src/gromacs/fileio/confio.h

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  37 #ifndef GMX_FILEIO_CONFIO_H
  38 #define GMX_FILEIO_CONFIO_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/fileio/trx.h"
  43 #include "gromacs/legacyheaders/types/simple.h"
  44
  45 /* For reading coordinate files it is assumed that enough memory
  46  * has been allocated beforehand.
  47  */
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 struct gmx_mtop_t;
  53 struct t_atoms;
  54 struct t_topology;
  55
  56 gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr);
  57 int gro_first_x_or_v(FILE *status, t_trxframe *fr);
  58 /* read first/next x and/or v frame from gro file */
  59
  60 void write_hconf_indexed_p(FILE *out, const char *title, struct t_atoms *atoms,
  61                            int nx, const atom_id index[], int ndec,
  62                            rvec *x, rvec *v, matrix box);
  63
  64 void write_hconf_p(FILE *out, const char *title, struct t_atoms *atoms, int ndec,
  65                    rvec *x, rvec *v, matrix box);
  66 /* Write a Gromos file with precision ndec: number of decimal places in x,
  67  * v has one place more. */
  68
  69 void write_sto_conf_indexed(const char *outfile, const char *title,
  70                             struct t_atoms *atoms,
  71                             rvec x[], rvec *v, int ePBC, matrix box,
  72                             atom_id nindex, atom_id index[]);
  73 /* like write_sto_conf, but indexed */
  74
  75 void write_sto_conf(const char *outfile, const char *title,
  76                     struct t_atoms *atoms,
  77                     rvec x[], rvec *v, int ePBC, matrix box);
  78 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
  79  * to an STO (.gro or .pdb) file */
  80
  81 void write_sto_conf_mtop(const char *outfile, const char *title,
  82                          struct gmx_mtop_t *mtop,
  83                          rvec x[], rvec *v, int ePBC, matrix box);
  84 /* As write_sto_conf, but uses a gmx_mtop_t struct */
  85
  86 void get_stx_coordnum (const char *infile, int *natoms);
  87 /* read the number of atoms from an STX file */
  88
  89 void read_stx_conf(const char *infile, char *title,
  90                    struct t_atoms *atoms,
  91                    rvec x[], rvec *v, int *ePBC, matrix box);
  92 /* Read atoms, x, v and box from an STX file.
  93  * If ePBC!=NULL return the type of pbc in *ePBC or -1 if unknown.
  94  */
  95
  96 gmx_bool read_tps_conf(const char *infile, char *title, struct t_topology *top,
  97                        int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
  98 /* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
  99  * memory for atoms, x and v will be allocated.
 100  * Return TRUE if a complete topology was read.
 101  * If infile is a TPX file read the whole top,
 102  * else if bMass=TRUE, read the masses into top.atoms from the mass database.
 103  */
 104
 105 #ifdef __cplusplus
 106 }
 107 #endif
 108
 109 #endif  /* GMX_FILEIO_CONFIO_H */