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tprplugin.C File Reference

#include "molfile_plugin.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "Gromacs.h"
#include "tprplugin.h"

Go to the source code of this file.

Defines

#define VMDPLUGIN_STATIC
#define STRLEN   4096
#define SAVELEN   8
#define TRUE   (1)
#define FALSE   (0)
#define MIN(a, b)   ((a)<(b)? (a):(b))

Functions

int readff (md_file *mf, int version)
int read_atomtypes (md_file *mf, int version)
int read_cmap (md_file *mf)
int read_groups (md_file *mf, int ngrp, tprdata *tpr)
void tpr_save_string (md_file *mf, char *saveloc, int genversion)
int readtprAfterPrecision (tprdata *tpr)
int read_tpr_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
void * open_tpr_read (const char *filename, const char *, int *natoms)
int read_tpr_timestep (void *v, int natoms, molfile_timestep_t *ts)
int read_tpr_bonds (void *v, int *nbonds, int **fromptr, int **toptr, float **bondorder, int **bondtype, int *nbondtypes, char ***bondtypename)
int read_tpr_angles (void *v, int *numangles, int **angles, int **angletypes, int *numangletypes, char ***angletypenames, int *numdihedrals, int **dihedrals, int **dihedraltypes, int *numdihedraltypes, char ***dihedraltypenames, int *numimpropers, int **impropers, int **impropertypes, int *numimpropertypes, char ***impropertypenames, int *numcterms, int **cterms, int *ctermcols, int *ctermrows)
int read_tpr_timestep_metadata (void *v, molfile_timestep_metadata_t *metadata)
void close_tpr_read (void *mydata)
VMDPLUGIN_API int VMDPLUGIN_init (void)
VMDPLUGIN_API int VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int VMDPLUGIN_fini (void)

Variables

molfile_plugin_t tpr_plugin

Define Documentation

#define FALSE   (0)
 

Definition at line 17 of file tprplugin.C.

Referenced by readtprAfterPrecision.

#define MIN (  a,
b    )     ((a)<(b)? (a):(b))
 

Definition at line 145 of file tprplugin.C.

#define SAVELEN   8
 

Definition at line 15 of file tprplugin.C.

Referenced by read_groups, read_tpr_structure, readtprAfterPrecision, and tpr_save_string.

#define STRLEN   4096
 

Definition at line 14 of file tprplugin.C.

Referenced by open_tpr_read, readtprAfterPrecision, and tpr_save_string.

#define TRUE   (1)
 

Definition at line 16 of file tprplugin.C.

Referenced by readtprAfterPrecision.

#define VMDPLUGIN_STATIC
 

Definition at line 1 of file tprplugin.C.

Function Documentation

void close_tpr_read (  void *    mydata )  [static]
 

Definition at line 1017 of file tprplugin.C.

References tprdata::atomicnumbers, tprdata::atomnameids, tprdata::atomsinmol, tprdata::atomtypeids, tprdata::charges, md_file::f, F_NRE, tprdata::interactionlist, tprdata::masses, tprdata::mf, tprdata::molbnatoms, tprdata::molbnmol, tprdata::molbtype, tprdata::molnames, tprdata::nmoltypes, tprdata::nr, tprdata::ptypes, tprdata::resids, tprdata::resinmol, tprdata::resnames, tprdata::symtab, and tprdata::types.

Referenced by VMDPLUGIN_init.

void* open_tpr_read (  const char *    filename,
const char *   ,
int *    natoms
)  [static]
 

Definition at line 624 of file tprplugin.C.

References md_file::f, tprdata::mf, tprdata::natoms, md_file::prec, readtprAfterPrecision, md_file::rev, STRLEN, tpr_string, and trx_int.

Referenced by VMDPLUGIN_init.

int read_atomtypes (  md_file *    mf,
int    version
) 
 

Definition at line 51 of file tprplugin.C.

References trx_int, and trx_real.

Referenced by readtprAfterPrecision.

int read_cmap (  md_file *    mf ) 
 

Definition at line 77 of file tprplugin.C.

References trx_int, and trx_real.

Referenced by readtprAfterPrecision.

int read_groups (  md_file *    mf,
int    ngrp,
tprdata *    tpr
) 
 

Definition at line 95 of file tprplugin.C.

References md_file::f, SAVELEN, tprdata::symtab, trx_int, and tprdata::wversion.

Referenced by readtprAfterPrecision.

int read_tpr_angles (  void *    v,
int *    numangles,
int **    angles,
int **    angletypes,
int *    numangletypes,
char ***    angletypenames,
int *    numdihedrals,
int **    dihedrals,
int **    dihedraltypes,
int *    numdihedraltypes,
char ***    dihedraltypenames,
int *    numimpropers,
int **    impropers,
int **    impropertypes,
int *    numimpropertypes,
char ***    impropertypenames,
int *    numcterms,
int **    cterms,
int *    ctermcols,
int *    ctermrows
)  [static]
 

Definition at line 813 of file tprplugin.C.

References tprdata::atomsinmol, F_ANGLES, F_CMAP, F_G96ANGLES, F_IDIHS, F_LINEAR_ANGLES, F_PDIHS, F_RESTRANGLES, F_SETTLE, F_UREY_BRADLEY, tprdata::interactionlist, tprdata::molbnmol, tprdata::molbtype, tprdata::nmolblock, and tprdata::nr.

Referenced by VMDPLUGIN_init.

int read_tpr_bonds (  void *    v,
int *    nbonds,
int **    fromptr,
int **    toptr,
float **    bondorder,
int **    bondtype,
int *    nbondtypes,
char ***    bondtypename
)  [static]
 

Definition at line 736 of file tprplugin.C.

References tprdata::atomsinmol, F_BONDS, F_CONSTR, F_G96BONDS, F_SETTLE, tprdata::interactionlist, tprdata::molbnmol, tprdata::molbtype, tprdata::nmolblock, and tprdata::nr.

Referenced by VMDPLUGIN_init.

int read_tpr_structure (  void *    mydata,
int *    optflags,
molfile_atom_t *    atoms
)  [static]
 

Definition at line 591 of file tprplugin.C.

References tprdata::atomnameids, tprdata::atomtypeids, molfile_atom_t::charge, tprdata::charges, molfile_atom_t::mass, tprdata::masses, tprdata::molbnatoms, tprdata::molbnmol, tprdata::molbtype, MOLFILE_CHARGE, MOLFILE_MASS, tprdata::molnames, name, tprdata::nmolblock, molfile_atom_t::resid, tprdata::resids, tprdata::resnames, SAVELEN, and tprdata::symtab.

Referenced by VMDPLUGIN_init.

int read_tpr_timestep (  void *    v,
int    natoms,
molfile_timestep_t *    ts
)  [static]
 

Definition at line 668 of file tprplugin.C.

References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, molfile_timestep_t::beta, tprdata::boxdims, molfile_timestep_t::C, molfile_timestep_t::coords, md_file::f, molfile_timestep_t::gamma, tprdata::has_velocities, tprdata::mf, MOLFILE_ERROR, tprdata::natoms, tprdata::readcoordinates, tpr_rvector, and molfile_timestep_t::velocities.

Referenced by VMDPLUGIN_init.

int read_tpr_timestep_metadata (  void *    v,
molfile_timestep_metadata_t *    metadata
)  [static]
 

Definition at line 1003 of file tprplugin.C.

References molfile_timestep_metadata::has_velocities, and tprdata::has_velocities.

Referenced by VMDPLUGIN_init.

int readff (  md_file *    mf,
int    version
) 
 

Definition at line 21 of file tprplugin.C.

References MOLFILE_ERROR, NFTUPD, readparams, trx_double, trx_int, and trx_real.

Referenced by readtprAfterPrecision.

int readtprAfterPrecision (  tprdata *    tpr ) 
 

Definition at line 172 of file tprplugin.C.

References tprdata::atomicnumbers, tprdata::atomnameids, tprdata::atomsinmol, tprdata::atomtypeids, tprdata::boxdims, tprdata::charges, egcNR, md_file::f, F_NRE, FALSE, tprdata::has_velocities, tprdata::interactionlist, tprdata::masses, tprdata::mf, tprdata::molbnatoms, tprdata::molbnmol, tprdata::molbtype, MOLFILE_ERROR, tprdata::molnames, tprdata::natoms, NFTUPD, tprdata::ngtc, tprdata::nmolblock, tprdata::nmoltypes, tprdata::nr, tprdata::ptypes, read_atomtypes, read_cmap, read_groups, tprdata::readcoordinates, readff, tprdata::resids, tprdata::resinmol, tprdata::resnames, SAVELEN, STRLEN, tprdata::symtab, tprdata::symtablen, tpr_ivector, tpr_save_string, tpr_string, TRUE, trx_int, trx_long, trx_real, trx_rvector, trx_string, tprdata::types, tprdata::version, and tprdata::wversion.

Referenced by open_tpr_read.

void tpr_save_string (  md_file *    mf,
char *    saveloc,
int    genversion
) 
 

Definition at line 147 of file tprplugin.C.

References md_file::f, MIN, SAVELEN, STRLEN, and trx_long.

Referenced by readtprAfterPrecision.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    ) 
 

Definition at line 1102 of file tprplugin.C.

References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init (  void    ) 
 

Definition at line 1076 of file tprplugin.C.

References molfile_plugin_t::close_file_read, close_tpr_read, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, molfile_plugin_t::open_file_read, open_tpr_read, molfile_plugin_t::read_angles, molfile_plugin_t::read_bonds, molfile_plugin_t::read_next_timestep, molfile_plugin_t::read_structure, molfile_plugin_t::read_timestep_metadata, read_tpr_angles, read_tpr_bonds, read_tpr_structure, read_tpr_timestep, read_tpr_timestep_metadata, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, and VMDPLUGIN_THREADUNSAFE.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v,
vmdplugin_register_cb    cb
) 
 

Definition at line 1097 of file tprplugin.C.

References VMDPLUGIN_API, and vmdplugin_register_cb.

Variable Documentation

molfile_plugin_t tpr_plugin [static]
 

Definition at line 1074 of file tprplugin.C.

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