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babelplugin.c File Reference

#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <unistd.h>
#include "molfile_plugin.h"
#include "readpdb.h"
#include "vmddir.h"
#include "periodic_table.h"

Go to the source code of this file.

Compounds
struct	pdbdata
Defines
#define	BABEL_TMPDIR   "/tmp/"
Functions
int	vmd_getuid (void)
int	vmd_delete_file (const char *path)
char *	file (const char *filename, int idx, int has_multi)
void	delete_all (const char *filename)
void *	open_pdb_read (const char *filepath, int *natoms)
const char *	babel16type_from_name (const char *name)
const char *	openbabel11type_from_name (const char *name)
void *	open_babel_read (const char *filename, const char *filetypename, int *natoms)
int	read_pdb_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int	read_next_timestep (void *v, int natoms, molfile_timestep_t *ts)
void	close_pdb_read (void *v)
VMDPLUGIN_API int	VMDPLUGIN_init ()
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int	VMDPLUGIN_fini ()
Variables
const char *	babel16filetypes []
const char *	babel16filetypenames []
const char *	openbabel11filetypes []
const char *	openbabel11filetypenames []
molfile_plugin_t *	plugins
int	nplugins

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Define Documentation

#define BABEL_TMPDIR   "/tmp/"

Definition at line 71 of file babelplugin.c. Referenced by file, and open_babel_read.

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Function Documentation

const char* babel16type_from_name (  const char *    name )  [static]

Definition at line 307 of file babelplugin.c. References babel16filetypenames, babel16filetypes, and name. Referenced by open_babel_read.

void close_pdb_read (  void *    v )  [static]

Definition at line 588 of file babelplugin.c. References pdbdata::current_file, pdbdata::fd, and vmd_delete_file. Referenced by VMDPLUGIN_init.

void delete_all (  const char *    filename )  [static]

Definition at line 118 of file babelplugin.c. References file. Referenced by open_babel_read.

char* file (  const char *    filename, int    idx, int    has_multi )  [static]

Definition at line 79 of file babelplugin.c. References BABEL_TMPDIR, and vmd_getuid. Referenced by delete_all, open_babel_read, and read_next_timestep.

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

Definition at line 336 of file babelplugin.c. References babel16type_from_name, pdbdata::babel_i, pdbdata::babel_num, BABEL_TMPDIR, pdbdata::current_file, delete_all, file, open_pdb_read, openbabel11type_from_name, pdbdata::original_file, vmd_closedir, vmd_opendir, and vmd_readdir. Referenced by VMDPLUGIN_init.

void* open_pdb_read (  const char *    filepath, int *    natoms )  [static]

Definition at line 133 of file babelplugin.c. References pdbdata::fd, pdbdata::natoms, PDB_ATOM, PDB_BUFFER_LENGTH, PDB_END, PDB_EOF, and read_pdb_record.

const char* openbabel11type_from_name (  const char *    name )  [static]

Definition at line 319 of file babelplugin.c. References name, openbabel11filetypenames, and openbabel11filetypes. Referenced by open_babel_read.

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

Definition at line 516 of file babelplugin.c. References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, pdbdata::babel_i, pdbdata::babel_num, molfile_timestep_t::beta, molfile_timestep_t::C, molfile_timestep_t::coords, pdbdata::current_file, pdbdata::fd, file, molfile_timestep_t::gamma, get_pdb_coordinates, get_pdb_cryst1, MOLFILE_ERROR, pdbdata::natoms, pdbdata::original_file, PDB_ATOM, PDB_BUFFER_LENGTH, PDB_CRYST1, PDB_EOF, read_pdb_record, and vmd_delete_file. Referenced by VMDPLUGIN_init.

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

Definition at line 462 of file babelplugin.c. References molfile_atom_t::altloc, molfile_atom_t::atomicnumber, molfile_atom_t::bfactor, molfile_atom_t::chain, pdbdata::fd, get_pdb_fields, get_pte_idx_from_string, get_pte_mass, get_pte_vdw_radius, molfile_atom_t::insertion, molfile_atom_t::mass, MOLFILE_ALTLOC, MOLFILE_ATOMICNUMBER, MOLFILE_BFACTOR, MOLFILE_INSERTION, MOLFILE_MASS, MOLFILE_OCCUPANCY, MOLFILE_RADIUS, molfile_atom_t::name, molfile_atom_t::occupancy, PDB_ATOM, PDB_BUFFER_LENGTH, PDB_END, PDB_EOF, molfile_atom_t::radius, read_pdb_record, molfile_atom_t::resid, molfile_atom_t::resname, molfile_atom_t::segid, and molfile_atom_t::type. Referenced by VMDPLUGIN_init.

int vmd_delete_file (  const char *    path )  [static]

Definition at line 60 of file babelplugin.c. Referenced by close_pdb_read, and read_next_timestep.

int vmd_getuid (  void    )  [static]

Definition at line 52 of file babelplugin.c. Referenced by file.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    )

Definition at line 675 of file babelplugin.c. References nplugins, VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init (  void    )

Definition at line 609 of file babelplugin.c. References babel16filetypenames, babel16filetypes, molfile_plugin_t::close_file_read, close_pdb_read, molfile_plugin_t::filename_extension, MOLFILE_CONVERTER_PLUGIN_TYPE, nplugins, open_babel_read, molfile_plugin_t::open_file_read, openbabel11filetypenames, openbabel11filetypes, 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_THREADUNSAFE.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v, vmdplugin_register_cb    cb )

Definition at line 663 of file babelplugin.c. References nplugins, VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

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Variable Documentation

const char* babel16filetypenames[] [static]

Initial value: { "Alchemy", "AMBERPREP", "BallStick", "MSIBGF", "BiosymCAR", "Boogie", "Cacao", "CADPAC", "CHARMm", "Chem3d-1", "Chem3d-2", "CSSR", "FDAT", "GSTAT", "Dock", "DockPDB", "Feature", "Fractional", "GAMESSoutput", "GaussianZmatrix", "Gaussian92output", "Gaussian94output", "Gromos96A", "Gromos96N", "HyperchemHIN", "IsisSDF", "M3D", "MacMolecule", "Macromodel", "MicroWorld", "MM2Input", "MM2Output", "MM3", "MMADS", "MDLMOL", "MOLIN", "MopacCartesian", "MopacInternal", "MopacOutput", "PCModel", "PSGVBin", "PSGVBout", "QuantaMSF", "Schakal", "ShelX", "SMILES", "Spartan", "SpartanSE", "SpartanMM", "SybylMol", "SybylMol2", "Conjure", "UniChemXYZ", "XYZ", "XED", 0 } Definition at line 217 of file babelplugin.c. Referenced by babel16type_from_name, and VMDPLUGIN_init.

const char* babel16filetypes[] [static]

Definition at line 155 of file babelplugin.c. Referenced by babel16type_from_name, and VMDPLUGIN_init.

int nplugins [static]

Definition at line 607 of file babelplugin.c. Referenced by VMDPLUGIN_fini, VMDPLUGIN_init, and VMDPLUGIN_register.

const char* openbabel11filetypenames[] [static]

Initial value: { "Alchemy", "AMBERPREP", "BallStick", "Cacao", "CCC", "Chem3d-1", "Chem3d-2", "ChemicalMarkup" "CRK2D", "CRK3D", "Dock35Box", "Dmol3Coord", "Feature", "GAMESSoutput", "GhemicalProj", "GhemicalMM", "GhemicalQM", "HyperchemHIN", "JaguarOutput", "OpenEyeBinary", "Macromodel", "BiosymCAR", "IsisSDF", "MDLMOL", "MopacCartesian", "MopacOutput", "MMADS", "MPQC", "MSIBGF", "NWChemOutput", "PQS", "QChemOutput", "ShelX", "SMILES", "SybylMol2", "UniChemXYZ", "ViewMol", "XYZ", 0 } Definition at line 289 of file babelplugin.c. Referenced by openbabel11type_from_name, and VMDPLUGIN_init.

const char* openbabel11filetypes[] [static]

Definition at line 244 of file babelplugin.c. Referenced by openbabel11type_from_name, and VMDPLUGIN_init.

molfile_plugin_t* plugins [static]

Definition at line 606 of file babelplugin.c.

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