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xbgfplugin.C File Reference

#include "molfile_plugin.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>

Go to the source code of this file.

Compounds

struct xbgfdata

Defines

#define LINESIZE 256

#define MAXBONDS 16

Functions

void * open_xbgf_read (const char *path, const char *filetype, int *natoms)

void adjust_xbgf_field_string (char *field)

void get_xbgf_coordinates (const char *record, float *x, float *y, float *z)

void get_xbgf_fields (const char *record, char *name, char *resname, char *chain, char *segname, float *occupancy, float *bfactor, int *elementindex, int *resid, char *type, float *charge, float *x, float *y, float *z, char *insert)

int read_xbgf_structure (void *v, int *optflags, molfile_atom_t *atoms)

int read_xbgf_timestep (void *v, int natoms, molfile_timestep_t *ts)

void * open_xbgf_write (const char *filename, const char *filetype, int natoms)

int write_xbgf_structure (void *mydata, int optflags, const molfile_atom_t *atoms)

int read_xbgf_bonds_aux (void *v, int *nbonds, int **fromptr, int **toptr, float **bondorderptr)

int read_xbgf_bonds (void *v, int *nbonds, int **fromptr, int **toptr, float **bondorderptr, int **bondtype, int *nbondtypes, char ***bondtypename)

int write_xbgf_timestep (void *mydata, const molfile_timestep_t *ts)

int write_xbgf_bonds (void *v, int nbonds, int *fromptr, int *toptr, float *bondorderptr, int *bondtype, int nbondtypes, char **bondtypename)

void close_xbgf_write (void *mydata)

void close_xbgf_read (void *v)

int read_xbgf_molecule_metadata (void *v, molfile_metadata_t **metadata)

VMDPLUGIN_API int VMDPLUGIN_init ()

VMDPLUGIN_API int VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)

VMDPLUGIN_API int VMDPLUGIN_fini ()

Variables

molfile_plugin_t plugin

Define Documentation

#define LINESIZE 256

Definition at line 28 of file xbgfplugin.C.
Referenced by open_xbgf_read, read_xbgf_bonds_aux, read_xbgf_structure, and read_xbgf_timestep.

#define MAXBONDS 16

Definition at line 29 of file xbgfplugin.C.
Referenced by read_xbgf_bonds_aux, and write_xbgf_timestep.

Function Documentation

void adjust_xbgf_field_string ( char * field ) [static]

Definition at line 117 of file xbgfplugin.C.
Referenced by get_xbgf_fields.

void close_xbgf_read ( void * v ) [static]

Definition at line 646 of file xbgfplugin.C.
References xbgfdata::bondorder, xbgfdata::file, xbgfdata::from, xbgfdata::meta, molfile_metadata_t::remarks, and xbgfdata::to.
Referenced by VMDPLUGIN_init.

void close_xbgf_write ( void * mydata ) [static]

Definition at line 627 of file xbgfplugin.C.
References xbgfdata::atomlist, xbgfdata::bondorder, xbgfdata::file, xbgfdata::from, and xbgfdata::to.
Referenced by VMDPLUGIN_init.

void get_xbgf_coordinates ( const char * record,

float * x,

float * y,

float * z

) [static]

Definition at line 133 of file xbgfplugin.C.
Referenced by get_xbgf_fields, and read_xbgf_timestep.

void get_xbgf_fields ( const char * record,

char * name,

char * resname,

char * chain,

char * segname,

float * occupancy,

float * bfactor,

int * elementindex,

int * resid,

char * type,

float * charge,

float * x,

float * y,

float * z,

char * insert

) [static]

Definition at line 154 of file xbgfplugin.C.
References adjust_xbgf_field_string, get_xbgf_coordinates, and name.
Referenced by read_xbgf_structure.

void* open_xbgf_read ( const char * path,

const char * filetype,

int * natoms

) [static]

Definition at line 43 of file xbgfplugin.C.
References xbgfdata::bondorder, xbgfdata::coords_read, xbgfdata::file, xbgfdata::from, LINESIZE, xbgfdata::meta, MOLFILE_ATOMICNUMBER, MOLFILE_BFACTOR, MOLFILE_CHARGE, MOLFILE_INSERTION, MOLFILE_OCCUPANCY, xbgfdata::natoms, xbgfdata::nbonds, xbgfdata::optflags, molfile_metadata_t::remarklen, molfile_metadata_t::remarks, and xbgfdata::to.
Referenced by VMDPLUGIN_init.

void* open_xbgf_write ( const char * filename,

const char * filetype,

int natoms

) [static]

Definition at line 315 of file xbgfplugin.C.
References xbgfdata::file, xbgfdata::natoms, and xbgfdata::nbonds.
Referenced by VMDPLUGIN_init.

int read_xbgf_bonds ( void * v,

int * nbonds,

int ** fromptr,

int ** toptr,

float ** bondorderptr,

int ** bondtype,

int * nbondtypes,

char *** bondtypename

) [static]

Definition at line 468 of file xbgfplugin.C.
References xbgfdata::bondorder, xbgfdata::file, xbgfdata::from, MOLFILE_ERROR, xbgfdata::nbonds, read_xbgf_bonds_aux, and xbgfdata::to.
Referenced by VMDPLUGIN_init.

int read_xbgf_bonds_aux ( void * v,

int * nbonds,

int ** fromptr,

int ** toptr,

float ** bondorderptr

) [static]

Definition at line 345 of file xbgfplugin.C.
References xbgfdata::bondorder, xbgfdata::file, xbgfdata::from, LINESIZE, MAXBONDS, MOLFILE_ERROR, xbgfdata::nbonds, and xbgfdata::to.
Referenced by read_xbgf_bonds.

int read_xbgf_molecule_metadata ( void * v,

molfile_metadata_t ** metadata

) [static]

Definition at line 664 of file xbgfplugin.C.
References xbgfdata::meta.
Referenced by VMDPLUGIN_init.

int read_xbgf_structure ( void * v,

int * optflags,

molfile_atom_t * atoms

) [static]

Definition at line 224 of file xbgfplugin.C.
References molfile_atom_t::atomicnumber, molfile_atom_t::bfactor, molfile_atom_t::chain, molfile_atom_t::charge, xbgfdata::file, get_xbgf_fields, molfile_atom_t::insertion, LINESIZE, MOLFILE_ERROR, molfile_atom_t::name, xbgfdata::natoms, molfile_atom_t::occupancy, xbgfdata::optflags, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type.
Referenced by VMDPLUGIN_init.

int read_xbgf_timestep ( void * v,

int natoms,

molfile_timestep_t * ts

) [static]

Definition at line 267 of file xbgfplugin.C.
References molfile_timestep_t::coords, xbgfdata::coords_read, xbgfdata::file, get_xbgf_coordinates, LINESIZE, MOLFILE_EOF, MOLFILE_ERROR, and xbgfdata::natoms.
Referenced by VMDPLUGIN_init.

VMDPLUGIN_API int VMDPLUGIN_fini ( void )

Definition at line 703 of file xbgfplugin.C.
References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init ( void )

Definition at line 673 of file xbgfplugin.C.
References molfile_plugin_t::close_file_read, molfile_plugin_t::close_file_write, close_xbgf_read, close_xbgf_write, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, molfile_plugin_t::open_file_read, molfile_plugin_t::open_file_write, open_xbgf_read, open_xbgf_write, molfile_plugin_t::read_bonds, molfile_plugin_t::read_molecule_metadata, molfile_plugin_t::read_next_timestep, molfile_plugin_t::read_structure, read_xbgf_bonds, read_xbgf_molecule_metadata, read_xbgf_structure, read_xbgf_timestep, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, VMDPLUGIN_THREADSAFE, molfile_plugin_t::write_bonds, molfile_plugin_t::write_structure, molfile_plugin_t::write_timestep, write_xbgf_bonds, write_xbgf_structure, and write_xbgf_timestep.

VMDPLUGIN_API int VMDPLUGIN_register ( void * v,

vmdplugin_register_cb cb

)

Definition at line 698 of file xbgfplugin.C.
References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

int write_xbgf_bonds ( void * v,

int nbonds,

int * fromptr,

int * toptr,

float * bondorderptr,

int * bondtype,

int nbondtypes,

char ** bondtypename

) [static]

Definition at line 600 of file xbgfplugin.C.
References xbgfdata::bondorder, xbgfdata::from, xbgfdata::nbonds, and xbgfdata::to.
Referenced by VMDPLUGIN_init.

int write_xbgf_structure ( void * mydata,

int optflags,

const molfile_atom_t * atoms

) [static]

Definition at line 335 of file xbgfplugin.C.
References xbgfdata::atomlist, and xbgfdata::natoms.
Referenced by VMDPLUGIN_init.

int write_xbgf_timestep ( void * mydata,

const molfile_timestep_t * ts

) [static]

Definition at line 504 of file xbgfplugin.C.
References molfile_atom_t::atomicnumber, xbgfdata::atomlist, molfile_atom_t::bfactor, xbgfdata::bondorder, molfile_atom_t::chain, molfile_atom_t::charge, molfile_timestep_t::coords, xbgfdata::file, xbgfdata::from, MAXBONDS, molfile_atom_t::name, xbgfdata::natoms, xbgfdata::nbonds, molfile_atom_t::occupancy, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, xbgfdata::to, and molfile_atom_t::type.
Referenced by VMDPLUGIN_init.

Variable Documentation

molfile_plugin_t plugin [static]

Definition at line 671 of file xbgfplugin.C.

Generated on Tue Oct 8 03:10:04 2024 for VMD Plugins (current) by

Compounds
struct	xbgfdata
Defines
#define	LINESIZE 256
#define	MAXBONDS 16
Functions
void *	open_xbgf_read (const char path, const char filetype, int *natoms)
void	adjust_xbgf_field_string (char *field)
void	get_xbgf_coordinates (const char record, float x, float y, float z)
void	get_xbgf_fields (const char record, char name, char resname, char chain, char segname, float occupancy, float bfactor, int elementindex, int resid, char type, float charge, float x, float y, float z, char *insert)
int	read_xbgf_structure (void v, int optflags, molfile_atom_t *atoms)
int	read_xbgf_timestep (void v, int natoms, molfile_timestep_t ts)
void *	open_xbgf_write (const char filename, const char filetype, int natoms)
int	write_xbgf_structure (void mydata, int optflags, const molfile_atom_t atoms)
int	read_xbgf_bonds_aux (void v, int nbonds, int fromptr, int toptr, float **bondorderptr)
int	read_xbgf_bonds (void v, int nbonds, int fromptr, int toptr, float bondorderptr, int bondtype, int nbondtypes, char **bondtypename)
int	write_xbgf_timestep (void mydata, const molfile_timestep_t ts)
int	write_xbgf_bonds (void v, int nbonds, int fromptr, int toptr, float bondorderptr, int bondtype, int nbondtypes, char *bondtypename)
void	close_xbgf_write (void *mydata)
void	close_xbgf_read (void *v)
int	read_xbgf_molecule_metadata (void v, molfile_metadata_t *metadata)
VMDPLUGIN_API int	VMDPLUGIN_init ()
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int	VMDPLUGIN_fini ()
Variables
molfile_plugin_t	plugin