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pdbxplugin.C File Reference

#include "largefiles.h"
#include "molfile_plugin.h"
#include "periodic_table.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/time.h>
#include "inthash.h"

Go to the source code of this file.

Compounds

struct  list_node
struct  pdbx_data
struct  pdbxParser
struct  pdbxWriter

Defines

#define VMDPLUGIN_STATIC
#define CHAIN_SIZE   4
#define TYPE_SIZE   8
#define BUFFER_SIZE   4096
#define COLUMN_BUFFER_SIZE   1024
#define MAX_COLUMNS   32
#define WB_SIZE   1024
#define ATOM_TYPE   0
#define ATOM_RESNAME   1
#define ATOM_INSERTION   2
#define ATOM_CHAIN   3
#define MAX_OPTIONAL_AUTH_FIELDS   2
#define FLAG_CHAIN_LENGTH   0x01
#define FLAG_CHARGE   0x02
#define FLAG_INSERTION   0x04
#define FLAG_BFACTOR   0x08
#define FLAG_OCCUPANCY   0x10
#define FLAG_MODEL_NUM   0x20
#define BOND_JUNK   0
#define BOND_NAME_1   1
#define BOND_CHAIN_1   2
#define BOND_RESNAME_1   3
#define BOND_RESID_1   4
#define BOND_NAME_2   5
#define BOND_CHAIN_2   6
#define BOND_RESNAME_2   7
#define BOND_RESID_2   8

Typedefs

typedef pdbxParser pdbxParser
typedef pdbxWriter pdbxWriter

Enumerations

enum  TableColums {
  COLUMN_NUMBER = 0, COLUMN_NAME, COLUMN_TYPE, COLUMN_TYPE_AUTH,
  COLUMN_RESNAME, COLUMN_RESID, COLUMN_RESID_AUTH, COLUMN_INSERTION,
  COLUMN_X, COLUMN_Y, COLUMN_Z, COLUMN_OCCUPANCY,
  COLUMN_BFACTOR, COLUMN_CHARGE, COLUMN_CHAIN, COLUMN_CHAIN_AUTH,
  COLUMN_MODEL_NUM, COLUMN_JUNK
}

Functions

pdbxParsercreate_pdbxParser (const char *filepath)
int parseStructure (molfile_atom_t *atoms, int *optflags, pdbxParser *parser)
bool readRMSDBonds (molfile_atom_t *atoms, pdbxParser *parser)
bool readAngleBonds (molfile_atom_t *atoms, pdbxParser *parser)
bool readBonds (molfile_atom_t *atoms, pdbxParser *parser)
int parseNumberAtoms (pdbxParser *parser)
bool isAtomSite (char *str)
bool isValidateRMSDBond (char *str)
float stringToFloat (char *str)
void getNextWord (char *str, void *word, int &pos, int maxstrlen, int maxwordlen)
void skipNextWord (char *str, void *word, int &pos, int maxlen)
int getUniqueResID (char *chainstr, int resid)
void initCharToNum ()
void writeBuffer (pdbxWriter *writer)
void writeIntro (pdbxWriter *writer)
void write (const char *str, pdbxWriter *writer)
void writeAtomSite (pdbxWriter *writer)
void close (pdbxWriter *writer)
pdbxWritercreate_pdbxWriter (const char *filename, int numAtoms)
void addAtoms (const molfile_atom_t *atoms, int optflags, pdbxWriter *writer)
void addCoordinates (const float *coords, pdbxWriter *writer)
void writeFile (pdbxWriter *writer)
void delete_pdbxParser (pdbxParser *parser)
bool isPDB_DevFile (pdbxParser *parser)
bool isStructureDataHeader (const char *strbuf)
bool parse_pdbx_ihm_sphere_data (pdbxParser *parser)
bool parse_pdbx_ihm_restraints_data (pdbxParser *parser)
bool parse_pdbx_graphics_data (pdbxParser *parser)
void * open_pdbx_read (const char *filepath, const char *filetype, int *natoms)
int read_pdbx_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_pdbx_timestep (void *mydata, int natoms, molfile_timestep_t *ts)
int read_rawgraphics (void *v, int *nelem, const molfile_graphics_t **g_data)
void close_pdbx_read (void *v)
void * open_file_write (const char *path, const char *filetypye, int natoms)
int write_structure (void *v, int optflags, const molfile_atom_t *atoms)
int write_timestep (void *v, const molfile_timestep_t *ts)
void close_file_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

unsigned char charToNum [128]
const char atomSiteHeader []
molfile_plugin_t plugin


Define Documentation

#define ATOM_CHAIN   3
 

Definition at line 718 of file pdbxplugin.C.

#define ATOM_INSERTION   2
 

Definition at line 717 of file pdbxplugin.C.

#define ATOM_RESNAME   1
 

Definition at line 716 of file pdbxplugin.C.

#define ATOM_TYPE   0
 

Definition at line 715 of file pdbxplugin.C.

#define BOND_CHAIN_1   2
 

Definition at line 1116 of file pdbxplugin.C.

#define BOND_CHAIN_2   6
 

Definition at line 1120 of file pdbxplugin.C.

#define BOND_JUNK   0
 

Definition at line 1114 of file pdbxplugin.C.

#define BOND_NAME_1   1
 

Definition at line 1115 of file pdbxplugin.C.

#define BOND_NAME_2   5
 

Definition at line 1119 of file pdbxplugin.C.

#define BOND_RESID_1   4
 

Definition at line 1118 of file pdbxplugin.C.

#define BOND_RESID_2   8
 

Definition at line 1122 of file pdbxplugin.C.

#define BOND_RESNAME_1   3
 

Definition at line 1117 of file pdbxplugin.C.

#define BOND_RESNAME_2   7
 

Definition at line 1121 of file pdbxplugin.C.

#define BUFFER_SIZE   4096
 

Definition at line 51 of file pdbxplugin.C.

Referenced by create_pdbxParser, isPDB_DevFile, parse_pdbx_ihm_restraints_data, parse_pdbx_ihm_sphere_data, parseNumberAtoms, parseStructure, readAngleBonds, readRMSDBonds, and writeAtomSite.

#define CHAIN_SIZE   4
 

Definition at line 49 of file pdbxplugin.C.

Referenced by create_pdbxParser, parseStructure, readAngleBonds, and readRMSDBonds.

#define COLUMN_BUFFER_SIZE   1024
 

Definition at line 52 of file pdbxplugin.C.

Referenced by parse_pdbx_ihm_restraints_data, parse_pdbx_ihm_sphere_data, parseStructure, readAngleBonds, and readRMSDBonds.

#define FLAG_BFACTOR   0x08
 

Definition at line 724 of file pdbxplugin.C.

Referenced by parseStructure.

#define FLAG_CHAIN_LENGTH   0x01
 

Definition at line 721 of file pdbxplugin.C.

Referenced by parseStructure.

#define FLAG_CHARGE   0x02
 

Definition at line 722 of file pdbxplugin.C.

Referenced by parseStructure.

#define FLAG_INSERTION   0x04
 

Definition at line 723 of file pdbxplugin.C.

Referenced by parseStructure.

#define FLAG_MODEL_NUM   0x20
 

Definition at line 726 of file pdbxplugin.C.

Referenced by parseStructure.

#define FLAG_OCCUPANCY   0x10
 

Definition at line 725 of file pdbxplugin.C.

Referenced by parseStructure.

#define MAX_COLUMNS   32
 

Definition at line 53 of file pdbxplugin.C.

Referenced by parseNumberAtoms, parseStructure, and readAngleBonds.

#define MAX_OPTIONAL_AUTH_FIELDS   2
 

Definition at line 719 of file pdbxplugin.C.

Referenced by parseStructure.

#define TYPE_SIZE   8
 

Definition at line 50 of file pdbxplugin.C.

Referenced by create_pdbxParser, parseStructure, readAngleBonds, and readRMSDBonds.

#define VMDPLUGIN_STATIC
 

Definition at line 43 of file pdbxplugin.C.

#define WB_SIZE   1024
 

Definition at line 150 of file pdbxplugin.C.

Referenced by write.


Typedef Documentation

typedef struct pdbxParser pdbxParser
 

typedef struct pdbxWriter pdbxWriter
 


Enumeration Type Documentation

enum TableColums
 

Enumeration values:
COLUMN_NUMBER 
COLUMN_NAME 
COLUMN_TYPE 
COLUMN_TYPE_AUTH 
COLUMN_RESNAME 
COLUMN_RESID 
COLUMN_RESID_AUTH 
COLUMN_INSERTION 
COLUMN_X 
COLUMN_Y 
COLUMN_Z 
COLUMN_OCCUPANCY 
COLUMN_BFACTOR 
COLUMN_CHARGE 
COLUMN_CHAIN 
COLUMN_CHAIN_AUTH 
COLUMN_MODEL_NUM 
COLUMN_JUNK 

Definition at line 84 of file pdbxplugin.C.


Function Documentation

void addAtoms const molfile_atom_t   atoms,
int    optflags,
pdbxWriter   writer
[static]
 

Definition at line 1934 of file pdbxplugin.C.

References molfile_atom_t::altloc, molfile_atom_t::atomicnumber, pdbxWriter::atoms, molfile_atom_t::bfactor, molfile_atom_t::insertion, MOLFILE_ALTLOC, MOLFILE_ATOMICNUMBER, MOLFILE_BFACTOR, MOLFILE_INSERTION, MOLFILE_OCCUPANCY, pdbxWriter::numatoms, and molfile_atom_t::occupancy.

Referenced by write_structure.

void addCoordinates const float *    coords,
pdbxWriter   writer
[static]
 

Definition at line 1929 of file pdbxplugin.C.

References pdbxWriter::coordinates.

Referenced by write_timestep.

void close pdbxWriter   writer [static]
 

Definition at line 2013 of file pdbxplugin.C.

References pdbxWriter::fd, and writeBuffer.

Referenced by fio_fclose, and writeFile.

void close_file_write void *    v [static]
 

Definition at line 2184 of file pdbxplugin.C.

References pdbxWriter::atoms, and pdbx_data::writer.

Referenced by VMDPLUGIN_init.

void close_pdbx_read void *    v [static]
 

Definition at line 2155 of file pdbxplugin.C.

References delete_pdbxParser, and pdbx_data::parser.

Referenced by VMDPLUGIN_init.

pdbxParser * create_pdbxParser const char *    filepath [static]
 

Definition at line 229 of file pdbxplugin.C.

References pdbxParser::bondsFrom, pdbxParser::bondsTo, BUFFER_SIZE, pdbxParser::chain_auth, CHAIN_SIZE, pdbxParser::error, pdbxParser::file, pdbxParser::g_data, pdbxParser::hashMem, initCharToNum, pdbxParser::n_graphics_elems, pdbxParser::natoms, pdbxParser::nbonds, parseNumberAtoms, pdbxParser::pdb_dev, pdbxParser::resid_auth, pdbxParser::type_auth, TYPE_SIZE, and pdbxParser::xyz.

Referenced by open_pdbx_read.

pdbxWriter * create_pdbxWriter const char *    filename,
int    numAtoms
[static]
 

Definition at line 1901 of file pdbxplugin.C.

References pdbxWriter::bufferCount, pdbxWriter::fd, pdbxWriter::numatoms, and pdbxWriter::pdbName.

Referenced by open_file_write.

void delete_pdbxParser pdbxParser   parser [static]
 

Definition at line 278 of file pdbxplugin.C.

References pdbxParser::bondHash, pdbxParser::bondsFrom, pdbxParser::bondsTo, pdbxParser::chain_auth, pdbxParser::file, pdbxParser::g_data, pdbxParser::hashMem, inthash_destroy, pdbxParser::natoms, pdbxParser::resid_auth, pdbxParser::type_auth, and pdbxParser::xyz.

Referenced by close_pdbx_read.

void getNextWord char *    str,
void *    word,
int &    pos,
int    maxstrlen,
int    maxwordlen
[static]
 

Definition at line 365 of file pdbxplugin.C.

Referenced by parse_pdbx_ihm_restraints_data, parse_pdbx_ihm_sphere_data, parseStructure, readAngleBonds, and readRMSDBonds.

int getUniqueResID char *    chainstr,
int    resid
[inline, static]
 

Definition at line 688 of file pdbxplugin.C.

References charToNum.

Referenced by parseStructure, readAngleBonds, and readRMSDBonds.

void initCharToNum   [static]
 

Definition at line 668 of file pdbxplugin.C.

References charToNum.

Referenced by create_pdbxParser.

bool isAtomSite char *    str [inline, static]
 

Definition at line 1890 of file pdbxplugin.C.

bool isPDB_DevFile pdbxParser   parser [static]
 

Definition at line 344 of file pdbxplugin.C.

References BUFFER_SIZE, and pdbxParser::file.

Referenced by parseNumberAtoms.

bool isStructureDataHeader const char *    strbuf [static]
 

Definition at line 468 of file pdbxplugin.C.

Referenced by parseNumberAtoms, and parseStructure.

bool isValidateRMSDBond char *    str [inline, static]
 

Definition at line 1878 of file pdbxplugin.C.

Referenced by readRMSDBonds.

void* open_file_write const char *    path,
const char *    filetypye,
int    natoms
[static]
 

Definition at line 2162 of file pdbxplugin.C.

References create_pdbxWriter, and pdbx_data::writer.

Referenced by VMDPLUGIN_init.

void* open_pdbx_read const char *    filepath,
const char *    filetype,
int *    natoms
[static]
 

Definition at line 2064 of file pdbxplugin.C.

References create_pdbxParser, pdbxParser::error, pdbxParser::natoms, pdbx_data::natoms, pdbx_data::parser, and pdbx_data::readTS.

Referenced by VMDPLUGIN_init.

bool parse_pdbx_graphics_data pdbxParser   parser [static]
 

Definition at line 1851 of file pdbxplugin.C.

References parse_pdbx_ihm_restraints_data, and parse_pdbx_ihm_sphere_data.

Referenced by read_rawgraphics.

bool parse_pdbx_ihm_restraints_data pdbxParser   parser [static]
 

Definition at line 1601 of file pdbxplugin.C.

References BUFFER_SIZE, COLUMN_BUFFER_SIZE, pdbxParser::file, getNextWord, and pdbxParser::nbonds.

Referenced by parse_pdbx_graphics_data.

bool parse_pdbx_ihm_sphere_data pdbxParser   parser [static]
 

Definition at line 1496 of file pdbxplugin.C.

References BUFFER_SIZE, COLUMN_BUFFER_SIZE, molfile_graphics_t::data, pdbxParser::file, pdbxParser::g_data, getNextWord, MOLFILE_SPHERE, pdbxParser::n_graphics_elems, pdbxParser::nbonds, molfile_graphics_t::size, molfile_graphics_t::style, and molfile_graphics_t::type.

Referenced by parse_pdbx_graphics_data.

int parseNumberAtoms pdbxParser   parser [static]
 

Definition at line 479 of file pdbxplugin.C.

References BUFFER_SIZE, COLUMN_BFACTOR, COLUMN_CHAIN, COLUMN_CHAIN_AUTH, COLUMN_CHARGE, COLUMN_INSERTION, COLUMN_JUNK, COLUMN_MODEL_NUM, COLUMN_NAME, COLUMN_NUMBER, COLUMN_OCCUPANCY, COLUMN_RESID, COLUMN_RESID_AUTH, COLUMN_RESNAME, COLUMN_TYPE, COLUMN_TYPE_AUTH, COLUMN_X, COLUMN_Y, COLUMN_Z, pdbxParser::file, isPDB_DevFile, isStructureDataHeader, MAX_COLUMNS, pdbxParser::pdb_dev, pdbxParser::table, and pdbxParser::tableSize.

Referenced by create_pdbxParser.

int parseStructure molfile_atom_t   atoms,
int *    optflags,
pdbxParser   parser
[static]
 

Definition at line 728 of file pdbxplugin.C.

References molfile_atom_t::altloc, molfile_atom_t::atomicnumber, molfile_atom_t::bfactor, pdbxParser::bondHash, BUFFER_SIZE, molfile_atom_t::chain, pdbxParser::chain_auth, CHAIN_SIZE, molfile_atom_t::charge, COLUMN_BFACTOR, COLUMN_BUFFER_SIZE, COLUMN_CHAIN, COLUMN_CHAIN_AUTH, COLUMN_CHARGE, COLUMN_INSERTION, COLUMN_JUNK, COLUMN_MODEL_NUM, COLUMN_NAME, COLUMN_NUMBER, COLUMN_OCCUPANCY, COLUMN_RESID, COLUMN_RESID_AUTH, COLUMN_RESNAME, COLUMN_TYPE, COLUMN_TYPE_AUTH, COLUMN_X, COLUMN_Y, COLUMN_Z, pdbxParser::error, pdbxParser::file, FLAG_BFACTOR, FLAG_CHAIN_LENGTH, FLAG_CHARGE, FLAG_INSERTION, FLAG_MODEL_NUM, FLAG_OCCUPANCY, get_pte_idx_from_string, get_pte_mass, get_pte_vdw_radius, getNextWord, getUniqueResID, pdbxParser::hashMem, list_node::index, molfile_atom_t::insertion, inthash_init, inthash_insert, isStructureDataHeader, molfile_atom_t::mass, MAX_COLUMNS, MAX_OPTIONAL_AUTH_FIELDS, MOLFILE_ALTLOC, MOLFILE_ATOMICNUMBER, MOLFILE_BFACTOR, MOLFILE_CHARGE, MOLFILE_INSERTION, MOLFILE_MASS, MOLFILE_OCCUPANCY, MOLFILE_RADIUS, molfile_atom_t::name, pdbxParser::natoms, list_node::next, molfile_atom_t::occupancy, molfile_atom_t::radius, molfile_atom_t::resid, pdbxParser::resid_auth, molfile_atom_t::resname, skipNextWord, pdbxParser::table, pdbxParser::tableSize, molfile_atom_t::type, pdbxParser::type_auth, TYPE_SIZE, and pdbxParser::xyz.

Referenced by read_pdbx_structure.

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

Definition at line 2105 of file pdbxplugin.C.

References pdbxParser::bondsFrom, pdbxParser::bondsTo, pdbxParser::nbonds, and pdbx_data::parser.

Referenced by VMDPLUGIN_init.

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

Definition at line 2081 of file pdbxplugin.C.

References MOLFILE_BONDSSPECIAL, MOLFILE_ERROR, MOLFILE_NOOPTIONS, MOLFILE_NOSTRUCTUREDATA, pdbxParser::natoms, pdbx_data::parser, parseStructure, pdbxParser::pdb_dev, and readBonds.

Referenced by VMDPLUGIN_init.

int read_pdbx_timestep void *    mydata,
int    natoms,
molfile_timestep_t   ts
[static]
 

Definition at line 2128 of file pdbxplugin.C.

References molfile_timestep_t::coords, MOLFILE_ERROR, pdbx_data::parser, pdbx_data::readTS, and pdbxParser::xyz.

Referenced by VMDPLUGIN_init.

int read_rawgraphics void *    v,
int *    nelem,
const molfile_graphics_t **    g_data
[static]
 

Definition at line 2140 of file pdbxplugin.C.

References pdbxParser::g_data, pdbxParser::n_graphics_elems, parse_pdbx_graphics_data, pdbx_data::parser, and pdbxParser::pdb_dev.

Referenced by VMDPLUGIN_init.

bool readAngleBonds molfile_atom_t   atoms,
pdbxParser   parser
[static]
 

Definition at line 1124 of file pdbxplugin.C.

References pdbxParser::bondHash, pdbxParser::bondsFrom, pdbxParser::bondsTo, BUFFER_SIZE, pdbxParser::chain_auth, CHAIN_SIZE, COLUMN_BUFFER_SIZE, pdbxParser::file, getNextWord, getUniqueResID, pdbxParser::hashMem, list_node::index, inthash_lookup, MAX_COLUMNS, pdbxParser::nbonds, list_node::next, pdbxParser::resid_auth, pdbxParser::type_auth, and TYPE_SIZE.

Referenced by readBonds.

bool readBonds molfile_atom_t   atoms,
pdbxParser   parser
[static]
 

Definition at line 1871 of file pdbxplugin.C.

References readAngleBonds, and readRMSDBonds.

Referenced by read_pdbx_structure.

bool readRMSDBonds molfile_atom_t   atoms,
pdbxParser   parser
[static]
 

Definition at line 1311 of file pdbxplugin.C.

References pdbxParser::bondHash, pdbxParser::bondsFrom, pdbxParser::bondsTo, BUFFER_SIZE, pdbxParser::chain_auth, CHAIN_SIZE, COLUMN_BUFFER_SIZE, pdbxParser::file, getNextWord, getUniqueResID, pdbxParser::hashMem, list_node::index, inthash_lookup, isValidateRMSDBond, pdbxParser::nbonds, list_node::next, pdbxParser::resid_auth, pdbxParser::type_auth, and TYPE_SIZE.

Referenced by readBonds.

void skipNextWord char *    str,
void *    word,
int &    pos,
int    maxlen
[static]
 

Definition at line 319 of file pdbxplugin.C.

Referenced by parseStructure.

float stringToFloat char *    str [static]
 

Definition at line 439 of file pdbxplugin.C.

VMDPLUGIN_API int VMDPLUGIN_fini void   
 

Definition at line 2227 of file pdbxplugin.C.

References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init void   
 

Definition at line 2198 of file pdbxplugin.C.

References molfile_plugin_t::close_file_read, close_file_write, molfile_plugin_t::close_file_write, close_pdbx_read, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, molfile_plugin_t::open_file_read, open_file_write, molfile_plugin_t::open_file_write, open_pdbx_read, read_bonds, molfile_plugin_t::read_bonds, molfile_plugin_t::read_next_timestep, read_pdbx_structure, read_pdbx_timestep, read_rawgraphics, molfile_plugin_t::read_rawgraphics, molfile_plugin_t::read_structure, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, VMDPLUGIN_THREADSAFE, write_structure, molfile_plugin_t::write_structure, write_timestep, and molfile_plugin_t::write_timestep.

VMDPLUGIN_API int VMDPLUGIN_register void *    v,
vmdplugin_register_cb    cb
 

Definition at line 2222 of file pdbxplugin.C.

References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

void write const char *    str,
pdbxWriter   writer
[static]
 

Definition at line 2019 of file pdbxplugin.C.

References pdbxWriter::bufferCount, WB_SIZE, pdbxWriter::writeBuf, and writeBuffer.

Referenced by fio_fwrite, writeAtomSite, writeFile, and writeIntro.

int write_structure void *    v,
int    optflags,
const molfile_atom_t   atoms
[static]
 

Definition at line 2169 of file pdbxplugin.C.

References addAtoms, and pdbx_data::writer.

Referenced by VMDPLUGIN_init.

int write_timestep void *    v,
const molfile_timestep_t   ts
[static]
 

Definition at line 2176 of file pdbxplugin.C.

References addCoordinates, molfile_timestep_t::coords, writeFile, and pdbx_data::writer.

Referenced by VMDPLUGIN_init.

void writeAtomSite pdbxWriter   writer [static]
 

Definition at line 1973 of file pdbxplugin.C.

References pdbxWriter::atoms, BUFFER_SIZE, pdbxWriter::coordinates, name, pdbxWriter::numatoms, and write.

Referenced by writeFile.

void writeBuffer pdbxWriter   writer [static]
 

Definition at line 2043 of file pdbxplugin.C.

References pdbxWriter::bufferCount, pdbxWriter::fd, and pdbxWriter::writeBuf.

Referenced by close, and write.

void writeFile pdbxWriter   writer [static]
 

Definition at line 1996 of file pdbxplugin.C.

References atomSiteHeader, close, write, writeAtomSite, and writeIntro.

Referenced by write_timestep.

void writeIntro pdbxWriter   writer [static]
 

Definition at line 2006 of file pdbxplugin.C.

References pdbxWriter::pdbName, and write.

Referenced by writeFile.


Variable Documentation

const char atomSiteHeader[] [static]
 

Initial value:

  "loop_\n"
  "_atom_site.group_PDB\n"
  "_atom_site.id\n"
  "_atom_site.type_symbol\n"
  "_atom_site.label_atom_id\n"
  "_atom_site.label_alt_id\n"
  "_atom_site.label_comp_id\n"
  "_atom_site.label_asym_id\n"
  "_atom_site.label_entity_id\n"
  "_atom_site.label_seq_id\n"
  "_atom_site.pdbx_PDB_ins_code\n"
  "_atom_site.Cartn_x\n"
  "_atom_site.Cartn_y\n"
  "_atom_site.Cartn_z\n"
  "_atom_site.occupancy\n"
  "_atom_site.pdbx_formal_charge\n"
  "_atom_site.auth_asym_id\n"

Definition at line 184 of file pdbxplugin.C.

Referenced by writeFile.

unsigned char charToNum[128] [static]
 

Definition at line 82 of file pdbxplugin.C.

Referenced by getUniqueResID, and initCharToNum.

molfile_plugin_t plugin [static]
 

Definition at line 2196 of file pdbxplugin.C.


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