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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_basis_t
struct	molfile_qm_hessian_t
struct	molfile_qm_metadata_t
struct	molfile_qm_sysinfo_t
struct	molfile_qm_t
struct	molfile_qm_timestep_metadata
struct	molfile_qm_timestep_t
struct	molfile_qm_wavefunction_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 */
#define	MOLFILE_BIGBUFSIZ   4096 /**< maximum chars in long strings */
#define	MOLFILE_MAXWAVEPERTS   25 /**< maximum number of wavefunctions
#define	MOLFILE_QMSTATUS_UNKNOWN   -1
#define	MOLFILE_QMSTATUS_OPT_CONV   0
#define	MOLFILE_QMSTATUS_SCF_NOT_CONV   1
#define	MOLFILE_QMSTATUS_OPT_NOT_CONV   2
#define	MOLFILE_QMSTATUS_FILE_TRUNCATED   3
#define	MOLFILE_SCFTYPE_UNKNOWN   -1
#define	MOLFILE_SCFTYPE_NONE   0
#define	MOLFILE_SCFTYPE_RHF   1
#define	MOLFILE_SCFTYPE_UHF   2
#define	MOLFILE_SCFTYPE_ROHF   3
#define	MOLFILE_SCFTYPE_GVB   4
#define	MOLFILE_SCFTYPE_MCSCF   5
#define	MOLFILE_SCFTYPE_FF   6
#define	MOLFILE_RUNTYPE_UNKNOWN   0
#define	MOLFILE_RUNTYPE_ENERGY   1
#define	MOLFILE_RUNTYPE_OPTIMIZE   2
#define	MOLFILE_RUNTYPE_SADPOINT   3
#define	MOLFILE_RUNTYPE_HESSIAN   4
#define	MOLFILE_RUNTYPE_SURFACE   5
#define	MOLFILE_RUNTYPE_GRADIENT   6
#define	MOLFILE_RUNTYPE_MEX   7
#define	MOLFILE_RUNTYPE_DYNAMICS   8
#define	MOLFILE_RUNTYPE_PROPERTIES   9
Typedefs
typedef molfile_timestep_metadata	molfile_timestep_metadata_t
typedef molfile_qm_timestep_metadata	molfile_qm_timestep_metadata_t
Enumerations
enum	molfile_qm_wavefunc_type {   MOLFILE_WAVE_CANON, MOLFILE_WAVE_GEMINAL, MOLFILE_WAVE_MCSCFNAT, MOLFILE_WAVE_MCSCFOPT,   MOLFILE_WAVE_CINATUR, MOLFILE_WAVE_PIPEK, MOLFILE_WAVE_BOYS, MOLFILE_WAVE_RUEDEN,   MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO, MOLFILE_WAVE_PNHO,   MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO, MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO,   MOLFILE_WAVE_MOAO, MOLFILE_WAVE_NATO, MOLFILE_WAVE_UNKNOWN }
enum	molfile_qm_charge_type {   MOLFILE_QMCHARGE_UNKNOWN, MOLFILE_QMCHARGE_MULLIKEN, MOLFILE_QMCHARGE_LOWDIN, MOLFILE_QMCHARGE_ESP,   MOLFILE_QMCHARGE_NPA }
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 124 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 125 of file molfile_plugin.h. Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, open_xbgf_read, read_cpmdlog_structure, read_cube_structure, read_gamess_structure, read_gaussian_structure, read_js_structure, read_lammps_structure, read_molden_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 130 of file molfile_plugin.h.

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

Plugin optional data field availability flag Definition at line 120 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_BIGBUFSIZ   4096 /**< maximum chars in long strings */

Definition at line 58 of file molfile_plugin.h. Referenced by hoomd_parse_line.

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

Plugin optional data field availability flag Definition at line 126 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 57 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_basis, get_basis_options, get_input_structure, get_internal_basis, get_proc_mem, get_traj_frame, get_wavefunction, have_cpmd, have_gaussian, parse_static_data, read_timestep, and xml_new_tag.

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

Plugin optional data field availability flag Definition at line 122 of file molfile_plugin.h. Referenced by open_bgf_read, open_mol2_read, open_xbgf_read, read_car_structure, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_js_structure, read_lammps_structure, read_mdf_structure, read_parm7_structure, read_parm_structure, read_pqr_structure, read_psf, vtf_parse_atom, write_hoomd_structure, write_js_structure, write_pqr_structure, and xml_new_tag.

#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 43 of file molfile_plugin.h. Referenced by VMDPLUGIN_init.

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

Definition at line 47 of file molfile_plugin.h. Referenced by DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, 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 48 of file molfile_plugin.h. Referenced by DEN_read_volumetric_data, DEN_read_volumetric_metadata, fill_basis_arrays, GEO_read_structure, get_basis, get_basis_options, hoomd_parse_line, open_hoomd_read, POT_read_volumetric_data, POT_read_volumetric_metadata, ReadPARM::preadln, read_amber_cdf_timestep, read_avsfield_data, read_bgf_bonds, read_bgf_bonds_aux, 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_hoomd_structure, read_hoomd_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_bonds_aux, read_mol2_timestep, read_molden_metadata, read_molden_rundata, read_molden_structure, read_next_timestep, read_pbeq_data, read_phi_data, read_plt_data, read_pqr_structure, read_pqr_timestep, read_psf, read_qm_timestep_metadata, read_rawgraphics, read_rst_timestep, read_situs_data, read_structure, read_timestep, read_tinker_structure, read_tinker_timestep, read_trr_timestep, read_uhbd_data, read_vaspchgcar_data, read_vaspchgcar_metadata, read_vaspoutcar_structure, read_vaspparchg_data, read_vaspparchg_metadata, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_volumetric_data, read_volumetric_metadata, read_xbgf_bonds, read_xbgf_bonds_aux, read_xbgf_structure, read_xbgf_timestep, read_xsf_data, read_xsf_structure, read_xsf_timestep, read_xyz_structure, read_xyz_timestep, ReadPARM::readparm, vtf_parse_atom, vtf_parse_bond, vtf_parse_pbc, vtf_parse_structure, vtf_parse_timestep, vtf_read_bonds, vtf_read_next_timestep, WFK_read_volumetric_data, WFK_read_volumetric_metadata, write_edm_data, write_pqr_timestep, write_situs_data, write_structure, 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 118 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 121 of file molfile_plugin.h. Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_hoomd_structure, read_js_structure, read_lammps_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, write_hoomd_structure, write_js_structure, and xml_new_tag.

#define MOLFILE_MAXWAVEPERTS   25 /**< maximum number of wavefunctions

Definition at line 60 of file molfile_plugin.h. Referenced by read_qm_timestep_metadata.

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

Plugin optional data field availability flag Definition at line 117 of file molfile_plugin.h. Referenced by open_hoomd_read, open_mol2_read, read_cor_structure, read_cpmd_structure, read_dlpoly_structure, read_g96_structure, read_gro_structure, read_js_structure, read_lammps_structure, read_mmtk_cdf_structure, read_parm7_structure, read_tinker_structure, and vtf_open_file_read.

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

Definition at line 49 of file molfile_plugin.h. Referenced by read_cdf_structure, read_js_structure, vtf_open_file_read, vtf_parse_structure, and write_js_structure.

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

Definition at line 52 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, and open_uhbd_read.

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

Definition at line 51 of file molfile_plugin.h. Referenced by main, open_crd_read, open_file_read, open_vaspchgcar_read, open_vaspoutcar_read, open_vaspparchg_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 119 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 37 of file molfile_plugin.h. Referenced by register_cb, and VMDPLUGIN_init.

#define MOLFILE_QMSTATUS_FILE_TRUNCATED   3

Definition at line 242 of file molfile_plugin.h. Referenced by analyze_traj, and get_wavefunction.

#define MOLFILE_QMSTATUS_OPT_CONV   0

Definition at line 239 of file molfile_plugin.h. Referenced by analyze_traj, and get_traj_frame.

#define MOLFILE_QMSTATUS_OPT_NOT_CONV   2

Definition at line 241 of file molfile_plugin.h. Referenced by analyze_traj, and get_traj_frame.

#define MOLFILE_QMSTATUS_SCF_NOT_CONV   1

Definition at line 240 of file molfile_plugin.h. Referenced by analyze_traj.

#define MOLFILE_QMSTATUS_UNKNOWN   -1

Definition at line 238 of file molfile_plugin.h. Referenced by analyze_traj, get_traj_frame, and init_qmdata.

#define MOLFILE_QMTS_GRADIENT   0x0001 /**< energy gradients provided */

Flags indicating availability of optional data fields for QM timesteps Definition at line 139 of file molfile_plugin.h.

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

Flags indicating availability of optional data fields for QM timesteps Definition at line 138 of file molfile_plugin.h.

#define MOLFILE_QMTS_SCFITER   0x0002

Flags indicating availability of optional data fields for QM timesteps Definition at line 140 of file molfile_plugin.h.

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

Plugin optional data field availability flag Definition at line 123 of file molfile_plugin.h. Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_hoomd_structure, read_js_structure, read_lammps_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_hoomd_structure, write_js_structure, write_pqr_structure, and xml_new_tag.

#define MOLFILE_RUNTYPE_DYNAMICS   8

Definition at line 263 of file molfile_plugin.h.

#define MOLFILE_RUNTYPE_ENERGY   1

Definition at line 256 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_RUNTYPE_GRADIENT   6

Definition at line 261 of file molfile_plugin.h. Referenced by get_contrl, get_contrl_firefly, and get_final_properties.

#define MOLFILE_RUNTYPE_HESSIAN   4

Definition at line 259 of file molfile_plugin.h. Referenced by get_contrl, get_contrl_firefly, get_final_properties, read_gamess_metadata, and read_gamess_rundata.

#define MOLFILE_RUNTYPE_MEX   7

Definition at line 262 of file molfile_plugin.h. Referenced by analyze_traj, get_contrl, get_contrl_firefly, and get_traj_frame.

#define MOLFILE_RUNTYPE_OPTIMIZE   2

Definition at line 257 of file molfile_plugin.h. Referenced by analyze_traj, get_contrl, get_contrl_firefly, and get_traj_frame.

#define MOLFILE_RUNTYPE_PROPERTIES   9

Definition at line 266 of file molfile_plugin.h.

#define MOLFILE_RUNTYPE_SADPOINT   3

Definition at line 258 of file molfile_plugin.h. Referenced by analyze_traj, get_contrl, get_contrl_firefly, and get_traj_frame.

#define MOLFILE_RUNTYPE_SURFACE   5

Definition at line 260 of file molfile_plugin.h. Referenced by analyze_traj, get_contrl, get_contrl_firefly, and get_traj_frame.

#define MOLFILE_RUNTYPE_UNKNOWN   0

Definition at line 255 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_FF   6

Definition at line 252 of file molfile_plugin.h.

#define MOLFILE_SCFTYPE_GVB   4

Definition at line 250 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_MCSCF   5

Definition at line 251 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_contrl, get_contrl_firefly, and parse_static_data.

#define MOLFILE_SCFTYPE_NONE   0

Definition at line 246 of file molfile_plugin.h. Referenced by get_contrl, get_contrl_firefly, and get_mcscf.

#define MOLFILE_SCFTYPE_RHF   1

Definition at line 247 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_ROHF   3

Definition at line 249 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_UHF   2

Definition at line 248 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_UNKNOWN   -1

Definition at line 245 of file molfile_plugin.h.

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

Definition at line 46 of file molfile_plugin.h.

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Typedef Documentation

typedef struct molfile_qm_timestep_metadata molfile_qm_timestep_metadata_t

Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data.

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 500 of file molfile_plugin.h.

enum molfile_qm_charge_type

Enumeration of all of the supported QM related charge types Enumeration values: MOLFILE_QMCHARGE_UNKNOWN  MOLFILE_QMCHARGE_MULLIKEN  MOLFILE_QMCHARGE_LOWDIN  MOLFILE_QMCHARGE_ESP  MOLFILE_QMCHARGE_NPA  Definition at line 423 of file molfile_plugin.h.

enum molfile_qm_wavefunc_type

Enumeration of all of the wavefunction types that can be read from QM file reader plugins. CANON = canonical (i.e diagonalized) wavefunction GEMINAL = GVB-ROHF geminal pairs MCSCFNAT = Multi-Configuration SCF natural orbitals MCSCFOPT = Multi-Configuration SCF optimized orbitals CINATUR = Configuration-Interaction natural orbitals BOYS = Boys localization RUEDEN = Ruedenberg localization PIPEK = Pipek-Mezey population localization NBO related localizations: -------------------------- NAO = Natural Atomic Orbitals PNAO = pre-orthogonal NAOs NBO = Natural Bond Orbitals PNBO = pre-orthogonal NBOs NHO = Natural Hybrid Orbitals PNHO = pre-orthogonal NHOs NLMO = Natural Localized Molecular Orbitals PNLMO = pre-orthogonal NLMOs UNKNOWN = Use this for any type not listed here You can use the string field for description Enumeration values: MOLFILE_WAVE_CANON  MOLFILE_WAVE_GEMINAL  MOLFILE_WAVE_MCSCFNAT  MOLFILE_WAVE_MCSCFOPT  MOLFILE_WAVE_CINATUR  MOLFILE_WAVE_PIPEK  MOLFILE_WAVE_BOYS  MOLFILE_WAVE_RUEDEN  MOLFILE_WAVE_NAO  MOLFILE_WAVE_PNAO  MOLFILE_WAVE_NHO  MOLFILE_WAVE_PNHO  MOLFILE_WAVE_NBO  MOLFILE_WAVE_PNBO  MOLFILE_WAVE_PNLMO  MOLFILE_WAVE_NLMO  MOLFILE_WAVE_MOAO  MOLFILE_WAVE_NATO  MOLFILE_WAVE_UNKNOWN  Definition at line 407 of file molfile_plugin.h.

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