Skip to content
GitLab
Commit f2259af4 authored by Berk Onat's avatar Berk Onat
Browse files

molfile_plugin libraries are compiled with GCC on MacOS

parent 3b405c2e
Hide whitespace changes
Inline Side-by-side
pymolfile/molfile/1 deleted 100644 → 0
View file @ 3b405c2e
import numpy
import ctypes
import _libpymolfile
class molatom_t(ctypes.Structure):
_fields_ = [
('name', ctypes.c_char * 16),
('type', ctypes.c_char * 16),
('resname', ctypes.c_char * 8),
('resid', ctypes.c_uint8),
('segid', ctypes.c_char * 8),
('chain', ctypes.c_char * 2),
('altloc', ctypes.c_char * 2),
('insertion', ctypes.c_char *2),
('occupancy', ctypes.c_float),
('bfactor', ctypes.c_float),
('mass', ctypes.c_float),
('charge', ctypes.c_float),
('radius', ctypes.c_float),
('atomicnumber', ctypes.c_uint8),
('ctnumber', ctypes.c_uint8),
]
class molplugin_t(ctypes.Structure):
_fields_ = [
('abiversion', ctypes.c_uint8),
('type', ctypes.c_char_p),
('name', ctypes.c_char_p),
('prettyname', ctypes.c_char_p),
('author', ctypes.c_char_p),
('majorv', ctypes.c_uint8),
('minorv', ctypes.c_uint8),
('is_reentrant', ctypes.c_uint8),
('filename_extension', ctypes.c_char_p),
('open_file_read', ctypes.CFUNCTYPE(ctypes.c_char_p,
ctypes.c_char_p, ctypes.POINTER(ctypes.c_uint8))),
('read_structure', ctypes.CFUNCTYPE(ctypes.c_void_p,
ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(molatom_t))),
('read_bonds', ctypes.CFUNCTYPE(ctypes.c_void_p,
ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_uint), ctypes.POINTER(ctypes.c_uint),
ctypes.c_char_p)),
('read_next_timestep', ctypes.c_int8),
('close_file_read', ctypes.c_void_p),
('open_file_write', ctypes.c_void_p),
('write_structure', ctypes.c_int8),
('write_timestep', ctypes.c_int8),
('close_file_write', ctypes.c_void_p),
('read_volumetric_metadata', ctypes.c_int8),
('read_volumetric_data', ctypes.c_int8),
('read_volumetric_data_ex', ctypes.c_int8),
('read_rawgraphics', ctypes.c_int8),
('read_molecule_metadata', ctypes.c_int8),
('write_bonds', ctypes.c_int8),
('write_volumetric_data', ctypes.c_int8),
('write_volumetric_data_ex', ctypes.c_int8),
('read_angles', ctypes.c_int8),
('write_angles', ctypes.c_int8),
('read_qm_metadata', ctypes.c_int8),
('read_qm_rundata', ctypes.c_int8),
('read_timestep', ctypes.c_int8),
('read_timestep_metadata', ctypes.c_int8),
('read_qm_timestep_metadata', ctypes.c_int8),
('read_timestep2', ctypes.c_int8),
('read_times', ctypes.c_ssize_t),
('cons_fputs', ctypes.c_uint8)
]
class moltimestep_t(ctypes.Structure):
_fields_ = [
('coords', ctypes.POINTER(ctypes.c_float)),
('velocities', ctypes.POINTER(ctypes.c_float)),
('A', ctypes.c_float),
('B', ctypes.c_float),
('C', ctypes.c_float),
('alpha', ctypes.c_float),
('beta', ctypes.c_float),
('gamma', ctypes.c_float),
('physical_time', ctypes.c_double),
('total_energy', ctypes.c_double),
('potential_energy', ctypes.c_double),
('kinetic_energy', ctypes.c_double),
('extended_energy', ctypes.c_double),
('force_energy', ctypes.c_double),
('total_pressure', ctypes.c_double)
]
class molhandle_t(ctypes.Structure):
_fields_ = [
('plugin', ctypes.POINTER(molplugin_t)),
('file_handle', ctypes.c_void_p),
('natoms', ctypes.c_int)
]
class molnatoms(ctypes.Structure):
_fields_ = [
('natoms', ctypes.c_int)
]
#callback_t = ctypes.CFUNCTYPE(None, ctypes.POINTER(molatom_t))
def get_open_file_read(output):
ctypes.open_file_read.restype = ctypes.POINTER(molhandle_t)
ctypes.open_file_read.argtypes = [ctypes.POINTER(molplugin_t), ctypes.c_void_p, ctypes.c_uint8]
return ctypes.pythonapi.PyCapsule_GetPointer(output, "plugin")
def get_capsule(capsule):
ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.c_void_p
ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
return ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
def get_plugincapsule(capsule):
data = ctypes.POINTER(molhandle_t)
ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
return data
def get_plugindata(capsule):
data = ctypes.POINTER(molhandle_t)
ctypes.pythonapi.PyCapsule_GetPointer.restype = ctypes.POINTER(molhandle_t)
ctypes.pythonapi.PyCapsule_GetPointer.argtypes = [ctypes.py_object, ctypes.c_char_p]
data = ctypes.pythonapi.PyCapsule_GetPointer(capsule, b"plugin")
return data
mylib = _libpymolfile
mylist = mylib.molfile_plugin_list(200)
numlist = mylib.molfile_init()
print(numlist)
for i in range(numlist):
testplugin = mylib.molfile_plugin_info(mylist, i)
print(i, testplugin)
plugin = mylib.get_plugin(mylist, 81)
print(plugin)
natoms=0
numatoms=molnatoms(natoms)
fname="../../test/md.gro"
ftype="gro"
pluginhandle = mylib.open_file_read(plugin, fname, ftype, natoms)
print("This passed")
print(pluginhandle)
print("This passed too")
print(pluginhandle.natoms)
print("Here")
x = numpy.array([
('C1','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6),
('C2','C','ACE',0,'','','','',1.0,1.0,12.011,6,1.0,6)
],
dtype=[
('name', 'S16'), ('type', 'S16'), ('resname', 'S8'),
('resid', 'i4'), ('segid', 'S8'), ('chain', 'S2'),
('altloc', 'S2'), ('insertion', 'S2'), ('occupancy', 'f8'),
('bfactor', 'f8'), ('mass', 'f8'), ('charge', 'f8'),
('radius', 'f8'), ('atomicnumber', 'i4')
]
)
print(x)
print(x.__array_interface__)
print(x.__array_interface__["descr"])
print(x.__array_struct__)
#y = mylib.read_fill_structure(pluginhandle, x)
y = mylib.print_array_struct(x)
print('Test')
print(y)
#outarray = mylib.get_structure(pluginhandle)
#print(outarray)
#print(type(outarray))
#for i in outarray:
# print(i)
pymolfile/molfile/compile.sh
View file @ f2259af4
swig -py3 -Wall -c++ -python libpymolfile.i
g++ -fPIC -Wall -Wextra -Wunused-function -shared -g -I/labEnv3/lib/python3.6/site-packages/numpy/core/include/ -I. libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so -Ivmd_molfile_plugins/include/ -Ilib/ -L. lib/libmolfile_plugin.a -I/labEnv3/include/python3.6m/ -L/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6
g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter -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/libpymolfile-backup3.i 0 → 100644
View file @ f2259af4
/* -*- C -*- (not really, but good for syntax highlighting) */
/* SWIG interface for libpymolfile of VMD molfile_plugins
Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
Published under UIUC LICENSE
swig -c++ -python -outdir . molfile/libpymolfile.i
*/
%define DOCSTRING
"
:Author: Berk Onat <b.onat@warwick.ac.uk>
:Year: 2017
:Licence: UIUC LICENSE
"
%enddef
%module(docstring=DOCSTRING) libpymolfile
%{
/* Python SWIG interface to libpymolfile
Copyright (c) 2017 Berk Onat <b.onat@warwick.ac.uk>
Published under BSD LICENSE
*/
#define SWIG_FILE_WITH_INIT
#define __STDC_FORMAT_MACROS
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <inttypes.h>
#include "molfile_plugin.h"
#include "libmolfile_plugin.h"
#include "vmdplugin.h"
#include "pymolfile.h"
%}
%include "numpy.i"
%init %{
Py_Initialize();
import_array();
%}
/*
Wrapping only high-level plugin functions to register VMD
plugins and to retrive the data through molfile_plugin interface.
Only modifing call signatures. This will help one to access functions
without dealing with pointers from python.
*/
/* plugin status codes for error handling */
enum { pluginOK, pluginNOINIT, pluginCLOSE, pluginNOMEM,
pluginENDOFFILE, pluginFILENOTFOUND, pluginFORMATERROR };
/* Definition of molfile_atoms_t from molfile_plugin.h */
%inline %{
/*
struct MolAtoms {
char name[16];
char type[16];
char resname[8];
int resid;
char segid[8];
char chain[2];
char altloc[2];
char insertion[2];
float occupancy;
float bfactor;
float mass;
float charge;
float radius;
float atomicnumber;
float ctnumber;
};
void del_plugin_structure(PyObject* pymolfile_atoms){
delete (MolAtoms*)PyCapsule_GetPointer(pymolfile_atoms, "plugin_structure");
}
static PyObject* alloc_plugin_structure(PyObject *self, PyObject *args) {
return PyCapsule_New((void*)new MolAtoms(), "plugin_structure", del_plugin_structure);
}
*/
void del_plugin(PyObject* pymolfile_plugin){
delete (MolObject*)PyCapsule_GetPointer(pymolfile_plugin, "plugin");
}
void del_atoms(PyObject* pymolfile_atoms){
delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atoms");
}
void del_atomname(PyObject* pymolfile_atoms){
delete (PyObject*)PyCapsule_GetPointer(pymolfile_atoms, "atomname");
}
static PyObject* alloc_plugin(PyObject *self, PyObject *args) {
return PyCapsule_New((void*)new MolObject(), "plugin_handle", del_plugin);
}
%}
/* pymolfile.c
initialize and finalize molfile plugins
*/
%feature("autodoc", "0") molfile_plugin_list;
extern molfile_plugin_t** molfile_plugin_list(int maxsize);
%feature("autodoc", "0") molfile_init;
extern int molfile_init(void);
%feature("autodoc", "0") molfile_finish;
extern int molfile_finish(void);
%feature("autodoc", "0") get_plugin;
extern molfile_plugin_t* get_plugin(molfile_plugin_t** plugin_list, int plugin_no);
%feature("autodoc", "0") molfile_plugin_info;
%exception molfile_plugin_info {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * molfile_plugin_info(molfile_plugin_t** plugin_list, int plugin_no) {
molfile_plugin_t *plugin;
int *plugno = &plugin_no;
int has_readstructure = 0;
int has_readbonds = 0;
int has_readangles = 0;
int has_writestructure = 0;
int has_writebonds = 0;
int has_writeangles = 0;
int has_readnexttimestep = 0;
int has_writetimestep = 0;
int plugin_list_size = sizeof(plugin_list) / sizeof(molfile_plugin_t**);
if (plugno==NULL || plugin_no<0){
PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin handle no should be given, be positive value and should not exceed the list length'%d'. You set '%d'", pluginNOINIT, plugin_list_size, plugin_no);
return 0;
}
plugin = plugin_list[plugin_no];
if(plugin==NULL || !plugin->open_file_read){
PyErr_Format(PyExc_IOError, "[%d] Error: molfile plugin '%d' is not initialized.", pluginNOINIT, plugin_no);
return 0;
}
if (plugin->read_structure) has_readstructure = 1;
if (plugin->read_bonds) has_readbonds = 1;
if (plugin->read_angles) has_readangles = 1;
if (plugin->read_next_timestep) has_readnexttimestep = 1;
if (plugin->write_structure) has_writestructure = 1;
if (plugin->write_bonds) has_writebonds = 1;
if (plugin->write_angles) has_writeangles = 1;
if (plugin->write_timestep) has_writetimestep = 1;
PyObject *tuple = PyTuple_New(17);
PyTuple_SET_ITEM(tuple, 0, PyString_FromString(plugin->filename_extension));
PyTuple_SET_ITEM(tuple, 1, PyString_FromString(plugin->name));
PyTuple_SET_ITEM(tuple, 2, PyInt_FromLong((long)has_readstructure));
PyTuple_SET_ITEM(tuple, 3, PyInt_FromLong((long)has_readbonds));
PyTuple_SET_ITEM(tuple, 4, PyInt_FromLong((long)has_readangles));
PyTuple_SET_ITEM(tuple, 5, PyInt_FromLong((long)has_readnexttimestep));
PyTuple_SET_ITEM(tuple, 6, PyInt_FromLong((long)has_writestructure));
PyTuple_SET_ITEM(tuple, 7, PyInt_FromLong((long)has_writebonds));
PyTuple_SET_ITEM(tuple, 8, PyInt_FromLong((long)has_writeangles));
PyTuple_SET_ITEM(tuple, 9, PyInt_FromLong((long)has_writetimestep));
PyTuple_SET_ITEM(tuple, 10, PyString_FromString(plugin->prettyname));
PyTuple_SET_ITEM(tuple, 11, PyString_FromString(plugin->type));
PyTuple_SET_ITEM(tuple, 12, PyString_FromString(plugin->author));
PyTuple_SET_ITEM(tuple, 13, PyInt_FromLong((long)plugin->majorv));
PyTuple_SET_ITEM(tuple, 14, PyInt_FromLong((long)plugin->minorv));
PyTuple_SET_ITEM(tuple, 15, PyInt_FromLong((long)plugin->abiversion));
PyTuple_SET_ITEM(tuple, 16, PyInt_FromLong((long)plugin->is_reentrant));
return tuple;
}
%}
%feature("autodoc", "0") my_open_file_read;
%rename (open_file_read) my_open_file_read;
%exception my_open_file_read {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * my_open_file_read(molfile_plugin_t* plugin, char* fname, char* ftype, int natoms) {
if (PyType_Ready(&MolObjectType) < 0)
return NULL;
PyTypeObject *type = &MolObjectType;
/*plugin_handle = PyCapsule_New((void*)new MolObject(), "plugin", del_plugin); */
/*MolObject* plugin_c = new MolObject;*/
MolObject *plugin_c;
plugin_c = (MolObject *)type->tp_alloc(type, 0);
/*PyObject * plugin_c = MolObject_new(&MolObjectType, args, kwds);*/
plugin_c->plugin = plugin;
plugin_c->file_handle = plugin->open_file_read(fname, ftype, &natoms);
plugin_c->natoms = natoms;
/* PyCapsule_SetPointer(plugin_handle, &plugin_c); */
/* PyObject* plugin_handle = PyCapsule_New((void*)plugin_c, "plugin", del_plugin); */
PyObject* plugin_handle = (PyObject *)plugin_c;
/*if(!plugin_handle) printf("Not assigned\n");*/
/*PyObject *tuple = PyTuple_New(2);
PyTuple_SET_ITEM(tuple, 0, PyInt_FromLong((long)natoms));
PyTuple_SET_ITEM(tuple, 1, plugin_handle);*/
return plugin_handle;
}
%}
/*
%typemap( argout ) ( char **MolfileAtomT_CharArray )
{
// The result variable is the return value from
// c_ephcom_read_constants, the number of actual values that are
// defined for cnames/values.
npy_intp dims[] = { result };
PyArray_Dims newshape_location;
PyArray_Dims * newshape = &newshape_location;
PyObject * status_check;
newshape->len = 1;
newshape->ptr = dims;
// resize array$argnum to actual size needed.
// Follow directions at http://www.mail-archive.com/numpy-discussion@scipy.org/msg13013.html
status_check = PyArray_Resize( (PyArrayObject *) array$argnum, newshape, 0, NPY_CORDER );
if ( !status_check )
SWIG_fail;
Py_DECREF( status_check );
$result = SWIG_Python_AppendOutput( $result, array$argnum );
}
%typemap( freearg ) ( char **MolfileAtomT_CharArray )
{
free( $1 );
}
*/
/*
#define DIM 3
typedef int imatrix[DIM][DIM];
typedef int ivec[DIM];
typedef float fmatrix[DIM][DIM];
typedef float fvec[DIM];
*/
/* Reading from xdr files */
/*
%apply (float INPLACE_ARRAY2[ANY][ANY]) {(matrix box)}
%apply (int DIM1, int DIM2, float* INPLACE_ARRAY2) {(int natoms, int _DIM, float *x),
(int vnatoms, int v_DIM, float *v),
(int fnatoms, int f_DIM, float *f)}
*/
/*
%apply (int INPLACE_IARRAY2[ANY][ANY]) {(imatrix intdata)}
%apply (float INPLACE_FARRAY2[ANY][ANY]) {(fmatrix floatdata)}
%apply (int DIM1, int* INPLACE_IARRAY2) {(int rnatoms, int* MolAtom_resid)}
%apply (int DIM1, float* INPLACE_FARRAY2) {(int mnatoms, float* MolAtom_mass),
(int anatoms, float* MolAtom_atomicnumber)}
*/
/*
%inline %{
int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
int* natoms, char** MolAtom_name,
int* natoms, char** MolAtom_type,
int* natoms, char** MolAtom_resname,
int* natoms, int** MolAtom_resid,
int* natoms, char** MolAtom_segid,
int* natoms, char** MolAtom_chain,
int* natoms, char** MolAtom_altloc,
int* natoms, char** MolAtom_insertion,
int* natoms, float** MolAtom_occupancy,
int* natoms, float** MolAtom_bfactor,
int* natoms, float** MolAtom_mass,
int* natoms, float** MolAtom_charge,
int* natoms, float** MolAtom_radius,
int* natoms, float** MolAtom_atomicnumber,
int* natoms, float** MolAtom_ctnumber) {
molfile_atom_t* atoms;
atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
plugin->read_structure(fhandle, options, atoms);
MolAtom_name = (char **)malloc(natoms,sizeof(char*));
MolAtom_type = (char **)malloc(natoms,sizeof(char*));
MolAtom_resname = (char **)malloc(natoms,sizeof(char*));
MolAtom_resid = (int **)malloc(natoms,sizeof(int*));
%}
*/
/*
%inline %{
int structure_read(molfile_plugin_t* plugin, void* fhandle, int *options,
int natoms, char** MolAtom_name,
int tnatoms, char** MolAtom_type,
int rnatoms, int* MolAtom_resid,
int mnatoms, float* MolAtom_mass,
int anatoms, float* MolAtom_atomicnumber) {
int i;
molfile_atom_t* atoms;
molfile_atom_t atm;
atoms = (molfile_atom_t *)calloc(natoms,sizeof(molfile_atom_t));
plugin->read_structure(fhandle, options, atoms);
if(atoms == NULL) { free(atoms); return 1; }
if(atoms->type == NULL || atoms->name == NULL){ free(atoms); return 1; }
MolAtom_name = (char **)malloc(natoms,sizeof(char*));
MolAtom_type = (char **)malloc(natoms,sizeof(char*));
MolAtom_resid = (int *)malloc(natoms,sizeof(int));
MolAtom_mass = (float *)malloc(natoms,sizeof(float));
MolAtom_atomicnumber = (float *)malloc(natoms,sizeof(float));
for (i=0;i<natoms;i++){
atm = atoms[i];
MolAtom_name[i] = atm.name;
MolAtom_type[i] = atm.type;
MolAtom_resid[i] = atm.resid;
MolAtom_mass[i] = atm.mass;
MolAtom_atomicnumber[i] = atm.atomicnumber;
}
return 0;
}
%}
*/
%feature("autodoc", "0") my_read_structure;
%rename (read_structure) my_read_structure;
extern PyObject * my_read_structure(PyObject* molpack);
%feature("autodoc", "0") get_structure;
extern PyObject * get_structure(PyObject* molpack);
%feature("autodoc", "0") read_fill_structure;
extern PyObject * read_fill_structure(PyObject* molpack, PyObject* prototype);
%feature("autodoc", "0") print_array_struct;
extern PyObject* print_array_struct(PyObject* prototype);
/*
%feature("autodoc", "0") my_read_structure;
%rename (read_structure) my_read_structure;
%exception my_read_structure {
$action
if (PyErr_Occurred()) SWIG_fail;
}
%inline %{
PyObject * my_read_structure(PyObject* molpack) {
int options = 0;
int i;
molfile_plugin_t* plugin;
void* file_handle;
molfile_atom_t* atoms;
int numatoms, status;
char** atom_names;
char** atom_types;
PyObject *npatoms = NULL; */
/*MolObject* plugin_handle = (MolObject*)PyCapsule_GetPointer(molpack, "plugin");*/
/* MolObject* plugin_handle = (MolObject*)molpack;
plugin = plugin_handle->plugin;
file_handle = plugin_handle->file_handle;
numatoms = plugin_handle->natoms;
atoms = (molfile_atom_t *)calloc(numatoms,sizeof(molfile_atom_t));
printf("Test1\n");
status = plugin->read_structure(file_handle, &options, atoms);
printf("Test2 %d\n",status);
if (status!=0){
PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
return NULL;
}
printf("Test3\n");
npy_intp natoms[1] = { numatoms };
PyArrayObject* oresid;
int64_t* cresid;
int typenum;
int nd = 1;
npy_intp dims[1] = { numatoms }; */
/*dims[0] = numatoms;*/
/* oresid = (PyArrayObject*) PyArray_SimpleNew(nd, dims, NPY_INT64);
npy_intp* n = PyArray_DIMS(oresid);
printf("dimensions %ld\n", n[0]);
cresid = (int64_t*) PyArray_DATA(oresid);
PyObject* npatomresid = NULL;
char** MolAtom_name = (char **)malloc(numatoms*sizeof(char*));
char** MolAtom_type = (char **)malloc(numatoms*sizeof(char*));
int64_t* MolAtom_resid = NULL; */
/*int64_t* MolAtom_resid = (int64_t *)malloc(numatoms*sizeof(int64_t));*/
/* float* MolAtom_mass = (float *)malloc(numatoms*sizeof(float));
float* MolAtom_atomicnumber = (float *)malloc(numatoms*sizeof(float));
for (i=0;i<numatoms;i++){
MolAtom_name[i] = atoms[i].name;
MolAtom_type[i] = atoms[i].type;
cresid[i] = (int64_t) atoms[i].resid;
MolAtom_mass[i] = atoms[i].mass;
MolAtom_atomicnumber[i] = atoms[i].atomicnumber;
} */
/*Py_DECREF( obj );*/
/*npy_intp dims[3];*/ /* PyArray_AsCArray is for ndim <= 3 */
/* PyArray_Descr *descr;
npatoms = PyArray_SimpleNewFromData(1, natoms, NPY_USERDEF, atoms);
printf("Test4 numatoms=%d\n", numatoms);
PyObject* npatomname = NULL;
npatomname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_name[0]);
PyObject* npatomtype = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, MolAtom_type); */
/*PyObject* npatomresname = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->resname);*/
/*PyObject* npatomsegid = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->segid);*/
/*PyObject* npatomchain = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->chain);*/
/*PyObject* npatomaltloc = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->altloc);*/
/*PyObject* npatominsert = PyArray_SimpleNewFromData(1, natoms, NPY_STRING, atoms->insertion);*/
/*PyObject* npatomoccup = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->occupancy);*/
/*PyObject* npatombfact = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->bfactor);*/
/* PyObject* npatommass = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, MolAtom_mass); */
/*PyObject* npatomcharge = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->charge);*/
/*PyObject* npatomradius = PyArray_SimpleNewFromData(1, natoms, NPY_FLOAT64, &atoms->radius);*/
/* PyObject* npatomicnumber = PyArray_SimpleNewFromData(1, natoms, NPY_INT64, MolAtom_atomicnumber); */
/*if (npatomname==NULL || npatomtype==NULL || npatomresname==NULL ||
npatomresid==NULL || npatomsegid==NULL || npatomchain==NULL )
{
free(atoms);
Py_XDECREF(npatomname); Py_XDECREF(npatomtype);
Py_XDECREF(npatomresname); Py_XDECREF(npatomresid); Py_XDECREF(npatomsegid);
Py_XDECREF(npatomchain); Py_XDECREF(npatomaltloc); Py_XDECREF(npatominsert);
Py_XDECREF(npatomoccup); Py_XDECREF(npatombfact); Py_XDECREF(npatommass);
Py_XDECREF(npatomcharge); Py_XDECREF(npatomradius); Py_XDECREF(npatomicnumber);
PyErr_Format(PyExc_IOError, "Error copying molfile_atom_t into Python.");
return 0;
}
PyArray_BASE(npatomname) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomtype) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomresname) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomresid) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomsegid) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomchain) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatomaltloc) = PyCObject_FromVoidPtr(*atoms, free);
PyArray_BASE(npatominsert) = PyCObject_FromVoidPtr(*atoms, free);