include/index.h

   1 /*
   2  * $Id$
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   8  *          GROningen MAchine for Chemical Simulations
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  10  *                        VERSION 3.2.0
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  14  * check out http://www.gromacs.org for more information.
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  36
  37 #ifndef _index_h
  38 #define _index_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include <typedefs.h>
  45
  46 #ifdef CPLUSPLUS
  47 extern "C" {
  48 #endif
  49
  50 extern void check_index(char *gname,int n,atom_id index[],
  51                         char *traj,int natoms);
  52 /* Checks if any index is smaller than zero or larger than natoms,
  53  * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
  54  * and traj (if traj=NULL, "the trajectory" is used).
  55  */
  56
  57 t_block *init_index(char *gfile, char ***grpname);
  58 /* Lower level routine than the next */
  59
  60 void rd_index(char *statfile,int ngrps,int isize[],
  61               atom_id *index[],char *grpnames[]);
  62 /* Assume the group file is generated, so the
  63  * format need not be user-friendly. The format is:
  64  * nr of groups, total nr of atoms
  65  * for each group: name nr of element, elements
  66  * The function opens a file, reads ngrps groups, puts the
  67  * sizes in isize, the atom_id s in index and the names of
  68  * the groups in grpnames.
  69  *
  70  * It is also assumed, that when ngrps groups are requested
  71  * memory has been allocated for ngrps index arrays, and that
  72  * the dimension of the isize and grpnames arrays are ngrps.
  73  */
  74
  75 void rd_index_nrs(char *statfile,int ngrps,int isize[],
  76                   atom_id *index[],char *grpnames[],int grpnr[]);
  77 /* the same but also reads the number of the selected group*/
  78
  79 void get_index(t_atoms *atoms, char *fnm, int ngrps,
  80                int isize[], atom_id *index[],char *grpnames[]);
  81 /* Does the same as rd_index, but if the fnm pointer is NULL it
  82  * will not read from fnm, but it will make default index groups
  83  * for the atoms in *atoms.
  84  */
  85
  86 typedef struct {
  87   int n;
  88   char **aa;
  89 } t_aa_names;
  90
  91 extern t_aa_names *get_aa_names(void);
  92 /* Read the database in aminoacids.dat */
  93
  94 extern bool is_protein(t_aa_names *aan,char *resnm);
  95 /* gives true if resnm occurs in aminoacids.dat */
  96
  97 extern void done_aa_names(t_aa_names **aan);
  98 /* Free memory. Pass address of the pointer youget from get_aa_names */
  99
 100 extern t_block *new_block(void);
 101 /* allocate new block */
 102
 103 extern void write_index(char *outf, t_block *b,char **gnames);
 104 /* Writes index blocks to outf (writes an indexfile) */
 105
 106 void add_grp(t_block *b,char ***gnames,int nra,atom_id a[],const char *name);
 107 /* Ads group a with name name to block b and namelist gnames */
 108
 109 extern void analyse(t_atoms *atoms,t_block *gb,char ***gn,
 110                     bool bASK,bool bVerb);
 111 /* Makes index groups gb with names gn for atoms in atoms.
 112  * bASK=FALSE gives default groups.
 113  */
 114
 115 extern int find_group(char s[], int ngrps, char **grpname);
 116
 117
 118 #ifdef CPLUSPLUS
 119 }
 120 #endif
 121
 122 #endif  /* _index_h */