+/*
+ * 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
+ * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
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+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
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+ */
+
+#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 "gmxfio.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0 /* avoid screwing up indentation */
+}
+#endif
+
+/* 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 */
+
+void clear_trxframe(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);
+/* 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,
+ 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);
+/* 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 atom_id *ind, 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 close_trx(t_trxstatus *status);
+/* Close trj 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 */
+
+/* get a fileio from a trxstatus */
+t_fileio *trx_get_fileio(t_trxstatus *status);
+
+
+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.
+ */
+
+#ifdef 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 output_env_t oenv, t_trxstatus **status,
+ const char *fn, 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.
+ * 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 output_env_t oenv, t_trxstatus *status,
+ 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 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 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 trj file as opened with read_first_x, read_frist_frame
+ * or open_trx. Identical to close_trx.
+ */
+
+void rewind_trj(t_trxstatus *status);
+/* Rewind trj file as opened with read_first_x */
+
+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