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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_DIRECTIO_MIN_BLOCK_SIZE   4096
#define	MOLFILE_DIRECTIO_MAX_BLOCK_SIZE   4096
#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 156 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 157 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 162 of file molfile_plugin.h.

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

Plugin optional data field availability flag Definition at line 152 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 158 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 154 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_DIRECTIO_MAX_BLOCK_SIZE   4096

Definition at line 76 of file molfile_plugin.h. Referenced by read_js_structure.

#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE   4096

Hard-coded direct-I/O page size constants for use by both VMD and the plugins that want to use direct, unbuffered I/O for high performance with SSDs etc. We use two constants to define the range of hardware page sizes that we can support, so that we can add support for larger 8KB or 16KB page sizes in the future as they become more prevalent in high-end storage systems. At present, VMD uses a hard-coded 4KB page size to reduce memory fragmentation, but these constants will make it easier to enable the use of larger page sizes in the future if it becomes necessary. Definition at line 75 of file molfile_plugin.h. Referenced by write_js_structure.

#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 150 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 153 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 149 of file molfile_plugin.h. Referenced by _vtf_open_file_read, 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, and read_tinker_structure.

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

Definition at line 49 of file molfile_plugin.h. Referenced by _vtf_open_file_read, 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 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 _vtf_open_file_read, main, open_crd_read, open_file_read, open_vaspchgcar_read, open_vaspoutcar_read, open_vaspparchg_read, open_vaspposcar_read, open_vaspxdatcar_read, and open_vaspxml_read.

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

Plugin optional data field availability flag Definition at line 151 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 274 of file molfile_plugin.h. Referenced by analyze_traj, and get_wavefunction.

#define MOLFILE_QMSTATUS_OPT_CONV   0

Definition at line 271 of file molfile_plugin.h. Referenced by analyze_traj, and get_traj_frame.

#define MOLFILE_QMSTATUS_OPT_NOT_CONV   2

Definition at line 273 of file molfile_plugin.h. Referenced by analyze_traj, and get_traj_frame.

#define MOLFILE_QMSTATUS_SCF_NOT_CONV   1

Definition at line 272 of file molfile_plugin.h. Referenced by analyze_traj.

#define MOLFILE_QMSTATUS_UNKNOWN   -1

Definition at line 270 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 171 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 170 of file molfile_plugin.h.

#define MOLFILE_QMTS_SCFITER   0x0002

Flags indicating availability of optional data fields for QM timesteps Definition at line 172 of file molfile_plugin.h.

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

Plugin optional data field availability flag Definition at line 155 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 295 of file molfile_plugin.h.

#define MOLFILE_RUNTYPE_ENERGY   1

Definition at line 288 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_RUNTYPE_GRADIENT   6

Definition at line 293 of file molfile_plugin.h. Referenced by get_contrl, get_contrl_firefly, and get_final_properties.

#define MOLFILE_RUNTYPE_HESSIAN   4

Definition at line 291 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 294 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 289 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 298 of file molfile_plugin.h.

#define MOLFILE_RUNTYPE_SADPOINT   3

Definition at line 290 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 292 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 287 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_FF   6

Definition at line 284 of file molfile_plugin.h.

#define MOLFILE_SCFTYPE_GVB   4

Definition at line 282 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_MCSCF   5

Definition at line 283 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 278 of file molfile_plugin.h. Referenced by get_contrl, get_contrl_firefly, and get_mcscf.

#define MOLFILE_SCFTYPE_RHF   1

Definition at line 279 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_ROHF   3

Definition at line 281 of file molfile_plugin.h. Referenced by get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_UHF   2

Definition at line 280 of file molfile_plugin.h. Referenced by check_add_wavefunctions, get_contrl, and get_contrl_firefly.

#define MOLFILE_SCFTYPE_UNKNOWN   -1

Definition at line 277 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 532 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 455 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 439 of file molfile_plugin.h.

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