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

#include "vmdplugin.h"

Classes
struct	PLMD::molfile::molfile_atom_t
	Per-atom attributes and information. More...

struct	PLMD::molfile::molfile_graphics_t
	Individual graphics object/element data. More...

struct	PLMD::molfile::molfile_metadata_t
	File level comments, origin information, and annotations. More...

struct	PLMD::molfile::molfile_plugin_t
	Main file reader API. More...

struct	PLMD::molfile::molfile_qm_basis_t
	Data for QM basis set. More...

struct	PLMD::molfile::molfile_qm_hessian_t
	Data from QM Hessian/normal mode runs. More...

struct	PLMD::molfile::molfile_qm_metadata_t
	Sizes of various QM-related, timestep independent data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data. More...

struct	PLMD::molfile::molfile_qm_sysinfo_t
	QM run info. More...

struct	PLMD::molfile::molfile_qm_t
	QM related information that is timestep independent. More...

struct	PLMD::molfile::molfile_qm_timestep_metadata
	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. More...

struct	PLMD::molfile::molfile_qm_timestep_t
	QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions. More...

struct	PLMD::molfile::molfile_qm_wavefunction_t
	QM wavefunction. More...

struct	PLMD::molfile::molfile_timestep_metadata

struct	PLMD::molfile::molfile_timestep_t

struct	PLMD::molfile::molfile_volumetric_readwrite_t
	Volumetric dataset read/write structure with both flag/parameter sets and VMD-allocated pointers for fields to be used by the plugin. More...

struct	PLMD::molfile::molfile_volumetric_t
	Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading. More...

Namespaces
	PLMD

	PLMD::molfile

Macros
#define	MOL_FILE_PLUGIN_H

#define	MOLFILE_BIGBUFSIZ 4096
	maximum chars in long strings More...

#define	MOLFILE_BUFSIZ 81
	Maximum string size macro. More...

#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. More...

#define	MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096

#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. More...

#define	MOLFILE_EOF -1
	end of file More...

#define	MOLFILE_ERROR -1
	error reading/opening a file More...

#define	MOLFILE_MAXWAVEPERTS 25
	maximum number of wavefunctions per timestep More...

#define	MOLFILE_NOSTRUCTUREDATA -2
	no structure data in this file More...

#define	MOLFILE_NUMATOMS_NONE 0
	no atoms in this file type More...

#define	MOLFILE_NUMATOMS_UNKNOWN -1
	unknown number of atoms More...

#define	MOLFILE_PLUGIN_TYPE "mol file reader"
	Define a common plugin type to be used when registering the plugin. More...

#define	MOLFILE_QMSTATUS_FILE_TRUNCATED 3 /* file was truncated */

#define	MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */

#define	MOLFILE_QMSTATUS_OPT_NOT_CONV 2 /* optimization not converged */

#define	MOLFILE_QMSTATUS_SCF_NOT_CONV 1 /* SCF convergence failed */

#define	MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */

#define	MOLFILE_RUNTYPE_DYNAMICS

#define	MOLFILE_RUNTYPE_ENERGY 1 /* single point run */

#define	MOLFILE_RUNTYPE_GRADIENT 6 /* energy gradient calculation */

#define	MOLFILE_RUNTYPE_HESSIAN 4 /* Hessian/frequency calculation */

#define	MOLFILE_RUNTYPE_MEX 7 /* minimum energy crossing */

#define	MOLFILE_RUNTYPE_OPTIMIZE 2 /* geometry optimization */

#define	MOLFILE_RUNTYPE_PROPERTIES

#define	MOLFILE_RUNTYPE_SADPOINT 3 /* saddle point search */

#define	MOLFILE_RUNTYPE_SURFACE 5 /* potential surface scan */

#define	MOLFILE_RUNTYPE_UNKNOWN 0 /* single point run */

#define	MOLFILE_SCFTYPE_FF 6 /* classical force-field based sim. */

#define	MOLFILE_SCFTYPE_GVB 4 /* generalized valence bond orbitals */

#define	MOLFILE_SCFTYPE_MCSCF 5 /* multi-configuration SCF */

#define	MOLFILE_SCFTYPE_NONE 0 /* calculation didn't make use of SCF */

#define	MOLFILE_SCFTYPE_RHF 1 /* restricted Hartree-Fock */

#define	MOLFILE_SCFTYPE_ROHF 3 /* restricted open-shell Hartree-Fock */

#define	MOLFILE_SCFTYPE_UHF 2 /* unrestricted Hartree-Fock */

#define	MOLFILE_SCFTYPE_UNKNOWN -1 /* no info about the method */

#define	MOLFILE_SUCCESS 0
	succeeded in reading file More...


#define	MOLFILE_NOOPTIONS 0x0000
	Plugin optional data field availability flag. More...

#define	MOLFILE_INSERTION 0x0001
	insertion codes provided More...

#define	MOLFILE_OCCUPANCY 0x0002
	occupancy data provided More...

#define	MOLFILE_BFACTOR 0x0004
	B-factor data provided. More...

#define	MOLFILE_MASS 0x0008
	Atomic mass provided. More...

#define	MOLFILE_CHARGE 0x0010
	Atomic charge provided. More...

#define	MOLFILE_RADIUS 0x0020
	Atomic VDW radius provided. More...

#define	MOLFILE_ALTLOC 0x0040
	Multiple conformations present. More...

#define	MOLFILE_ATOMICNUMBER 0x0080
	Atomic element number provided. More...

#define	MOLFILE_BONDSSPECIAL 0x0100
	Only non-standard bonds provided. More...

#define	MOLFILE_BADOPTIONS 0xFFFFFFFF
	Detect badly behaved plugins. More...


#define	MOLFILE_QMTS_NOOPTIONS 0x0000
	Flags indicating availability of optional data fields for QM timesteps. More...

#define	MOLFILE_QMTS_GRADIENT 0x0001
	energy gradients provided More...

#define	MOLFILE_QMTS_SCFITER 0x0002

Typedefs
typedef struct PLMD::molfile::molfile_qm_timestep_metadata	PLMD::molfile::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. More...

typedef struct PLMD::molfile::molfile_timestep_metadata	PLMD::molfile::molfile_timestep_metadata_t

Enumerations
enum	PLMD::molfile::molfile_graphics_type { PLMD::molfile::MOLFILE_POINT, PLMD::molfile::MOLFILE_TRIANGLE, PLMD::molfile::MOLFILE_TRINORM, PLMD::molfile::MOLFILE_NORMS, PLMD::molfile::MOLFILE_LINE, PLMD::molfile::MOLFILE_CYLINDER, PLMD::molfile::MOLFILE_CAPCYL, PLMD::molfile::MOLFILE_CONE, PLMD::molfile::MOLFILE_SPHERE, PLMD::molfile::MOLFILE_TEXT, PLMD::molfile::MOLFILE_COLOR, PLMD::molfile::MOLFILE_TRICOLOR }
	Enumeration of all of the supported graphics objects that can be read from graphics file reader plugins. More...

enum	PLMD::molfile::molfile_qm_charge_type { PLMD::molfile::MOLFILE_QMCHARGE_UNKNOWN, PLMD::molfile::MOLFILE_QMCHARGE_MULLIKEN, PLMD::molfile::MOLFILE_QMCHARGE_LOWDIN, PLMD::molfile::MOLFILE_QMCHARGE_ESP, PLMD::molfile::MOLFILE_QMCHARGE_NPA }
	Enumeration of all of the supported QM related charge types. More...

enum	PLMD::molfile::molfile_qm_wavefunc_type { PLMD::molfile::MOLFILE_WAVE_CANON, PLMD::molfile::MOLFILE_WAVE_GEMINAL, PLMD::molfile::MOLFILE_WAVE_MCSCFNAT, PLMD::molfile::MOLFILE_WAVE_MCSCFOPT, PLMD::molfile::MOLFILE_WAVE_CINATUR, PLMD::molfile::MOLFILE_WAVE_PIPEK, PLMD::molfile::MOLFILE_WAVE_BOYS, PLMD::molfile::MOLFILE_WAVE_RUEDEN, PLMD::molfile::MOLFILE_WAVE_NAO, PLMD::molfile::MOLFILE_WAVE_PNAO, PLMD::molfile::MOLFILE_WAVE_NHO, PLMD::molfile::MOLFILE_WAVE_PNHO, PLMD::molfile::MOLFILE_WAVE_NBO, PLMD::molfile::MOLFILE_WAVE_PNBO, PLMD::molfile::MOLFILE_WAVE_PNLMO, PLMD::molfile::MOLFILE_WAVE_NLMO, PLMD::molfile::MOLFILE_WAVE_MOAO, PLMD::molfile::MOLFILE_WAVE_NATO, PLMD::molfile::MOLFILE_WAVE_UNKNOWN }
	Enumeration of all of the wavefunction types that can be read from QM file reader plugins. More...

Detailed Description

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

Macro Definition Documentation

◆ MOL_FILE_PLUGIN_H

#define MOL_FILE_PLUGIN_H

◆ MOLFILE_ALTLOC

#define MOLFILE_ALTLOC 0x0040

Multiple conformations present.

◆ MOLFILE_ATOMICNUMBER

#define MOLFILE_ATOMICNUMBER 0x0080

Atomic element number provided.

◆ MOLFILE_BADOPTIONS

#define MOLFILE_BADOPTIONS 0xFFFFFFFF

Detect badly behaved plugins.

◆ MOLFILE_BFACTOR

#define MOLFILE_BFACTOR 0x0004

B-factor data provided.

◆ MOLFILE_BIGBUFSIZ

#define MOLFILE_BIGBUFSIZ 4096

maximum chars in long strings

◆ MOLFILE_BONDSSPECIAL

#define MOLFILE_BONDSSPECIAL 0x0100

Only non-standard bonds provided.

◆ MOLFILE_BUFSIZ

#define MOLFILE_BUFSIZ 81

Maximum string size macro.

maximum chars in string data

◆ MOLFILE_CHARGE

#define MOLFILE_CHARGE 0x0010

Atomic charge provided.

◆ MOLFILE_CONVERTER_PLUGIN_TYPE

#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.

◆ MOLFILE_DIRECTIO_MAX_BLOCK_SIZE

#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096

◆ MOLFILE_DIRECTIO_MIN_BLOCK_SIZE

#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.

◆ MOLFILE_EOF

#define MOLFILE_EOF -1

end of file

◆ MOLFILE_ERROR

#define MOLFILE_ERROR -1

error reading/opening a file

◆ MOLFILE_INSERTION

#define MOLFILE_INSERTION 0x0001

insertion codes provided

◆ MOLFILE_MASS

#define MOLFILE_MASS 0x0008

Atomic mass provided.

◆ MOLFILE_MAXWAVEPERTS

#define MOLFILE_MAXWAVEPERTS 25

maximum number of wavefunctions per timestep

◆ MOLFILE_NOOPTIONS

#define MOLFILE_NOOPTIONS 0x0000

Plugin optional data field availability flag.

no optional data

◆ MOLFILE_NOSTRUCTUREDATA

#define MOLFILE_NOSTRUCTUREDATA -2

no structure data in this file

◆ MOLFILE_NUMATOMS_NONE

#define MOLFILE_NUMATOMS_NONE 0

no atoms in this file type

◆ MOLFILE_NUMATOMS_UNKNOWN

#define MOLFILE_NUMATOMS_UNKNOWN -1

unknown number of atoms

◆ MOLFILE_OCCUPANCY

#define MOLFILE_OCCUPANCY 0x0002

occupancy data provided

◆ MOLFILE_PLUGIN_TYPE

#define MOLFILE_PLUGIN_TYPE "mol file reader"

Define a common plugin type to be used when registering the plugin.

◆ MOLFILE_QMSTATUS_FILE_TRUNCATED

#define MOLFILE_QMSTATUS_FILE_TRUNCATED 3 /* file was truncated */

◆ MOLFILE_QMSTATUS_OPT_CONV

#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */

◆ MOLFILE_QMSTATUS_OPT_NOT_CONV

#define MOLFILE_QMSTATUS_OPT_NOT_CONV 2 /* optimization not converged */

◆ MOLFILE_QMSTATUS_SCF_NOT_CONV

#define MOLFILE_QMSTATUS_SCF_NOT_CONV 1 /* SCF convergence failed */

◆ MOLFILE_QMSTATUS_UNKNOWN

#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */

◆ MOLFILE_QMTS_GRADIENT

#define MOLFILE_QMTS_GRADIENT 0x0001

energy gradients provided

◆ MOLFILE_QMTS_NOOPTIONS

#define MOLFILE_QMTS_NOOPTIONS 0x0000

Flags indicating availability of optional data fields for QM timesteps.

no optional data

◆ MOLFILE_QMTS_SCFITER

#define MOLFILE_QMTS_SCFITER 0x0002

◆ MOLFILE_RADIUS

#define MOLFILE_RADIUS 0x0020

Atomic VDW radius provided.

◆ MOLFILE_RUNTYPE_DYNAMICS

#define MOLFILE_RUNTYPE_DYNAMICS

Value:

8  /* Any type of molecular dynamics
                                       * e.g. Born-Oppenheimer, Car-Parinello,
                                       * or classical MD */

◆ MOLFILE_RUNTYPE_ENERGY

#define MOLFILE_RUNTYPE_ENERGY 1 /* single point run */

◆ MOLFILE_RUNTYPE_GRADIENT

#define MOLFILE_RUNTYPE_GRADIENT 6 /* energy gradient calculation */

◆ MOLFILE_RUNTYPE_HESSIAN

#define MOLFILE_RUNTYPE_HESSIAN 4 /* Hessian/frequency calculation */

◆ MOLFILE_RUNTYPE_MEX

#define MOLFILE_RUNTYPE_MEX 7 /* minimum energy crossing */

◆ MOLFILE_RUNTYPE_OPTIMIZE

#define MOLFILE_RUNTYPE_OPTIMIZE 2 /* geometry optimization */

◆ MOLFILE_RUNTYPE_PROPERTIES

#define MOLFILE_RUNTYPE_PROPERTIES

Value:

9 /* Properties were calculated from a

* wavefunction that was read from file */

◆ MOLFILE_RUNTYPE_SADPOINT

#define MOLFILE_RUNTYPE_SADPOINT 3 /* saddle point search */

◆ MOLFILE_RUNTYPE_SURFACE

#define MOLFILE_RUNTYPE_SURFACE 5 /* potential surface scan */

◆ MOLFILE_RUNTYPE_UNKNOWN

#define MOLFILE_RUNTYPE_UNKNOWN 0 /* single point run */

◆ MOLFILE_SCFTYPE_FF

#define MOLFILE_SCFTYPE_FF 6 /* classical force-field based sim. */

◆ MOLFILE_SCFTYPE_GVB

#define MOLFILE_SCFTYPE_GVB 4 /* generalized valence bond orbitals */

◆ MOLFILE_SCFTYPE_MCSCF

#define MOLFILE_SCFTYPE_MCSCF 5 /* multi-configuration SCF */

◆ MOLFILE_SCFTYPE_NONE

#define MOLFILE_SCFTYPE_NONE 0 /* calculation didn't make use of SCF */

◆ MOLFILE_SCFTYPE_RHF

#define MOLFILE_SCFTYPE_RHF 1 /* restricted Hartree-Fock */

◆ MOLFILE_SCFTYPE_ROHF

#define MOLFILE_SCFTYPE_ROHF 3 /* restricted open-shell Hartree-Fock */

◆ MOLFILE_SCFTYPE_UHF

#define MOLFILE_SCFTYPE_UHF 2 /* unrestricted Hartree-Fock */

◆ MOLFILE_SCFTYPE_UNKNOWN

#define MOLFILE_SCFTYPE_UNKNOWN -1 /* no info about the method */

◆ MOLFILE_SUCCESS

#define MOLFILE_SUCCESS 0

succeeded in reading file

Classes

Namespaces

Macros

Typedefs

Enumerations