/usr/include/gromacs/fileio/trxio.h is in libgromacs-dev 2016.1-2.
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* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
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#ifndef GMX_FILEIO_TRXIO_H
#define GMX_FILEIO_TRXIO_H
#include "gromacs/fileio/pdbio.h"
#ifdef __cplusplus
extern "C" {
#endif
struct gmx_mtop_t;
struct gmx_output_env_t;
struct t_atoms;
struct t_fileio;
struct t_topology;
struct t_trxframe;
/* a dedicated status type contains fp, etc. */
typedef struct t_trxstatus t_trxstatus;
/* I/O function types */
/************************************************
* Trajectory functions
************************************************/
int prec2ndec(real prec);
/* Convert precision in 1/(nm) to number of decimal places */
/*! \brief Convert number of decimal places to trajectory precision in
* 1/(nm) */
real ndec2prec(int ndec);
void clear_trxframe(struct t_trxframe *fr, gmx_bool bFirst);
/* Set all content gmx_booleans to FALSE.
* When bFirst = TRUE, set natoms=-1, all pointers to NULL
* and all data to zero.
*/
void set_trxframe_ePBC(struct t_trxframe *fr, int ePBC);
/* Set the type of periodic boundary conditions, ePBC=-1 is not set */
int nframes_read(t_trxstatus *status);
/* Returns the number of frames read from the trajectory */
int write_trxframe_indexed(t_trxstatus *status, const t_trxframe *fr, int nind,
const int *ind, gmx_conect gc);
/* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
int write_trxframe(t_trxstatus *status, struct t_trxframe *fr, gmx_conect gc);
/* Write a frame to a TRX file.
* Only entries for which the gmx_boolean is TRUE will be written,
* except for step, time, lambda and/or box, which may not be
* omitted for certain trajectory formats.
* The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
* the precision is set to 1000.
* gc is important for pdb file writing only and may be NULL.
*/
int write_trx(t_trxstatus *status, int nind, const int *ind, const t_atoms *atoms,
int step, real time, matrix box, rvec x[], rvec *v,
gmx_conect gc);
/* Write an indexed frame to a TRX file.
* v can be NULL.
* atoms can be NULL for file types which don't need atom names.
*/
void trjtools_gmx_prepare_tng_writing(const char *filename,
char filemode,
t_trxstatus *in,
t_trxstatus **out,
const char *infile,
const int natoms,
const struct gmx_mtop_t *mtop,
const int *index,
const char *index_group_name);
/* Sets up *out for writing TNG. If *in != NULL and contains a TNG trajectory
* some data, e.g. molecule system, will be copied over from *in to *out.
* If *in == NULL a file name (infile) of a TNG file can be provided instead
* and used for copying data to *out.
* If there is no TNG input natoms is used to create "implicit atoms" (no atom
* or molecular data present). If natoms == -1 the number of atoms are
* not known (or there is already a TNG molecule system to copy, in which case
* natoms is not required anyhow). If an group of indexed atoms are written
* natoms must be the length of index. index_group_name is the name of the
* index group.
*/
/*! \brief Write a trxframe to the TNG file in status.
*
* This function is needed because both t_trxstatus and
* tng_trajectory_t are encapsulated, so client trajectory-writing
* code with a t_trxstatus can't just call the TNG writing
* function. */
void write_tng_frame(t_trxstatus *status,
struct t_trxframe *fr);
void close_trx(t_trxstatus *status);
/* Close trajectory file as opened with read_first_x, read_frist_frame
* or open_trx. Identical to close_trj.
*/
t_trxstatus *open_trx(const char *outfile, const char *filemode);
/* Open a TRX file and return an allocated status pointer */
struct t_fileio *trx_get_fileio(t_trxstatus *status);
/* get a fileio from a trxstatus */
float trx_get_time_of_final_frame(t_trxstatus *status);
/* get time of final frame. Only supported for TNG and XTC */
gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
/* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
* larger than the float/double precision.
*/
#if GMX_DOUBLE
#define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
#else
#define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
#endif
int check_times2(real t, real t0, gmx_bool bDouble);
/* This routine checkes if the read-in time is correct or not;
* returns -1 if t<tbegin or t MOD dt = t0,
* 0 if tbegin <= t <=tend+margin,
* 1 if t>tend
* where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
* tp and tpp should be the time of the previous frame and the one before.
* The mod is done with single or double precision accuracy depending
* on the value of bDouble.
*/
int check_times(real t);
/* This routine checkes if the read-in time is correct or not;
* returns -1 if t<tbegin,
* 0 if tbegin <= t <=tend,
* 1 if t>tend
*/
/* For trxframe.flags, used in trxframe read routines.
* When a READ flag is set, the field will be read when present,
* but a frame might be returned which does not contain the field.
* When a NEED flag is set, frames not containing the field will be skipped.
*/
#define TRX_READ_X (1<<0)
#define TRX_NEED_X (1<<1)
#define TRX_READ_V (1<<2)
#define TRX_NEED_V (1<<3)
#define TRX_READ_F (1<<4)
#define TRX_NEED_F (1<<5)
/* Useful for reading natoms from a trajectory without skipping */
#define TRX_DONT_SKIP (1<<6)
/* For trxframe.not_ok */
#define HEADER_NOT_OK (1<<0)
#define DATA_NOT_OK (1<<1)
#define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
int read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, struct t_trxframe *fr, int flags);
/* Read the first frame which is in accordance with flags, which are
* defined further up in this file.
* Memory will be allocated for flagged entries.
* The flags are copied to fr for subsequent calls to read_next_frame.
* Returns TRUE when succeeded, FALSE otherwise.
*/
gmx_bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status,
struct t_trxframe *fr);
/* Reads the next frame which is in accordance with fr->flags.
* Returns TRUE when succeeded, FALSE otherwise.
*/
int read_first_x(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, real *t, rvec **x, matrix box);
/* These routines read first coordinates and box, and allocates
* memory for the coordinates, for a trajectory file.
* The routine returns the number of atoms, or 0 when something is wrong.
* The integer in status should be passed to calls of read_next_x
*/
gmx_bool read_next_x(const gmx_output_env_t *oenv, t_trxstatus *status, real *t, rvec x[], matrix box);
/* Read coordinates and box from a trajectory file. Return TRUE when all well,
* or FALSE when end of file (or last frame requested by user).
* status is the integer set in read_first_x.
*/
void close_trj(t_trxstatus *status);
/* Close trajectory file as opened with read_first_x, read_first_frame
* or open_trx. Identical to close_trx.
*/
void rewind_trj(t_trxstatus *status);
/* Rewind trajectory file as opened with read_first_x */
struct t_topology *read_top(const char *fn, int *ePBC);
/* Extract a topology data structure from a topology file.
* If ePBC!=NULL *ePBC gives the pbc type.
*/
#ifdef __cplusplus
}
#endif
#endif
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