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43 #include "types/atoms.h"
44 #include "types/block.h"
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).
57 t_blocka *init_index(const char *gfile, char ***grpname);
58 /* Lower level routine than the next */
60 void rd_index(const 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.
67 * The function opens a file, reads ngrps groups, asks the
68 * user for group numbers, and puts the resulting sizes in
69 * isize, the atom_id s in index and the names of
70 * the groups in grpnames.
72 * It is also assumed, that when ngrps groups are requested
73 * memory has been allocated for ngrps index arrays, and that
74 * the dimension of the isize and grpnames arrays are ngrps.
77 void rd_index_nrs(char *statfile, int ngrps, int isize[],
78 atom_id *index[], char *grpnames[], int grpnr[]);
79 /* the same but also reads the number of the selected group*/
81 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
82 int isize[], atom_id *index[], char *grpnames[]);
83 /* Does the same as rd_index, but if the fnm pointer is NULL it
84 * will not read from fnm, but it will make default index groups
85 * for the atoms in *atoms.
95 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
102 typedef struct gmx_residuetype *
106 gmx_residuetype_init(gmx_residuetype_t *rt);
109 gmx_residuetype_destroy(gmx_residuetype_t rt);
112 gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype);
115 gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
118 gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
119 const char *** p_typenames,
123 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
126 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
129 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
132 gmx_residuetype_get_size(gmx_residuetype_t rt);
135 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
138 gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
145 t_blocka *new_blocka(void);
146 /* allocate new block */
148 void write_index(const char *outf, t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
149 /* Writes index blocks to outf (writes an indexfile) */
151 void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name);
152 /* Ads group a with name name to block b and namelist gnames */
154 void analyse(t_atoms *atoms, t_blocka *gb, char ***gn,
155 gmx_bool bASK, gmx_bool bVerb);
156 /* Makes index groups gb with names gn for atoms in atoms.
157 * bASK=FALSE gives default groups.
160 int find_group(char s[], int ngrps, char **grpname);
167 #endif /* _index_h */