Sort all includes in src/gromacs

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

diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index 3f7305984c6d19e9e779a4421ad1366d6dfc09c6..0d32e364051a95bccbe9a4cecb6bae2050dc91e4 100644 (file)
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -38,12 +38,11 @@
 #ifndef GMX_FILEIO_TRXIO_H
 #define GMX_FILEIO_TRXIO_H
 
-#include "../legacyheaders/readinp.h"
-#include "../legacyheaders/oenv.h"
-
-#include "filenm.h"
-#include "gmxfio.h"
-#include "pdbio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/readinp.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -54,6 +53,8 @@ extern "C" {
 
 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;
@@ -71,23 +72,23 @@ int prec2ndec(real prec);
  * 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
@@ -132,11 +133,11 @@ void trjtools_gmx_prepare_tng_writing(const char               *filename,
  * 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.
  */
 
@@ -202,7 +203,7 @@ int check_times(real t);
 #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.
@@ -212,7 +213,7 @@ int read_first_frame(const output_env_t oenv, t_trxstatus **status,
  */
 
 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.
  */
@@ -232,14 +233,14 @@ gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec
  */
 
 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.
  */