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molfile_plugin.h File Reference

#include "vmdplugin.h"

Go to the source code of this file.

Compounds
struct	molfile_atom_t
struct	molfile_graphics_t
struct	molfile_metadata_t
struct	molfile_plugin_t
struct	molfile_qm_hessian_t
struct	molfile_qm_metadata_t
struct	molfile_qm_orbital_t
struct	molfile_qm_sysinfo_t
struct	molfile_qm_t
struct	molfile_qm_timestep_t
struct	molfile_timestep_metadata
struct	molfile_timestep_t
struct	molfile_volumetric_t
Defines
#define	MOLFILE_PLUGIN_TYPE   "mol file reader"
#define	MOLFILE_CONVERTER_PLUGIN_TYPE   "mol file converter"
#define	MOLFILE_SUCCESS   0 /**< succeeded in reading file */
#define	MOLFILE_EOF   -1 /**< end of file */
#define	MOLFILE_ERROR   -1 /**< error reading/opening a file */
#define	MOLFILE_NOSTRUCTUREDATA   -2 /**< no structure data in this file */
#define	MOLFILE_NUMATOMS_UNKNOWN   -1 /**< unknown number of atoms */
#define	MOLFILE_NUMATOMS_NONE   0 /**< no atoms in this file type */
#define	MOLFILE_BUFSIZ   81 /**< maximum chars in string data */
Typedefs
typedef molfile_timestep_metadata	molfile_timestep_metadata_t
Enumerations
enum	molfile_graphics_type {   MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,   MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,   MOLFILE_SPHERE, MOLFILE_TEXT, MOLFILE_COLOR, MOLFILE_TRICOLOR }

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Detailed Description

API for C extensions to define a way to load structure, coordinate, trajectory, and volumetric data files

Definition in file molfile_plugin.h.

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Define Documentation

#define MOLFILE_ALTLOC   0x0040 /**< Multiple conformations present */

Plugin optional data field availability flag Definition at line 111 of file molfile_plugin.h. Referenced by read_pdb_structure, vtf_parse_atom, and write_structure.

#define MOLFILE_ATOMICNUMBER   0x0080 /**< Atomic element number provided */

Plugin optional data field availability flag Definition at line 112 of file molfile_plugin.h. Referenced by open_xbgf_read, read_cube_structure, read_js_structure, read_pdb_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, write_js_structure, and write_structure.

#define MOLFILE_BADOPTIONS   0xFFFFFFFF /**< Detect badly behaved plugins */

Plugin optional data field availability flag Definition at line 114 of file molfile_plugin.h.

#define MOLFILE_BFACTOR   0x0004 /**< B-factor data provided */

Plugin optional data field availability flag Definition at line 107 of file molfile_plugin.h. Referenced by open_xbgf_read, read_js_structure, read_pdb_structure, vtf_parse_atom, write_js_structure, and write_structure.

#define MOLFILE_BONDSSPECIAL   0x0100 /**< Only non-standard bonds provided */

Plugin optional data field availability flag Definition at line 113 of file molfile_plugin.h. Referenced by read_pdb_structure.

#define MOLFILE_BUFSIZ   81 /**< maximum chars in string data */

Maximum string size macro Definition at line 51 of file molfile_plugin.h.

#define MOLFILE_CHARGE   0x0010 /**< Atomic charge provided */

Plugin optional data field availability flag Definition at line 109 of file molfile_plugin.h. Referenced by open_bgf_read, open_mol2_read, open_xbgf_read, read_car_structure, read_js_structure, read_mdf_structure, read_parm7_structure, read_parm_structure, read_pqr_structure, read_psf, vtf_parse_atom, write_js_structure, and write_pqr_structure.

#define MOLFILE_CONVERTER_PLUGIN_TYPE   "mol file converter"

File converter plugins use the same API but register under a different type so that regular file readers can have priority. Definition at line 37 of file molfile_plugin.h. Referenced by VMDPLUGIN_init.

#define MOLFILE_EOF   -1 /**< end of file */

Definition at line 41 of file molfile_plugin.h. Referenced by read_bgf_timestep, read_car_timestep, read_cube_timestep, read_dlpoly_structure, read_dlpoly_timestep, read_js_timestep, read_next_timestep, read_pqr_timestep, read_vaspoutcar_timestep, read_vaspposcar_timestep, read_vaspxdatcar_timestep, read_vaspxml_timestep, read_xbgf_timestep, and vtf_read_next_timestep.

#define MOLFILE_ERROR   -1 /**< error reading/opening a file */

Definition at line 42 of file molfile_plugin.h. Referenced by atomic_basis, get_basis, ReadPARM::preadln, read_amber_cdf_timestep, read_avsfield_data, read_bgf_bonds, read_bgf_structure, read_bgf_timestep, read_binary_dx_data, read_biomocca_data, read_bonds, read_brix_data, read_car_structure, read_car_timestep, read_ccp4_data, read_cdf_structure, read_cdf_timestep, read_cor_structure, read_cor_timestep, read_cpmd_structure, read_cpmd_timestep, read_crd_timestep, read_cube_data, read_cube_structure, read_cube_timestep, read_dlpoly_structure, read_dlpoly_timestep, read_dsn6_data, read_dx_data, read_edm_data, read_fs4_data, read_g96_structure, read_g96_timestep, read_grd_data, read_grid_data, read_gro_structure, read_gro_timestep, read_lammps_structure, read_lammps_timestep, read_map_data, read_mdf_bonds, read_mdf_structure, read_mmcif_structure, read_mmcif_timestep, read_mmtk_cdf_structure, read_mmtk_cdf_timestep, read_mol2, read_mol2_bonds, read_mol2_timestep, read_molden_structure, read_next_timestep, read_pbeq_data, read_phi_data, read_plt_data, read_pqr_structure, read_pqr_timestep, read_psf, read_rawgraphics, read_rst_timestep, read_situs_data, read_tinker_structure, read_tinker_timestep, read_trr_timestep, read_uhbd_data, read_vaspchgcar_data, read_vaspchgcar_metadata, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_bonds, read_xbgf_structure, read_xbgf_timestep, read_xsf_data, read_xsf_structure, read_xsf_timestep, read_xyz_structure, read_xyz_timestep, ReadPARM::readparm, vtf_open_file_read, vtf_parse_atom, vtf_parse_bond, vtf_parse_pbc, vtf_parse_structure, vtf_parse_timestep, vtf_read_next_timestep, write_pqr_timestep, write_situs_data, write_timestep, write_trr_timestep, write_vaspposcar_structure, and write_vaspposcar_timestep.

#define MOLFILE_INSERTION   0x0001 /**< insertion codes provided */

Plugin optional data field availability flag Definition at line 105 of file molfile_plugin.h. Referenced by open_bgf_read, open_xbgf_read, read_pdb_structure, vtf_parse_atom, and write_structure.

#define MOLFILE_MASS   0x0008 /**< Atomic mass provided */

Plugin optional data field availability flag Definition at line 108 of file molfile_plugin.h. Referenced by read_cube_structure, read_js_structure, read_parm7_structure, read_parm_structure, read_pdb_structure, read_psf, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, and write_js_structure.

#define MOLFILE_NOOPTIONS   0x0000 /**< no optional data */

Plugin optional data field availability flag Definition at line 104 of file molfile_plugin.h. Referenced by open_mol2_read, read_cor_structure, read_cpmd_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gro_structure, read_js_structure, read_lammps_structure, read_mmtk_cdf_structure, read_molden_structure, read_parm7_structure, read_tinker_structure, and vtf_parse_structure.

#define MOLFILE_NOSTRUCTUREDATA   -2 /**< no structure data in this file */

Definition at line 43 of file molfile_plugin.h. Referenced by read_cdf_structure, read_js_structure, vtf_parse_structure, and write_js_structure.

#define MOLFILE_NUMATOMS_NONE   0 /**< no atoms in this file type */

Definition at line 46 of file molfile_plugin.h. Referenced by open_avsfield_read, open_biomocca_read, open_brix_read, open_ccp4_read, open_cor_file, open_dsn6_read, open_dx_read, open_edm_read, open_fs4_read, open_grd_read, open_grid_read, open_map_read, open_pbeq_read, open_phi_read, open_plt_read, open_psf_read, open_situs_read, open_spider_read, open_uhbd_read, and vtf_parse_structure.

#define MOLFILE_NUMATOMS_UNKNOWN   -1 /**< unknown number of atoms */

Definition at line 45 of file molfile_plugin.h. Referenced by open_crd_read, open_vaspchgcar_read, open_vaspoutcar_read, open_vaspposcar_read, open_vaspxdatcar_read, open_vaspxml_read, and vtf_open_file_read.

#define MOLFILE_OCCUPANCY   0x0002 /**< occupancy data provided */

Plugin optional data field availability flag Definition at line 106 of file molfile_plugin.h. Referenced by open_xbgf_read, read_js_structure, read_mdf_structure, read_pdb_structure, vtf_parse_atom, write_js_structure, and write_structure.

#define MOLFILE_PLUGIN_TYPE   "mol file reader"

Define a common plugin type to be used when registering the plugin. Definition at line 31 of file molfile_plugin.h. Referenced by register_cb, and VMDPLUGIN_init.

#define MOLFILE_RADIUS   0x0020 /**< Atomic VDW radius provided */

Plugin optional data field availability flag Definition at line 110 of file molfile_plugin.h. Referenced by read_cube_structure, read_js_structure, read_pdb_structure, read_pqr_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, write_js_structure, and write_pqr_structure.

#define MOLFILE_SUCCESS   0 /**< succeeded in reading file */

Definition at line 40 of file molfile_plugin.h. Referenced by read_amber_cdf_timestep, read_angles, read_avsfield_data, read_avsfield_metadata, read_bgf_bonds, read_bgf_structure, read_bgf_timestep, read_binary_dx_data, read_biomocca_data, read_biomocca_metadata, read_bonds, read_brix_data, read_brix_metadata, read_car_structure, read_car_timestep, read_ccp4_data, read_ccp4_metadata, read_cor_structure, read_cor_timestep, read_cpmd_structure, read_cpmd_timestep, read_crd_timestep, read_cube_data, read_cube_metadata, read_cube_structure, read_cube_timestep, read_dlpoly_structure, read_dlpoly_timestep, read_dsn6_data, read_dsn6_metadata, read_dx_data, read_dx_metadata, read_edm_data, read_edm_metadata, read_fs4_data, read_fs4_metadata, read_g96_structure, read_g96_timestep, read_gamess_structure, read_grd_data, read_grd_metadata, read_grid_data, read_grid_metadata, read_gro_structure, read_gro_timestep, read_js_angles, read_js_bonds, read_js_structure, read_js_timestep, read_lammps_structure, read_lammps_timestep, read_map_data, read_map_metadata, read_mdf_bonds, read_mdf_structure, read_mmtk_cdf_structure, read_mmtk_cdf_timestep, read_mol2, read_mol2_bonds, read_mol2_timestep, read_molden_structure, read_molecule_metadata, read_next_timestep, read_orbital_data, read_orbital_metadata, read_parm7_bonds, read_parm7_structure, read_parm_bonds, read_parm_structure, read_pbeq_data, read_pbeq_metadata, read_pdb_structure, read_phi_data, read_phi_metadata, read_plt_data, read_plt_metadata, read_pqr_structure, read_pqr_timestep, read_psf, read_rawgraphics, read_rst_timestep, read_situs_data, read_situs_metadata, read_spider_data, read_spider_metadata, read_tinker_structure, read_tinker_timestep, read_trr_timestep, read_uhbd_data, read_uhbd_metadata, read_vaspchgcar_data, read_vaspchgcar_metadata, read_vaspoutcar_structure, read_vaspoutcar_timestep, read_vaspposcar_structure, read_vaspposcar_timestep, read_vaspxdatcar_structure, read_vaspxdatcar_timestep, read_vaspxml_structure, read_vaspxml_timestep, read_xbgf_bonds, read_xbgf_structure, read_xbgf_timestep, read_xsf_data, read_xsf_metadata, read_xsf_structure, read_xsf_timestep, read_xyz_structure, read_xyz_timestep, ReadPARM::readparm, vtf_open_file_read, vtf_parse_atom, vtf_parse_bond, vtf_parse_pbc, vtf_parse_structure, vtf_parse_timestep, vtf_read_bonds, vtf_read_next_timestep, vtf_read_structure, write_angles, write_bgf_structure, write_bgf_timestep, write_bonds, write_crd_timestep, write_dx_data, write_js_angles, write_js_bonds, write_js_structure, write_js_timestep, write_mol2_structure, write_mol2_timestep, write_pqr_structure, write_pqr_timestep, write_psf_structure, write_rst_timestep, write_situs_data, write_structure, write_timestep, write_trr_timestep, write_vaspposcar_structure, write_vaspposcar_timestep, write_xbgf_structure, write_xbgf_timestep, write_xyz_structure, and write_xyz_timestep.

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Typedef Documentation

typedef struct molfile_timestep_metadata molfile_timestep_metadata_t

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Enumeration Type Documentation

enum molfile_graphics_type

Enumeration of all of the supported graphics objects that can be read from graphics file reader plugins. Enumeration values: MOLFILE_POINT  MOLFILE_TRIANGLE  MOLFILE_TRINORM  MOLFILE_NORMS  MOLFILE_LINE  MOLFILE_CYLINDER  MOLFILE_CAPCYL  MOLFILE_CONE  MOLFILE_SPHERE  MOLFILE_TEXT  MOLFILE_COLOR  MOLFILE_TRICOLOR  Definition at line 307 of file molfile_plugin.h.

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