include/index.h

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  38
  39 #ifndef _index_h
  40 #define _index_h
  41
  42 #include "visibility.h"
  43 #include "typedefs.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 GMX_LIBGMX_EXPORT
  50 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 GMX_LIBGMX_EXPORT
  58 t_blocka *init_index(const char *gfile, char ***grpname);
  59 /* Lower level routine than the next */
  60
  61 GMX_LIBGMX_EXPORT
  62 void rd_index(const char *statfile, int ngrps, int isize[],
  63               atom_id *index[], char *grpnames[]);
  64 /* Assume the group file is generated, so the
  65  * format need not be user-friendly. The format is:
  66  * nr of groups, total nr of atoms
  67  * for each group: name nr of element, elements.
  68  *
  69  * The function opens a file, reads ngrps groups, asks the
  70  * user for group numbers, and puts the resulting sizes in
  71  * isize, the atom_id s in index and the names of
  72  * the groups in grpnames.
  73  *
  74  * It is also assumed, that when ngrps groups are requested
  75  * memory has been allocated for ngrps index arrays, and that
  76  * the dimension of the isize and grpnames arrays are ngrps.
  77  */
  78
  79 void rd_index_nrs(char *statfile, int ngrps, int isize[],
  80                   atom_id *index[], char *grpnames[], int grpnr[]);
  81 /* the same but also reads the number of the selected group*/
  82
  83 GMX_LIBGMX_EXPORT
  84 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
  85                int isize[], atom_id *index[], char *grpnames[]);
  86 /* Does the same as rd_index, but if the fnm pointer is NULL it
  87  * will not read from fnm, but it will make default index groups
  88  * for the atoms in *atoms.
  89  */
  90
  91 typedef struct {
  92     int        maxframe;
  93     char     **grpname;
  94     t_blocka  *clust;
  95     atom_id   *inv_clust;
  96 } t_cluster_ndx;
  97
  98 GMX_LIBGMX_EXPORT
  99 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
 100
 101 typedef struct {
 102     int    n;
 103     char **name;
 104 } t_names;
 105
 106 typedef struct gmx_residuetype *
 107     gmx_residuetype_t;
 108
 109 GMX_LIBGMX_EXPORT
 110 int
 111 gmx_residuetype_init(gmx_residuetype_t *rt);
 112
 113 GMX_LIBGMX_EXPORT
 114 int
 115 gmx_residuetype_destroy(gmx_residuetype_t rt);
 116
 117 GMX_LIBGMX_EXPORT
 118 int
 119 gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype);
 120
 121 GMX_LIBGMX_EXPORT
 122 int
 123 gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
 124
 125 int
 126 gmx_residuetype_get_alltypes(gmx_residuetype_t    rt,
 127                              const char ***       p_typenames,
 128                              int *                ntypes);
 129
 130 GMX_LIBGMX_EXPORT
 131 gmx_bool
 132 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
 133
 134 GMX_LIBGMX_EXPORT
 135 gmx_bool
 136 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
 137
 138 GMX_LIBGMX_EXPORT
 139 gmx_bool
 140 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
 141
 142 GMX_LIBGMX_EXPORT
 143 int
 144 gmx_residuetype_get_size(gmx_residuetype_t rt);
 145
 146 GMX_LIBGMX_EXPORT
 147 int
 148 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
 149
 150 GMX_LIBGMX_EXPORT
 151 const char *
 152 gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
 153
 154
 155
 156
 157
 158
 159 GMX_LIBGMX_EXPORT
 160 t_blocka *new_blocka(void);
 161 /* allocate new block */
 162
 163 GMX_LIBGMX_EXPORT
 164 void write_index(const char *outf, t_blocka *b, char **gnames);
 165 /* Writes index blocks to outf (writes an indexfile) */
 166
 167 GMX_LIBGMX_EXPORT
 168 void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name);
 169 /* Ads group a with name name to block b and namelist gnames */
 170
 171 GMX_LIBGMX_EXPORT
 172 void analyse(t_atoms *atoms, t_blocka *gb, char ***gn,
 173              gmx_bool bASK, gmx_bool bVerb);
 174 /* Makes index groups gb with names gn for atoms in atoms.
 175  * bASK=FALSE gives default groups.
 176  */
 177
 178 GMX_LIBGMX_EXPORT
 179 int find_group(char s[], int ngrps, char **grpname);
 180
 181
 182 #ifdef __cplusplus
 183 }
 184 #endif
 185
 186 #endif  /* _index_h */