One Cmake call for all

build/lib.macosx-10.12-x86_64-3.6/pymolfile/__init__.py

-
-from __future__ import absolute_import
-import warnings
-
-try:
-    from .molfile import libpymolfile
-except ImportError:
-    warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
-
-from . import plugin_list
-from . import pymolfile
-
-__all__ = [ "pymolfile" ]
-
-from .pymolfile import OpenMolfile, list_plugins
-

build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/__init__.py

-
-# Stand-alone python bindings for libpymolfile
-# Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
-# Published under the UIUC OpenSource LICENSE 
-"""libpymolfile library.
-
-"""

build/lib.macosx-10.12-x86_64-3.6/pymolfile/molfile/libpymolfile.py

-# This file was automatically generated by SWIG (http://www.swig.org).
-# Version 3.0.12
-#
-# Do not make changes to this file unless you know what you are doing--modify
-# the SWIG interface file instead.
-
-"""
-
-:Author:  Berk Onat <b.onat@warwick.ac.uk>
-:Year:    2017
-:Licence: UIUC LICENSE
-
-
-
-"""
-
-
-from sys import version_info as _swig_python_version_info
-if _swig_python_version_info >= (2, 7, 0):
-    def swig_import_helper():
-        import importlib
-        pkg = __name__.rpartition('.')[0]
-        mname = '.'.join((pkg, '_libpymolfile')).lstrip('.')
-        try:
-            return importlib.import_module(mname)
-        except ImportError:
-            return importlib.import_module('_libpymolfile')
-    _libpymolfile = swig_import_helper()
-    del swig_import_helper
-elif _swig_python_version_info >= (2, 6, 0):
-    def swig_import_helper():
-        from os.path import dirname
-        import imp
-        fp = None
-        try:
-            fp, pathname, description = imp.find_module('_libpymolfile', [dirname(__file__)])
-        except ImportError:
-            import _libpymolfile
-            return _libpymolfile
-        try:
-            _mod = imp.load_module('_libpymolfile', fp, pathname, description)
-        finally:
-            if fp is not None:
-                fp.close()
-        return _mod
-    _libpymolfile = swig_import_helper()
-    del swig_import_helper
-else:
-    import _libpymolfile
-del _swig_python_version_info
-
-try:
-    _swig_property = property
-except NameError:
-    pass  # Python < 2.2 doesn't have 'property'.
-
-try:
-    import builtins as __builtin__
-except ImportError:
-    import __builtin__
-
-def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
-    if (name == "thisown"):
-        return self.this.own(value)
-    if (name == "this"):
-        if type(value).__name__ == 'SwigPyObject':
-            self.__dict__[name] = value
-            return
-    method = class_type.__swig_setmethods__.get(name, None)
-    if method:
-        return method(self, value)
-    if (not static):
-        if _newclass:
-            object.__setattr__(self, name, value)
-        else:
-            self.__dict__[name] = value
-    else:
-        raise AttributeError("You cannot add attributes to %s" % self)
-
-
-def _swig_setattr(self, class_type, name, value):
-    return _swig_setattr_nondynamic(self, class_type, name, value, 0)
-
-
-def _swig_getattr(self, class_type, name):
-    if (name == "thisown"):
-        return self.this.own()
-    method = class_type.__swig_getmethods__.get(name, None)
-    if method:
-        return method(self)
-    raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
-
-
-def _swig_repr(self):
-    try:
-        strthis = "proxy of " + self.this.__repr__()
-    except __builtin__.Exception:
-        strthis = ""
-    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
-
-try:
-    _object = object
-    _newclass = 1
-except __builtin__.Exception:
-    class _object:
-        pass
-    _newclass = 0
-
-
-def molfile_plugin_list(maxsize: 'int') -> "PyObject *":
-    """molfile_plugin_list(maxsize) -> PyObject *"""
-    return _libpymolfile.molfile_plugin_list(maxsize)
-
-def molfile_init() -> "int":
-    """molfile_init() -> int"""
-    return _libpymolfile.molfile_init()
-
-def molfile_finish() -> "int":
-    """molfile_finish() -> int"""
-    return _libpymolfile.molfile_finish()
-
-def get_plugin(molcapsule: 'PyObject *', plug_no: 'int') -> "PyObject *":
-    """get_plugin(molcapsule, plug_no) -> PyObject *"""
-    return _libpymolfile.get_plugin(molcapsule, plug_no)
-
-def molfile_plugin_info(molcapsule: 'PyObject *', plugin_no: 'int') -> "PyObject *":
-    """molfile_plugin_info(molcapsule, plugin_no) -> PyObject *"""
-    return _libpymolfile.molfile_plugin_info(molcapsule, plugin_no)
-
-def open_file_read(molcapsule: 'PyObject *', fname: 'char *', ftype: 'char *', natoms: 'int') -> "PyObject *":
-    """open_file_read(molcapsule, fname, ftype, natoms) -> PyObject *"""
-    return _libpymolfile.open_file_read(molcapsule, fname, ftype, natoms)
-
-def close_file_read(molpack: 'PyObject *') -> "PyObject *":
-    """close_file_read(molpack) -> PyObject *"""
-    return _libpymolfile.close_file_read(molpack)
-
-def read_fill_structure(molpack: 'PyObject *', prototype: 'PyObject *') -> "PyObject *":
-    """read_fill_structure(molpack, prototype) -> PyObject *"""
-    return _libpymolfile.read_fill_structure(molpack, prototype)
-
-def read_fill_bonds(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_bonds(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_bonds(molpack)
-
-def read_fill_angles(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_angles(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_angles(molpack)
-
-def read_fill_next_timestep(molpack: 'PyObject *') -> "PyObject *":
-    """read_fill_next_timestep(molpack) -> PyObject *"""
-    return _libpymolfile.read_fill_next_timestep(molpack)
-
-def are_plugins_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
-    """are_plugins_same(molpack_a, molpack_b) -> PyObject *"""
-    return _libpymolfile.are_plugins_same(molpack_a, molpack_b)
-
-def are_filehandles_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
-    """are_filehandles_same(molpack_a, molpack_b) -> PyObject *"""
-    return _libpymolfile.are_filehandles_same(molpack_a, molpack_b)
-# This file is compatible with both classic and new-style classes.
-
-

build/lib.macosx-10.12-x86_64-3.6/pymolfile/plugin_list.py

-import warnings
-import sys
-
-from .molfile import libpymolfile
-try:
-    from .molfile import libpymolfile
-except ImportError:
-    warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
-
-MAX_NUM_PLUGINS = 200
-C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
-
-def byte_str_decode(data, dectype=None):
-    try:
-        return data.decode(dectype).replace('\x00', '')
-    except AttributeError:
-        return data
-
-def plugins():
-    """ Information on the available molfile plugins
-
-        Example tuple: ('psf', 'psf', 1, 1, 1, 0, 1, 1, 1, 0, 
-            'CHARMM,NAMD,XPLOR PSF', 'mol file reader', 
-            'Justin Gullingsrud, John Stone', 1, 9, 17, 1)
-
-        The fields in the tuple represent info in ordered as follows:
-            1: format extension
-            2: format name
-            3: read_structure is avaliable if 1
-            4: read_bonds is avaliable if 1
-            5: read_angles is avaliable if 1
-            6: read_next_timestep is avaliable if 1
-            7: write_structure is avaliable if 1
-            8: write_bonds is avaliable if 1
-            9: write_angles is avaliable if 1
-           10: write_timestep is avaliable if 1
-           11: long name of the plugin
-           12: type of plugin
-           13: authors of the plugin
-           14: major version of the plugin
-           15: minor version of the plugin
-           16: ABI version of the plugin
-           17: 1 if is reentrant (returns is_reentrant) 
-
-    Returns: A list of tuples that includes the information and 
-             capabilities of each molfile plugin. The information is 
-             extracted from molfile_plugin_t. 
-    """
-    global C_MOLFILE_PLUGINS
-    numlist = libpymolfile.molfile_init()
-    if sys.version_info > (3,):
-        basestring = str
-    plugins_list = [
-        [byte_str_decode(item, 
-            dectype="unicode_escape") for item in libpymolfile.molfile_plugin_info(
-            C_MOLFILE_PLUGINS, i)
-            ] for i in range(numlist)
-        ]
-    libpymolfile.molfile_finish()
-    return plugins_list
-
-MOLFILE_PLUGINS = plugins()
-

build/lib.macosx-10.12-x86_64-3.6/pymolfile/test_libpymolfile.py

-import numpy
-import molfile.libpymolfile as pym
-
-mylist  = pym.molfile_plugin_list(200)
-print(mylist)
-numlist = pym.molfile_init()
-print(numlist)
-for i in range(numlist):
-    testplugin = pym.molfile_plugin_info(mylist, i)
-    print(i, testplugin)
-
-#splugin = pym.get_plugin(mylist, 99) #pdb
-#cplugin = pym.get_plugin(mylist, 83) #trr
-#cplugin = pym.get_plugin(mylist, 85) #xtc
-splugin = pym.get_plugin(mylist, 105) #psf
-#splugin = pym.get_plugin(mylist, 81) #gro
-cplugin = pym.get_plugin(mylist, 69) #dcd
-#cplugin = pym.get_plugin(mylist, 126) #nc
-print(splugin)
-print(cplugin)
-natoms=0
-#sfname="../test/DPDP.pdb"
-#cfname="../test/DPDP.nc"
-
-#sfname="../test/ala3.pdb"
-sfname="../test/ala3.psf"
-cfname="../test/ala3.dcd"
-
-#sfname="../test/md.gro"
-#cfname="../test/md.trr"
-#cfname="../test/md.xtc"
-
-#sfname="../test/md_1u19.gro"
-#cfname="../test/md_1u19.xtc"
-
-#sftype="pdb"
-#cftype="trr"
-#cftype="xtc"
-sftype="psf"
-#sftype="gro"
-cftype="dcd"
-#cftype="nc"
-
-print("Structure plugin:")
-spluginhandle = pym.open_file_read(splugin, sfname, sftype, natoms)
-print("Coordinate plugin:")
-cpluginhandle = pym.open_file_read(cplugin, cfname, cftype, natoms)
-print(cpluginhandle)
-print(cpluginhandle.natoms)
-print(spluginhandle)
-print(spluginhandle.natoms)
-if cpluginhandle.natoms != spluginhandle.natoms:
-    print("Number of atoms do not match in structure and coordinate files.")
-    
-
-if pym.is_plugin_same(spluginhandle, cpluginhandle):
-    pym.close_file_read(cpluginhandle)
-    cpluginhandle = spluginhandle
-
-#if 0 && vmdplugin_ABIVERSION > 17
-#  /* The new PDB file formats allows for much larger structures, */
-#  /* which can therefore require longer chain ID strings.  The   */
-#  /* new PDBx/mmCIF file formats do not have length limits on    */
-#  /* fields, so PDB chains could be arbitrarily long strings     */
-#  /* in such files.  At present, we know we need at least 3-char */
-#  /* chains for existing PDBx/mmCIF files.                       */
-#  char chain[4];      /**< required chain name, or ""            */
-#else
-#  char chain[2];      /**< required chain name, or ""            */
-#endif
-# Change 'chain', 'S4' to S2 for PDB
-if 'pdb' in [sftype, cftype]:
-    print("file chain is set to S2")
-    chain_size = 'S2'
-else:
-    chain_size = 'S4'
-x = numpy.array([
-    ('C1','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6), 
-    ('C2','C','ACE',0,'','','','',1.0,1.0,1.0,1.0,1.0,6)
-    ],
-    dtype=[
-        ('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
-        ('resid', 'i4'), ('segid', 'S8'), ('chain', chain_size),
-        ('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f4'),
-        ('bfactor', 'f4'), ('mass', 'f4'), ('charge', 'f4'),
-        ('radius', 'f4'), ('atomicnumber', 'i4')
-        ]
-    )
-y = pym.read_fill_structure(spluginhandle, x)
-if y is not None:
-    print(y)
-    print(len(y))
-
-try:
-    z = pym.read_fill_bonds(spluginhandle)
-    if z is not None:
-        print(z)
-        print(len(z))
-except (AttributeError, SystemError):
-    pass
-
-try:
-    a = pym.read_fill_angles(spluginhandle)
-    if a is not None:
-        print(a)
-        print(len(a))
-except (AttributeError, SystemError):
-    pass
-
-if pym.is_plugin_same(spluginhandle, cpluginhandle):
-    pass
-else:
-    pym.close_file_read(spluginhandle)
-
-step=0
-while True:
-#while False:
-    try:
-        c = pym.read_fill_next_timestep(cpluginhandle)
-        if c is None:
-            break
-        step=step+1
-        print("Step:",step)
-        print(c)
-        if c["coords"] is not None:
-            print(len(c["coords"]))
-    except (AttributeError,OSError):
-        pass
-
-pym.close_file_read(cpluginhandle)
-pym.molfile_finish()
-
-

pymolfile/molfile/CMakeLists.txt

@@ -3,9 +3,10 @@ cmake_minimum_required(VERSION 2.8.12)
 project(molfile)
 
 add_subdirectory(external)
-add_subdirectory(molfile_plugins)
+add_subdirectory(molfile_plugins/compile)
 
-set_source_files_properties( external/tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
+#set_source_files_properties( tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
 
 add_dependencies( molfile_plugins_comp tngio_comp )
+#add_dependencies( molfile_plugins_comp TNGBuilder )
 

pymolfile/molfile/_libpymolfile.so.dSYM/Contents/Info.plist

-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
-<plist version="1.0">
-	<dict>
-		<key>CFBundleDevelopmentRegion</key>
-		<string>English</string>
-		<key>CFBundleIdentifier</key>
-		<string>com.apple.xcode.dsym._libpymolfile.so</string>
-		<key>CFBundleInfoDictionaryVersion</key>
-		<string>6.0</string>
-		<key>CFBundlePackageType</key>
-		<string>dSYM</string>
-		<key>CFBundleSignature</key>
-		<string>????</string>
-		<key>CFBundleShortVersionString</key>
-		<string>1.0</string>
-		<key>CFBundleVersion</key>
-		<string>1</string>
-	</dict>
-</plist>