy re-wrapping --> " , npa)
+# #ni.modify()
+# #print("object after modification in C space --> {0}", npa)
+
+# Wrap the different objects with the NumInd class
+# and execute some actions on it
+#for obj in [np]:
+# ni = numind.NumInd(obj)
+# print("original object type-->", type(ni.undarray))
+# # Print some values
+# print("typestr -->", ni.typestr)
+# print("shape -->", ni.shape)
+# print("strides -->", ni.strides)
+# npa = numpy.asarray(ni)
+# print("object after a numpy re-wrapping -->", npa)
+# ni.modify()
+# print("object after modification in C space -->", npa)
+