src/gromacs/fileio/trxio.h

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  37
  38 #ifndef GMX_FILEIO_TRXIO_H
  39 #define GMX_FILEIO_TRXIO_H
  40
  41 #include "../legacyheaders/types/topology.h"
  42 #include "../legacyheaders/readinp.h"
  43 #include "../legacyheaders/oenv.h"
  44
  45 #include "filenm.h"
  46 #include "gmxfio.h"
  47 #include "pdbio.h"
  48
  49 #ifdef __cplusplus
  50 extern "C" {
  51 #endif
  52 #if 0 /* avoid screwing up indentation */
  53 }
  54 #endif
  55
  56 struct t_atoms;
  57
  58 /* a dedicated status type contains fp, etc. */
  59 typedef struct t_trxstatus t_trxstatus;
  60
  61 /* I/O function types */
  62
  63 /************************************************
  64  *             Trajectory functions
  65  ************************************************/
  66
  67 int prec2ndec(real prec);
  68 /* Convert precision in 1/(nm) to number of decimal places */
  69
  70 /*! \brief Convert number of decimal places to trajectory precision in
  71  * 1/(nm) */
  72 real ndec2prec(int ndec);
  73
  74 void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
  75 /* Set all content gmx_booleans to FALSE.
  76  * When bFirst = TRUE, set natoms=-1, all pointers to NULL
  77  *                     and all data to zero.
  78  */
  79
  80 void set_trxframe_ePBC(t_trxframe *fr, int ePBC);
  81 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
  82
  83 int nframes_read(t_trxstatus *status);
  84 /* Returns the number of frames read from the trajectory */
  85
  86 int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
  87                            const atom_id *ind, gmx_conect gc);
  88 /* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
  89
  90 int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc);
  91 /* Write a frame to a TRX file.
  92  * Only entries for which the gmx_boolean is TRUE will be written,
  93  * except for step, time, lambda and/or box, which may not be
  94  * omitted for certain trajectory formats.
  95  * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
  96  * the precision is set to 1000.
  97  * gc is important for pdb file writing only and may be NULL.
  98  */
  99
 100 int write_trx(t_trxstatus *status, int nind, const atom_id *ind, struct t_atoms *atoms,
 101               int step, real time, matrix box, rvec x[], rvec *v,
 102               gmx_conect gc);
 103 /* Write an indexed frame to a TRX file.
 104  * v can be NULL.
 105  * atoms can be NULL for file types which don't need atom names.
 106  */
 107
 108 void trjtools_gmx_prepare_tng_writing(const char       *filename,
 109                                       char              filemode,
 110                                       t_trxstatus      *in,
 111                                       t_trxstatus     **out,
 112                                       const char       *infile,
 113                                       const int         natoms,
 114                                       const gmx_mtop_t *mtop,
 115                                       const atom_id    *index,
 116                                       const char       *index_group_name);
 117 /* Sets up *out for writing TNG. If *in != NULL and contains a TNG trajectory
 118  * some data, e.g. molecule system, will be copied over from *in to *out.
 119  * If *in == NULL a file name (infile) of a TNG file can be provided instead
 120  * and used for copying data to *out.
 121  * If there is no TNG input natoms is used to create "implicit atoms" (no atom
 122  * or molecular data present). If natoms == -1 the number of atoms are
 123  * not known (or there is already a TNG molecule system to copy, in which case
 124  * natoms is not required anyhow). If an group of indexed atoms are written
 125  * natoms must be the length of index. index_group_name is the name of the
 126  * index group.
 127  */
 128
 129 /*! \brief Write a trxframe to the TNG file in status.
 130  *
 131  * This function is needed because both t_trxstatus and
 132  * tng_trajectory_t are encapsulated, so client trajectory-writing
 133  * code with a t_trxstatus can't just call the TNG writing
 134  * function. */
 135 void write_tng_frame(t_trxstatus *status,
 136                      t_trxframe  *fr);
 137
 138 void close_trx(t_trxstatus *status);
 139 /* Close trj file as opened with read_first_x, read_frist_frame
 140  * or open_trx. Identical to close_trj.
 141  */
 142
 143 t_trxstatus *open_trx(const char *outfile, const char *filemode);
 144 /* Open a TRX file and return an allocated status pointer */
 145
 146 t_fileio *trx_get_fileio(t_trxstatus *status);
 147 /* get a fileio from a trxstatus */
 148
 149 float trx_get_time_of_final_frame(t_trxstatus *status);
 150 /* get time of final frame. Only supported for TNG and XTC */
 151
 152 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
 153 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
 154  * larger than the float/double precision.
 155  */
 156
 157 #ifdef GMX_DOUBLE
 158 #define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
 159 #else
 160 #define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
 161 #endif
 162
 163 int check_times2(real t, real t0, gmx_bool bDouble);
 164 /* This routine checkes if the read-in time is correct or not;
 165  * returns -1 if t<tbegin or t MOD dt = t0,
 166  *          0 if tbegin <= t <=tend+margin,
 167  *          1 if t>tend
 168  * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
 169  * tp and tpp should be the time of the previous frame and the one before.
 170  * The mod is done with single or double precision accuracy depending
 171  * on the value of bDouble.
 172  */
 173
 174 int check_times(real t);
 175 /* This routine checkes if the read-in time is correct or not;
 176  * returns -1 if t<tbegin,
 177  *          0 if tbegin <= t <=tend,
 178  *          1 if t>tend
 179  */
 180
 181
 182
 183
 184
 185 /* For trxframe.flags, used in trxframe read routines.
 186  * When a READ flag is set, the field will be read when present,
 187  * but a frame might be returned which does not contain the field.
 188  * When a NEED flag is set, frames not containing the field will be skipped.
 189  */
 190 #define TRX_READ_X    (1<<0)
 191 #define TRX_NEED_X    (1<<1)
 192 #define TRX_READ_V    (1<<2)
 193 #define TRX_NEED_V    (1<<3)
 194 #define TRX_READ_F    (1<<4)
 195 #define TRX_NEED_F    (1<<5)
 196 /* Useful for reading natoms from a trajectory without skipping */
 197 #define TRX_DONT_SKIP (1<<6)
 198
 199 /* For trxframe.not_ok */
 200 #define HEADER_NOT_OK (1<<0)
 201 #define DATA_NOT_OK   (1<<1)
 202 #define FRAME_NOT_OK  (HEADER_NOT_OK | DATA_NOT_OK)
 203
 204 int read_first_frame(const output_env_t oenv, t_trxstatus **status,
 205                      const char *fn, t_trxframe *fr, int flags);
 206 /* Read the first frame which is in accordance with flags, which are
 207  * defined further up in this file.
 208  * Returns natoms when succeeded, 0 otherwise.
 209  * Memory will be allocated for flagged entries.
 210  * The flags are copied to fr for subsequent calls to read_next_frame.
 211  * Returns TRUE when succeeded, FALSE otherwise.
 212  */
 213
 214 gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
 215                          t_trxframe *fr);
 216 /* Reads the next frame which is in accordance with fr->flags.
 217  * Returns TRUE when succeeded, FALSE otherwise.
 218  */
 219
 220 int read_first_x(const output_env_t oenv, t_trxstatus **status,
 221                  const char *fn, real *t, rvec **x, matrix box);
 222 /* These routines read first coordinates and box, and allocates
 223  * memory for the coordinates, for a trajectory file.
 224  * The routine returns the number of atoms, or 0 when something is wrong.
 225  * The integer in status should be passed to calls of read_next_x
 226  */
 227
 228 gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec x[], matrix box);
 229 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
 230  * or FALSE when end of file (or last frame requested by user).
 231  * status is the integer set in read_first_x.
 232  */
 233
 234 void close_trj(t_trxstatus *status);
 235 /* Close trj file as opened with read_first_x, read_frist_frame
 236  * or open_trx. Identical to close_trx.
 237  */
 238
 239 void rewind_trj(t_trxstatus *status);
 240 /* Rewind trj file as opened with read_first_x */
 241
 242 t_topology *read_top(const char *fn, int *ePBC);
 243 /* Extract a topology data structure from a topology file.
 244  * If ePBC!=NULL *ePBC gives the pbc type.
 245  */
 246
 247 #ifdef __cplusplus
 248 }
 249 #endif
 250
 251 #endif