include/index.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
   8  *
   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
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _index_h
  37 #define _index_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <typedefs.h>
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 extern void check_index(char *gname,int n,atom_id index[],
  50                         char *traj,int natoms);
  51 /* Checks if any index is smaller than zero or larger than natoms,
  52  * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
  53  * and traj (if traj=NULL, "the trajectory" is used).
  54  */
  55
  56 t_blocka *init_index(const char *gfile, char ***grpname);
  57 /* Lower level routine than the next */
  58
  59 void rd_index(const char *statfile,int ngrps,int isize[],
  60               atom_id *index[],char *grpnames[]);
  61 /* Assume the group file is generated, so the
  62  * format need not be user-friendly. The format is:
  63  * nr of groups, total nr of atoms
  64  * for each group: name nr of element, elements
  65  * The function opens a file, reads ngrps groups, puts the
  66  * sizes in isize, the atom_id s in index and the names of
  67  * the groups in grpnames.
  68  *
  69  * It is also assumed, that when ngrps groups are requested
  70  * memory has been allocated for ngrps index arrays, and that
  71  * the dimension of the isize and grpnames arrays are ngrps.
  72  */
  73
  74 void rd_index_nrs(char *statfile,int ngrps,int isize[],
  75                   atom_id *index[],char *grpnames[],int grpnr[]);
  76 /* the same but also reads the number of the selected group*/
  77
  78 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
  79                int isize[], atom_id *index[],char *grpnames[]);
  80 /* Does the same as rd_index, but if the fnm pointer is NULL it
  81  * will not read from fnm, but it will make default index groups
  82  * for the atoms in *atoms.
  83  */
  84
  85 typedef struct {
  86   int      maxframe;
  87   char     **grpname;
  88   t_blocka *clust;
  89   atom_id  *inv_clust;
  90 } t_cluster_ndx;
  91
  92 extern t_cluster_ndx *cluster_index(FILE *fplog,const char *ndx);
  93
  94 typedef struct {
  95   int n;
  96   char **aa;
  97 } t_aa_names;
  98
  99 extern t_aa_names *get_aa_names(void);
 100 /* Read the database in aminoacids.dat */
 101
 102 extern bool is_protein(t_aa_names *aan,char *resnm);
 103 /* gives true if resnm occurs in aminoacids.dat */
 104
 105 extern void done_aa_names(t_aa_names **aan);
 106 /* Free memory. Pass address of the pointer youget from get_aa_names */
 107
 108 extern t_blocka *new_blocka(void);
 109 /* allocate new block */
 110
 111 extern void write_index(const char *outf, t_blocka *b,char **gnames);
 112 /* Writes index blocks to outf (writes an indexfile) */
 113
 114 void add_grp(t_blocka *b,char ***gnames,int nra,atom_id a[],const char *name);
 115 /* Ads group a with name name to block b and namelist gnames */
 116
 117 extern void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,
 118                     bool bASK,bool bVerb);
 119 /* Makes index groups gb with names gn for atoms in atoms.
 120  * bASK=FALSE gives default groups.
 121  */
 122
 123 extern int find_group(char s[], int ngrps, char **grpname);
 124
 125
 126 #ifdef __cplusplus
 127 }
 128 #endif
 129
 130 #endif  /* _index_h */