include/confio.h

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
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   7  *
   8  *          GROningen MAchine for Chemical Simulations
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  10  *                        VERSION 3.2.0
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  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
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  16  * This program is free software; you can redistribute it and/or
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  36
  37 #ifndef _confio_h
  38 #define _confio_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include "typedefs.h"
  45
  46 /* For reading coordinate files it is assumed that enough memory
  47  * has been allocated beforehand.
  48  */
  49 #ifdef CPLUSPLUS
  50 extern "C" {
  51 #endif
  52
  53 extern void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
  54 /* allocate memory for the arrays, set nr to natoms and nres to 0
  55  * set pdbinfo to NULL or allocate memory for it */
  56
  57 extern void free_t_atoms(t_atoms *atoms);
  58 /* free all the arrays and set the nr and nres to 0 */
  59
  60 int read_g96_conf(FILE *fp,char *infile,t_trxframe *fr);
  61 /* read a Gromos96 coordinate or trajectory file,                       *
  62  * returns the number of atoms                                          *
  63  * sets what's in the frame in info                                     *
  64  * read from fp, infile is only needed for error messages               *
  65  * nwanted is the number of wanted coordinates,                         *
  66  * set this to -1 if you want to know the number of atoms in the file   *
  67  * title, atoms, x, v can all be NULL, in which case they won't be read */
  68
  69 void write_g96_conf(FILE *out,t_trxframe *fr,int nindex,atom_id *index);
  70 /* write a Gromos96 coordinate file or trajectory frame *
  71  * index can be NULL                                    */
  72
  73 extern bool gro_next_x_or_v(FILE *status,t_trxframe *fr);
  74 extern int gro_first_x_or_v(FILE *status,t_trxframe *fr);
  75 /* read first/next x and/or v frame from gro file */
  76
  77 extern void write_hconf_indexed_p(FILE *out,char *title,t_atoms *atoms,
  78                                   int nx,atom_id index[],int ndec,
  79                                   rvec *x,rvec *v,matrix box);
  80
  81 extern void write_hconf_p(FILE *out,char *title,t_atoms *atoms, int ndec,
  82                           rvec *x,rvec *v,matrix box);
  83 /* Write a Gromos file with precision ndec: number of decimal places in x,
  84  * v has one place more. */
  85
  86 void write_sto_conf_indexed(char *outfile,char *title,t_atoms *atoms,
  87                             rvec x[],rvec *v,matrix box,
  88                             atom_id nindex,atom_id index[]);
  89 /* like write_sto_conf, but indexed */
  90
  91 extern void write_sto_conf(char *outfile, char *title,t_atoms *atoms,
  92                            rvec x[],rvec *v, matrix box);
  93 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
  94  * to an STO (.gro or .pdb) file */
  95
  96 extern void get_stx_coordnum (char *infile,int *natoms);
  97 /* read the number of atoms from an STX file */
  98
  99 extern void read_stx_conf(char *infile, char *title,t_atoms *atoms,
 100                           rvec x[],rvec *v, matrix box);
 101 /* read atoms, x, v and box from an STX file */
 102
 103 #ifdef CPLUSPLUS
 104 }
 105 #endif
 106
 107 #endif  /* _confio_h */