include/confio.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Good ROcking Metal Altar for Chronical Sinners
  28  */
  29
  30 #ifndef _confio_h
  31 #define _confio_h
  32
  33 static char *SRCID_confio_h = "$Id$";
  34
  35 #ifdef HAVE_IDENT
  36 #ident  "@(#) confio.h 1.16 11/23/92"
  37 #endif /* HAVE_IDENT */
  38
  39 #include "typedefs.h"
  40
  41 /* For reading coordinate files it is assumed that enough memory
  42  * has been allocated beforehand.
  43  */
  44 #ifdef CPLUSPLUS
  45 extern "C" {
  46 #endif
  47
  48   typedef struct {
  49     bool bTitle;
  50     bool bTime;
  51     bool bAtoms;
  52     bool bPos;
  53     bool bVel;
  54     bool bBox;
  55     int  step;
  56     real time;
  57   } t_g96info;
  58
  59 extern void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
  60 /* allocate memory for the arrays, set nr to natoms and nres to 0
  61  * set pdbinfo to NULL or allocate memory for it */
  62
  63 extern void free_t_atoms(t_atoms *atoms);
  64 /* free all the arrays and set the nr and nres to 0 */
  65
  66 void clear_g96info(t_g96info *info);
  67 /* set all bools in the info struct to FALSE */
  68
  69 int read_g96_conf(FILE *fp,char *infile,int nwanted,t_g96info *info,
  70                   char *title,t_atoms *atoms,rvec *x, rvec *v,matrix box);
  71 /* read a Gromos96 coordinate or trajectory file,                       *
  72  * returns the number of atoms                                          *
  73  * sets what's in the frame in info                                     *
  74  * read from fp, infile is only needed for error messages               *
  75  * nwanted is the number of wanted coordinates,                         *
  76  * set this to -1 if you want to know the number of atoms in the file   *
  77  * title, atoms, x, v can all be NULL, in which case they won't be read */
  78
  79 void write_g96_conf(FILE *out,char *title,t_atoms *atoms,
  80                     rvec *x,rvec *v,matrix box,
  81                     int nindex,atom_id *index);
  82 /* write a Gromos96 coordinate file *
  83  * x, v and index can be NULL       */
  84
  85 extern bool gro_next_x(FILE *status,real *t,int natoms,rvec x[],matrix box);
  86 extern int gro_first_x(FILE *status, real *t, rvec **x, matrix box);
  87 /* read first/next x frame from gro file */
  88
  89 extern bool gro_next_x_or_v(FILE *status,real *t,int natoms,
  90                             rvec x[],rvec *v,matrix box);
  91 extern int gro_first_x_or_v(FILE *status, real *t,
  92                             rvec **x, rvec **v, matrix box);
  93 /* read first/next x and/or v frame from gro file */
  94
  95 extern bool gro_next_v(FILE *status,real *t,int natoms,rvec *v,matrix box);
  96 extern int gro_first_v(FILE *status, real *t, rvec **v, matrix box);
  97 /* read first/next v frame from gro file */
  98
  99 extern bool gro_next_x_v(FILE *status,real *t,int natoms,
 100                          rvec x[],rvec *v,matrix box);
 101 extern int gro_first_x_v(FILE *status, real *t,
 102                          rvec **x, rvec **v, matrix box);
 103 /* read first/next x and v frame from gro file */
 104
 105 extern void write_hconf(FILE *out,char *title,
 106                         t_atoms *atoms,rvec *x,
 107                         rvec *v,matrix box);
 108
 109 extern void write_hconf_indexed(FILE *out,char *title,t_atoms *atoms,
 110                                 int nx,atom_id index[],
 111                                 rvec *x,rvec *v,matrix box);
 112
 113 extern void write_hconf_p(FILE *out,char *title,t_atoms *atoms, int pr,
 114                           rvec *x,rvec *v,matrix box);
 115 /* Write a Gromos file with precision pr: number of decimal places in x,
 116  * v has one place more. */
 117
 118 extern void write_xdr_conf(char *outfile,char *title,t_atoms *atoms,
 119                            rvec x[],rvec *v,matrix box);
 120
 121 extern void read_xdr_coordnum(char *infile,int *natoms);
 122
 123 extern void read_xdr_conf(char *infile,char *title,t_atoms *atoms,
 124                           rvec x[],rvec *v,matrix box);
 125
 126 void write_sto_conf_indexed(char *outfile,char *title,t_atoms *atoms,
 127                             rvec x[],rvec *v,matrix box,
 128                             atom_id nindex,atom_id index[]);
 129 /* like write_sto_conf, but indexed */
 130
 131 extern void write_sto_conf(char *outfile, char *title,t_atoms *atoms,
 132                            rvec x[],rvec *v, matrix box);
 133 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
 134  * to an STO (.gro or .pdb) file */
 135
 136 extern void get_stx_coordnum (char *infile,int *natoms);
 137 /* read the number of atoms from an STX file */
 138
 139 extern void read_stx_conf(char *infile, char *title,t_atoms *atoms,
 140                           rvec x[],rvec *v, matrix box);
 141 /* read atoms, x, v and box from an STX file */
 142
 143 #ifdef CPLUSPLUS
 144 }
 145 #endif
 146
 147 #endif  /* _confio_h */