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psfplugin.c File Reference

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

Go to the source code of this file.

Compounds

struct psfdata

Defines

#define PSF_RECORD_LENGTH 256

Functions

int strnwscpy_shift (char *target, const char *source, const int len, const int maxlen)

int atoifw (char **ptr, int fw)

int get_psf_atom (FILE *f, char *name, char *atype, char *resname, char *segname, int *resid, char *insertion, float *q, float *m, int namdfmt, int charmmext, int charmmdrude)

int psf_start_block (FILE *file, const char *blockname)

int psf_get_bonds (FILE *f, int nbond, int fromAtom[], int toAtom[], int charmmext, int namdfmt)

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

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

int read_bonds (void *v, int *nbonds, int **fromptr, int **toptr, float **bondorder, int **bondtype, int *nbondtypes, char ***bondtypename)

int psf_get_angles (FILE *f, int n, int *angles, int charmmext)

int psf_get_dihedrals_impropers (FILE *f, int n, int *dihedrals, int charmmext)

int read_angles (void *v, int *numangles, int **angles, double **angleforces, int *numdihedrals, int **dihedrals, double **dihedralforces, int *numimpropers, int **impropers, double **improperforces, int *numcterms, int **cterms, int *ctermcols, int *ctermrows, double **ctermforces)

void close_psf_read (void *mydata)

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

int write_psf_structure (void *v, int optflags, const molfile_atom_t *atoms)

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

int write_angles (void *v, int numangles, const int *angles, const double *angleforces, int numdihedrals, const int *dihedrals, const double *dihedralforces, int numimpropers, const int *impropers, const double *improperforces, int numcterms, const int *cterms, int ctermcols, int ctermrows, const double *ctermforces)

void close_psf_write (void *v)

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 PSF_RECORD_LENGTH 256

Definition at line 27 of file psfplugin.c.
Referenced by get_psf_atom, open_psf_read, psf_get_angles, psf_get_bonds, psf_get_dihedrals_impropers, and psf_start_block.

Function Documentation

int atoifw ( char ** ptr,

int fw

) [static]

Definition at line 88 of file psfplugin.c.
Referenced by psf_get_angles, psf_get_bonds, and psf_get_dihedrals_impropers.

void close_psf_read ( void * mydata ) [static]

Definition at line 708 of file psfplugin.c.
References psfdata::angles, psfdata::cterms, psfdata::dihedrals, psfdata::fp, psfdata::from, psfdata::impropers, and psfdata::to.
Referenced by VMDPLUGIN_init.

void close_psf_write ( void * v ) [static]

Definition at line 1059 of file psfplugin.c.
References psfdata::angles, psfdata::cterms, psfdata::dihedrals, psfdata::fp, psfdata::from, psfdata::impropers, and psfdata::to.
Referenced by VMDPLUGIN_init.

int get_psf_atom ( FILE * f,

char * name,

char * atype,

char * resname,

char * segname,

int * resid,

char * insertion,

float * q,

float * m,

int namdfmt,

int charmmext,

int charmmdrude

) [static]

Definition at line 115 of file psfplugin.c.
References name, PSF_RECORD_LENGTH, strnwscpy, and strnwscpy_shift.
Referenced by read_psf.

void* open_psf_read ( const char * path,

const char * filetype,

int * natoms

) [static]

Definition at line 351 of file psfplugin.c.
References psfdata::charmmcheq, psfdata::charmmcmap, psfdata::charmmdrude, psfdata::charmmext, psfdata::charmmfmt, psfdata::fp, MOLFILE_NUMATOMS_NONE, psfdata::namdfmt, psfdata::numatoms, and PSF_RECORD_LENGTH.
Referenced by VMDPLUGIN_init.

void* open_psf_write ( const char * path,

const char * filetype,

int natoms

) [static]

Definition at line 737 of file psfplugin.c.
References psfdata::charmmcheq, psfdata::charmmcmap, psfdata::charmmdrude, psfdata::charmmext, psfdata::charmmfmt, psfdata::fp, psfdata::from, psfdata::namdfmt, psfdata::nbonds, psfdata::numatoms, and psfdata::to.
Referenced by VMDPLUGIN_init.

int psf_get_angles ( FILE * f,

int n,

int * angles,

int charmmext

) [static]

Definition at line 503 of file psfplugin.c.
References atoifw, and PSF_RECORD_LENGTH.
Referenced by read_angles.

int psf_get_bonds ( FILE * f,

int nbond,

int fromAtom[],

int toAtom[],

int charmmext,

int namdfmt

) [static]

Definition at line 282 of file psfplugin.c.
References atoifw, and PSF_RECORD_LENGTH.
Referenced by read_bonds.

int psf_get_dihedrals_impropers ( FILE * f,

int n,

int * dihedrals,

int charmmext

) [static]

Definition at line 530 of file psfplugin.c.
References atoifw, and PSF_RECORD_LENGTH.
Referenced by read_angles.

int psf_start_block ( FILE * file,

const char * blockname

) [static]

Definition at line 256 of file psfplugin.c.
References PSF_RECORD_LENGTH.
Referenced by read_angles, and read_bonds.

int read_angles ( void * v,

int * numangles,

int ** angles,

double ** angleforces,

int * numdihedrals,

int ** dihedrals,

double ** dihedralforces,

int * numimpropers,

int ** impropers,

double ** improperforces,

int * numcterms,

int ** cterms,

int * ctermcols,

int * ctermrows,

double ** ctermforces

) [static]

Definition at line 643 of file psfplugin.c.
References psfdata::angles, psfdata::cterms, psfdata::dihedrals, psfdata::fp, psfdata::impropers, psfdata::numangles, psfdata::numcterms, psfdata::numdihedrals, psfdata::numimpropers, psf_get_angles, psf_get_dihedrals_impropers, and psf_start_block.
Referenced by VMDPLUGIN_init.

int read_bonds ( void * v,

int * nbonds,

int ** fromptr,

int ** toptr,

float ** bondorder,

int ** bondtype,

int * nbondtypes,

char *** bondtypename

) [static]

Definition at line 466 of file psfplugin.c.
References psfdata::charmmext, psfdata::fp, psfdata::from, MOLFILE_ERROR, psfdata::namdfmt, psf_get_bonds, psf_start_block, and psfdata::to.
Referenced by VMDPLUGIN_init.

int read_psf ( void * v,

int * optflags,

molfile_atom_t * atoms

) [static]

Definition at line 440 of file psfplugin.c.
References molfile_atom_t::chain, molfile_atom_t::charge, psfdata::charmmdrude, psfdata::charmmext, psfdata::fp, get_psf_atom, molfile_atom_t::insertion, molfile_atom_t::mass, MOLFILE_CHARGE, MOLFILE_ERROR, MOLFILE_INSERTION, MOLFILE_MASS, psfdata::namdfmt, molfile_atom_t::name, psfdata::numatoms, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type.
Referenced by VMDPLUGIN_init.

int strnwscpy_shift ( char * target,

const char * source,

const int len,

const int maxlen

) [static]

Definition at line 61 of file psfplugin.c.
Referenced by get_psf_atom.

VMDPLUGIN_API int VMDPLUGIN_fini ( void )

Definition at line 1124 of file psfplugin.c.
References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init ( void )

Definition at line 1091 of file psfplugin.c.
References molfile_plugin_t::close_file_read, molfile_plugin_t::close_file_write, close_psf_read, close_psf_write, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, molfile_plugin_t::open_file_read, molfile_plugin_t::open_file_write, open_psf_read, open_psf_write, read_angles, molfile_plugin_t::read_angles, read_bonds, molfile_plugin_t::read_bonds, read_psf, molfile_plugin_t::read_structure, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, VMDPLUGIN_THREADSAFE, write_angles, molfile_plugin_t::write_angles, write_bonds, molfile_plugin_t::write_bonds, write_psf_structure, and molfile_plugin_t::write_structure.

VMDPLUGIN_API int VMDPLUGIN_register ( void * v,

vmdplugin_register_cb cb

)

Definition at line 1119 of file psfplugin.c.
References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

int write_angles ( void * v,

int numangles,

const int * angles,

const double * angleforces,

int numdihedrals,

const int * dihedrals,

const double * dihedralforces,

int numimpropers,

const int * impropers,

const double * improperforces,

int numcterms,

const int * cterms,

int ctermcols,

int ctermrows,

const double * ctermforces

) [static]

Definition at line 1029 of file psfplugin.c.
References psfdata::angles, psfdata::cterms, psfdata::dihedrals, psfdata::impropers, psfdata::numangles, psfdata::numcterms, psfdata::numdihedrals, and psfdata::numimpropers.
Referenced by VMDPLUGIN_init.

int write_bonds ( void * v,

int nbonds,

int * fromptr,

int * toptr,

float * bondorderptr,

int * bondtype,

int nbondtypes,

char ** bondtypename

) [static]

Definition at line 981 of file psfplugin.c.
References psfdata::from, psfdata::nbonds, and psfdata::to.
Referenced by VMDPLUGIN_init.

int write_psf_structure ( void * v,

int optflags,

const molfile_atom_t * atoms

) [static]

Definition at line 763 of file psfplugin.c.
References psfdata::angles, molfile_atom_t::charge, psfdata::charmmcmap, psfdata::charmmext, psfdata::charmmfmt, psfdata::cterms, psfdata::dihedrals, psfdata::fp, psfdata::from, psfdata::impropers, molfile_atom_t::mass, psfdata::namdfmt, molfile_atom_t::name, name, psfdata::nbonds, psfdata::numangles, psfdata::numatoms, psfdata::numcterms, psfdata::numdihedrals, psfdata::numimpropers, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, psfdata::to, and molfile_atom_t::type.
Referenced by VMDPLUGIN_init.

Variable Documentation

molfile_plugin_t plugin [static]

Definition at line 1089 of file psfplugin.c.

Generated on Mon Feb 17 03:09:32 2025 for VMD Plugins (current) by

Compounds
struct	psfdata
Defines
#define	PSF_RECORD_LENGTH 256
Functions
int	strnwscpy_shift (char target, const char source, const int len, const int maxlen)
int	atoifw (char **ptr, int fw)
int	get_psf_atom (FILE f, char name, char atype, char resname, char segname, int resid, char insertion, float q, float *m, int namdfmt, int charmmext, int charmmdrude)
int	psf_start_block (FILE file, const char blockname)
int	psf_get_bonds (FILE *f, int nbond, int fromAtom[], int toAtom[], int charmmext, int namdfmt)
void *	open_psf_read (const char path, const char filetype, int *natoms)
int	read_psf (void v, int optflags, molfile_atom_t *atoms)
int	read_bonds (void v, int nbonds, int fromptr, int toptr, float bondorder, int bondtype, int nbondtypes, char **bondtypename)
int	psf_get_angles (FILE f, int n, int angles, int charmmext)
int	psf_get_dihedrals_impropers (FILE f, int n, int dihedrals, int charmmext)
int	read_angles (void v, int numangles, int angles, double angleforces, int numdihedrals, int dihedrals, double dihedralforces, int numimpropers, int impropers, double improperforces, int numcterms, int cterms, int ctermcols, int ctermrows, double *ctermforces)
void	close_psf_read (void *mydata)
void *	open_psf_write (const char path, const char filetype, int natoms)
int	write_psf_structure (void v, int optflags, const molfile_atom_t atoms)
int	write_bonds (void v, int nbonds, int fromptr, int toptr, float bondorderptr, int bondtype, int nbondtypes, char *bondtypename)
int	write_angles (void v, int numangles, const int angles, const double angleforces, int numdihedrals, const int dihedrals, const double dihedralforces, int numimpropers, const int impropers, const double improperforces, int numcterms, const int cterms, int ctermcols, int ctermrows, const double *ctermforces)
void	close_psf_write (void *v)
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