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 #include "typedefs.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 void check_index(char *gname,int n,atom_id index[],
  46                         char *traj,int natoms);
  47 /* Checks if any index is smaller than zero or larger than natoms,
  48  * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
  49  * and traj (if traj=NULL, "the trajectory" is used).
  50  */
  51
  52 t_blocka *init_index(const char *gfile, char ***grpname);
  53 /* Lower level routine than the next */
  54
  55 void rd_index(const char *statfile,int ngrps,int isize[],
  56               atom_id *index[],char *grpnames[]);
  57 /* Assume the group file is generated, so the
  58  * format need not be user-friendly. The format is:
  59  * nr of groups, total nr of atoms
  60  * for each group: name nr of element, elements.
  61  *
  62  * The function opens a file, reads ngrps groups, asks the
  63  * user for group numbers, and puts the resulting sizes in
  64  * isize, the atom_id s in index and the names of
  65  * the groups in grpnames.
  66  *
  67  * It is also assumed, that when ngrps groups are requested
  68  * memory has been allocated for ngrps index arrays, and that
  69  * the dimension of the isize and grpnames arrays are ngrps.
  70  */
  71
  72 void rd_index_nrs(char *statfile,int ngrps,int isize[],
  73                   atom_id *index[],char *grpnames[],int grpnr[]);
  74 /* the same but also reads the number of the selected group*/
  75
  76 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
  77                int isize[], atom_id *index[],char *grpnames[]);
  78 /* Does the same as rd_index, but if the fnm pointer is NULL it
  79  * will not read from fnm, but it will make default index groups
  80  * for the atoms in *atoms.
  81  */
  82
  83 typedef struct {
  84   int      maxframe;
  85   char     **grpname;
  86   t_blocka *clust;
  87   atom_id  *inv_clust;
  88 } t_cluster_ndx;
  89
  90 t_cluster_ndx *cluster_index(FILE *fplog,const char *ndx);
  91
  92 typedef struct {
  93   int n;
  94   char **name;
  95 } t_names;
  96
  97 typedef struct gmx_residuetype *
  98 gmx_residuetype_t;
  99
 100 int
 101 gmx_residuetype_init(gmx_residuetype_t *rt);
 102
 103 int
 104 gmx_residuetype_destroy(gmx_residuetype_t rt);
 105
 106 int
 107 gmx_residuetype_get_type(gmx_residuetype_t rt,const char * resname, const char ** p_restype);
 108
 109 int
 110 gmx_residuetype_add(gmx_residuetype_t rt,const char *newresname, const char *newrestype);
 111
 112 int
 113 gmx_residuetype_get_alltypes(gmx_residuetype_t    rt,
 114                              const char ***       p_typenames,
 115                              int *                ntypes);
 116
 117 gmx_bool
 118 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
 119
 120 gmx_bool
 121 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
 122
 123 gmx_bool
 124 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
 125
 126 int
 127 gmx_residuetype_get_size(gmx_residuetype_t rt);
 128
 129 int
 130 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
 131
 132 const char *
 133 gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
 134
 135
 136
 137
 138
 139
 140 t_blocka *new_blocka(void);
 141 /* allocate new block */
 142
 143 void write_index(const char *outf, t_blocka *b,char **gnames);
 144 /* Writes index blocks to outf (writes an indexfile) */
 145
 146 void add_grp(t_blocka *b,char ***gnames,int nra,atom_id a[],const char *name);
 147 /* Ads group a with name name to block b and namelist gnames */
 148
 149 void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,
 150                     gmx_bool bASK,gmx_bool bVerb);
 151 /* Makes index groups gb with names gn for atoms in atoms.
 152  * bASK=FALSE gives default groups.
 153  */
 154
 155 int find_group(char s[], int ngrps, char **grpname);
 156
 157
 158 #ifdef __cplusplus
 159 }
 160 #endif
 161
 162 #endif  /* _index_h */