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
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  18  * of the License, or (at your option) any later version.
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  21  * scientific software is very special. Version control is crucial -
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  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  *
  66  * The function opens a file, reads ngrps groups, asks the
  67  * user for group numbers, and puts the resulting sizes in
  68  * isize, the atom_id s in index and the names of
  69  * the groups in grpnames.
  70  *
  71  * It is also assumed, that when ngrps groups are requested
  72  * memory has been allocated for ngrps index arrays, and that
  73  * the dimension of the isize and grpnames arrays are ngrps.
  74  */
  75
  76 void rd_index_nrs(char *statfile,int ngrps,int isize[],
  77                   atom_id *index[],char *grpnames[],int grpnr[]);
  78 /* the same but also reads the number of the selected group*/
  79
  80 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
  81                int isize[], atom_id *index[],char *grpnames[]);
  82 /* Does the same as rd_index, but if the fnm pointer is NULL it
  83  * will not read from fnm, but it will make default index groups
  84  * for the atoms in *atoms.
  85  */
  86
  87 typedef struct {
  88   int      maxframe;
  89   char     **grpname;
  90   t_blocka *clust;
  91   atom_id  *inv_clust;
  92 } t_cluster_ndx;
  93
  94 extern t_cluster_ndx *cluster_index(FILE *fplog,const char *ndx);
  95
  96 typedef struct {
  97   int n;
  98   char **aa;
  99 } t_aa_names;
 100
 101 extern t_aa_names *get_aa_names(void);
 102 /* Read the database in aminoacids.dat */
 103
 104 extern bool is_protein(t_aa_names *aan,char *resnm);
 105 /* gives true if resnm occurs in aminoacids.dat */
 106
 107 extern void done_aa_names(t_aa_names **aan);
 108 /* Free memory. Pass address of the pointer youget from get_aa_names */
 109
 110 extern t_blocka *new_blocka(void);
 111 /* allocate new block */
 112
 113 extern void write_index(const char *outf, t_blocka *b,char **gnames);
 114 /* Writes index blocks to outf (writes an indexfile) */
 115
 116 void add_grp(t_blocka *b,char ***gnames,int nra,atom_id a[],const char *name);
 117 /* Ads group a with name name to block b and namelist gnames */
 118
 119 extern void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,
 120                     bool bASK,bool bVerb);
 121 /* Makes index groups gb with names gn for atoms in atoms.
 122  * bASK=FALSE gives default groups.
 123  */
 124
 125 extern int find_group(char s[], int ngrps, char **grpname);
 126
 127
 128 #ifdef __cplusplus
 129 }
 130 #endif
 131
 132 #endif  /* _index_h */