pdbxplugin.C File Reference

  "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"

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
pdbxParser *	create_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)
pdbxWriter *	create_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

pdbxplugin.C File Reference

Compounds

Defines

Typedefs

Enumerations

Functions

Variables

Define Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation