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Commit 672baac3 authored by Berk Onat's avatar Berk Onat
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Added Numpy example wrapper for molfile_atom_t

parent c013427c
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Showing with 21638 additions and 170 deletions
pymolfile/molfile/compile.sh
View file @ 672baac3
swig -Wall -c++ -python libpymolfile.i
swig -py3 -Wall -c++ -python libpymolfile.i
g++ -fPIC -Wall -Wextra -Wunused-function -shared -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ -I. libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so -Ivmd_molfile_plugins/include/ -Ilib/ -L. lib/libmolfile_plugin.a -I/labEnv3/include/python3.6m/ -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6
pymolfile/molfile/deneme 0 → 100644
View file @ 672baac3
This diff is collapsed.
pymolfile/molfile/libpymolfile.i
View file @ 672baac3
......@@ -24,10 +24,12 @@
Published under BSD LICENSE
*/
#define SWIG_FILE_WITH_INIT
#define __STDC_FORMAT_MACROS
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <inttypes.h>
#include "molfile_plugin.h"
#include "libmolfile_plugin.h"
#include "vmdplugin.h"
......@@ -37,6 +39,7 @@
%include "numpy.i"
%init %{
Py_Initialize();
import_array();
%}
......@@ -54,6 +57,57 @@ import_array();
enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
/* Definition of molfile_atoms_t from molfile_plugin.h */
%inline %{
/*
struct MolAtoms {
char name[16];
char type[16];
char resname[8];
int resid;
char segid[8];
char chain[2];
char altloc[2];
char insertion[2];
float occupancy;
float bfactor;
float mass;
float charge;
float radius;
float atomicnumber;
float ctnumber;
};
void del_plugin_structure(PyObject* pymolfile_atoms){
delete (MolAtoms*)PyCapsule_GetPointer(pymolfile_atoms, "plugin_structure");
}
static PyObject* alloc_plugin_structure(PyObject *self, PyObject *args) {
return PyCapsule_New((void*)new MolAtoms(), "plugin_structure", del_plugin_structure);
}
*/
void del_plugin(PyObject* pymolfile_plugin){
delete (MolObject*)PyCapsule_GetPointer(pymolfile_plugin, "plugin");
}
void del_atoms(PyObject* pymolfile_atoms){
delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atoms");
}
void del_atomname(PyObject* pymolfile_atoms){
delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atomname");
}
static PyObject* alloc_plugin(PyObject *self, PyObject *args) {
return PyCapsule_New((void*)new MolObject(), "plugin_handle", del_plugin);
}
%}
/* pymolfile.c
initialize and finalize molfile plugins
*/
......@@ -126,20 +180,290 @@ PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
}
%}
%feature("autodoc", "0") my_open_file_read;
%rename (open_file_read) my_open_file_read;
%exception my_open_file_read {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
if (PyType_Ready(&MolObjectType) < 0)
return NULL;
PyTypeObject *type = &MolObjectType;
/*plugin_handle = PyCapsule_New((void*)new MolObject(), "plugin", del_plugin); */
/*MolObject* plugin_c = new MolObject;*/
MolObject *plugin_c;
plugin_c = (MolObject *)type->tp_alloc(type, 0);
/*PyObject * plugin_c = MolObject_new(&MolObjectType, args, kwds);*/
plugin_c->plugin = plugin;
plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
plugin_c->natoms = natoms;
/* PyCapsule_SetPointer(plugin_handle, &plugin_c); */
/* PyObject* plugin_handle = PyCapsule_New((void*)plugin_c, "plugin", del_plugin); */
PyObject* plugin_handle = (PyObject *)plugin_c;
/*if(!plugin_handle) printf("Not assigned\n");*/
/*PyObject *tuple = PyTuple_New(2);
PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
PyTuple_SET_ITEM(tuple, 1, plugin_handle);*/
return plugin_handle;
}
%}
/*
%typemap( argout ) ( char **MolfileAtomT_CharArray )
{
// The result variable is the return value from
// c_ephcom_read_constants, the number of actual values that are
// defined for cnames/values.
npy_intp dims[] = { result };
PyArray_Dims newshape_location;
PyArray_Dims * newshape = &newshape_location;
PyObject * status_check;
newshape->len = 1;
newshape->ptr = dims;
// resize array$argnum to actual size needed.
// Follow directions at http://www.mail-archive.com/numpy-discussion@scipy.org/msg13013.html
status_check = PyArray_Resize( (PyArrayObject *) array$argnum, newshape, 0, NPY_CORDER );
if ( !status_check )
SWIG_fail;
Py_DECREF( status_check );
$result = SWIG_Python_AppendOutput( $result, array$argnum );
}
%typemap( freearg ) ( char **MolfileAtomT_CharArray )
{
free( $1 );
}
*/
/*
%feature("autodoc", "0") molfile_open;
%exception molfile_open {
#define DIM 3
typedef int imatrix[DIM][DIM];
typedef int ivec[DIM];
typedef float fmatrix[DIM][DIM];
typedef float fvec[DIM];
*/
/* Reading from xdr files */
/*
%apply (float INPLACE_ARRAY2[ANY][ANY]) {(matrix box)}
%apply (int DIM1, int DIM2, float* INPLACE_ARRAY2) {(int natoms, int _DIM, float *x),
(int vnatoms, int v_DIM, float *v),
(int fnatoms, int f_DIM, float *f)}
*/
/*
%apply (int INPLACE_IARRAY2[ANY][ANY]) {(imatrix intdata)}
%apply (float INPLACE_FARRAY2[ANY][ANY]) {(fmatrix floatdata)}
%apply (int DIM1, int* INPLACE_IARRAY2) {(int rnatoms, int* MolAtom_resid)}
%apply (int DIM1, float* INPLACE_FARRAY2) {(int mnatoms, float* MolAtom_mass),
(int anatoms, float* MolAtom_atomicnumber)}
*/
/*
%inline %{
int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
int* natoms, char** MolAtom_name,
int* natoms, char** MolAtom_type,
int* natoms, char** MolAtom_resname,
int* natoms, int** MolAtom_resid,
int* natoms, char** MolAtom_segid,
int* natoms, char** MolAtom_chain,
int* natoms, char** MolAtom_altloc,
int* natoms, char** MolAtom_insertion,
int* natoms, float** MolAtom_occupancy,
int* natoms, float** MolAtom_bfactor,
int* natoms, float** MolAtom_mass,
int* natoms, float** MolAtom_charge,
int* natoms, float** MolAtom_radius,
int* natoms, float** MolAtom_atomicnumber,
int* natoms, float** MolAtom_ctnumber) {
molfile_atom_t* atoms;
atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
plugin->read_structure(fhandle, options, atoms);
MolAtom_name = (char **)malloc(natoms,sizeof(char*));
MolAtom_type = (char **)malloc(natoms,sizeof(char*));
MolAtom_resname = (char **)malloc(natoms,sizeof(char*));
MolAtom_resid = (int **)malloc(natoms,sizeof(int*));
%}
*/
/*
%inline %{
int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
int natoms, char** MolAtom_name,
int tnatoms, char** MolAtom_type,
int rnatoms, int* MolAtom_resid,
int mnatoms, float* MolAtom_mass,
int anatoms, float* MolAtom_atomicnumber) {
int i;
molfile_atom_t* atoms;
molfile_atom_t atm;
atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
plugin->read_structure(fhandle, options, atoms);
if(atoms == NULL) { free(atoms); return 1; }
if(atoms->type == NULL || atoms->name == NULL){ free(atoms); return 1; }
MolAtom_name = (char **)malloc(natoms,sizeof(char*));
MolAtom_type = (char **)malloc(natoms,sizeof(char*));
MolAtom_resid = (int *)malloc(natoms,sizeof(int));
MolAtom_mass = (float *)malloc(natoms,sizeof(float));
MolAtom_atomicnumber = (float *)malloc(natoms,sizeof(float));
for (i=0;i<natoms;i++){
atm = atoms[i];
MolAtom_name[i] = atm.name;
MolAtom_type[i] = atm.type;
MolAtom_resid[i] = atm.resid;
MolAtom_mass[i] = atm.mass;
MolAtom_atomicnumber[i] = atm.atomicnumber;
}
return 0;
}
%}
*/
%feature("autodoc", "0") my_read_structure;
%rename (read_structure) my_read_structure;
extern PyObject * my_read_structure(PyObject* molpack);
/*
%feature("autodoc", "0") my_read_structure;
%rename (read_structure) my_read_structure;
%exception my_read_structure {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * molfile_open(molfile_plugin_t* plugin, ) {
int *plugno = &plugin_no;
return plugin;
PyObject * my_read_structure(PyObject* molpack) {
int options = 0;
int i;
molfile_plugin_t* plugin;
void* file_handle;
molfile_atom_t* atoms;
int numatoms, status;
char** atom_names;
char** atom_types;
PyObject *npatoms = NULL; */
/*MolObject* plugin_handle = (MolObject*)PyCapsule_GetPointer(molpack, "plugin");*/
/* MolObject* plugin_handle = (MolObject*)molpack;
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
printf("Test1\n");
status = plugin->read_structure(file_handle, &options, atoms);
printf("Test2 %d\n",status);
if (status!=0){
PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
return NULL;
}
printf("Test3\n");
npy_intp natoms[1] = { numatoms };
PyArrayObject* oresid;
int64_t* cresid;
int typenum;
int nd = 1;
npy_intp dims[1] = { numatoms }; */
/*dims[0] = numatoms;*/
/* oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
npy_intp* n = PyArray_DIMS(oresid);
printf("dimensions %ld\n", n[0]);
cresid = (int64_t*) PyArray_DATA(oresid);
PyObject* npatomresid = NULL;
char** MolAtom_name = (char **)malloc(numatoms*sizeof(char*));
char** MolAtom_type = (char **)malloc(numatoms*sizeof(char*));
int64_t* MolAtom_resid = NULL; */
/*int64_t* MolAtom_resid = (int64_t *)malloc(numatoms*sizeof(int64_t));*/
/* float* MolAtom_mass = (float *)malloc(numatoms*sizeof(float));
float* MolAtom_atomicnumber = (float *)malloc(numatoms*sizeof(float));
for (i=0;i<numatoms;i++){
MolAtom_name[i] = atoms[i].name;
MolAtom_type[i] = atoms[i].type;
cresid[i] = (int64_t) atoms[i].resid;
MolAtom_mass[i] = atoms[i].mass;
MolAtom_atomicnumber[i] = atoms[i].atomicnumber;
} */
/*Py_DECREF( obj );*/
/*npy_intp dims[3];*/ /* PyArray_AsCArray is for ndim <= 3 */
/* PyArray_Descr *descr;
npatoms = PyArray_SimpleNewFromData(1, natoms, NPY_USERDEF, atoms);
printf("Test4 numatoms=%d\n", numatoms);
PyObject* npatomname = NULL;
npatomname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_name[0]);
PyObject* npatomtype = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_type); */
/*PyObject* npatomresname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->resname);*/
/*PyObject* npatomsegid = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->segid);*/
/*PyObject* npatomchain = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->chain);*/
/*PyObject* npatomaltloc = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->altloc);*/
/*PyObject* npatominsert = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->insertion);*/
/*PyObject* npatomoccup = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->occupancy);*/
/*PyObject* npatombfact = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->bfactor);*/
/* PyObject* npatommass = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, MolAtom_mass); */
/*PyObject* npatomcharge = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->charge);*/
/*PyObject* npatomradius = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->radius);*/
/* PyObject* npatomicnumber = PyArray_SimpleNewFromData(1, natoms, NPY_INT64, MolAtom_atomicnumber); */
/*if (npatomname==NULL || npatomtype==NULL || npatomresname==NULL ||
npatomresid==NULL || npatomsegid==NULL || npatomchain==NULL )
{
free(atoms);
Py_XDECREF(npatomname); Py_XDECREF(npatomtype);
Py_XDECREF(npatomresname); Py_XDECREF(npatomresid); Py_XDECREF(npatomsegid);
Py_XDECREF(npatomchain); Py_XDECREF(npatomaltloc); Py_XDECREF(npatominsert);
Py_XDECREF(npatomoccup); Py_XDECREF(npatombfact); Py_XDECREF(npatommass);
Py_XDECREF(npatomcharge); Py_XDECREF(npatomradius); Py_XDECREF(npatomicnumber);
PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
return 0;
}
PyArray_BASE(npatomname) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomtype) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomresname) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomresid) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomsegid) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomchain) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomaltloc) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatominsert) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomoccup) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatombfact) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatommass) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomcharge) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomradius) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomicnumber) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatoms) = PyCObject_FromVoidPtr(atoms, free);
PyArray_BASE((PyArrayObject *)npatoms) = PyCapsule_New(atoms, "atoms", del_atoms);*/
/*PyArray_BASE((PyArrayObject *)npatoms); */
/* printf("Test4-2\n"); */
/*PyObject* Py_MolAtom_name = PyCapsule_New((void*)MolAtom_name, "atomname", del_atomname);*/
/*PyObject* Py_MolAtom_name;
Py_INCREF(Py_MolAtom_name);*/
/* printf("Test4-3\n"); */
/*PyArray_SetBaseObject((PyArrayObject *)npatomname, Py_MolAtom_name);*/
/*PyArray_SetBaseObject((PyArrayObject *)npatomtype, MolAtom_type);
PyArray_SetBaseObject((PyArrayObject *)npatomresid, MolAtom_resid);
PyArray_SetBaseObject((PyArrayObject *)npatommass, MolAtom_mass);
PyArray_SetBaseObject((PyArrayObject *)npatomicnumber, MolAtom_atomicnumber); */
/* printf("Test5\n");
PyObject *tuple = PyTuple_New(2);
PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
printf("Test6\n");
PyTuple_SET_ITEM(tuple, 1, npatomname); */
/*PyTuple_SET_ITEM(tuple, 2, npatomtype);
PyTuple_SET_ITEM(tuple, 3, npatomresid);
PyTuple_SET_ITEM(tuple, 4, npatommass);
PyTuple_SET_ITEM(tuple, 5, npatomicnumber);
PyObject* vars = PyDict_New();
printf("Test7\n");
PyDict_SetItemString( vars, "name", npatomname ); */
/* printf("Test8\n"); */
/*PyDict_SetItemString( vars, "resid", npatomresid ); */
/*return Py_BuildValue("O", oresid); */
/*return PyArray_FromArray(oresid, PyArray_DESCR(oresid), 0);*/
/* return 0;
}
%}
*/
/*
python wrappers for functions
and structure data in molfile_plugin.h
......@@ -167,7 +491,20 @@ PyObject * molfile_open(molfile_plugin_t* plugin, ) {
/* molfile_plugin_t */
/*
%feature("autodoc", "0") molfile_open_file_read;
%rename (open_file_read) molfile_open_file_read;
%exception molfile_open_file_read {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * molfile_open_file_read(molfile_plugin_t* plugin, char *fname, int natoms) {
int *plugno = &plugin_no;
return plugin;
}
%}
*/
/*
void *(* open_file_read)(const char *filepath, const char *filetype,
int *natoms);
......
pymolfile/molfile/libpymolfile.py
View file @ 672baac3
......@@ -8,7 +8,7 @@
:Author: Berk Onat <b.onat@warwick.ac.uk>
:Year: 2017
:Licence: BSD LICENSE
:Licence: UIUC LICENSE
......@@ -113,26 +113,136 @@ pluginNOMEM = _libpymolfile.pluginNOMEM
pluginENDOFFILE = _libpymolfile.pluginENDOFFILE
pluginFILENOTFOUND = _libpymolfile.pluginFILENOTFOUND
pluginFORMATERROR = _libpymolfile.pluginFORMATERROR
class MolAtoms(_object):
__swig_setmethods__ = {}
__setattr__ = lambda self, name, value: _swig_setattr(self, MolAtoms, name, value)
__swig_getmethods__ = {}
__getattr__ = lambda self, name: _swig_getattr(self, MolAtoms, name)
__repr__ = _swig_repr
__swig_setmethods__["name"] = _libpymolfile.MolAtoms_name_set
__swig_getmethods__["name"] = _libpymolfile.MolAtoms_name_get
if _newclass:
name = _swig_property(_libpymolfile.MolAtoms_name_get, _libpymolfile.MolAtoms_name_set)
__swig_setmethods__["type"] = _libpymolfile.MolAtoms_type_set
__swig_getmethods__["type"] = _libpymolfile.MolAtoms_type_get
if _newclass:
type = _swig_property(_libpymolfile.MolAtoms_type_get, _libpymolfile.MolAtoms_type_set)
__swig_setmethods__["resname"] = _libpymolfile.MolAtoms_resname_set
__swig_getmethods__["resname"] = _libpymolfile.MolAtoms_resname_get
if _newclass:
resname = _swig_property(_libpymolfile.MolAtoms_resname_get, _libpymolfile.MolAtoms_resname_set)
__swig_setmethods__["resid"] = _libpymolfile.MolAtoms_resid_set
__swig_getmethods__["resid"] = _libpymolfile.MolAtoms_resid_get
if _newclass:
resid = _swig_property(_libpymolfile.MolAtoms_resid_get, _libpymolfile.MolAtoms_resid_set)
__swig_setmethods__["segid"] = _libpymolfile.MolAtoms_segid_set
__swig_getmethods__["segid"] = _libpymolfile.MolAtoms_segid_get
if _newclass:
segid = _swig_property(_libpymolfile.MolAtoms_segid_get, _libpymolfile.MolAtoms_segid_set)
__swig_setmethods__["chain"] = _libpymolfile.MolAtoms_chain_set
__swig_getmethods__["chain"] = _libpymolfile.MolAtoms_chain_get
if _newclass:
chain = _swig_property(_libpymolfile.MolAtoms_chain_get, _libpymolfile.MolAtoms_chain_set)
__swig_setmethods__["altloc"] = _libpymolfile.MolAtoms_altloc_set
__swig_getmethods__["altloc"] = _libpymolfile.MolAtoms_altloc_get
if _newclass:
altloc = _swig_property(_libpymolfile.MolAtoms_altloc_get, _libpymolfile.MolAtoms_altloc_set)
__swig_setmethods__["insertion"] = _libpymolfile.MolAtoms_insertion_set
__swig_getmethods__["insertion"] = _libpymolfile.MolAtoms_insertion_get
if _newclass:
insertion = _swig_property(_libpymolfile.MolAtoms_insertion_get, _libpymolfile.MolAtoms_insertion_set)
__swig_setmethods__["occupancy"] = _libpymolfile.MolAtoms_occupancy_set
__swig_getmethods__["occupancy"] = _libpymolfile.MolAtoms_occupancy_get
if _newclass:
occupancy = _swig_property(_libpymolfile.MolAtoms_occupancy_get, _libpymolfile.MolAtoms_occupancy_set)
__swig_setmethods__["bfactor"] = _libpymolfile.MolAtoms_bfactor_set
__swig_getmethods__["bfactor"] = _libpymolfile.MolAtoms_bfactor_get
if _newclass:
bfactor = _swig_property(_libpymolfile.MolAtoms_bfactor_get, _libpymolfile.MolAtoms_bfactor_set)
__swig_setmethods__["mass"] = _libpymolfile.MolAtoms_mass_set
__swig_getmethods__["mass"] = _libpymolfile.MolAtoms_mass_get
if _newclass:
mass = _swig_property(_libpymolfile.MolAtoms_mass_get, _libpymolfile.MolAtoms_mass_set)
__swig_setmethods__["charge"] = _libpymolfile.MolAtoms_charge_set
__swig_getmethods__["charge"] = _libpymolfile.MolAtoms_charge_get
if _newclass:
charge = _swig_property(_libpymolfile.MolAtoms_charge_get, _libpymolfile.MolAtoms_charge_set)
__swig_setmethods__["radius"] = _libpymolfile.MolAtoms_radius_set
__swig_getmethods__["radius"] = _libpymolfile.MolAtoms_radius_get
if _newclass:
radius = _swig_property(_libpymolfile.MolAtoms_radius_get, _libpymolfile.MolAtoms_radius_set)
__swig_setmethods__["atomicnumber"] = _libpymolfile.MolAtoms_atomicnumber_set
__swig_getmethods__["atomicnumber"] = _libpymolfile.MolAtoms_atomicnumber_get
if _newclass:
atomicnumber = _swig_property(_libpymolfile.MolAtoms_atomicnumber_get, _libpymolfile.MolAtoms_atomicnumber_set)
__swig_setmethods__["ctnumber"] = _libpymolfile.MolAtoms_ctnumber_set
__swig_getmethods__["ctnumber"] = _libpymolfile.MolAtoms_ctnumber_get
if _newclass:
ctnumber = _swig_property(_libpymolfile.MolAtoms_ctnumber_get, _libpymolfile.MolAtoms_ctnumber_set)
def __init__(self):
this = _libpymolfile.new_MolAtoms()
try:
self.this.append(this)
except __builtin__.Exception:
self.this = this
__swig_destroy__ = _libpymolfile.delete_MolAtoms
__del__ = lambda self: None
MolAtoms_swigregister = _libpymolfile.MolAtoms_swigregister
MolAtoms_swigregister(MolAtoms)
def del_plugin_structure(pymolfile_atoms: 'PyObject *') -> "void":
return _libpymolfile.del_plugin_structure(pymolfile_atoms)
del_plugin_structure = _libpymolfile.del_plugin_structure
def alloc_plugin_structure(arg1: 'PyObject *', args: 'PyObject *') -> "PyObject *":
return _libpymolfile.alloc_plugin_structure(arg1, args)
alloc_plugin_structure = _libpymolfile.alloc_plugin_structure
def del_plugin(pymolfile_plugin: 'PyObject *') -> "void":
return _libpymolfile.del_plugin(pymolfile_plugin)
del_plugin = _libpymolfile.del_plugin
def molfile_plugin_list(maxsize):
def del_atoms(pymolfile_atoms: 'PyObject *') -> "void":
return _libpymolfile.del_atoms(pymolfile_atoms)
del_atoms = _libpymolfile.del_atoms
def del_atomname(pymolfile_atoms: 'PyObject *') -> "void":
return _libpymolfile.del_atomname(pymolfile_atoms)
del_atomname = _libpymolfile.del_atomname
def alloc_plugin(arg1: 'PyObject *', args: 'PyObject *') -> "PyObject *":
return _libpymolfile.alloc_plugin(arg1, args)
alloc_plugin = _libpymolfile.alloc_plugin
def molfile_plugin_list(maxsize: 'int') -> "molfile_plugin_t **":
"""molfile_plugin_list(maxsize) -> molfile_plugin_t **"""
return _libpymolfile.molfile_plugin_list(maxsize)
def molfile_init():
def molfile_init() -> "int":
"""molfile_init() -> int"""
return _libpymolfile.molfile_init()
def molfile_finish():
def molfile_finish() -> "int":
"""molfile_finish() -> int"""
return _libpymolfile.molfile_finish()
def get_plugin(plugin_list, plugin_no):
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 molfile_plugin_info(plugin_list, plugin_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 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 read_structure(molpack: 'PyObject *') -> "PyObject *":
"""read_structure(molpack) -> PyObject *"""
return _libpymolfile.read_structure(molpack)
# This file is compatible with both classic and new-style classes.
pymolfile/molfile/libpymolfile_wrap.c
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pymolfile/molfile/libpymolfile_wrap.cxx
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pymolfile/molfile/pymolfile.c
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......@@ -36,6 +36,9 @@
int numplugins=0;
molfile_plugin_t** plugin_list;
/* * * * * * * * * * * * * * * * * * * * * * *
* Helper functions to set and store plugins *
* * * * * * * * * * * * * * * * * * * * * * */
......@@ -58,11 +61,13 @@ struct DICTHOLDER * plugin_find(struct DICTHOLDER *dict, const char *pluginname)
molfile_plugin_t* get_plugin(molfile_plugin_t** plug_list, int plug_no)
{
molfile_plugin_t* plugin;
if(plug_no < 0){
return NULL;
plugin = NULL;
} else {
return plug_list[plug_no];
plugin = plug_list[plug_no];
}
return plugin;
}
#if 0
......@@ -245,4 +250,55 @@ int molfile_finish(void)
/* Functions in molfile_plugin_t */
PyObject * my_read_structure(PyObject* molpack) {
Py_Initialize();
import_array();
int options = 0;
int i;
molfile_plugin_t* plugin;
void* file_handle;
molfile_atom_t* atoms;
int numatoms, status;
PyArray_Descr *descr;
PyObject p*;
if (PyType_Ready(&MolAtomType) < 0)
return NULL;
PyTypeObject *atype = &MolAtomType;
MolAtom *atom_t;
atom_t = (MolAtom *)atype->tp_alloc(atype, 0);
p = (PyObject*) atom_t;
descr = PyArray_DescrFromObject(p, NULL)
MolObject* plugin_handle = (MolObject*) molpack;
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
status = plugin->read_structure(file_handle, &options, atoms);