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dcdplugin.c File Reference

#include "largefiles.h"
#include "fastio.h"
#include <stdio.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <stdlib.h>
#include <stddef.h>
#include <string.h>
#include <math.h>
#include <time.h>
#include "endianswap.h"
#include "molfile_plugin.h"

Go to the source code of this file.

Compounds

struct dcdhandle

Defines

#define M_PI_2   1.57079632679489661922

#define RECSCALE32BIT   1

#define RECSCALE64BIT   2

#define RECSCALEMAX   2

#define DCD_SUCCESS   0

#define DCD_EOF   -1

#define DCD_DNE   -2

#define DCD_OPENFAILED   -3

#define DCD_BADREAD   -4

#define DCD_BADEOF   -5

#define DCD_BADFORMAT   -6

#define DCD_FILEEXISTS   -7

#define DCD_BADMALLOC   -8

#define DCD_BADWRITE   -9

#define DCD_IS_XPLOR   0x00

#define DCD_IS_CHARMM   0x01

#define DCD_HAS_4DIMS   0x02

#define DCD_HAS_EXTRA_BLOCK   0x04

#define DCD_HAS_64BIT_REC   0x08

#define NFILE_POS   8L

#define NSTEP_POS   20L

#define READ(fd, buf, size)   fio_fread(((void *) buf), (size), 1, (fd))

#define WRITE(fd, buf, size)   fio_fwrite(((void *) buf), (size), 1, (fd))

#define CHECK_FREAD(X, msg)   if (X==-1) { return(DCD_BADREAD); }

#define CHECK_FEOF(X, msg)   if (X==0) { return(DCD_BADEOF); }

Functions

void print_dcderror (const char *func, int errcode)

int read_dcdheader (fio_fd fd, int *N, int *NSET, int *ISTART, int *NSAVC, double *DELTA, int *NAMNF, int **FREEINDEXES, float **fixedcoords, int *reverseEndian, int *charmm)

int read_charmm_extrablock (fio_fd fd, int charmm, int reverseEndian, float *unitcell)

int read_fixed_atoms (fio_fd fd, int N, int num_free, const int *indexes, int reverseEndian, const float *fixedcoords, float *freeatoms, float *pos, int charmm)

int read_charmm_4dim (fio_fd fd, int charmm, int reverseEndian)

int read_dcdstep (fio_fd fd, int N, float *X, float *Y, float *Z, float *unitcell, int num_fixed, int first, int *indexes, float *fixedcoords, int reverseEndian, int charmm)

int skip_dcdstep (fio_fd fd, int natoms, int nfixed, int charmm)

int write_dcdstep (fio_fd fd, int curframe, int curstep, int N, const float *X, const float *Y, const float *Z, const double *unitcell, int charmm)

int write_dcdheader (fio_fd fd, const char *remarks, int N, int ISTART, int NSAVC, double DELTA, int with_unitcell, int charmm)

void close_dcd_read (int *indexes, float *fixedcoords)

void * open_dcd_read (const char *path, const char *filetype, int *natoms)

int read_next_timestep (void *v, int natoms, molfile_timestep_t *ts)

void close_file_read (void *v)

void * open_dcd_write (const char *path, const char *filetype, int natoms)

int write_timestep (void *v, const molfile_timestep_t *ts)

void close_file_write (void *v)

VMDPLUGIN_API int VMDPLUGIN_init ()

VMDPLUGIN_API int VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)

VMDPLUGIN_API int VMDPLUGIN_fini ()

Variables

molfile_plugin_t plugin

Define Documentation

#define CHECK_FEOF ( X,
msg ) if (X==0) { return(DCD_BADEOF); }

Definition at line 116 of file dcdplugin.c.
Referenced by read_dcdheader.

#define CHECK_FREAD ( X,
msg ) if (X==-1) { return(DCD_BADREAD); }

Definition at line 115 of file dcdplugin.c.
Referenced by read_dcdheader.

#define DCD_BADEOF -5

Definition at line 91 of file dcdplugin.c.
Referenced by print_dcderror, and skip_dcdstep.

#define DCD_BADFORMAT -6

Definition at line 92 of file dcdplugin.c.
Referenced by print_dcderror, read_dcdheader, read_dcdstep, and read_fixed_atoms.

#define DCD_BADMALLOC -8

Definition at line 94 of file dcdplugin.c.
Referenced by print_dcderror, and read_dcdheader.

#define DCD_BADREAD -4

Definition at line 90 of file dcdplugin.c.
Referenced by print_dcderror, read_charmm_4dim, read_charmm_extrablock, read_dcdstep, and read_fixed_atoms.

#define DCD_BADWRITE -9

Definition at line 95 of file dcdplugin.c.
Referenced by print_dcderror, and write_dcdstep.

#define DCD_DNE -2

Definition at line 88 of file dcdplugin.c.
Referenced by print_dcderror.

#define DCD_EOF -1

Definition at line 87 of file dcdplugin.c.
Referenced by print_dcderror.

#define DCD_FILEEXISTS -7

Definition at line 93 of file dcdplugin.c.
Referenced by print_dcderror.

#define DCD_HAS_4DIMS 0x02

Definition at line 100 of file dcdplugin.c.
Referenced by open_dcd_read, read_charmm_4dim, read_dcdheader, and skip_dcdstep.

#define DCD_HAS_64BIT_REC 0x08

Definition at line 102 of file dcdplugin.c.
Referenced by read_charmm_4dim, read_charmm_extrablock, read_dcdheader, read_dcdstep, read_fixed_atoms, and skip_dcdstep.

#define DCD_HAS_EXTRA_BLOCK 0x04

Definition at line 101 of file dcdplugin.c.
Referenced by open_dcd_read, open_dcd_write, read_charmm_extrablock, read_dcdheader, and skip_dcdstep.

#define DCD_IS_CHARMM 0x01

Definition at line 99 of file dcdplugin.c.
Referenced by open_dcd_write, read_charmm_4dim, read_charmm_extrablock, read_dcdheader, and skip_dcdstep.

#define DCD_IS_XPLOR 0x00

Definition at line 98 of file dcdplugin.c.
Referenced by open_dcd_write, and read_dcdheader.

#define DCD_OPENFAILED -3

Definition at line 89 of file dcdplugin.c.
Referenced by print_dcderror.

#define DCD_SUCCESS 0

Definition at line 86 of file dcdplugin.c.
Referenced by print_dcderror, read_charmm_4dim, read_charmm_extrablock, read_dcdheader, read_dcdstep, read_fixed_atoms, skip_dcdstep, write_dcdheader, and write_dcdstep.

#define M_PI_2 1.57079632679489661922

Definition at line 60 of file dcdplugin.c.
Referenced by read_next_timestep, and write_timestep.

#define NFILE_POS 8L

Definition at line 105 of file dcdplugin.c.
Referenced by write_dcdstep.

#define NSTEP_POS 20L

Definition at line 106 of file dcdplugin.c.
Referenced by write_dcdstep.

#define READ ( fd,
buf,
size ) fio_fread(((void *) buf), (size), 1, (fd))

Definition at line 109 of file dcdplugin.c.
Referenced by read_dcdheader.

#define RECSCALE32BIT 1

Definition at line 63 of file dcdplugin.c.
Referenced by read_charmm_4dim, read_charmm_extrablock, read_dcdheader, read_dcdstep, read_fixed_atoms, and skip_dcdstep.

#define RECSCALE64BIT 2

Definition at line 64 of file dcdplugin.c.
Referenced by read_charmm_4dim, read_charmm_extrablock, read_dcdheader, read_dcdstep, read_fixed_atoms, and skip_dcdstep.

#define RECSCALEMAX 2

Definition at line 65 of file dcdplugin.c.
Referenced by read_dcdstep.

#define WRITE ( fd,
buf,
size ) fio_fwrite(((void *) buf), (size), 1, (fd))

Definition at line 112 of file dcdplugin.c.
Referenced by write_dcdheader, and write_dcdstep.

Function Documentation

void close_dcd_read ( int * indexes,

float * fixedcoords

) [static]

Definition at line 859 of file dcdplugin.c.
Referenced by close_file_read.

void close_file_read ( void * v ) [static]

Definition at line 1057 of file dcdplugin.c.
References close_dcd_read, dcdhandle::fd, fio_fclose, dcdhandle::fixedcoords, dcdhandle::freeind, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

void close_file_write ( void * v ) [static]

Definition at line 1162 of file dcdplugin.c.
References dcdhandle::fd, fio_fclose, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

void* open_dcd_read ( const char * path,

const char * filetype,

int * natoms

) [static]

Definition at line 865 of file dcdplugin.c.
References dcdhandle::charmm, DCD_HAS_4DIMS, DCD_HAS_EXTRA_BLOCK, dcdhandle::delta, dcdhandle::fd, fio_fclose, fio_fd, fio_fseek, fio_ftell, fio_open, FIO_READ, FIO_SEEK_END, FIO_SEEK_SET, fio_size_t, dcdhandle::first, dcdhandle::fixedcoords, dcdhandle::freeind, dcdhandle::istart, dcdhandle::natoms, dcdhandle::nfixed, dcdhandle::nsavc, dcdhandle::nsets, print_dcderror, read_dcdheader, dcdhandle::reverse, dcdhandle::setsread, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

void* open_dcd_write ( const char * path,

const char * filetype,

int natoms

) [static]

Definition at line 1068 of file dcdplugin.c.
References dcdhandle::charmm, DCD_HAS_EXTRA_BLOCK, DCD_IS_CHARMM, DCD_IS_XPLOR, dcdhandle::fd, fio_fclose, fio_fd, fio_open, FIO_WRITE, dcdhandle::istart, dcdhandle::natoms, dcdhandle::nsavc, dcdhandle::nsets, print_dcderror, dcdhandle::with_unitcell, write_dcdheader, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

void print_dcderror ( const char * func,

int errcode

) [static]

Definition at line 120 of file dcdplugin.c.
References DCD_BADEOF, DCD_BADFORMAT, DCD_BADMALLOC, DCD_BADREAD, DCD_BADWRITE, DCD_DNE, DCD_EOF, DCD_FILEEXISTS, DCD_OPENFAILED, and DCD_SUCCESS.
Referenced by open_dcd_read, open_dcd_write, read_next_timestep, and write_timestep.

int read_charmm_4dim ( fio_fd fd,

int charmm,

int reverseEndian

) [static]

Definition at line 504 of file dcdplugin.c.
References DCD_BADREAD, DCD_HAS_4DIMS, DCD_HAS_64BIT_REC, DCD_IS_CHARMM, DCD_SUCCESS, fio_fd, fio_fread, fio_fseek, FIO_SEEK_CUR, RECSCALE32BIT, RECSCALE64BIT, and swap4_aligned.
Referenced by read_dcdstep.

int read_charmm_extrablock ( fio_fd fd,

int charmm,

int reverseEndian,

float * unitcell

) [static]

Definition at line 434 of file dcdplugin.c.
References DCD_BADREAD, DCD_HAS_64BIT_REC, DCD_HAS_EXTRA_BLOCK, DCD_IS_CHARMM, DCD_SUCCESS, fio_fd, fio_fread, fio_fseek, FIO_SEEK_CUR, RECSCALE32BIT, RECSCALE64BIT, swap4_aligned, and swap8_aligned.
Referenced by read_dcdstep.

int read_dcdheader ( fio_fd fd,

int * N,

int * NSET,

int * ISTART,

int * NSAVC,

double * DELTA,

int * NAMNF,

int ** FREEINDEXES,

float ** fixedcoords,

int * reverseEndian,

int * charmm

) [static]

Definition at line 156 of file dcdplugin.c.
References CHECK_FEOF, CHECK_FREAD, DCD_BADFORMAT, DCD_BADMALLOC, DCD_HAS_4DIMS, DCD_HAS_64BIT_REC, DCD_HAS_EXTRA_BLOCK, DCD_IS_CHARMM, DCD_IS_XPLOR, DCD_SUCCESS, fio_fd, fio_fseek, FIO_SEEK_CUR, READ, RECSCALE32BIT, RECSCALE64BIT, swap4_aligned, swap4_unaligned, and swap8_unaligned.
Referenced by open_dcd_read.

int read_dcdstep ( fio_fd fd,

int N,

float * X,

float * Y,

float * Z,

float * unitcell,

int num_fixed,

int first,

int * indexes,

float * fixedcoords,

int reverseEndian,

int charmm

) [static]

Definition at line 541 of file dcdplugin.c.
References DCD_BADFORMAT, DCD_BADREAD, DCD_HAS_64BIT_REC, DCD_SUCCESS, fio_fd, fio_fread, fio_readv, fio_iovec::iov_base, fio_iovec::iov_len, read_charmm_4dim, read_charmm_extrablock, read_fixed_atoms, RECSCALE32BIT, RECSCALE64BIT, RECSCALEMAX, and swap4_aligned.
Referenced by read_next_timestep.

int read_fixed_atoms ( fio_fd fd,

int N,

int num_free,

const int * indexes,

int reverseEndian,

const float * fixedcoords,

float * freeatoms,

float * pos,

int charmm

) [static]

Definition at line 467 of file dcdplugin.c.
References DCD_BADFORMAT, DCD_BADREAD, DCD_HAS_64BIT_REC, DCD_SUCCESS, fio_fd, fio_fread, RECSCALE32BIT, RECSCALE64BIT, and swap4_aligned.
Referenced by read_dcdstep.

int read_next_timestep ( void * v,

int natoms,

molfile_timestep_t * ts

) [static]

Definition at line 976 of file dcdplugin.c.
References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, molfile_timestep_t::beta, molfile_timestep_t::C, dcdhandle::charmm, molfile_timestep_t::coords, dcdhandle::fd, dcdhandle::first, dcdhandle::fixedcoords, dcdhandle::freeind, molfile_timestep_t::gamma, M_PI_2, MOLFILE_EOF, MOLFILE_ERROR, dcdhandle::natoms, dcdhandle::nfixed, dcdhandle::nsets, print_dcderror, read_dcdstep, dcdhandle::reverse, dcdhandle::setsread, skip_dcdstep, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

int skip_dcdstep ( fio_fd fd,

int natoms,

int nfixed,

int charmm

) [static]

Definition at line 698 of file dcdplugin.c.
References DCD_BADEOF, DCD_HAS_4DIMS, DCD_HAS_64BIT_REC, DCD_HAS_EXTRA_BLOCK, DCD_IS_CHARMM, DCD_SUCCESS, fio_fd, fio_fseek, FIO_SEEK_CUR, RECSCALE32BIT, and RECSCALE64BIT.
Referenced by read_next_timestep.

VMDPLUGIN_API int VMDPLUGIN_fini ( void )

Definition at line 1202 of file dcdplugin.c.
References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init ( void )

Definition at line 1177 of file dcdplugin.c.
References close_file_read, molfile_plugin_t::close_file_read, close_file_write, molfile_plugin_t::close_file_write, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, open_dcd_read, open_dcd_write, molfile_plugin_t::open_file_read, molfile_plugin_t::open_file_write, read_next_timestep, molfile_plugin_t::read_next_timestep, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, VMDPLUGIN_THREADSAFE, write_timestep, and molfile_plugin_t::write_timestep.

VMDPLUGIN_API int VMDPLUGIN_register ( void * v,

vmdplugin_register_cb cb

)

Definition at line 1197 of file dcdplugin.c.
References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

int write_dcdheader ( fio_fd fd,

const char * remarks,

int N,

int ISTART,

int NSAVC,

double DELTA,

int with_unitcell,

int charmm

) [static]

Definition at line 784 of file dcdplugin.c.
References DCD_SUCCESS, fio_fd, fio_write_int32, and WRITE.
Referenced by open_dcd_write.

int write_dcdstep ( fio_fd fd,

int curframe,

int curstep,

int N,

const float * X,

const float * Y,

const float * Z,

const double * unitcell,

int charmm

) [static]

Definition at line 737 of file dcdplugin.c.
References DCD_BADWRITE, DCD_SUCCESS, fio_fd, fio_fseek, fio_fwrite, FIO_SEEK_END, FIO_SEEK_SET, fio_write_int32, NFILE_POS, NSTEP_POS, and WRITE.
Referenced by write_timestep.

int write_timestep ( void * v,

const molfile_timestep_t * ts

) [static]

Definition at line 1126 of file dcdplugin.c.
References molfile_timestep_t::A, molfile_timestep_t::alpha, molfile_timestep_t::B, molfile_timestep_t::beta, molfile_timestep_t::C, dcdhandle::charmm, molfile_timestep_t::coords, dcdhandle::fd, molfile_timestep_t::gamma, dcdhandle::istart, M_PI_2, MOLFILE_ERROR, dcdhandle::natoms, dcdhandle::nsavc, dcdhandle::nsets, print_dcderror, dcdhandle::with_unitcell, write_dcdstep, dcdhandle::x, dcdhandle::y, and dcdhandle::z.
Referenced by VMDPLUGIN_init.

Variable Documentation

molfile_plugin_t plugin [static]

Definition at line 1175 of file dcdplugin.c.

Generated on Fri Apr 26 03:08:39 2024 for VMD Plugins (current) by

Compounds
struct	dcdhandle
Defines
#define	M_PI_2 1.57079632679489661922
#define	RECSCALE32BIT 1
#define	RECSCALE64BIT 2
#define	RECSCALEMAX 2
#define	DCD_SUCCESS 0
#define	DCD_EOF -1
#define	DCD_DNE -2
#define	DCD_OPENFAILED -3
#define	DCD_BADREAD -4
#define	DCD_BADEOF -5
#define	DCD_BADFORMAT -6
#define	DCD_FILEEXISTS -7
#define	DCD_BADMALLOC -8
#define	DCD_BADWRITE -9
#define	DCD_IS_XPLOR 0x00
#define	DCD_IS_CHARMM 0x01
#define	DCD_HAS_4DIMS 0x02
#define	DCD_HAS_EXTRA_BLOCK 0x04
#define	DCD_HAS_64BIT_REC 0x08
#define	NFILE_POS 8L
#define	NSTEP_POS 20L
#define	READ(fd, buf, size) fio_fread(((void *) buf), (size), 1, (fd))
#define	WRITE(fd, buf, size) fio_fwrite(((void *) buf), (size), 1, (fd))
#define	CHECK_FREAD(X, msg) if (X==-1) { return(DCD_BADREAD); }
#define	CHECK_FEOF(X, msg) if (X==0) { return(DCD_BADEOF); }
Functions
void	print_dcderror (const char *func, int errcode)
int	read_dcdheader (fio_fd fd, int N, int NSET, int ISTART, int NSAVC, double DELTA, int NAMNF, int FREEINDEXES, float fixedcoords, int reverseEndian, int charmm)
int	read_charmm_extrablock (fio_fd fd, int charmm, int reverseEndian, float *unitcell)
int	read_fixed_atoms (fio_fd fd, int N, int num_free, const int indexes, int reverseEndian, const float fixedcoords, float freeatoms, float pos, int charmm)
int	read_charmm_4dim (fio_fd fd, int charmm, int reverseEndian)
int	read_dcdstep (fio_fd fd, int N, float X, float Y, float Z, float unitcell, int num_fixed, int first, int indexes, float fixedcoords, int reverseEndian, int charmm)
int	skip_dcdstep (fio_fd fd, int natoms, int nfixed, int charmm)
int	write_dcdstep (fio_fd fd, int curframe, int curstep, int N, const float X, const float Y, const float Z, const double unitcell, int charmm)
int	write_dcdheader (fio_fd fd, const char *remarks, int N, int ISTART, int NSAVC, double DELTA, int with_unitcell, int charmm)
void	close_dcd_read (int indexes, float fixedcoords)
void *	open_dcd_read (const char path, const char filetype, int *natoms)
int	read_next_timestep (void v, int natoms, molfile_timestep_t ts)
void	close_file_read (void *v)
void *	open_dcd_write (const char path, const char filetype, int natoms)
int	write_timestep (void v, const molfile_timestep_t ts)
void	close_file_write (void *v)
VMDPLUGIN_API int	VMDPLUGIN_init ()
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int	VMDPLUGIN_fini ()
Variables
molfile_plugin_t	plugin