diff --git a/src/USER-MOLFILE/README b/src/USER-MOLFILE/README
index f6defed6ae849e87456f4df61b81b163e30cc34a..9a2833365dd9ebd526930af9b6cb6c5b0e96c398 100644
--- a/src/USER-MOLFILE/README
+++ b/src/USER-MOLFILE/README
@@ -28,8 +28,7 @@ taken from. These header files can be found inside the VMD
installation tree under: "plugins/include".
For convenience, this package includes a set of header files that is
-compatible with VMD 1.9 and 1.9.1 (the current version in June 2012)
-and should be compilable with VMD versions back to about version 1.8.4
+compatible with VMD 1.9.3 (the current version in April 2017)
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
diff --git a/src/USER-MOLFILE/molfile_plugin.h b/src/USER-MOLFILE/molfile_plugin.h
index 7a2d7ca42e6f35293e8d609a2c1c469b02c145cb..714b06539fb061dd73b3575fdf68e881508c91ec 100644
--- a/src/USER-MOLFILE/molfile_plugin.h
+++ b/src/USER-MOLFILE/molfile_plugin.h
@@ -11,14 +11,14 @@
*
* $RCSfile: molfile_plugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
- * $Revision: 1.103 $ $Date: 2011/03/05 03:56:11 $
+ * $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
*
***************************************************************************/
-/** @file
+/** @file
* API for C extensions to define a way to load structure, coordinate,
- * trajectory, and volumetric data files
- */
+ * trajectory, and volumetric data files
+ */
#ifndef MOL_FILE_PLUGIN_H
#define MOL_FILE_PLUGIN_H
@@ -60,6 +60,21 @@ typedef ssize_t molfile_ssize_t; /**< for frame counts */
#define MOLFILE_MAXWAVEPERTS 25 /**< maximum number of wavefunctions
* per timestep */
+/**
+ * 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.
+ */
+#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE 4096
+#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096
+
/**
* File level comments, origin information, and annotations.
@@ -74,16 +89,16 @@ typedef struct {
} molfile_metadata_t;
-/*
- * Struct for specifying atoms in a molecular structure. The first
- * six components are required, the rest are optional and their presence is
+/*
+ * Struct for specifying atoms in a molecular structure. The first
+ * six components are required, the rest are optional and their presence is
* indicating by setting the corresponding bit in optsflag. When omitted,
- * the application (for read_structure) or plugin (for write_structure)
- * must be able to supply default values if the missing parameters are
+ * the application (for read_structure) or plugin (for write_structure)
+ * must be able to supply default values if the missing parameters are
* part of its internal data structure.
* Note that it is not possible to specify coordinates with this structure.
- * This is intentional; all coordinate I/O is done with the read_timestep and
- * write_timestep functions.
+ * This is intentional; all coordinate I/O is done with the read_timestep and
+ * write_timestep functions.
*/
/**
@@ -96,8 +111,17 @@ typedef struct {
char resname[8]; /**< required residue name string */
int resid; /**< required integer residue ID */
char segid[8]; /**< required segment name string, or "" */
+#if 0 && vmdplugin_ABIVERSION > 17
+ /* The new PDB file formats allows for much larger structures, */
+ /* which can therefore require longer chain ID strings. The */
+ /* new PDBx/mmCIF file formats do not have length limits on */
+ /* fields, so PDB chains could be arbitrarily long strings */
+ /* in such files. At present, we know we need at least 3-char */
+ /* chains for existing PDBx/mmCIF files. */
+ char chain[4]; /**< required chain name, or "" */
+#else
char chain[2]; /**< required chain name, or "" */
-
+#endif
/* rest are optional; use optflags to specify what's present */
char altloc[2]; /**< optional PDB alternate location code */
char insertion[2]; /**< optional PDB insertion code */
@@ -107,6 +131,23 @@ typedef struct {
float charge; /**< optional charge value */
float radius; /**< optional radius value */
int atomicnumber; /**< optional element atomic number */
+
+#if 0
+ char complex[16];
+ char assembly[16];
+ int qmregion;
+ int qmregionlink;
+ int qmlayer;
+ int qmlayerlink;
+ int qmfrag;
+ int qmfraglink;
+ string qmecp;
+ int qmadapt;
+ int qmect; /**< boolean */
+ int qmparam;
+ int autoparam;
+#endif
+
#if defined(DESRES_CTNUMBER)
int ctnumber; /**< mae ct block, 0-based, including meta */
#endif
@@ -128,7 +169,7 @@ typedef struct {
#define MOLFILE_CTNUMBER 0x0200 /**< ctnumber provided */
#endif
#define MOLFILE_BADOPTIONS 0xFFFFFFFF /**< Detect badly behaved plugins */
-
+
/*@}*/
/*@{*/
@@ -140,38 +181,32 @@ typedef struct {
#define MOLFILE_QMTS_SCFITER 0x0002
/*@}*/
-#if vmdplugin_ABIVERSION > 10
typedef struct molfile_timestep_metadata {
unsigned int count; /**< total # timesteps; -1 if unknown */
unsigned int avg_bytes_per_timestep; /** bytes per timestep */
int has_velocities; /**< if timesteps have velocities */
} molfile_timestep_metadata_t;
-#endif
/*
* Per-timestep atom coordinates and periodic cell information
- */
+ */
typedef struct {
float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
-#if vmdplugin_ABIVERSION > 10
float *velocities; /**< space for velocities of all atoms; same layout */
/**< NULL unless has_velocities is set */
-#endif
- /*@{*/
+ /*@{*/
/**
* Unit cell specification of the form A, B, C, alpha, beta, gamma.
* notes: A, B, C are side lengths of the unit cell
* alpha = angle between b and c
* beta = angle between a and c
* gamma = angle between a and b
- */
- float A, B, C, alpha, beta, gamma;
- /*@}*/
+ */
+ float A, B, C, alpha, beta, gamma;
+ /*@}*/
-#if vmdplugin_ABIVERSION > 10
double physical_time; /**< physical time point associated with this frame */
-#endif
#if defined(DESRES_READ_TIMESTEP2)
/* HACK to support generic trajectory information */
@@ -188,7 +223,7 @@ typedef struct {
/**
* Metadata for volumetric datasets, read initially and used for subsequent
- * memory allocations and file loading.
+ * memory allocations and file loading.
*/
typedef struct {
char dataname[256]; /**< name of volumetric data set */
@@ -198,29 +233,48 @@ typedef struct {
* x/y/z axis:
* These the three cell sides, providing both direction and length
* (not unit vectors) for the x, y, and z axes. In the simplest
- * case, these would be <size,0,0> <0,size,0> and <0,0,size) for
+ * case, these would be <size,0,0> <0,size,0> and <0,0,size) for
* an orthogonal cubic volume set. For other cell shapes these
* axes can be oriented non-orthogonally, and the parallelpiped
* may have different side lengths, not just a cube/rhombus.
*/
- float xaxis[3]; /**< direction (and length) for X axis */
+ float xaxis[3]; /**< direction (and length) for X axis */
float yaxis[3]; /**< direction (and length) for Y axis */
float zaxis[3]; /**< direction (and length) for Z axis */
/*
- * x/y/z size:
+ * x/y/z size:
* Number of grid cells along each axis. This is _not_ the
* physical size of the box, this is the number of voxels in each
- * direction, independent of the shape of the volume set.
+ * direction, independent of the shape of the volume set.
*/
- int xsize; /**< number of grid cells along the X axis */
- int ysize; /**< number of grid cells along the Y axis */
- int zsize; /**< number of grid cells along the Z axis */
-
- int has_color; /**< flag indicating presence of voxel color data */
+ int xsize; /**< number of grid cells along the X axis */
+ int ysize; /**< number of grid cells along the Y axis */
+ int zsize; /**< number of grid cells along the Z axis */
+
+#if vmdplugin_ABIVERSION > 16
+ int has_scalar; /**< flag indicating presence of scalar volume */
+ int has_gradient; /**< flag indicating presence of vector volume */
+ int has_variance; /**< flag indicating presence of variance map */
+#endif
+ int has_color; /**< flag indicating presence of voxel color data */
} molfile_volumetric_t;
+#if vmdplugin_ABIVERSION > 16
+/**
+ * Volumetric dataset read/write structure with both flag/parameter sets
+ * and VMD-allocated pointers for fields to be used by the plugin.
+ */
+typedef struct {
+ int setidx; /**< volumetric dataset index to load/save */
+ float *scalar; /**< scalar density/potential field data */
+ float *gradient; /**< gradient vector field */
+ float *variance; /**< variance map indicating signal/noise */
+ float *rgb3f; /**< RGB floating point color texture map */
+ unsigned char *rgb3u; /**< RGB unsigned byte color texture map */
+} molfile_volumetric_readwrite_t;
+#endif
/**************************************************************
@@ -231,9 +285,6 @@ typedef struct {
**************************************************************
**************************************************************/
-#if vmdplugin_ABIVERSION > 9
-
-
/* macros for the convergence status of a QM calculation. */
#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */
#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */
@@ -297,10 +348,10 @@ typedef struct {
/**
* QM run info. Parameters that stay unchanged during a single file.
- */
+ */
typedef struct {
int nproc; /**< number of processors used. */
- int memory; /**< amount of memory used in Mbyte. */
+ int memory; /**< amount of memory used in Mbyte. */
int runtype; /**< flag indicating the calculation method. */
int scftype; /**< SCF type: RHF, UHF, ROHF, GVB or MCSCF wfn. */
int status; /**< indicates wether SCF and geometry optimization
@@ -333,9 +384,9 @@ typedef struct {
* array size = 2*num_basis_funcs
* The basis must NOT be normalized. */
int *atomic_number; /**< atomic numbers (chem. element) of atoms in basis set */
- int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
+ int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
* cartesian components of the angular momentum.
- * E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
+ * E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
*/
int *shell_types; /**< type for each shell in basis */
} molfile_qm_basis_t;
@@ -409,9 +460,9 @@ enum molfile_qm_wavefunc_type {
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_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
};
@@ -442,7 +493,7 @@ typedef struct molfile_qm_timestep_metadata {
int has_orben_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital energy flags */
int has_occup_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital occupancy flags */
int num_wavef ; /**< # wavefunctions in this ts */
- int wavef_size; /**< size of one wavefunction
+ int wavef_size; /**< size of one wavefunction
* (# of gaussian basis fctns) */
int num_charge_sets; /**< # of charge values per atom */
} molfile_qm_timestep_metadata_t;
@@ -485,8 +536,6 @@ typedef struct {
} molfile_qm_timestep_t;
-#endif
-
/**************************************************************
**************************************************************/
@@ -498,14 +547,14 @@ typedef struct {
* from graphics file reader plugins.
*/
enum molfile_graphics_type {
- MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
- MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
+ MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
+ MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
MOLFILE_SPHERE, MOLFILE_TEXT, MOLFILE_COLOR, MOLFILE_TRICOLOR
};
/**
* Individual graphics object/element data
- */
+ */
typedef struct {
int type; /* One of molfile_graphics_type */
int style; /* A general style parameter */
@@ -521,13 +570,13 @@ typedef struct {
type data style size
---- ---- ----- ----
point x, y, z pixel size
-triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
-trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
+triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
+trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
the next array element must be NORMS
-tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
+tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
the next array elements must be NORMS
the following element must be COLOR, with three RGB triples
-norms x1,y1,z1,x2,y2,z2,x3,y3,z3
+norms x1,y1,z1,x2,y2,z2,x3,y3,z3
line x1,y1,z1,x2,y2,z2 0=solid pixel width
1=stippled
cylinder x1,y1,z1,x2,y2,z2 resolution radius
@@ -541,41 +590,41 @@ color r, g, b
/**
* Main file reader API. Any function in this struct may be NULL
* if not implemented by the plugin; the application checks this to determine
- * what functionality is present in the plugin.
- */
+ * what functionality is present in the plugin.
+ */
typedef struct {
/**
- * Required header
+ * Required header
*/
vmdplugin_HEAD
/**
- * Filename extension for this file type. May be NULL if no filename
+ * Filename extension for this file type. May be NULL if no filename
* 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;
/**
* 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.
*/
- 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.
*/
@@ -587,15 +636,15 @@ typedef struct {
* 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.
- * 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.
*
* 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
+
diff --git a/src/USER-MOLFILE/vmdplugin.h b/src/USER-MOLFILE/vmdplugin.h
index 37299408fefe51a4ce9b80a613562349c402cd89..bbbc53c9bbfd9980028a7fff6ece2d06cfa08127 100644
--- a/src/USER-MOLFILE/vmdplugin.h
+++ b/src/USER-MOLFILE/vmdplugin.h
@@ -11,26 +11,26 @@
*
* $RCSfile: vmdplugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
- * $Revision: 1.32 $ $Date: 2009/02/24 05:12:35 $
+ * $Revision: 1.33 $ $Date: 2015/10/29 05:10:54 $
*
***************************************************************************/
/** @file
* This header must be included by every VMD plugin library. It defines the
- * API for every plugin so that VMD can organize the plugins it finds.
+ * API for every plugin so that VMD can organize the plugins it finds.
*/
#ifndef VMD_PLUGIN_H
#define VMD_PLUGIN_H
-/*
+/*
* Preprocessor tricks to make it easier for us to redefine the names of
* functions when building static plugins.
*/
#if !defined(VMDPLUGIN)
-/**
- * macro defining VMDPLUGIN if it hasn't already been set to the name of
+/**
+ * macro defining VMDPLUGIN if it hasn't already been set to the name of
* a static plugin that is being compiled. This is the catch-all case.
*/
#define VMDPLUGIN vmdplugin
@@ -38,11 +38,11 @@
/** concatenation macro, joins args x and y together as a single string */
#define xcat(x, y) cat(x, y)
/** concatenation macro, joins args x and y together as a single string */
-#define cat(x, y) x ## y
+#define cat(x, y) x ## y
/*
- * macros to correctly define plugin function names depending on whether
- * the plugin is being compiled for static linkage or dynamic loading.
+ * macros to correctly define plugin function names depending on whether
+ * the plugin is being compiled for static linkage or dynamic loading.
* When compiled for static linkage, each plugin needs to have unique
* function names for all of its entry points. When compiled for dynamic
* loading, the plugins must name their entry points consistently so that
@@ -59,13 +59,13 @@
/** "WIN32" is defined on both WIN32 and WIN64 platforms... */
-#if (defined(WIN32))
+#if (defined(WIN32))
#define WIN32_LEAN_AND_MEAN
#include <windows.h>
#if !defined(STATIC_PLUGIN)
#if defined(VMDPLUGIN_EXPORTS)
-/**
+/**
* Only define DllMain for plugins, not in VMD or in statically linked plugins
* VMDPLUGIN_EXPORTS is only defined when compiling dynamically loaded plugins
*/
@@ -86,7 +86,7 @@ BOOL APIENTRY DllMain( HANDLE hModule,
#endif /* ! STATIC_PLUGIN */
#else
/** If we're not compiling on Windows, then this macro is defined empty */
-#define VMDPLUGIN_API
+#define VMDPLUGIN_API
#endif
/** define plugin linkage correctly for both C and C++ based plugins */
@@ -96,13 +96,13 @@ BOOL APIENTRY DllMain( HANDLE hModule,
#define VMDPLUGIN_EXTERN extern VMDPLUGIN_API
#endif /* __cplusplus */
-/*
- * Plugin API functions start here
+/*
+ * Plugin API functions start here
*/
-/**
- * Init routine: called the first time the library is loaded by the
+/**
+ * Init routine: called the first time the library is loaded by the
* application and before any other API functions are referenced.
* Return 0 on success.
*/
@@ -110,15 +110,15 @@ VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
/**
* Macro for creating a struct header used in all plugin structures.
- *
- * This header should be placed at the top of every plugin API definition
+ *
+ * This header should be placed at the top of every plugin API definition
* so that it can be treated as a subtype of the base plugin type.
*
* abiversion: Defines the ABI for the base plugin type (not for other plugins)
* type: A string descriptor of the plugin type.
* name: A name for the plugin.
* author: A string identifier, possibly including newlines.
- * Major and minor version.
+ * Major and minor version.
* is_reentrant: Whether this library can be run concurrently with itself.
*/
#define vmdplugin_HEAD \
@@ -129,12 +129,12 @@ VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
const char *author; \
int majorv; \
int minorv; \
- int is_reentrant;
+ int is_reentrant;
-/**
+/**
* Typedef for generic plugin header, individual plugins can
- * make their own structures as long as the header info remains
- * the same as the generic plugin header, most easily done by
+ * make their own structures as long as the header info remains
+ * the same as the generic plugin header, most easily done by
* using the vmdplugin_HEAD macro.
*/
typedef struct {
@@ -144,7 +144,7 @@ typedef struct {
/**
* Use this macro to initialize the abiversion member of each plugin
*/
-#define vmdplugin_ABIVERSION 16
+#define vmdplugin_ABIVERSION 17
/*@{*/
/** Use this macro to indicate a plugin's thread-safety at registration time */
@@ -158,7 +158,7 @@ typedef struct {
#define VMDPLUGIN_ERROR -1
/*@}*/
-/**
+/**
* Function pointer typedef for register callback functions
*/
typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
@@ -175,16 +175,16 @@ typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
VMDPLUGIN_EXTERN int VMDPLUGIN_register(void *, vmdplugin_register_cb);
/**
- * Allow the library to register Tcl extensions.
+ * Allow the library to register Tcl extensions.
* This API is optional; if found by dlopen, it will be called after first
- * calling init and register.
+ * calling init and register.
*/
-VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp,
+VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp,
vmdplugin_register_cb);
/**
- * The Fini method is called when the application will no longer use
- * any plugins in the library.
+ * The Fini method is called when the application will no longer use
+ * any plugins in the library.
*/
VMDPLUGIN_EXTERN int VMDPLUGIN_fini(void);