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webpdbplugin.c File Reference

#include <tcl.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "molfile_plugin.h"
#include "readpdb.h"
#include "periodic_table.h"

Go to the source code of this file.

Compounds

struct  pdbdata

Functions

int my_read_pdb_record (const char *pdb, char **pos)
void * pdb_read (char *pdbstr, int *natoms)
void * open_file_read (const char *filename, const char *filetype, int *natoms)
int read_pdb_structure (void *mydata, 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 read_next_timestep (void *v, int natoms, molfile_timestep_t *ts)
void close_pdb_read (void *v)
int read_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

const char * rcsbmsg []
int show_msg = 1
molfile_plugin_t plugin


Function Documentation

void close_pdb_read void *    v [static]
 

Definition at line 394 of file webpdbplugin.c.

References pdbdata::idxmap, pdbdata::meta, pdbdata::pdbstr, and molfile_metadata_t::remarks.

Referenced by VMDPLUGIN_init.

int my_read_pdb_record const char *    pdb,
char **    pos
[static]
 

Definition at line 37 of file webpdbplugin.c.

References PDB_ATOM, PDB_CRYST1, PDB_END, PDB_EOF, PDB_HEADER, PDB_REMARK, and PDB_UNKNOWN.

Referenced by pdb_read, read_next_timestep, and read_pdb_structure.

void* open_file_read const char *    filename,
const char *    filetype,
int *    natoms
[static]
 

Definition at line 162 of file webpdbplugin.c.

References pdb_read, rcsbmsg, and show_msg.

Referenced by VMDPLUGIN_init.

void* pdb_read char *    pdbstr,
int *    natoms
[static]
 

Definition at line 87 of file webpdbplugin.c.

References molfile_metadata_t::accession, molfile_metadata_t::database, molfile_metadata_t::date, pdbdata::from, get_pdb_header, pdbdata::idxmap, pdbdata::maxbnum, pdbdata::meta, my_read_pdb_record, pdbdata::natoms, pdbdata::nbonds, pdbdata::nconect, PDB_ATOM, PDB_CONECT, PDB_END, PDB_EOF, PDB_HEADER, PDB_REMARK, PDB_UNKNOWN, pdbdata::pdbstr, pdbdata::pos, molfile_metadata_t::remarklen, molfile_metadata_t::remarks, and pdbdata::to.

Referenced by open_file_read.

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

Definition at line 313 of file webpdbplugin.c.

References pdbdata::from, pdbdata::natoms, pdbdata::nbonds, pdbdata::nconect, and pdbdata::to.

Referenced by VMDPLUGIN_init.

int read_molecule_metadata void *    v,
molfile_metadata_t **    metadata
[static]
 

Definition at line 408 of file webpdbplugin.c.

References pdbdata::meta.

Referenced by VMDPLUGIN_init.

int read_next_timestep void *    v,
int    natoms,
molfile_timestep_t   ts
[static]
 

Definition at line 351 of file webpdbplugin.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, molfile_timestep_t::gamma, get_pdb_coordinates, get_pdb_cryst1, MOLFILE_ERROR, my_read_pdb_record, pdbdata::natoms, PDB_ATOM, PDB_CRYST1, PDB_END, PDB_EOF, and pdbdata::pos.

Referenced by VMDPLUGIN_init.

int read_pdb_structure void *    mydata,
int *    optflags,
molfile_atom_t   atoms
[static]
 

Definition at line 233 of file webpdbplugin.c.

References molfile_atom_t::altloc, molfile_atom_t::atomicnumber, molfile_atom_t::bfactor, molfile_atom_t::chain, pdbdata::from, get_pdb_conect, get_pdb_fields, get_pte_idx_from_string, get_pte_mass, get_pte_vdw_radius, pdbdata::idxmap, molfile_atom_t::insertion, molfile_atom_t::mass, pdbdata::maxbnum, MOLFILE_ALTLOC, MOLFILE_ATOMICNUMBER, MOLFILE_BFACTOR, MOLFILE_BONDSSPECIAL, MOLFILE_INSERTION, MOLFILE_MASS, MOLFILE_OCCUPANCY, MOLFILE_RADIUS, my_read_pdb_record, molfile_atom_t::name, pdbdata::natoms, pdbdata::nbonds, molfile_atom_t::occupancy, PDB_ATOM, PDB_BUFFER_LENGTH, PDB_CONECT, PDB_END, PDB_EOF, pdbdata::pdbstr, molfile_atom_t::radius, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, pdbdata::to, and molfile_atom_t::type.

Referenced by VMDPLUGIN_init.

VMDPLUGIN_API int VMDPLUGIN_fini void   
 

Definition at line 445 of file webpdbplugin.c.

References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init void   
 

Definition at line 420 of file webpdbplugin.c.

References molfile_plugin_t::close_file_read, close_pdb_read, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, open_file_read, molfile_plugin_t::open_file_read, read_bonds, molfile_plugin_t::read_bonds, read_molecule_metadata, molfile_plugin_t::read_molecule_metadata, read_next_timestep, molfile_plugin_t::read_next_timestep, read_pdb_structure, molfile_plugin_t::read_structure, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, and VMDPLUGIN_THREADSAFE.

VMDPLUGIN_API int VMDPLUGIN_register void *    v,
vmdplugin_register_cb    cb
 

Definition at line 440 of file webpdbplugin.c.

References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.


Variable Documentation

molfile_plugin_t plugin [static]
 

Definition at line 418 of file webpdbplugin.c.

const char* rcsbmsg[] [static]
 

Initial value:

 {
  "  The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,",
  "and US DoE, who are not liable for the data.  PDB files shall not be",
  "sold.  See ftp://ftp.rcsb.org/advisory.doc for full details."
}

Definition at line 154 of file webpdbplugin.c.

Referenced by open_file_read.

int show_msg = 1 [static]
 

Definition at line 160 of file webpdbplugin.c.

Referenced by open_file_read.


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