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47 void check_index(char *gname, int n, atom_id index[],
48 char *traj, int natoms);
49 /* Checks if any index is smaller than zero or larger than natoms,
50 * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
51 * and traj (if traj=NULL, "the trajectory" is used).
54 t_blocka *init_index(const char *gfile, char ***grpname);
55 /* Lower level routine than the next */
57 void rd_index(const char *statfile, int ngrps, int isize[],
58 atom_id *index[], char *grpnames[]);
59 /* Assume the group file is generated, so the
60 * format need not be user-friendly. The format is:
61 * nr of groups, total nr of atoms
62 * for each group: name nr of element, elements.
64 * The function opens a file, reads ngrps groups, asks the
65 * user for group numbers, and puts the resulting sizes in
66 * isize, the atom_id s in index and the names of
67 * the groups in grpnames.
69 * It is also assumed, that when ngrps groups are requested
70 * memory has been allocated for ngrps index arrays, and that
71 * the dimension of the isize and grpnames arrays are ngrps.
74 void rd_index_nrs(char *statfile, int ngrps, int isize[],
75 atom_id *index[], char *grpnames[], int grpnr[]);
76 /* the same but also reads the number of the selected group*/
78 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
79 int isize[], atom_id *index[], char *grpnames[]);
80 /* Does the same as rd_index, but if the fnm pointer is NULL it
81 * will not read from fnm, but it will make default index groups
82 * for the atoms in *atoms.
92 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
99 typedef struct gmx_residuetype *
103 gmx_residuetype_init(gmx_residuetype_t *rt);
106 gmx_residuetype_destroy(gmx_residuetype_t rt);
109 gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype);
112 gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
115 gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
116 const char *** p_typenames,
120 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
123 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
126 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
129 gmx_residuetype_get_size(gmx_residuetype_t rt);
132 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
135 gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
142 t_blocka *new_blocka(void);
143 /* allocate new block */
145 void write_index(const char *outf, t_blocka *b, char **gnames);
146 /* Writes index blocks to outf (writes an indexfile) */
148 void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name);
149 /* Ads group a with name name to block b and namelist gnames */
151 void analyse(t_atoms *atoms, t_blocka *gb, char ***gn,
152 gmx_bool bASK, gmx_bool bVerb);
153 /* Makes index groups gb with names gn for atoms in atoms.
154 * bASK=FALSE gives default groups.
157 int find_group(char s[], int ngrps, char **grpname);
164 #endif /* _index_h */