forked from lijiext/lammps
Updated to 1.108 from 1.103
This commit is contained in:
ketankhare
GitHub
parent
8051b12ffc
commit
b9177fd6dc
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@ -11,14 +11,14 @@
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*
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* $RCSfile: molfile_plugin.h,v $
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* $Author: johns $ $Locker: $ $State: Exp $
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* $Revision: 1.103 $ $Date: 2011/03/05 03:56:11 $
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* $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
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*
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***************************************************************************/
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/** @file
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/** @file
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* API for C extensions to define a way to load structure, coordinate,
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* trajectory, and volumetric data files
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*/
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* trajectory, and volumetric data files
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*/
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#ifndef MOL_FILE_PLUGIN_H
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#define MOL_FILE_PLUGIN_H
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@ -60,6 +60,21 @@ typedef ssize_t molfile_ssize_t; /**< for frame counts */
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#define MOLFILE_MAXWAVEPERTS 25 /**< maximum number of wavefunctions
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* per timestep */
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/**
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* Hard-coded direct-I/O page size constants for use by both VMD
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* and the plugins that want to use direct, unbuffered I/O for high
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* performance with SSDs etc. We use two constants to define the
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* range of hardware page sizes that we can support, so that we can
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* add support for larger 8KB or 16KB page sizes in the future
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* as they become more prevalent in high-end storage systems.
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*
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* At present, VMD uses a hard-coded 4KB page size to reduce memory
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* fragmentation, but these constants will make it easier to enable the
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* use of larger page sizes in the future if it becomes necessary.
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*/
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#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE 4096
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#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096
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/**
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* File level comments, origin information, and annotations.
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@ -74,16 +89,16 @@ typedef struct {
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} molfile_metadata_t;
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/*
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* Struct for specifying atoms in a molecular structure. The first
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* six components are required, the rest are optional and their presence is
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/*
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* Struct for specifying atoms in a molecular structure. The first
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* six components are required, the rest are optional and their presence is
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* indicating by setting the corresponding bit in optsflag. When omitted,
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* the application (for read_structure) or plugin (for write_structure)
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* must be able to supply default values if the missing parameters are
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* the application (for read_structure) or plugin (for write_structure)
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* must be able to supply default values if the missing parameters are
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* part of its internal data structure.
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* Note that it is not possible to specify coordinates with this structure.
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* This is intentional; all coordinate I/O is done with the read_timestep and
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* write_timestep functions.
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* This is intentional; all coordinate I/O is done with the read_timestep and
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* write_timestep functions.
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*/
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/**
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@ -96,8 +111,17 @@ typedef struct {
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char resname[8]; /**< required residue name string */
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int resid; /**< required integer residue ID */
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char segid[8]; /**< required segment name string, or "" */
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#if 0 && vmdplugin_ABIVERSION > 17
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/* The new PDB file formats allows for much larger structures, */
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/* which can therefore require longer chain ID strings. The */
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/* new PDBx/mmCIF file formats do not have length limits on */
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/* fields, so PDB chains could be arbitrarily long strings */
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/* in such files. At present, we know we need at least 3-char */
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/* chains for existing PDBx/mmCIF files. */
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char chain[4]; /**< required chain name, or "" */
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#else
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char chain[2]; /**< required chain name, or "" */
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#endif
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/* rest are optional; use optflags to specify what's present */
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char altloc[2]; /**< optional PDB alternate location code */
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char insertion[2]; /**< optional PDB insertion code */
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@ -107,6 +131,23 @@ typedef struct {
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float charge; /**< optional charge value */
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float radius; /**< optional radius value */
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int atomicnumber; /**< optional element atomic number */
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#if 0
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char complex[16];
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char assembly[16];
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int qmregion;
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int qmregionlink;
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int qmlayer;
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int qmlayerlink;
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int qmfrag;
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int qmfraglink;
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string qmecp;
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int qmadapt;
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int qmect; /**< boolean */
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int qmparam;
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int autoparam;
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#endif
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#if defined(DESRES_CTNUMBER)
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int ctnumber; /**< mae ct block, 0-based, including meta */
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#endif
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@ -128,7 +169,7 @@ typedef struct {
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#define MOLFILE_CTNUMBER 0x0200 /**< ctnumber provided */
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#endif
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#define MOLFILE_BADOPTIONS 0xFFFFFFFF /**< Detect badly behaved plugins */
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/*@}*/
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/*@{*/
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@ -140,38 +181,32 @@ typedef struct {
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#define MOLFILE_QMTS_SCFITER 0x0002
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/*@}*/
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#if vmdplugin_ABIVERSION > 10
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typedef struct molfile_timestep_metadata {
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unsigned int count; /**< total # timesteps; -1 if unknown */
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unsigned int avg_bytes_per_timestep; /** bytes per timestep */
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int has_velocities; /**< if timesteps have velocities */
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} molfile_timestep_metadata_t;
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#endif
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/*
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* Per-timestep atom coordinates and periodic cell information
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*/
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*/
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typedef struct {
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float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
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#if vmdplugin_ABIVERSION > 10
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float *velocities; /**< space for velocities of all atoms; same layout */
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/**< NULL unless has_velocities is set */
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#endif
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/*@{*/
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/*@{*/
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/**
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* Unit cell specification of the form A, B, C, alpha, beta, gamma.
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* notes: A, B, C are side lengths of the unit cell
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* alpha = angle between b and c
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* beta = angle between a and c
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* gamma = angle between a and b
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*/
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float A, B, C, alpha, beta, gamma;
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/*@}*/
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*/
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float A, B, C, alpha, beta, gamma;
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/*@}*/
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#if vmdplugin_ABIVERSION > 10
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double physical_time; /**< physical time point associated with this frame */
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#endif
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#if defined(DESRES_READ_TIMESTEP2)
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/* HACK to support generic trajectory information */
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@ -188,7 +223,7 @@ typedef struct {
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/**
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* Metadata for volumetric datasets, read initially and used for subsequent
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* memory allocations and file loading.
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* memory allocations and file loading.
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*/
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typedef struct {
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char dataname[256]; /**< name of volumetric data set */
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@ -198,29 +233,48 @@ typedef struct {
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* x/y/z axis:
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* These the three cell sides, providing both direction and length
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* (not unit vectors) for the x, y, and z axes. In the simplest
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* case, these would be <size,0,0> <0,size,0> and <0,0,size) for
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* case, these would be <size,0,0> <0,size,0> and <0,0,size) for
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* an orthogonal cubic volume set. For other cell shapes these
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* axes can be oriented non-orthogonally, and the parallelpiped
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* may have different side lengths, not just a cube/rhombus.
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*/
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float xaxis[3]; /**< direction (and length) for X axis */
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float xaxis[3]; /**< direction (and length) for X axis */
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float yaxis[3]; /**< direction (and length) for Y axis */
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float zaxis[3]; /**< direction (and length) for Z axis */
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/*
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* x/y/z size:
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* x/y/z size:
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* Number of grid cells along each axis. This is _not_ the
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* physical size of the box, this is the number of voxels in each
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* direction, independent of the shape of the volume set.
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* direction, independent of the shape of the volume set.
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*/
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int xsize; /**< number of grid cells along the X axis */
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int ysize; /**< number of grid cells along the Y axis */
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int zsize; /**< number of grid cells along the Z axis */
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int xsize; /**< number of grid cells along the X axis */
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int ysize; /**< number of grid cells along the Y axis */
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int zsize; /**< number of grid cells along the Z axis */
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int has_color; /**< flag indicating presence of voxel color data */
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#if vmdplugin_ABIVERSION > 16
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int has_scalar; /**< flag indicating presence of scalar volume */
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int has_gradient; /**< flag indicating presence of vector volume */
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int has_variance; /**< flag indicating presence of variance map */
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#endif
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int has_color; /**< flag indicating presence of voxel color data */
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} molfile_volumetric_t;
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#if vmdplugin_ABIVERSION > 16
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/**
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* Volumetric dataset read/write structure with both flag/parameter sets
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* and VMD-allocated pointers for fields to be used by the plugin.
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*/
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typedef struct {
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int setidx; /**< volumetric dataset index to load/save */
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float *scalar; /**< scalar density/potential field data */
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float *gradient; /**< gradient vector field */
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float *variance; /**< variance map indicating signal/noise */
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float *rgb3f; /**< RGB floating point color texture map */
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unsigned char *rgb3u; /**< RGB unsigned byte color texture map */
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} molfile_volumetric_readwrite_t;
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#endif
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/**************************************************************
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@ -231,9 +285,6 @@ typedef struct {
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**************************************************************
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**************************************************************/
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#if vmdplugin_ABIVERSION > 9
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/* macros for the convergence status of a QM calculation. */
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#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */
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#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */
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@ -297,10 +348,10 @@ typedef struct {
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/**
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* QM run info. Parameters that stay unchanged during a single file.
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*/
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*/
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typedef struct {
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int nproc; /**< number of processors used. */
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int memory; /**< amount of memory used in Mbyte. */
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int memory; /**< amount of memory used in Mbyte. */
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int runtype; /**< flag indicating the calculation method. */
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int scftype; /**< SCF type: RHF, UHF, ROHF, GVB or MCSCF wfn. */
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int status; /**< indicates wether SCF and geometry optimization
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@ -333,9 +384,9 @@ typedef struct {
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* array size = 2*num_basis_funcs
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* The basis must NOT be normalized. */
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int *atomic_number; /**< atomic numbers (chem. element) of atoms in basis set */
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int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
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int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
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* cartesian components of the angular momentum.
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* E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
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* E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
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*/
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int *shell_types; /**< type for each shell in basis */
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} molfile_qm_basis_t;
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@ -409,9 +460,9 @@ enum molfile_qm_wavefunc_type {
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MOLFILE_WAVE_MCSCFNAT, MOLFILE_WAVE_MCSCFOPT,
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MOLFILE_WAVE_CINATUR,
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MOLFILE_WAVE_PIPEK, MOLFILE_WAVE_BOYS, MOLFILE_WAVE_RUEDEN,
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MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO,
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MOLFILE_WAVE_PNHO, MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO,
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MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO, MOLFILE_WAVE_MOAO,
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MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO,
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MOLFILE_WAVE_PNHO, MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO,
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MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO, MOLFILE_WAVE_MOAO,
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MOLFILE_WAVE_NATO, MOLFILE_WAVE_UNKNOWN
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};
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@ -442,7 +493,7 @@ typedef struct molfile_qm_timestep_metadata {
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int has_orben_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital energy flags */
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int has_occup_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital occupancy flags */
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int num_wavef ; /**< # wavefunctions in this ts */
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int wavef_size; /**< size of one wavefunction
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int wavef_size; /**< size of one wavefunction
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* (# of gaussian basis fctns) */
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int num_charge_sets; /**< # of charge values per atom */
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} molfile_qm_timestep_metadata_t;
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@ -485,8 +536,6 @@ typedef struct {
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} molfile_qm_timestep_t;
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#endif
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/**************************************************************
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**************************************************************/
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@ -498,14 +547,14 @@ typedef struct {
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* from graphics file reader plugins.
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*/
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enum molfile_graphics_type {
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MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
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MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
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MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
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MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
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MOLFILE_SPHERE, MOLFILE_TEXT, MOLFILE_COLOR, MOLFILE_TRICOLOR
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};
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/**
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* Individual graphics object/element data
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*/
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*/
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typedef struct {
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int type; /* One of molfile_graphics_type */
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int style; /* A general style parameter */
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@ -521,13 +570,13 @@ typedef struct {
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type data style size
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---- ---- ----- ----
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point x, y, z pixel size
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triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
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trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
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triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
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trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
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the next array element must be NORMS
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tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
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tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
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the next array elements must be NORMS
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the following element must be COLOR, with three RGB triples
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norms x1,y1,z1,x2,y2,z2,x3,y3,z3
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norms x1,y1,z1,x2,y2,z2,x3,y3,z3
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line x1,y1,z1,x2,y2,z2 0=solid pixel width
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1=stippled
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cylinder x1,y1,z1,x2,y2,z2 resolution radius
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@ -541,41 +590,41 @@ color r, g, b
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/**
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* Main file reader API. Any function in this struct may be NULL
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* if not implemented by the plugin; the application checks this to determine
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* what functionality is present in the plugin.
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*/
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* what functionality is present in the plugin.
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*/
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typedef struct {
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/**
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* Required header
|
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* Required header
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*/
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vmdplugin_HEAD
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/**
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* Filename extension for this file type. May be NULL if no filename
|
||||
* Filename extension for this file type. May be NULL if no filename
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||||
* extension exists and/or is known. For file types that match several
|
||||
* common extensions, list them in a comma separated list such as:
|
||||
* "pdb,ent,foo,bar,baz,ban"
|
||||
* The comma separated list will be expanded when filename extension matching
|
||||
* is performed. If multiple plugins solicit the same filename extensions,
|
||||
* the one that lists the extension earliest in its list is selected. In the
|
||||
* the one that lists the extension earliest in its list is selected. In the
|
||||
* case of a "tie", the first one tried/checked "wins".
|
||||
*/
|
||||
const char *filename_extension;
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||||
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||||
/**
|
||||
* Try to open the file for reading. Return an opaque handle, or NULL on
|
||||
* failure. Set the number of atoms; if the number of atoms cannot be
|
||||
* determined, set natoms to MOLFILE_NUMATOMS_UNKNOWN.
|
||||
* failure. Set the number of atoms; if the number of atoms cannot be
|
||||
* determined, set natoms to MOLFILE_NUMATOMS_UNKNOWN.
|
||||
* Filetype should be the name under which this plugin was registered;
|
||||
* this is provided so that plugins can provide the same function pointer
|
||||
* to handle multiple file types.
|
||||
*/
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||||
void *(* open_file_read)(const char *filepath, const char *filetype,
|
||||
void *(* open_file_read)(const char *filepath, const char *filetype,
|
||||
int *natoms);
|
||||
|
||||
|
||||
/**
|
||||
* Read molecular structure from the given file handle. atoms is allocated
|
||||
* by the caller and points to space for natoms.
|
||||
* On success, place atom information in the passed-in pointer.
|
||||
* On success, place atom information in the passed-in pointer.
|
||||
* optflags specifies which optional fields in the atoms will be set by
|
||||
* the plugin.
|
||||
*/
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||||
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@ -587,15 +636,15 @@ typedef struct {
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|||
* Each unique bond should be specified only once, so file formats that list
|
||||
* bonds twice will need post-processing before the results are returned to
|
||||
* the caller.
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||||
* If the plugin provides bond information, but the file loaded doesn't
|
||||
* If the plugin provides bond information, but the file loaded doesn't
|
||||
* actually contain any bond info, the nbonds parameter should be
|
||||
* set to 0 and from/to should be set to NULL to indicate that no bond
|
||||
* information was actually present, and automatic bond search should be
|
||||
* performed.
|
||||
* performed.
|
||||
*
|
||||
* If the plugin provides bond order information, the bondorder array
|
||||
* will contain the bond order for each from/to pair. If not, the bondorder
|
||||
* pointer should be set to NULL, in which case the caller will provide a
|
||||
* pointer should be set to NULL, in which case the caller will provide a
|
||||
* default bond order value of 1.0.
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||||
*
|
||||
* If the plugin provides bond type information, the bondtype array
|
||||
|
|
@ -606,27 +655,23 @@ typedef struct {
|
|||
* and consistency checking.
|
||||
*
|
||||
* These arrays must be freed by the plugin in the close_file_read function.
|
||||
* This function can be called only after read_structure().
|
||||
* Return MOLFILE_SUCCESS if no errors occur.
|
||||
* This function can be called only after read_structure().
|
||||
* Return MOLFILE_SUCCESS if no errors occur.
|
||||
*/
|
||||
#if vmdplugin_ABIVERSION > 14
|
||||
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
|
||||
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
|
||||
int **bondtype, int *nbondtypes, char ***bondtypename);
|
||||
#else
|
||||
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder);
|
||||
#endif
|
||||
|
||||
/**
|
||||
* XXX this function will be augmented and possibly superceded by a
|
||||
* XXX this function will be augmented and possibly superceded by a
|
||||
* new QM-capable version named read_timestep(), when finished.
|
||||
*
|
||||
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
|
||||
* MOLFILE_EOF on EOF. If the molfile_timestep_t argument is NULL, then
|
||||
* the frame should be skipped. Otherwise, the application must prepare
|
||||
* molfile_timestep_t by allocating space in coords for the corresponding
|
||||
* number of coordinates.
|
||||
* The natoms parameter exists because some coordinate file formats
|
||||
* (like CRD) cannot determine for themselves how many atoms are in a
|
||||
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
|
||||
* MOLFILE_EOF on EOF. If the molfile_timestep_t argument is NULL, then
|
||||
* the frame should be skipped. Otherwise, the application must prepare
|
||||
* molfile_timestep_t by allocating space in coords for the corresponding
|
||||
* number of coordinates.
|
||||
* The natoms parameter exists because some coordinate file formats
|
||||
* (like CRD) cannot determine for themselves how many atoms are in a
|
||||
* timestep; the app must therefore obtain this information elsewhere
|
||||
* and provide it to the plugin.
|
||||
*/
|
||||
|
|
@ -636,16 +681,16 @@ typedef struct {
|
|||
* Close the file and release all data. The handle cannot be reused.
|
||||
*/
|
||||
void (* close_file_read)(void *);
|
||||
|
||||
|
||||
/**
|
||||
* Open a coordinate file for writing using the given header information.
|
||||
* Return an opaque handle, or NULL on failure. The application must
|
||||
* specify the number of atoms to be written.
|
||||
* specify the number of atoms to be written.
|
||||
* filetype should be the name under which this plugin was registered.
|
||||
*/
|
||||
void *(* open_file_write)(const char *filepath, const char *filetype,
|
||||
void *(* open_file_write)(const char *filepath, const char *filetype,
|
||||
int natoms);
|
||||
|
||||
|
||||
/**
|
||||
* Write structure information. Return success.
|
||||
*/
|
||||
|
|
@ -653,12 +698,12 @@ typedef struct {
|
|||
|
||||
/**
|
||||
* Write a timestep to the coordinate file. Return MOLFILE_SUCCESS if no
|
||||
* errors occur. If the file contains structure information in each
|
||||
* timestep (like a multi-entry PDB), it will have to cache the information
|
||||
* errors occur. If the file contains structure information in each
|
||||
* timestep (like a multi-entry PDB), it will have to cache the information
|
||||
* from the initial calls from write_structure.
|
||||
*/
|
||||
int (* write_timestep)(void *, const molfile_timestep_t *);
|
||||
|
||||
|
||||
/**
|
||||
* Close the file and release all data. The handle cannot be reused.
|
||||
*/
|
||||
|
|
@ -671,24 +716,27 @@ typedef struct {
|
|||
* the plugin and should be freed by close_file_read(). The application
|
||||
* may call this function any number of times.
|
||||
*/
|
||||
int (* read_volumetric_metadata)(void *, int *nsets,
|
||||
int (* read_volumetric_metadata)(void *, int *nsets,
|
||||
molfile_volumetric_t **metadata);
|
||||
|
||||
/**
|
||||
* Read the specified volumetric data set into the space pointed to by
|
||||
* datablock. The set is specified with a zero-based index. The space
|
||||
/**
|
||||
* Read the specified volumetric data set into the space pointed to by
|
||||
* datablock. The set is specified with a zero-based index. The space
|
||||
* allocated for the datablock must be equal to
|
||||
* xsize * ysize * zsize. No space will be allocated for colorblock
|
||||
* xsize * ysize * zsize. No space will be allocated for colorblock
|
||||
* unless has_color is nonzero; in that case, colorblock should be
|
||||
* filled in with three RGB floats per datapoint.
|
||||
*/
|
||||
int (* read_volumetric_data)(void *, int set, float *datablock,
|
||||
int (* read_volumetric_data)(void *, int set, float *datablock,
|
||||
float *colorblock);
|
||||
#if vmdplugin_ABIVERSION > 16
|
||||
int (* read_volumetric_data_ex)(void *, molfile_volumetric_readwrite_t *v);
|
||||
#endif
|
||||
|
||||
/**
|
||||
* Read raw graphics data stored in this file. Return the number of data
|
||||
* elements and the data itself as an array of molfile_graphics_t in the
|
||||
* pointer provided by the application. The plugin is responsible for
|
||||
* elements and the data itself as an array of molfile_graphics_t in the
|
||||
* pointer provided by the application. The plugin is responsible for
|
||||
* freeing the data when the file is closed.
|
||||
*/
|
||||
int (* read_rawgraphics)(void *, int *nelem, const molfile_graphics_t **data);
|
||||
|
|
@ -698,19 +746,19 @@ typedef struct {
|
|||
* came from, what the accession code for the database is, textual remarks
|
||||
* and other notes pertaining to the contained structure/trajectory/volume
|
||||
* and anything else that's informative at the whole file level.
|
||||
*/
|
||||
*/
|
||||
int (* read_molecule_metadata)(void *, molfile_metadata_t **metadata);
|
||||
|
||||
|
||||
/**
|
||||
* Write bond information for the molecule. The arrays from
|
||||
* and to point to the (one-based) indices of bonded atoms.
|
||||
* Each unique bond will be specified only once by the caller.
|
||||
* File formats that list bonds twice will need to emit both the
|
||||
* Each unique bond will be specified only once by the caller.
|
||||
* File formats that list bonds twice will need to emit both the
|
||||
* from/to and to/from versions of each.
|
||||
* This function must be called before write_structure().
|
||||
* This function must be called before write_structure().
|
||||
*
|
||||
* Like the read_bonds() routine, the bondorder pointer is set to NULL
|
||||
* if the caller doesn't have such information, in which case the
|
||||
* if the caller doesn't have such information, in which case the
|
||||
* plugin should assume a bond order of 1.0 if the file format requires
|
||||
* bond order information.
|
||||
*
|
||||
|
|
@ -721,76 +769,47 @@ typedef struct {
|
|||
* scheme is different from the index numbers.
|
||||
* if the pointers are set to NULL, then this information is not available.
|
||||
* bondtypenames can only be used of bondtypes is also given.
|
||||
* Return MOLFILE_SUCCESS if no errors occur.
|
||||
* Return MOLFILE_SUCCESS if no errors occur.
|
||||
*/
|
||||
#if vmdplugin_ABIVERSION > 14
|
||||
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
|
||||
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
|
||||
int *bondtype, int nbondtypes, char **bondtypename);
|
||||
#else
|
||||
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
|
||||
#endif
|
||||
|
||||
#if vmdplugin_ABIVERSION > 9
|
||||
/**
|
||||
* Write the specified volumetric data set into the space pointed to by
|
||||
* Write the specified volumetric data set into the space pointed to by
|
||||
* datablock. The * allocated for the datablock must be equal to
|
||||
* xsize * ysize * zsize. No space will be allocated for colorblock
|
||||
* xsize * ysize * zsize. No space will be allocated for colorblock
|
||||
* unless has_color is nonzero; in that case, colorblock should be
|
||||
* filled in with three RGB floats per datapoint.
|
||||
*/
|
||||
int (* write_volumetric_data)(void *, molfile_volumetric_t *metadata,
|
||||
float *datablock, float *colorblock);
|
||||
#if vmdplugin_ABIVERSION > 16
|
||||
int (* write_volumetric_data_ex)(void *, molfile_volumetric_t *metadata,
|
||||
molfile_volumetric_readwrite_t *v);
|
||||
#endif
|
||||
|
||||
#if vmdplugin_ABIVERSION > 15
|
||||
/**
|
||||
/**
|
||||
* Read in Angles, Dihedrals, Impropers, and Cross Terms and optionally types.
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
|
||||
*/
|
||||
int (* read_angles)(void *handle, int *numangles, int **angles, int **angletypes,
|
||||
int *numangletypes, char ***angletypenames, int *numdihedrals,
|
||||
int **dihedrals, int **dihedraltypes, int *numdihedraltypes,
|
||||
char ***dihedraltypenames, int *numimpropers, int **impropers,
|
||||
char ***dihedraltypenames, int *numimpropers, int **impropers,
|
||||
int **impropertypes, int *numimpropertypes, char ***impropertypenames,
|
||||
int *numcterms, int **cterms, int *ctermcols, int *ctermrows);
|
||||
|
||||
/**
|
||||
/**
|
||||
* Write out Angles, Dihedrals, Impropers, and Cross Terms
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
|
||||
*/
|
||||
int (* write_angles)(void *handle, int numangles, const int *angles, const int *angletypes,
|
||||
int numangletypes, const char **angletypenames, int numdihedrals,
|
||||
const int *dihedrals, const int *dihedraltypes, int numdihedraltypes,
|
||||
const char **dihedraltypenames, int numimpropers,
|
||||
const char **dihedraltypenames, int numimpropers,
|
||||
const int *impropers, const int *impropertypes, int numimpropertypes,
|
||||
const char **impropertypenames, int numcterms, const int *cterms,
|
||||
const char **impropertypenames, int numcterms, const int *cterms,
|
||||
int ctermcols, int ctermrows);
|
||||
#else
|
||||
/**
|
||||
* Read in Angles, Dihedrals, Impropers, and Cross Terms
|
||||
* Forces are in Kcal/mol
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
|
||||
* as a 2-D matrix)
|
||||
*/
|
||||
int (* read_angles)(void *,
|
||||
int *numangles, int **angles, double **angleforces,
|
||||
int *numdihedrals, int **dihedrals, double **dihedralforces,
|
||||
int *numimpropers, int **impropers, double **improperforces,
|
||||
int *numcterms, int **cterms,
|
||||
int *ctermcols, int *ctermrows, double **ctermforces);
|
||||
|
||||
/**
|
||||
* Write out Angles, Dihedrals, Impropers, and Cross Terms
|
||||
* Forces are in Kcal/mol
|
||||
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
|
||||
* as a 2-D matrix)
|
||||
*/
|
||||
int (* write_angles)(void *,
|
||||
int numangles, const int *angles, const double *angleforces,
|
||||
int numdihedrals, const int *dihedrals, const double *dihedralforces,
|
||||
int numimpropers, const int *impropers, const double *improperforces,
|
||||
int numcterms, const int *cterms,
|
||||
int ctermcols, int ctermrows, const double *ctermforces);
|
||||
#endif
|
||||
|
||||
|
||||
/**
|
||||
|
|
@ -798,7 +817,7 @@ typedef struct {
|
|||
* QM datasets in this file.
|
||||
*
|
||||
* The metadata are the sizes of the QM related data structure
|
||||
* arrays that will be populated by the plugin when
|
||||
* arrays that will be populated by the plugin when
|
||||
* read_qm_rundata() is called. Since the allocation of these
|
||||
* arrays is done by VMD rather than the plugin, VMD needs to
|
||||
* know the sizes beforehand. Consequently read_qm_metadata()
|
||||
|
|
@ -811,7 +830,7 @@ typedef struct {
|
|||
* Read timestep independent QM data.
|
||||
*
|
||||
* Typical data that are defined only once per trajectory are
|
||||
* general info about the calculation (such as the used method),
|
||||
* general info about the calculation (such as the used method),
|
||||
* the basis set and normal modes.
|
||||
* The data structures to be populated must have been allocated
|
||||
* before by VMD according to sizes obtained through
|
||||
|
|
@ -821,32 +840,27 @@ typedef struct {
|
|||
|
||||
|
||||
/**
|
||||
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
|
||||
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
|
||||
* MOLFILE_EOF on EOF. If the molfile_timestep_t or molfile_qm_metadata_t
|
||||
* arguments are NULL, then the coordinate or qm data should be skipped.
|
||||
* Otherwise, the application must prepare molfile_timestep_t and
|
||||
* molfile_qm_timestep_t by allocating space for the corresponding
|
||||
* arguments are NULL, then the coordinate or qm data should be skipped.
|
||||
* Otherwise, the application must prepare molfile_timestep_t and
|
||||
* molfile_qm_timestep_t by allocating space for the corresponding
|
||||
* number of coordinates, orbital wavefunction coefficients, etc.
|
||||
* Since it is common for users to want to load only the final timestep
|
||||
* Since it is common for users to want to load only the final timestep
|
||||
* data from a QM run, the application may provide any combination of
|
||||
* valid, or NULL pointers for the molfile_timestep_t and
|
||||
* valid, or NULL pointers for the molfile_timestep_t and
|
||||
* molfile_qm_timestep_t parameters, depending on what information the
|
||||
* user is interested in.
|
||||
* The natoms and qm metadata parameters exist because some file formats
|
||||
* cannot determine for themselves how many atoms etc are in a
|
||||
* The natoms and qm metadata parameters exist because some file formats
|
||||
* cannot determine for themselves how many atoms etc are in a
|
||||
* timestep; the app must therefore obtain this information elsewhere
|
||||
* and provide it to the plugin.
|
||||
*/
|
||||
int (* read_timestep)(void *, int natoms, molfile_timestep_t *,
|
||||
molfile_qm_metadata_t *, molfile_qm_timestep_t *);
|
||||
#endif
|
||||
|
||||
#if vmdplugin_ABIVERSION > 10
|
||||
int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
|
||||
#endif
|
||||
#if vmdplugin_ABIVERSION > 11
|
||||
int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
|
||||
#endif
|
||||
|
||||
#if defined(DESRES_READ_TIMESTEP2)
|
||||
/**
|
||||
|
|
@ -864,7 +878,6 @@ typedef struct {
|
|||
double * times );
|
||||
#endif
|
||||
|
||||
#if vmdplugin_ABIVERSION > 13
|
||||
/**
|
||||
* Console output, READ-ONLY function pointer.
|
||||
* Function pointer that plugins can use for printing to the host
|
||||
|
|
@ -883,8 +896,8 @@ typedef struct {
|
|||
* application-provided services
|
||||
*/
|
||||
int (* cons_fputs)(const int, const char*);
|
||||
#endif
|
||||
|
||||
} molfile_plugin_t;
|
||||
|
||||
#endif
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue