Sort all includes in src/gromacs

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

diff --git a/src/gromacs/fileio/pdbio.h b/src/gromacs/fileio/pdbio.h
index c5c86e7cf25e0f3b1323e62c7a16faf9799ac58a..3e13161126c3d9c07b9765b303f720c8a21cb8b1 100644 (file)
--- a/src/gromacs/fileio/pdbio.h
+++ b/src/gromacs/fileio/pdbio.h
@@ -40,36 +40,53 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/atomprop.h"
-#include "../legacyheaders/types/topology.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-typedef struct gmx_conect_t *gmx_conect;
+struct gmx_atomprop;
+struct t_atoms;
+struct t_topology;
 
-/* THE pdb format (for ATOM/HETATOM lines) */
-const char* get_pdbformat(void);
-const char* get_pdbformat4(void);
+typedef struct gmx_conect_t *gmx_conect;
 
 /* Enumerated type for pdb records. The other entries are ignored
  * when reading a pdb file
  */
-enum {
+enum PDB_record {
     epdbATOM,   epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
     epdbMODEL,  epdbENDMDL, epdbTER,    epdbHEADER, epdbTITLE, epdbREMARK,
     epdbCONECT, epdbNR
 };
 
+/* Write a PDB line with an ATOM or HETATM record directly to a file pointer.
+ *
+ * Returns the number of characters printed.
+ */
+int
+gmx_fprintf_pdb_atomline(FILE *            fp,
+                         enum PDB_record   record,
+                         int               atom_seq_number,
+                         const char *      atom_name,
+                         char              alternate_location,
+                         const char *      res_name,
+                         char              chain_id,
+                         int               res_seq_number,
+                         char              res_insertion_code,
+                         real              x,
+                         real              y,
+                         real              z,
+                         real              occupancy,
+                         real              b_factor,
+                         const char *      element);
+
 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
 enum {
     U11, U22, U33, U12, U13, U23
 };
 
-void set_pdb_wide_format(gmx_bool bSet);
-/* If bSet, use wider format for occupancy and bfactor */
-
 void pdb_use_ter(gmx_bool bSet);
 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
    This function is fundamentally broken as far as thread-safety is concerned.*/
@@ -80,13 +97,13 @@ void gmx_write_pdb_box(FILE *out, int ePBC, matrix box);
  * This function is fundamentally broken as far as thread-safety is concerned.
  */
 
-void write_pdbfile_indexed(FILE *out, const char *title, t_atoms *atoms,
+void write_pdbfile_indexed(FILE *out, const char *title, struct t_atoms *atoms,
                            rvec x[], int ePBC, matrix box, char chain,
                            int model_nr, atom_id nindex, const atom_id index[],
                            gmx_conect conect, gmx_bool bTerSepChains);
 /* REALLY low level */
 
-void write_pdbfile(FILE *out, const char *title, t_atoms *atoms,
+void write_pdbfile(FILE *out, const char *title, struct t_atoms *atoms,
                    rvec x[], int ePBC, matrix box, char chain,
                    int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
 /* Low level pdb file writing routine.
@@ -102,18 +119,18 @@ void write_pdbfile(FILE *out, const char *title, t_atoms *atoms,
  * which may be useful for visualization purposes.
  */
 
-void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps);
+void get_pdb_atomnumber(struct t_atoms *atoms, struct gmx_atomprop *aps);
 /* Routine to extract atomic numbers from the atom names */
 
 int read_pdbfile(FILE *in, char *title, int *model_nr,
-                 t_atoms *atoms, rvec x[], int *ePBC, matrix box,
+                 struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
                  gmx_bool bChange, gmx_conect conect);
 /* Function returns number of atoms found.
  * ePBC and gmx_conect structure may be NULL.
  */
 
 void read_pdb_conf(const char *infile, char *title,
-                   t_atoms *atoms, rvec x[], int *ePBC, matrix box,
+                   struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
                    gmx_bool bChange, gmx_conect conect);
 /* Read a pdb file and extract ATOM and HETATM fields.
  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
@@ -139,7 +156,7 @@ gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
 void gmx_conect_add(gmx_conect conect, int ai, int aj);
 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 
-gmx_conect gmx_conect_generate(t_topology *top);
+gmx_conect gmx_conect_generate(struct t_topology *top);
 /* Generate a conect structure from a topology */
 
 gmx_conect gmx_conect_init(void);