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
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  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
  40 #include "typedefs.h"
  41
  42 /* For reading coordinate files it is assumed that enough memory
  43  * has been allocated beforehand.
  44  */
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
  50 /* allocate memory for the arrays, set nr to natoms and nres to 0
  51  * set pdbinfo to NULL or allocate memory for it */
  52
  53 int read_g96_conf(FILE *fp,const char *infile,t_trxframe *fr, char *line);
  54 /* read a Gromos96 coordinate or trajectory file,                       *
  55  * returns the number of atoms                                          *
  56  * sets what's in the frame in info                                     *
  57  * read from fp, infile is only needed for error messages               *
  58  * nwanted is the number of wanted coordinates,                         *
  59  * set this to -1 if you want to know the number of atoms in the file   *
  60  * title, atoms, x, v can all be NULL, in which case they won't be read *
  61  * line holds the previous line for trajectory reading                  */
  62
  63 void write_g96_conf(FILE *out,t_trxframe *fr,int nindex,atom_id *index);
  64 /* write a Gromos96 coordinate file or trajectory frame *
  65  * index can be NULL                                    */
  66
  67 gmx_bool gro_next_x_or_v(FILE *status,t_trxframe *fr);
  68 int gro_first_x_or_v(FILE *status,t_trxframe *fr);
  69 /* read first/next x and/or v frame from gro file */
  70
  71 void write_hconf_indexed_p(FILE *out,const char *title,t_atoms *atoms,
  72                                   int nx,atom_id index[],int ndec,
  73                                   rvec *x,rvec *v,matrix box);
  74
  75 void write_hconf_p(FILE *out,const char *title,t_atoms *atoms, int ndec,
  76                           rvec *x,rvec *v,matrix box);
  77 /* Write a Gromos file with precision ndec: number of decimal places in x,
  78  * v has one place more. */
  79
  80 void write_sto_conf_indexed(const char *outfile,const char *title,
  81                             t_atoms *atoms,
  82                             rvec x[],rvec *v,int ePBC,matrix box,
  83                             atom_id nindex,atom_id index[]);
  84 /* like write_sto_conf, but indexed */
  85
  86 void write_sto_conf(const char *outfile,const char *title,
  87                            t_atoms *atoms,
  88                            rvec x[],rvec *v,int ePBC,matrix box);
  89 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
  90  * to an STO (.gro or .pdb) file */
  91
  92 void write_sto_conf_mtop(const char *outfile,const char *title,
  93                                 gmx_mtop_t *mtop,
  94                                 rvec x[],rvec *v,int ePBC,matrix box);
  95 /* As write_sto_conf, but uses a gmx_mtop_t struct */
  96
  97 void get_stx_coordnum (const char *infile,int *natoms);
  98 /* read the number of atoms from an STX file */
  99
 100 void read_stx_conf(const char *infile,char *title,
 101                           t_atoms *atoms,
 102                           rvec x[],rvec *v,int *ePBC,matrix box);
 103 /* Read atoms, x, v and box from an STX file.
 104  * If ePBC!=NULL return the type of pbc in *ePBC or -1 if unknown.
 105  */
 106
 107 #ifdef __cplusplus
 108 }
 109 #endif
 110
 111 #endif  /* _confio_h */