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gromacsplugin.C File Reference

#include "largefiles.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "Gromacs.h"
#include "molfile_plugin.h"

Go to the source code of this file.

Compounds

struct  gmxdata

Defines

#define M_PI   3.14159265358979323846
#define GROMACS_PLUGIN_MAJOR_VERSION   0
#define GROMACS_PLUGIN_MINOR_VERSION   8

Functions

void * open_gro_read (const char *filename, const char *, int *natoms)
int read_gro_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int read_gro_timestep (void *v, int natoms, molfile_timestep_t *ts)
void close_gro_read (void *v)
void * open_g96_read (const char *filename, const char *, int *natoms)
int read_g96_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int read_g96_timestep (void *v, int natoms, molfile_timestep_t *ts)
void close_g96_read (void *v)
void * open_trr_read (const char *filename, const char *filetype, int *natoms)
int read_trr_timestep (void *v, int natoms, molfile_timestep_t *ts)
void close_trr_read (void *v)
void * open_trr_write (const char *filename, const char *filetype, int natoms)
int write_trr_timestep (void *mydata, const molfile_timestep_t *ts)
void close_trr_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 gro_plugin
molfile_plugin_t g96_plugin
molfile_plugin_t trr_plugin
molfile_plugin_t xtc_plugin

Define Documentation

#define GROMACS_PLUGIN_MAJOR_VERSION   0
 

Definition at line 491 of file gromacsplugin.C.

#define GROMACS_PLUGIN_MINOR_VERSION   8
 

Definition at line 492 of file gromacsplugin.C.

#define M_PI   3.14159265358979323846
 

Definition at line 33 of file gromacsplugin.C.

Referenced by write_trr_timestep.

Function Documentation

void close_g96_read (  void *    v )  [static]
 

Definition at line 296 of file gromacsplugin.C.

References mdio_close, and gmxdata::mf.

void close_gro_read (  void *    v )  [static]
 

Definition at line 132 of file gromacsplugin.C.

References mdio_close, and gmxdata::mf.

void close_trr_read (  void *    v )  [static]
 

Definition at line 377 of file gromacsplugin.C.

References mdio_close, and gmxdata::mf.

void close_trr_write (  void *    v )  [static]
 

Definition at line 485 of file gromacsplugin.C.

References mdio_close, and gmxdata::mf.

void* open_g96_read (  const char *    filename,
const char *   ,
int *    natoms
)  [static]
 

Definition at line 138 of file gromacsplugin.C.

References g96_countatoms, g96_header, MAX_G96_LINE, MAX_MDIO_TITLE, MDFMT_G96, mdio_errmsg, mdio_errno, mdio_open, mdio_readline, gmxdata::mf, gmxdata::natoms, md_header::timeval, and md_header::title.

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

Definition at line 46 of file gromacsplugin.C.

References gro_header, MAX_MDIO_TITLE, MDFMT_GRO, mdio_errmsg, mdio_errno, mdio_open, gmxdata::mf, gmxdata::natoms, md_header::natoms, md_header::timeval, and md_header::title.

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

Definition at line 307 of file gromacsplugin.C.

References MDFMT_TRR, MDFMT_XTC, mdio_close, mdio_errmsg, mdio_errno, mdio_header, mdio_open, gmxdata::mf, gmxdata::natoms, and md_header::natoms.

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

Definition at line 384 of file gromacsplugin.C.

References host_is_little_endian, MDFMT_TRR, MDFMT_XTC, mdio_errmsg, mdio_errno, mdio_open, MDIO_WRITE, gmxdata::mf, gmxdata::natoms, md_file::prec, md_file::rev, and gmxdata::step.

int read_g96_structure (  void *    mydata,
int *    optflags,
molfile_atom_t *    atoms
)  [static]
 

Definition at line 187 of file gromacsplugin.C.

References md_atom::atomname, molfile_atom_t::chain, md_file::f, g96_rec, MAX_G96_LINE, mdio_errmsg, mdio_errno, mdio_readline, gmxdata::mf, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_SUCCESS, molfile_atom_t::name, gmxdata::natoms, md_atom::resid, molfile_atom_t::resid, md_atom::resname, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type.

int read_g96_timestep (  void *    v,
int    natoms,
molfile_timestep_t *    ts
)  [static]
 

Definition at line 272 of file gromacsplugin.C.

References md_box::A, molfile_timestep_t::A, md_box::alpha, molfile_timestep_t::alpha, md_box::B, molfile_timestep_t::B, md_box::beta, molfile_timestep_t::beta, md_ts::box, md_box::C, molfile_timestep_t::C, molfile_timestep_t::coords, md_box::gamma, molfile_timestep_t::gamma, mdio_timestep, mdio_tsfree, gmxdata::mf, MOLFILE_ERROR, MOLFILE_SUCCESS, gmxdata::natoms, md_ts::natoms, and md_ts::pos.

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

Definition at line 75 of file gromacsplugin.C.

References md_atom::atomname, molfile_atom_t::chain, md_file::f, gro_rec, MAX_GRO_LINE, mdio_errmsg, mdio_errno, mdio_readline, gmxdata::mf, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_SUCCESS, molfile_atom_t::name, gmxdata::natoms, md_atom::resid, molfile_atom_t::resid, md_atom::resname, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type.

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

Definition at line 109 of file gromacsplugin.C.

References md_box::A, molfile_timestep_t::A, md_box::alpha, molfile_timestep_t::alpha, md_box::B, molfile_timestep_t::B, md_box::beta, molfile_timestep_t::beta, md_ts::box, md_box::C, molfile_timestep_t::C, molfile_timestep_t::coords, md_box::gamma, molfile_timestep_t::gamma, mdio_timestep, mdio_tsfree, gmxdata::mf, MOLFILE_ERROR, MOLFILE_SUCCESS, gmxdata::natoms, md_ts::natoms, and md_ts::pos.

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

Definition at line 341 of file gromacsplugin.C.

References md_box::A, molfile_timestep_t::A, md_box::alpha, molfile_timestep_t::alpha, md_box::B, molfile_timestep_t::B, md_box::beta, molfile_timestep_t::beta, md_ts::box, md_box::C, molfile_timestep_t::C, molfile_timestep_t::coords, md_box::gamma, molfile_timestep_t::gamma, MDIO_EOF, mdio_errmsg, mdio_errno, MDIO_IOERROR, mdio_timestep, mdio_tsfree, gmxdata::mf, MOLFILE_ERROR, MOLFILE_SUCCESS, gmxdata::natoms, md_ts::natoms, and md_ts::pos.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    ) 
 

Definition at line 605 of file gromacsplugin.C.

References VMDPLUGIN_API.

VMDPLUGIN_API int VMDPLUGIN_init (  void    ) 
 

Definition at line 593 of file gromacsplugin.C.

References VMDPLUGIN_API.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v,
vmdplugin_register_cb    cb
) 
 

Definition at line 597 of file gromacsplugin.C.

References VMDPLUGIN_API, and vmdplugin_register_cb.

int write_trr_timestep (  void *    mydata,
const molfile_timestep_t *    ts
)  [static]
 

Definition at line 416 of file gromacsplugin.C.

References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, molfile_timestep_t::beta, molfile_timestep_t::C, molfile_timestep_t::coords, md_file::fmt, molfile_timestep_t::gamma, M_PI, MDFMT_TRR, gmxdata::mf, MOLFILE_ERROR, MOLFILE_SUCCESS, gmxdata::natoms, put_trx_int, put_trx_real, put_trx_string, gmxdata::step, and TRX_MAGIC.

Variable Documentation

molfile_plugin_t g96_plugin [static]
 

Initial value:

 {
  vmdplugin_ABIVERSION,               
  MOLFILE_PLUGIN_TYPE,                
  "g96",                              
  "Gromacs g96",                      
  "David Norris, Justin Gullingsrud", 
  GROMACS_PLUGIN_MAJOR_VERSION,       
  GROMACS_PLUGIN_MINOR_VERSION,       
  VMDPLUGIN_THREADUNSAFE,             
  "g96",                              
  open_g96_read,
  read_g96_structure,
  0,
  read_g96_timestep,
  close_g96_read,
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0                                   
}

Definition at line 521 of file gromacsplugin.C.

molfile_plugin_t gro_plugin [static]
 

Initial value:

 {
  vmdplugin_ABIVERSION,               
  MOLFILE_PLUGIN_TYPE,                
  "gro",                              
  "Gromacs GRO",                      
  "David Norris, Justin Gullingsrud", 
  GROMACS_PLUGIN_MAJOR_VERSION,       
  GROMACS_PLUGIN_MINOR_VERSION,       
  VMDPLUGIN_THREADUNSAFE,             
  "gro",                              
  open_gro_read,
  read_gro_structure,
  0,
  read_gro_timestep,
  close_gro_read,
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0                                   
}

Definition at line 497 of file gromacsplugin.C.

molfile_plugin_t trr_plugin [static]
 

Initial value:

 {
  vmdplugin_ABIVERSION,               
  MOLFILE_PLUGIN_TYPE,                
  "trr",                              
  "Gromacs TRR Trajectory",           
  "David Norris, Justin Gullingsrud, Axel Kohlmeyer", 
  GROMACS_PLUGIN_MAJOR_VERSION,       
  GROMACS_PLUGIN_MINOR_VERSION,       
  VMDPLUGIN_THREADUNSAFE,             
  "trr",                              
  open_trr_read,
  0,
  0,
  read_trr_timestep,
  close_trr_read,
  open_trr_write,
  0,                            
  write_trr_timestep,
  close_trr_write,
  0,                            
  0,                            
  0                             
}

Definition at line 545 of file gromacsplugin.C.

molfile_plugin_t xtc_plugin [static]
 

Initial value:

 {
  vmdplugin_ABIVERSION,                
  MOLFILE_PLUGIN_TYPE,                 
  "xtc",                               
  "Gromacs XTC Compressed Trajectory", 
  "David Norris, Justin Gullingsrud",  
  GROMACS_PLUGIN_MAJOR_VERSION,        
  GROMACS_PLUGIN_MINOR_VERSION,        
  VMDPLUGIN_THREADUNSAFE,              
  "xtc",                               
  open_trr_read,
  0,
  0,
  read_trr_timestep,
  close_trr_read,
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0,                                  
  0                                   
}

Definition at line 569 of file gromacsplugin.C.

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