diff --git a/pymolfile/] b/pymolfile/]
deleted file mode 100644
index 3667a47ab4607d1e5a9a3d67121514c96b30af25..0000000000000000000000000000000000000000
--- a/pymolfile/]
+++ /dev/null
@@ -1,254 +0,0 @@
-
-from __future__ import absolute_import
-from __future__ import print_function
-
-import os
-import re
-import sys
-import numpy as np
-import warnings
-
-if sys.version_info > (3,):
- long = int
-
-try:
- from .molfile import libpymolfile
-except ImportError:
- warnings.warn("libpymolfile package not available, pymolfile does not work without its library!")
-
-
-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.
- """
- max_num_plugins = 200
- c_list = libpymolfile.molfile_plugin_list(max_num_plugins)
- numlist = libpymolfile.molfile_init()
- plugins_list = [libpymolfile.molfile_plugin_info(c_list, i) for i in range(numlist)]
- libpymolfile.molfile_finish()
- return plugins_list
-
-def open(file_name_with_path, topology=None,
- file_format=None, topology_format=None,
- plugin=None, topology_plugin=None):
- """ The main function to read topology and
- trajectory files
-
- Returns: Depends on the file format and arguments:
- If structure file is supplied, it returns topology class.
- If only trajectory file is supplied, it returns trajectory class
- without topology information. (the number of atoms must be known)
- If both files are supplied, it returns trajectory class with
- topology information.
- """
- pass
-
-def get_dir_base_extension(file_name):
- """ Splits directory, file base and file extensions
-
- Returns: directory without leading '/',
- file base name, and file extension without '.'
- """
- file_base, file_extension_with_dot = os.path.splitext(os.path.basename(file_name))
- file_extension = file_extension_with_dot.split(".")[-1]
- file_dir = os.path.dirname(file_name)
- return file_dir, file_base, file_extension
-
-def get_extension(file_name):
- """ Gets file extension of a file
-
- Returns: file extension without '.'
- """
- file_extension_with_dot = os.path.splitext(os.path.basename(file_name))[1]
- return file_extension_with_dot.split(".")[-1]
-
-def get_plugin_with_ext(file_ext):
- """ Search molfile plugins list and returns the plugin info
- for the first matched extension.
-
- Returns: Plugin no in the list and the list item (the plugin info tuple)
- """
- if not MOLFILE_PLUGINS:
- MOLFILE_PLUGINS = plugins()
-
- if MOLFILE_PLUGINS:
- plugin_no = -1
- for plugin_info in MOLFILE_PLUGINS:
- plugin_no += 1
- if file_ext == plugin_info[1]:
- return (plugin_no, plugin_info)
-
- return None
-
-def get_plugin_with_name(plugin_name):
- """ Search molfile plugins list and returns the plugin info
- for the first matching name in plugin name field.
-
- Returns: Plugin no in the list and the list item (the plugin info tuple)
- """
- if not MOLFILE_PLUGINS:
- MOLFILE_PLUGINS = plugins()
-
- if MOLFILE_PLUGINS:
- plugin_no = -1
- for plugin_info in MOLFILE_PLUGINS:
- plugin_no += 1
- if plugin_name == plugin_info[2]:
- return (plugin_no, plugin_info)
-
- return None
-
-
-class OpenMolfile(object):
-
- self.plugin_list = MOLFILE_PLUGINS
- self.trajectory = None
- self.topology = None
- self.smolobject = None
- self.cmolobject = None
- self.kwords = {
- "file_format" : None,
- "file_plugin" : None,
- "topology" : None,
- "topology_format" : None,
- "topology_plugin" : None,
- "natoms" : None
- }
-
- def __init__(self, file_name, **kwargs):
- if kwargs:
- for k, v in kwargs.items():
- if k in self.kwords:
- self.kwords[k] = v
-
- if file_name:
- if self.kwords["file_format"] is None:
- file_dir, file_base, file_ext = get_dir_base_extension(file_name)
- if file_ext:
- self.kwords["file_format"] = file_ext
- else:
- self.kwords["file_format"] = file_base
-
- if self.kwords["file_plugin"] is None:
- self.kwords["file_plugin"] = "auto"
-
- if "auto" in self.kwords["file_plugin"]:
- plugin_item = get_plugin_with_ext(self.kwords["file_format"])
- self.kwords["file_plugin"] =
-
- if self.kwords["file_plugin"]:
- if not MOLFILE_PLUGINS:
- MOLFILE_PLUGINS = plugins()
-
-
-
-
- c_list = libpymolfile.molfile_plugin_list(max_num_plugins)
- numlist = libpymolfile.molfile_init()
- self.cmolobject = libpymolfile.get_plugin(MOLFILE_PLUGINS, 83) #trr
-
-
-
- else:
- return None
-
-
-
-
-
-
-
-
-
-
-
-def get_listof_parts( filename, filepath, fileformats ):
- pattern = re.escape( filename[1:-4] ) + "\.part[0-9]{4,4}\.(xtc|trr)$"
- parts = []
- for f in os.listdir( directory ):
- m = re.match( pattern, f )
- if m and os.path.isfile( os.path.join( directory, f ) ):
- parts.append( os.path.join( directory, f ) )
- return sorted( parts )
-
-
-def get_trajectory( file_name ):
- ext = os.path.splitext( file_name )[1].lower()
- types = {
- ".xtc": XtcTrajectory,
- ".trr": TrrTrajectory,
- ".netcdf": NetcdfTrajectory,
- ".nc": NetcdfTrajectory,
- ".dcd": DcdTrajectory,
- }
- if ext in types:
- return types[ ext ]( file_name )
- else:
- raise Exception( "extension '%s' not supported" % ext )
-
-class Topology( object ):
-
- self.structure = None
- self.bonds = None
- self.angles = None
-
- def __init__( self, file_name ):
- pass
-
-
-
-class Trajectory( object ):
- def __init__( self, file_name ):
- pass
-
- def update( self, force=False ):
- pass
-
- def _get_frame( self, index ):
- pass
-
- def get_frame( self, index, atom_indices=None ):
- box, coords, time = self._get_frame( int( index ) )
- if atom_indices:
- coords = np.concatenate([
- ])
- return {
- "coords": coords
- "velocities": coords
- }
-
- def get_frame_string( self, index, atom_indices=None ):
- frame = self.get_frame( index, atom_indices=atom_indices )
- return (
- )
-
- def __del__( self ):
- pass
-
-
diff --git a/pymolfile/__init__.py b/pymolfile/__init__.py
index 62fae02b838f8df5482f3f643ceacdf3ddc3a1ee..0e4f244a9fecb0fa27699383764a33f9bd9b22cf 100644
--- a/pymolfile/__init__.py
+++ b/pymolfile/__init__.py
@@ -5,5 +5,7 @@ from . import pymolfile
__all__ = [ "pymolfile" ]
+MAX_NUM_PLUGINS = 200
+C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
MOLFILE_PLUGINS = pymolfile.plugins()
diff --git a/pymolfile/__pycache__/pymolfile.cpython-36.pyc b/pymolfile/__pycache__/pymolfile.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..1e19a06a51bf6003652eb8cfb19bc4b9a0a26c52
Binary files /dev/null and b/pymolfile/__pycache__/pymolfile.cpython-36.pyc differ
diff --git a/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc
index 09623bd45a3e5dc77246c0a88f466113249b2ab2..bc43e9aae4503301f6e3a92af0ca934b25c01e4b 100644
Binary files a/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc and b/pymolfile/molfile/__pycache__/libpymolfile.cpython-36.pyc differ
diff --git a/pymolfile/molfile/_libpymolfile.so b/pymolfile/molfile/_libpymolfile.so
index e72261324ff900aeaa9dbe33df442ea998472857..fdfdcc550fe4a6a7dba7e86c38a4b9974d2da208 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 c62a68708ff5b2653918f126239f92fabd92fefb..a0b3a8c49d4db6f95fffdd9921c301f5d99e2fdd 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/compile.sh b/pymolfile/molfile/compile.sh
index 100753d1b510ba934722e4328b09af79d11eb990..b04a1dd781331d66c0b4a562a414fcfecdd11ea2 100644
--- a/pymolfile/molfile/compile.sh
+++ b/pymolfile/molfile/compile.sh
@@ -1,4 +1,6 @@
+echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
swig -py3 -Wall -c++ -python libpymolfile.i
+echo "'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'-._.-'"
g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter \
-I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ \
-I./include \
diff --git a/pymolfile/molfile/libpymolfile.i b/pymolfile/molfile/libpymolfile.i
index 263d94239065b3e5ea31358fbbff2d9961ec0d35..4531072d9c1840d9e5080f4ec2a81303a30575ea 100644
--- a/pymolfile/molfile/libpymolfile.i
+++ b/pymolfile/molfile/libpymolfile.i
@@ -30,9 +30,6 @@
#include <ctype.h>
#include <string.h>
#include <inttypes.h>
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
#include "pymolfile.h"
%}
@@ -57,7 +54,7 @@ import_array();
initialize and finalize molfile plugins
*/
%feature("autodoc", "0") molfile_plugin_list;
-extern molfile_plugin_t** molfile_plugin_list(int maxsize);
+extern PyObject* molfile_plugin_list(int maxsize);
%feature("autodoc", "0") molfile_init;
extern int molfile_init(void);
@@ -66,16 +63,20 @@ extern int molfile_init(void);
extern int molfile_finish(void);
%feature("autodoc", "0") get_plugin;
-extern molfile_plugin_t* get_plugin(molfile_plugin_t** plugin_list, int plugin_no);
+extern PyObject* get_plugin(PyObject* molcapsule, int plug_no);
+
%feature("autodoc", "0") molfile_plugin_info;
+extern PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no);
+/*
%exception molfile_plugin_info {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
-PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
+PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no) {
molfile_plugin_t *plugin;
+ molfile_plugin_t** plugin_list = (molfile_plugin_t**) PyMolfileCapsule_AsVoidPtr(molcapsule);
int *plugno = &plugin_no;
int has_readstructure = 0;
int has_readbonds = 0;
@@ -87,12 +88,12 @@ PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
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);
+ PyErr_Format(PyExc_IOError, "Error: molfile plugin handle no should be given, be positive value and should not exceed the list length'%d'. You set '%d'", 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);
+ PyErr_Format(PyExc_IOError, "Error: molfile plugin '%d' is not initialized.", plugin_no);
return 0;
}
if (plugin->read_structure) has_readstructure = 1;
@@ -124,6 +125,7 @@ PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
return tuple;
}
%}
+*/
%feature("autodoc", "0") my_open_file_read;
@@ -133,11 +135,12 @@ PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
-PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
+PyObject * my_open_file_read(PyObject* molcapsule, char* fname, char* ftype, int natoms) {
if (PyType_Ready(&MolObjectType) < 0)
return NULL;
PyTypeObject *type = &MolObjectType;
MolObject *plugin_c;
+ molfile_plugin_t* plugin = (molfile_plugin_t*) PyMolfileCapsule_AsVoidPtr(molcapsule);
plugin_c = (MolObject *)type->tp_alloc(type, 0);
plugin_c->plugin = plugin;
plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
@@ -159,7 +162,7 @@ PyObject * my_close_file_read(PyObject* molpack) {
void* file_handle;
int numatoms;
MolObject* plugin_handle = (MolObject*) molpack;
- plugin = plugin_handle->plugin;
+ plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
plugin->close_file_read(file_handle);
diff --git a/pymolfile/molfile/libpymolfile.py b/pymolfile/molfile/libpymolfile.py
index cb5776343d31d4f4d488fc87d9d25dc3ea21901d..a57642aa6cb2eb903f6ce95a5d4ac44f7d63d090 100644
--- a/pymolfile/molfile/libpymolfile.py
+++ b/pymolfile/molfile/libpymolfile.py
@@ -107,8 +107,8 @@ except __builtin__.Exception:
_newclass = 0
-def molfile_plugin_list(maxsize: 'int') -> "molfile_plugin_t **":
- """molfile_plugin_list(maxsize) -> molfile_plugin_t **"""
+def molfile_plugin_list(maxsize: 'int') -> "PyObject *":
+ """molfile_plugin_list(maxsize) -> PyObject *"""
return _libpymolfile.molfile_plugin_list(maxsize)
def molfile_init() -> "int":
@@ -119,17 +119,17 @@ def molfile_finish() -> "int":
"""molfile_finish() -> int"""
return _libpymolfile.molfile_finish()
-def get_plugin(plugin_list: 'molfile_plugin_t **', plugin_no: 'int') -> "molfile_plugin_t *":
- """get_plugin(plugin_list, plugin_no) -> molfile_plugin_t *"""
- return _libpymolfile.get_plugin(plugin_list, plugin_no)
+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(plugin_list: 'molfile_plugin_t **', plugin_no: 'int') -> "PyObject *":
- """molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"""
- return _libpymolfile.molfile_plugin_info(plugin_list, plugin_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(plugin: 'molfile_plugin_t *', fname: 'char *', ftype: 'char *', natoms: 'int') -> "PyObject *":
- """open_file_read(plugin, fname, ftype, natoms) -> PyObject *"""
- return _libpymolfile.open_file_read(plugin, fname, ftype, natoms)
+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 *"""
diff --git a/pymolfile/molfile/libpymolfile_wrap.cxx b/pymolfile/molfile/libpymolfile_wrap.cxx
index e6fbc91446d74b4a71d28b0aaff7f349ea61e78c..533687b00f09f7f7734804817b5a34f0917f375f 100644
--- a/pymolfile/molfile/libpymolfile_wrap.cxx
+++ b/pymolfile/molfile/libpymolfile_wrap.cxx
@@ -3004,10 +3004,8 @@ SWIG_Python_NonDynamicSetAttr(PyObject *obj, PyObject *name, PyObject *value) {
/* -------- TYPES TABLE (BEGIN) -------- */
#define SWIGTYPE_p_char swig_types[0]
-#define SWIGTYPE_p_molfile_plugin_t swig_types[1]
-#define SWIGTYPE_p_p_molfile_plugin_t swig_types[2]
-static swig_type_info *swig_types[4];
-static swig_module_info swig_module = {swig_types, 3, 0, 0, 0, 0};
+static swig_type_info *swig_types[2];
+static swig_module_info swig_module = {swig_types, 1, 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)
@@ -3123,9 +3121,6 @@ namespace swig {
#include <ctype.h>
#include <string.h>
#include <inttypes.h>
-#include "molfile_plugin.h"
-#include "libmolfile_plugin.h"
-#include "vmdplugin.h"
#include "pymolfile.h"
@@ -3298,62 +3293,12 @@ SWIGINTERNINLINE PyObject*
}
-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;
- }
-
-
-PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
+PyObject * my_open_file_read(PyObject* molcapsule, char* fname, char* ftype, int natoms) {
if (PyType_Ready(&MolObjectType) < 0)
return NULL;
PyTypeObject *type = &MolObjectType;
MolObject *plugin_c;
+ molfile_plugin_t* plugin = (molfile_plugin_t*) PyMolfileCapsule_AsVoidPtr(molcapsule);
plugin_c = (MolObject *)type->tp_alloc(type, 0);
plugin_c->plugin = plugin;
plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
@@ -3497,7 +3442,7 @@ PyObject * my_close_file_read(PyObject* molpack) {
void* file_handle;
int numatoms;
MolObject* plugin_handle = (MolObject*) molpack;
- plugin = plugin_handle->plugin;
+ plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
plugin->close_file_read(file_handle);
@@ -3515,7 +3460,7 @@ SWIGINTERN PyObject *_wrap_molfile_plugin_list(PyObject *SWIGUNUSEDPARM(self), P
int val1 ;
int ecode1 = 0 ;
PyObject * obj0 = 0 ;
- molfile_plugin_t **result = 0 ;
+ PyObject *result = 0 ;
if (!PyArg_ParseTuple(args,(char *)"O:molfile_plugin_list",&obj0)) SWIG_fail;
ecode1 = SWIG_AsVal_int(obj0, &val1);
@@ -3523,8 +3468,8 @@ SWIGINTERN PyObject *_wrap_molfile_plugin_list(PyObject *SWIGUNUSEDPARM(self), P
SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "molfile_plugin_list" "', argument " "1"" of type '" "int""'");
}
arg1 = static_cast< int >(val1);
- result = (molfile_plugin_t **)molfile_plugin_list(arg1);
- resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
+ result = (PyObject *)molfile_plugin_list(arg1);
+ resultobj = result;
return resultobj;
fail:
return NULL;
@@ -3559,29 +3504,23 @@ fail:
SWIGINTERN PyObject *_wrap_get_plugin(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- molfile_plugin_t **arg1 = (molfile_plugin_t **) 0 ;
+ PyObject *arg1 = (PyObject *) 0 ;
int arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
int val2 ;
int ecode2 = 0 ;
PyObject * obj0 = 0 ;
PyObject * obj1 = 0 ;
- molfile_plugin_t *result = 0 ;
+ PyObject *result = 0 ;
if (!PyArg_ParseTuple(args,(char *)"OO:get_plugin",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "get_plugin" "', argument " "1"" of type '" "molfile_plugin_t **""'");
- }
- arg1 = reinterpret_cast< molfile_plugin_t ** >(argp1);
+ arg1 = obj0;
ecode2 = SWIG_AsVal_int(obj1, &val2);
if (!SWIG_IsOK(ecode2)) {
SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "get_plugin" "', argument " "2"" of type '" "int""'");
}
arg2 = static_cast< int >(val2);
- result = (molfile_plugin_t *)get_plugin(arg1,arg2);
- resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
+ result = (PyObject *)get_plugin(arg1,arg2);
+ resultobj = result;
return resultobj;
fail:
return NULL;
@@ -3590,10 +3529,8 @@ fail:
SWIGINTERN PyObject *_wrap_molfile_plugin_info(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- molfile_plugin_t **arg1 = (molfile_plugin_t **) 0 ;
+ PyObject *arg1 = (PyObject *) 0 ;
int arg2 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
int val2 ;
int ecode2 = 0 ;
PyObject * obj0 = 0 ;
@@ -3601,20 +3538,13 @@ SWIGINTERN PyObject *_wrap_molfile_plugin_info(PyObject *SWIGUNUSEDPARM(self), P
PyObject *result = 0 ;
if (!PyArg_ParseTuple(args,(char *)"OO:molfile_plugin_info",&obj0,&obj1)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_p_molfile_plugin_t, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "molfile_plugin_info" "', argument " "1"" of type '" "molfile_plugin_t **""'");
- }
- arg1 = reinterpret_cast< molfile_plugin_t ** >(argp1);
+ arg1 = obj0;
ecode2 = SWIG_AsVal_int(obj1, &val2);
if (!SWIG_IsOK(ecode2)) {
SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "molfile_plugin_info" "', argument " "2"" of type '" "int""'");
}
arg2 = static_cast< int >(val2);
- {
- result = (PyObject *)molfile_plugin_info(arg1,arg2);
- if (PyErr_Occurred()) SWIG_fail;
- }
+ result = (PyObject *)molfile_plugin_info(arg1,arg2);
resultobj = result;
return resultobj;
fail:
@@ -3624,12 +3554,10 @@ fail:
SWIGINTERN PyObject *_wrap_open_file_read(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
- molfile_plugin_t *arg1 = (molfile_plugin_t *) 0 ;
+ PyObject *arg1 = (PyObject *) 0 ;
char *arg2 = (char *) 0 ;
char *arg3 = (char *) 0 ;
int arg4 ;
- void *argp1 = 0 ;
- int res1 = 0 ;
int res2 ;
char *buf2 = 0 ;
int alloc2 = 0 ;
@@ -3645,11 +3573,7 @@ SWIGINTERN PyObject *_wrap_open_file_read(PyObject *SWIGUNUSEDPARM(self), PyObje
PyObject *result = 0 ;
if (!PyArg_ParseTuple(args,(char *)"OOOO:open_file_read",&obj0,&obj1,&obj2,&obj3)) SWIG_fail;
- res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_molfile_plugin_t, 0 | 0 );
- if (!SWIG_IsOK(res1)) {
- SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "open_file_read" "', argument " "1"" of type '" "molfile_plugin_t *""'");
- }
- arg1 = reinterpret_cast< molfile_plugin_t * >(argp1);
+ arg1 = obj0;
res2 = SWIG_AsCharPtrAndSize(obj1, &buf2, NULL, &alloc2);
if (!SWIG_IsOK(res2)) {
SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "open_file_read" "', argument " "2"" of type '" "char *""'");
@@ -3806,12 +3730,12 @@ fail:
static PyMethodDef SwigMethods[] = {
{ (char *)"SWIG_PyInstanceMethod_New", (PyCFunction)SWIG_PyInstanceMethod_New, METH_O, NULL},
- { (char *)"molfile_plugin_list", _wrap_molfile_plugin_list, METH_VARARGS, (char *)"molfile_plugin_list(maxsize) -> molfile_plugin_t **"},
+ { (char *)"molfile_plugin_list", _wrap_molfile_plugin_list, METH_VARARGS, (char *)"molfile_plugin_list(maxsize) -> PyObject *"},
{ (char *)"molfile_init", _wrap_molfile_init, METH_VARARGS, (char *)"molfile_init() -> int"},
{ (char *)"molfile_finish", _wrap_molfile_finish, METH_VARARGS, (char *)"molfile_finish() -> int"},
- { (char *)"get_plugin", _wrap_get_plugin, METH_VARARGS, (char *)"get_plugin(plugin_list, plugin_no) -> molfile_plugin_t *"},
- { (char *)"molfile_plugin_info", _wrap_molfile_plugin_info, METH_VARARGS, (char *)"molfile_plugin_info(plugin_list, plugin_no) -> PyObject *"},
- { (char *)"open_file_read", _wrap_open_file_read, METH_VARARGS, (char *)"open_file_read(plugin, fname, ftype, natoms) -> PyObject *"},
+ { (char *)"get_plugin", _wrap_get_plugin, METH_VARARGS, (char *)"get_plugin(molcapsule, plug_no) -> PyObject *"},
+ { (char *)"molfile_plugin_info", _wrap_molfile_plugin_info, METH_VARARGS, (char *)"molfile_plugin_info(molcapsule, plugin_no) -> PyObject *"},
+ { (char *)"open_file_read", _wrap_open_file_read, METH_VARARGS, (char *)"open_file_read(molcapsule, fname, ftype, natoms) -> PyObject *"},
{ (char *)"close_file_read", _wrap_close_file_read, METH_VARARGS, (char *)"close_file_read(molpack) -> PyObject *"},
{ (char *)"read_fill_structure", _wrap_read_fill_structure, METH_VARARGS, (char *)"read_fill_structure(molpack, prototype) -> PyObject *"},
{ (char *)"read_fill_bonds", _wrap_read_fill_bonds, METH_VARARGS, (char *)"read_fill_bonds(molpack) -> PyObject *"},
@@ -3826,23 +3750,15 @@ static PyMethodDef SwigMethods[] = {
/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
static swig_type_info _swigt__p_char = {"_p_char", "char *", 0, 0, (void*)0, 0};
-static swig_type_info _swigt__p_molfile_plugin_t = {"_p_molfile_plugin_t", "molfile_plugin_t *", 0, 0, (void*)0, 0};
-static swig_type_info _swigt__p_p_molfile_plugin_t = {"_p_p_molfile_plugin_t", "molfile_plugin_t **", 0, 0, (void*)0, 0};
static swig_type_info *swig_type_initial[] = {
&_swigt__p_char,
- &_swigt__p_molfile_plugin_t,
- &_swigt__p_p_molfile_plugin_t,
};
static swig_cast_info _swigc__p_char[] = { {&_swigt__p_char, 0, 0, 0},{0, 0, 0, 0}};
-static swig_cast_info _swigc__p_molfile_plugin_t[] = { {&_swigt__p_molfile_plugin_t, 0, 0, 0},{0, 0, 0, 0}};
-static swig_cast_info _swigc__p_p_molfile_plugin_t[] = { {&_swigt__p_p_molfile_plugin_t, 0, 0, 0},{0, 0, 0, 0}};
static swig_cast_info *swig_cast_initial[] = {
_swigc__p_char,
- _swigc__p_molfile_plugin_t,
- _swigc__p_p_molfile_plugin_t,
};
diff --git a/pymolfile/molfile/pymolfile.c b/pymolfile/molfile/pymolfile.c
index f334813e74554d4d367eee2e4b249ba1fb9fd94b..fa2f689ce0c327c9cede5e774b51ebbf6d76e27e 100644
--- a/pymolfile/molfile/pymolfile.c
+++ b/pymolfile/molfile/pymolfile.c
@@ -1,16 +1,14 @@
/* Hey emacs this is -*- C -*- and this is my editor vim.
*
- * molfile.c : C and Fortran interfaces for molfile_plugins
+ * pymolfile.c : C and Python interfaces for molfile_plugins
* Copyright (c) Berk Onat <b.onat@warwick.ac.uk> 2017
*
- * This program is under BSD LICENSE
+ * This program is under UIUC Open Source License please see LICENSE file
*/
/*
* 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.
+ * context of main.c in molfile_plugin/src/
*/
/* Get HAVE_CONFIG_H */
@@ -36,39 +34,44 @@
int numplugins=0;
molfile_plugin_t** plugin_list;
-/* * * * * * * * * * * * * * * * * * * * * * *
- * 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
+void del_molfile_plugin_list(PyObject* molcapsule)
+{
+ plugin_list = (molfile_plugin_t**) PyMolfileCapsule_AsVoidPtr(molcapsule);
+ free(plugin_list);
+ Py_XDECREF(molcapsule);
+}
#else
-#define PyBytes_FromString PyString_FromString
+void* del_molfile_plugin_list(void* molcapsule)
+{
+ plugin_list = PyMolfileCapsule_AsVoidPtr((PyObject*)molcapsule);
+ free(plugin_list);
+ Py_XDECREF(molcapsule);
+}
#endif
+/* * * * * * * * * * * * * * * * * * * * * * *
+ * Helper functions to set and store plugins *
+ * * * * * * * * * * * * * * * * * * * * * * */
-#define NPY_NEXT_ALIGNED_OFFSET(offset, alignment) \
- (((offset) + (alignment) - 1) & (-(alignment)))
-
-molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no)
+PyObject* get_plugin(PyObject* molcapsule, int plug_no)
{
molfile_plugin_t* plugin;
+ molfile_plugin_t** plug_list = (molfile_plugin_t**) PyMolfileCapsule_AsVoidPtr(molcapsule);
if(plug_no < 0){
plugin = NULL;
} else {
- plugin = plug_list[plug_no];
+ if(plug_list != NULL){
+ plugin = plug_list[plug_no];
+ } else {
+ plugin = NULL;
+ }
}
- return plugin;
+ return PyMolfileCapsule_FromVoidPtr((void *)plugin, NULL);
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * *
@@ -99,13 +102,13 @@ static int molfile_register(void*, vmdplugin_t *plugin) {
return VMDPLUGIN_SUCCESS;
}
-molfile_plugin_t** molfile_plugin_list(int maxsize)
+PyObject* molfile_plugin_list(int maxsize)
{
if(maxsize < MAXPLUGINS){
maxsize = MAXPLUGINS;
}
plugin_list = (molfile_plugin_t**) malloc(sizeof(molfile_plugin_t*)*maxsize);
- return plugin_list;
+ return PyMolfileCapsule_FromVoidPtr((void *)plugin_list, del_molfile_plugin_list);
}
/* register all available plugins and clear handles. */
@@ -132,6 +135,57 @@ int molfile_finish(void)
/* Functions in molfile_plugin_t */
+PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no) {
+ molfile_plugin_t *plugin;
+ molfile_plugin_t** plugin_list = (molfile_plugin_t**) PyMolfileCapsule_AsVoidPtr(molcapsule);
+ 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, "Error: molfile plugin handle no should be given, be positive value and should not exceed the list length'%d'. You set '%d'", plugin_list_size, plugin_no);
+ return 0;
+ }
+ plugin = plugin_list[plugin_no];
+ if(plugin==NULL || !plugin->open_file_read){
+ PyErr_Format(PyExc_IOError, "Error: molfile plugin '%d' is not initialized.", 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;
+}
+
PyObject* read_fill_structure(PyObject* molpack, PyObject* prototype)
{
// Py_Initialize();
@@ -146,14 +200,14 @@ PyObject* read_fill_structure(PyObject* molpack, PyObject* prototype)
// Access plugin_handle values
MolObject* plugin_handle = (MolObject*) molpack;
if (plugin_handle->plugin) {
- plugin = plugin_handle->plugin;
- } else {
+ plugin = plugin_handle->plugin;
+ } else {
PyErr_Format(PyExc_IOError, "molfile plugin is not active.");
return NULL;
}
if (plugin_handle->file_handle) {
file_handle = plugin_handle->file_handle;
- } else {
+ } else {
PyErr_Format(PyExc_IOError, "no file handle in molfile plugin handle.");
return NULL;
}
@@ -206,8 +260,18 @@ PyObject* read_fill_bonds(PyObject* molpack)
PyObject *ret = NULL;
// Access plugin_handle values
MolObject* plugin_handle = (MolObject*) molpack;
- plugin = plugin_handle->plugin;
- file_handle = plugin_handle->file_handle;
+ if (plugin_handle->plugin) {
+ plugin = plugin_handle->plugin;
+ } else {
+ PyErr_Format(PyExc_IOError, "molfile plugin is not active.");
+ return NULL;
+ }
+ if (plugin_handle->file_handle) {
+ file_handle = plugin_handle->file_handle;
+ } else {
+ PyErr_Format(PyExc_IOError, "no file handle in molfile plugin handle.");
+ return NULL;
+ }
numatoms = plugin_handle->natoms;
if (plugin->read_bonds) {
int nbonds, *from, *to, *bondtype, nbondtypes;
@@ -290,8 +354,18 @@ PyObject* read_fill_angles(PyObject* molpack)
PyObject *ret = NULL;
// Access plugin_handle values
MolObject* plugin_handle = (MolObject*) molpack;
- plugin = plugin_handle->plugin;
- file_handle = plugin_handle->file_handle;
+ if (plugin_handle->plugin) {
+ plugin = plugin_handle->plugin;
+ } else {
+ PyErr_Format(PyExc_IOError, "molfile plugin is not active.");
+ return NULL;
+ }
+ if (plugin_handle->file_handle) {
+ file_handle = plugin_handle->file_handle;
+ } else {
+ PyErr_Format(PyExc_IOError, "no file handle in molfile plugin handle.");
+ return NULL;
+ }
numatoms = plugin_handle->natoms;
// Check if there is read_angles support in this plugin
if (plugin->read_angles) {
@@ -476,16 +550,16 @@ PyObject* read_fill_next_timestep(PyObject* molpack)
// Access plugin_handle values
MolObject* plugin_handle = (MolObject*) molpack;
if (plugin_handle->plugin) {
- plugin = plugin_handle->plugin;
- } else {
+ plugin = plugin_handle->plugin;
+ } else {
PyErr_Format(PyExc_IOError, "molfile plugin is not active.");
- return NULL;
+ return NULL;
}
if (plugin_handle->file_handle) {
file_handle = plugin_handle->file_handle;
- } else {
+ } else {
PyErr_Format(PyExc_IOError, "no file handle in molfile plugin handle.");
- return NULL;
+ return NULL;
}
if (plugin_handle->natoms) {
numatoms = plugin_handle->natoms;
@@ -597,14 +671,14 @@ PyObject* is_plugin_same(PyObject* molpack_a, PyObject* molpack_b)
MolObject* plugin_handle_a = (MolObject*) molpack_a;
MolObject* plugin_handle_b = (MolObject*) molpack_b;
if (plugin_handle_a->plugin) {
- plugin_a = plugin_handle_a->plugin;
- } else {
+ plugin_a = plugin_handle_a->plugin;
+ } else {
PyErr_Format(PyExc_IOError, "Arg 1 of the molfile plugin is not active.");
- return NULL;
+ return NULL;
}
if (plugin_handle_b->plugin) {
- plugin_b = plugin_handle_b->plugin;
- } else {
+ plugin_b = plugin_handle_b->plugin;
+ } else {
PyErr_Format(PyExc_IOError, "Arg 2 of the molfile plugin is not active.");
return NULL;
}
@@ -619,18 +693,18 @@ PyObject* is_filehandle_same(PyObject* molpack_a, PyObject* molpack_b)
{
MolObject* plugin_handle_a = (MolObject*) molpack_a;
MolObject* plugin_handle_b = (MolObject*) molpack_b;
- void* file_handle_a;
- void* file_handle_b;
+ void* file_handle_a;
+ void* file_handle_b;
if (plugin_handle_a->file_handle) {
- file_handle_a = plugin_handle_a->file_handle;
- } else {
+ file_handle_a = plugin_handle_a->file_handle;
+ } else {
PyErr_Format(PyExc_IOError, "no file handle in arg 1 of molfile plugin.");
return NULL;
}
if (plugin_handle_b->file_handle) {
- file_handle_b = plugin_handle_b->file_handle;
- } else {
- PyErr_Format(PyExc_IOError, "no file handle in arg 1 of molfile plugin.");
+ file_handle_b = plugin_handle_b->file_handle;
+ } else {
+ PyErr_Format(PyExc_IOError, "no file handle in arg 2 of molfile plugin.");
return NULL;
}
if(file_handle_a == file_handle_b){
diff --git a/pymolfile/molfile/pymolfile.h b/pymolfile/molfile/pymolfile.h
index 98dbf324bdd1fbc5f74048b68cac8007561eedc7..94a0b42d5dcb259684cb942600e482c97e5ed797 100644
--- a/pymolfile/molfile/pymolfile.h
+++ b/pymolfile/molfile/pymolfile.h
@@ -31,9 +31,6 @@ extern "C"
#include <numpy/arrayobject.h>
-//enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
-// pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
-
#ifndef MAXPLUGINS
#define MAXPLUGINS 200
#endif
@@ -46,6 +43,55 @@ struct MolObject {
MolObject(void) {}
};
+static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj);
+static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*data)(PyObject *));
+void del_molfile_plugin_list(PyObject* molcapsule);
+
+#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
+
+static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
+{
+ void *ret = PyCapsule_GetPointer(obj, NULL);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+
+static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(PyObject *))
+{
+ PyObject *ret = PyCapsule_New(ptr, NULL, destr);
+ if (ret == NULL) {
+ PyErr_Clear();
+ }
+ return ret;
+}
+
+#else
+#define PyBytes_FromString PyString_FromString
+
+static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
+{
+ return PyCObject_AsVoidPtr(obj);
+}
+
+static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(void *))
+{
+ return PyCObject_FromVoidPtr(ptr, destr);
+}
+
+#endif
+
static void MolObject_dealloc(MolObject* self)
{
Py_XDECREF(self->plugin);
@@ -184,16 +230,15 @@ static PyTypeObject MolObjectType = {
MolObject_new, /* tp_new */
};
+PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no);
PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
PyObject * read_fill_bonds(PyObject* molpack);
PyObject * read_fill_angles(PyObject* molpack);
PyObject * read_fill_next_timestep(PyObject* molpack);
PyObject * is_plugin_same(PyObject* molpack_a, PyObject* molpack_b);
PyObject * is_filehandle_same(PyObject* molpack_a, PyObject* molpack_b);
-
-molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no);
-
-molfile_plugin_t** molfile_plugin_list(int maxsize);
+PyObject * get_plugin(PyObject* molcapsule, int plug_no);
+PyObject * molfile_plugin_list(int maxsize);
int molfile_init(void);
diff --git a/pymolfile/pymolfile.py b/pymolfile/pymolfile.py
index 8902abaa5629d35f9bad7c4d2cb5f5d65a955243..b96887b61467d291b7a59818c779864098ea0ce0 100644
--- a/pymolfile/pymolfile.py
+++ b/pymolfile/pymolfile.py
@@ -47,28 +47,11 @@ def plugins():
capabilities of each molfile plugin. The information is
extracted from molfile_plugin_t.
"""
- max_num_plugins = 200
- c_list = libpymolfile.molfile_plugin_list(max_num_plugins)
numlist = libpymolfile.molfile_init()
- plugins_list = [libpymolfile.molfile_plugin_info(c_list, i) for i in range(numlist)]
+ plugins_list = [libpymolfile.molfile_plugin_info(C_MOLFILE_PLUGINS, i) for i in range(numlist)]
libpymolfile.molfile_finish()
return plugins_list
-def open(file_name_with_path, topology=None,
- file_format=None, topology_format=None,
- plugin=None, topology_plugin=None):
- """ The main function to read topology and
- trajectory files
-
- Returns: Depends on the file format and arguments:
- If structure file is supplied, it returns topology class.
- If only trajectory file is supplied, it returns trajectory class
- without topology information. (the number of atoms must be known)
- If both files are supplied, it returns trajectory class with
- topology information.
- """
- pass
-
def get_dir_base_extension(file_name):
""" Splits directory, file base and file extensions
@@ -115,6 +98,13 @@ def get_plugin_with_ext(file_ext):
return None
+def plugins_same(plugin_one, plugin_two):
+ if((plugin_one[1] == plugin_two[1]) and
+ (plugin_one[2][2] == plugin_two[2][2])):
+ return True
+ else:
+ return False
+
def get_plugin_with_name(plugin_name):
""" Search molfile plugins list and returns the plugin info
for the first matching name in plugin name field.
@@ -135,54 +125,197 @@ def get_plugin_with_name(plugin_name):
class Topology( object ):
- self.structure = None
- self.bonds = None
- self.angles = None
-
def __init__(self):
+ self.natoms = None
+ self.structure = None
+ self.bonds = None
+ self.angles = None
+
+ def __del__( self ):
pass
class Trajectory( object ):
- self.atoms = None
+ def __init__(self, file_name, file_format, plugin, natoms):
+ self.natoms = None
+ self.atoms = None
+ self.plugin = None
+ self.fname = None
+ self.ftype = None
+ self.fname = file_name
+ self.ftype = file_format
+ self.plugin = plugin
+ self.natoms = natoms
- def __init__(self):
- pass
-
- def get_frame(self, index):
-
def iread(self, chunk=None):
+ numlist = libpymolfile.molfile_init()
+ tplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+ self.plugin[1])
+ pluginhandle = libpymolfile.open_file_read(tplugin,
+ file_name, file_format, natoms)
+
+ step=0
+ while True:
+ try:
+ x = libpymolfile.read_fill_next_timestep(
+ pluginhandle)
+ if x is None:
+ break
+ step=step+1
+ if x is not None:
+ self.atoms = x
+ yield x
+ except (AttributeError,OSError):
+ pass
+
+ libpymolfile.close_file_read(pluginhandle)
+ libpymolfile.molfile_finish()
+
+# def read_frame(self, index_no):
+# numlist = libpymolfile.molfile_init()
+# tplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+# self.plugin[1])
+# pluginhandle = libpymolfile.open_file_read(tplugin,
+# file_name, file_format, natoms)
+# libpymolfile.molfile_finish()
+
+# def read(self, index_list, chunk=None):
+# numlist = libpymolfile.molfile_init()
+# tplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+# self.plugin[1])
+# pluginhandle = libpymolfile.open_file_read(tplugin,
+# file_name, file_format, natoms)
+# libpymolfile.molfile_finish()
- def read(self, index, chunk=None):
-
- def __del__(self):
+ def __del__( self ):
pass
class Molfile(object):
- self.plugin_list = MOLFILE_PLUGINS
- self.trajectory = None
- self.topology = None
- self.fplugin = None
- self.tplugin = None
- self.fmolobject = None
- self.tmolobject = None
- self.kwords = {
- "file_format" : None,
- "file_plugin" : None,
- "topology" : None,
- "topology_format" : None,
- "topology_plugin" : None,
- "natoms" : None
- }
-
def __init__(self, file_name, **kwargs):
- pass
+ self.plugin_list = MOLFILE_PLUGINS
+ self.c_plugin_list = C_MOLFILE_PLUGINS
+ self.trajectory = None
+ self.topology = None
+ self.fplugin = None
+ self.tplugin = None
+ self.smolplugin = None
+ self.cmolplugin = None
+ self.kwords = {
+ "file_format" : None,
+ "file_plugin" : None,
+ "topology" : None,
+ "topology_format" : None,
+ "topology_plugin" : None,
+ "natoms" : None
+ }
+
+ if not C_MOLFILE_PLUGINS:
+ C_MOLFILE_PLUGINS = libpymolfile.molfile_plugin_list(MAX_NUM_PLUGINS)
+ if not MOLFILE_PLUGINS:
+ MOLFILE_PLUGINS = plugins()
+ if(MOLFILE_PLUGINS and self.plugin_list is None):
+ self.plugin_list = MOLFILE_PLUGINS
+ if(C_MOLFILE_PLUGINS and self.c_plugin_list is None):
+ self.c_plugin_list = C_MOLFILE_PLUGINS
def __del__( self ):
pass
+def read_topology(self, file_name, file_format, plugin):
+ """ Reads structure, bonds, angles, dihedrals, impropers and
+ additional informations through molfile_plugin if the
+ data is available
+
+ The topology data in pymolfile is a list of tuples that include
+ the following fields:
+ (name, type, resname, resid, segid, chain, altloc, insertion,
+ occupancy, bfactor, mass, charge, radius, atomicnumber)
+
+ The data types are as follows in the tuple:
+ s = string, i = integer, f = float
+ (s, s, s, i, s, s, s, s, f, f, f, f, f, i)
+
+ Returns: Topology class if at least one of the topology
+ data is available. If non of the data is accessible,
+ function returns None
+ """
+ topo = None
+ if(file_name is not None and
+ file_format is not None and
+ plugin is not None):
+ natoms=0
+ pluginhandle = libpymolfile.open_file_read(plugin,
+ file_name, file_format, natoms)
+ natoms = pluginhandle.natoms
+ #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 file_format:
+ chain_size = 'S2'
+ else:
+ chain_size = 'S4'
+ prototype = 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')
+ ]
+ )
+ structure = libpymolfile.read_fill_structure(pluginhandle, prototype)
+ try:
+ bonds = libpymolfile.read_fill_bonds(pluginhandle)
+ except (AttributeError, SystemError):
+ pass
+
+ try:
+ angles = libpymolfile.read_fill_angles(pluginhandle)
+ except (AttributeError, SystemError):
+ pass
+
+ if structure:
+ topo = Topology()
+ topo.natoms = natoms
+ topo.structure = structure
+ if bonds:
+ topo.bonds = bonds
+ if angles:
+ topo.angles = angles
+
+ libpymolfile.close_file_read(pluginhandle)
+
+ if topo:
+ return topo
+ else:
+ return None
+
class OpenMolfile(Molfile):
+ """ The main class/function to read topology and
+ trajectory files
+
+ Returns: Depends on the file format and arguments:
+ If structure file is supplied, it returns topology class.
+ If only trajectory file is supplied, it returns trajectory class
+ without topology information. (the number of atoms must be known)
+ If both files are supplied, it returns trajectory class with
+ topology information.
+ """
def __init__(self, file_name, **kwargs):
if kwargs:
@@ -206,6 +339,8 @@ class OpenMolfile(Molfile):
if plugin_item:
self.fplugin = plugin_item
self.kwords["file_plugin"] = plugin_item[2][2]
+ else:
+ self.kwords["file_plugin"] = None
if self.kwords["file_plugin"]:
# Check if file_plugin reads structure info
@@ -214,34 +349,78 @@ class OpenMolfile(Molfile):
# Topology may be read with the plugin.
# This will override topology information
# if a 'topology' is supplied in keywords.
- else:
+ if self.kwords["file_format"] is not None:
+ numlist = libpymolfile.molfile_init()
+ self.smolplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+ self.fplugin[1])
+ self.topology = read_topology(file_name,
+ self.kwords["file_format"],
+ self.smolplugin)
+ libpymolfile.molfile_finish()
+
+ if self.fplugin[2][3] == 0:
# Topology can not be read with plugin from
# the file. If 'topology' is not set but 'natoms'
- # is only the trajectory will be available.
-
-
-
-
-
-
-
- c_list = libpymolfile.molfile_plugin_list(max_num_plugins)
- numlist = libpymolfile.molfile_init()
- self.cmolobject = libpymolfile.get_plugin(MOLFILE_PLUGINS, 83) #trr
-
-
-
- return self
- else:
- return None
-
-
-
-
-
-
-
-
-
+ # is set, only the trajectory will be available.
+ if self.kwords["topology"] is not None:
+ if isinstance(self.kwords["topology"], Molfile):
+ self.topology = self.kwords["topology"].topology
+ elif isinstance(elf.kwords["topology"], Topology):
+ self.topology = self.kwords["topology"]
+ else:
+ if self.kwords["topology_format"] is None:
+ topo_file_dir, topo_file_base, topo_file_ext = get_dir_base_extension(
+ self.kwords["topology"])
+ if topo_file_ext:
+ self.kwords["topology_format"] = topo_file_ext
+ else:
+ self.kwords["topology_format"] = topo_file_base
+
+ if self.kwords["topology_plugin"] is None:
+ self.kwords["topology_plugin"] = "auto"
+
+ if "auto" in self.kwords["topology_plugin"]:
+ topo_plugin_item = get_plugin_with_ext(self.kwords["topology_format"])
+ if topo_plugin_item:
+ self.tplugin = topo_plugin_item
+ self.kwords["topology_plugin"] = topo_plugin_item[2][2]
+ else:
+ self.kwords["topology_plugin"] = None
+
+ if self.kwords["topology_plugin"]:
+ # Check if topology_plugin reads structure info
+ # for the given file format.
+ if self.tplugin[2][3] == 1:
+ # Topology may be read with the plugin.
+ # This will override the topology information.
+ if self.kwords["topology_format"] is not None:
+ numlist = libpymolfile.molfile_init()
+ self.smolplugin = libpymolfile.get_plugin(C_MOLFILE_PLUGINS,
+ self.fplugin[1])
+ self.topology = read_topology(file_name,
+ self.kwords["topology_format"],
+ self.smolplugin)
+ libpymolfile.molfile_finish()
+ else:
+ print("Pymolfile can not determine the {0} file format " +
+ "of the file {1}" % (self.kwords["topology_format"],
+ topo_file_base + "." + topo_file_ext))
+
+ if(self.fplugin[2][6] == 1):
+ num_atoms = 0
+ if self.topology:
+ num_atoms = self.topology.natoms
+ elif natoms is not None:
+ num_atoms = natoms
+ # Trajectory can be read if num_atoms is set
+ if num_atoms>0:
+ self.trajectory = Trajectory(file_name,
+ self.kwords["file_format"],
+ self.kwords["file_plugin"],
+ num_atoms)
+ else:
+ print("Pymolfile can not determine the {0} file format " +
+ "of the file {1}" % (self.kwords["file_format"],
+ file_base + "." + file_ext))
diff --git a/pymolfile/test.py b/pymolfile/test.py
index c081c3845eb113a85432766127def8062bf51bc6..35fb3d9cfb303bc5ded90f2ca018938d5d82bc26 100644
--- a/pymolfile/test.py
+++ b/pymolfile/test.py
@@ -1,131 +1,20 @@
import numpy
-import molfile.libpymolfile as pym
+import pymolfile as pym
-mylist = pym.molfile_plugin_list(200)
-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/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"
+#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)
-print(y)
-if y is not None:
- print(len(y))
-
-try:
- z = pym.read_fill_bonds(spluginhandle)
- print(z)
- if z is not None:
- print(len(z))
-except (AttributeError, SystemError):
- pass
-
-try:
- a = pym.read_fill_angles(spluginhandle)
- print(a)
- if a is not None:
- 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:
-# 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()
-
+molfile = pym.OpenMolfile(sfname)
+print(molfile)
diff --git a/pymolfile/test_libpymolfile.py b/pymolfile/test_libpymolfile.py
new file mode 100644
index 0000000000000000000000000000000000000000..59d978e27129152aa349c63f7f60354467f772c1
--- /dev/null
+++ b/pymolfile/test_libpymolfile.py
@@ -0,0 +1,133 @@
+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()
+
+