OpenMolfile Class is added with trajectory and topology functions

pymolfile/]

-
-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
-
-

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()
 

pymolfile/molfile/compile.sh

+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 \

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); 

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 *"""

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"},