Add TNG writing and reading support

[alexxy/gromacs.git] / src / gromacs / fileio / trxio.h

diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index b5ba5bb8b5d7f4059adc5d319d71216b43f9bc00..28cc436aef2aba7821549dfd307da7927e706fc7 100644 (file)
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -44,6 +44,7 @@
 #include "pdbio.h"
 #include "../legacyheaders/oenv.h"
 #include "gmxfio.h"
+#include "../../external/tng_io/include/tng_io_fwd.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -64,6 +65,10 @@ typedef struct t_trxstatus t_trxstatus;
 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(t_trxframe *fr, gmx_bool bFirst);
 /* Set all content gmx_booleans to FALSE.
  * When bFirst = TRUE, set natoms=-1, all pointers to NULL
@@ -98,6 +103,36 @@ int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
  * 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);
+/* 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,
+                     t_trxframe  *fr);
+
 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.
@@ -106,9 +141,11 @@ void close_trx(t_trxstatus *status);
 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);
+/* get a fileio from a trxstatus */
 
+tng_trajectory_t trx_get_tng(t_trxstatus *status);
+/* get a tng trajectory container from a trxstatus */
 
 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