include/confio.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _confio_h
  37 #define _confio_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.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 extern void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
  53 /* allocate memory for the arrays, set nr to natoms and nres to 0
  54  * set pdbinfo to NULL or allocate memory for it */
  55
  56 int read_g96_conf(FILE *fp,const char *infile,t_trxframe *fr);
  57 /* read a Gromos96 coordinate or trajectory file,                       *
  58  * returns the number of atoms                                          *
  59  * sets what's in the frame in info                                     *
  60  * read from fp, infile is only needed for error messages               *
  61  * nwanted is the number of wanted coordinates,                         *
  62  * set this to -1 if you want to know the number of atoms in the file   *
  63  * title, atoms, x, v can all be NULL, in which case they won't be read */
  64
  65 void write_g96_conf(FILE *out,t_trxframe *fr,int nindex,atom_id *index);
  66 /* write a Gromos96 coordinate file or trajectory frame *
  67  * index can be NULL                                    */
  68
  69 extern bool gro_next_x_or_v(FILE *status,t_trxframe *fr);
  70 extern int gro_first_x_or_v(FILE *status,t_trxframe *fr);
  71 /* read first/next x and/or v frame from gro file */
  72
  73 extern void write_hconf_indexed_p(FILE *out,const char *title,t_atoms *atoms,
  74                                   int nx,atom_id index[],int ndec,
  75                                   rvec *x,rvec *v,matrix box);
  76
  77 extern void write_hconf_p(FILE *out,const char *title,t_atoms *atoms, int ndec,
  78                           rvec *x,rvec *v,matrix box);
  79 /* Write a Gromos file with precision ndec: number of decimal places in x,
  80  * v has one place more. */
  81
  82 void write_sto_conf_indexed(const char *outfile,const char *title,
  83                             t_atoms *atoms,
  84                             rvec x[],rvec *v,int ePBC,matrix box,
  85                             atom_id nindex,atom_id index[]);
  86 /* like write_sto_conf, but indexed */
  87
  88 extern void write_sto_conf(const char *outfile,const char *title,
  89                            t_atoms *atoms,
  90                            rvec x[],rvec *v,int ePBC,matrix box);
  91 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
  92  * to an STO (.gro or .pdb) file */
  93
  94 extern void write_sto_conf_mtop(const char *outfile,const char *title,
  95                                 gmx_mtop_t *mtop,
  96                                 rvec x[],rvec *v,int ePBC,matrix box);
  97 /* As write_sto_conf, but uses a gmx_mtop_t struct */
  98
  99 extern void get_stx_coordnum (const char *infile,int *natoms);
 100 /* read the number of atoms from an STX file */
 101
 102 extern void read_stx_conf(const char *infile,char *title,
 103                           t_atoms *atoms,
 104                           rvec x[],rvec *v,int *ePBC,matrix box);
 105 /* Read atoms, x, v and box from an STX file.
 106  * If ePBC!=NULL return the type of pbc in *ePBC or -1 if unknown.
 107  */
 108
 109 #ifdef __cplusplus
 110 }
 111 #endif
 112
 113 #endif  /* _confio_h */