* 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, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_TRXIO_H
#define GMX_FILEIO_TRXIO_H
-#include "../legacyheaders/typedefs.h"
-#include "filenm.h"
#include "../legacyheaders/readinp.h"
-#include "pdbio.h"
#include "../legacyheaders/oenv.h"
+
+#include "filenm.h"
#include "gmxfio.h"
-#include "../../external/tng_io/include/tng_io_fwd.h"
+#include "pdbio.h"
#ifdef __cplusplus
extern "C" {
}
#endif
+struct gmx_mtop_t;
+struct t_atoms;
+struct t_topology;
+struct t_trxframe;
+
/* a dedicated status type contains fp, etc. */
typedef struct t_trxstatus t_trxstatus;
* 1/(nm) */
real ndec2prec(int ndec);
-void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
+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(t_trxframe *fr, int ePBC);
+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, t_trxframe *fr, int nind,
+int write_trxframe_indexed(t_trxstatus *status, struct t_trxframe *fr, int nind,
const atom_id *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, t_trxframe *fr, gmx_conect gc);
+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
* gc is important for pdb file writing only and may be NULL.
*/
-int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
+int write_trx(t_trxstatus *status, int nind, const atom_id *ind, struct t_atoms *atoms,
int step, real time, matrix box, rvec x[], rvec *v,
gmx_conect gc);
/* Write an indexed frame to a TRX file.
* 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 gmx_mtop_t *mtop,
- const atom_id *index,
- const char *index_group_name);
+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 atom_id *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
* 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,
- t_trxframe *fr);
+void write_tng_frame(t_trxstatus *status,
+ struct t_trxframe *fr);
void close_trx(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* Close trajectory file as opened with read_first_x, read_frist_frame
* or open_trx. Identical to close_trj.
*/
t_fileio *trx_get_fileio(t_trxstatus *status);
/* get a fileio from a trxstatus */
-tng_trajectory_t trx_get_tng(t_trxstatus *status);
-/* get a tng trajectory container 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
#define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
- const char *fn, t_trxframe *fr, int flags);
+ 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.
* Returns natoms when succeeded, 0 otherwise.
*/
gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
- t_trxframe *fr);
+ struct t_trxframe *fr);
/* Reads the next frame which is in accordance with fr->flags.
* Returns TRUE when succeeded, FALSE otherwise.
*/
*/
void close_trj(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* 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 trj file as opened with read_first_x */
+/* Rewind trajectory file as opened with read_first_x */
-t_topology *read_top(const char *fn, int *ePBC);
+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.
*/
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