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42 #include "visibility.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).
58 t_blocka
*init_index(const char *gfile
, char ***grpname
);
59 /* Lower level routine than the next */
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.
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.
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.
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*/
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.
99 t_cluster_ndx
*cluster_index(FILE *fplog
, const char *ndx
);
106 typedef struct gmx_residuetype
*
111 gmx_residuetype_init(gmx_residuetype_t
*rt
);
115 gmx_residuetype_destroy(gmx_residuetype_t rt
);
119 gmx_residuetype_get_type(gmx_residuetype_t rt
, const char * resname
, const char ** p_restype
);
123 gmx_residuetype_add(gmx_residuetype_t rt
, const char *newresname
, const char *newrestype
);
126 gmx_residuetype_get_alltypes(gmx_residuetype_t rt
,
127 const char *** p_typenames
,
132 gmx_residuetype_is_protein(gmx_residuetype_t rt
, const char *resnm
);
136 gmx_residuetype_is_dna(gmx_residuetype_t rt
, const char *resnm
);
140 gmx_residuetype_is_rna(gmx_residuetype_t rt
, const char *resnm
);
144 gmx_residuetype_get_size(gmx_residuetype_t rt
);
148 gmx_residuetype_get_index(gmx_residuetype_t rt
, const char *resnm
);
152 gmx_residuetype_get_name(gmx_residuetype_t rt
, int index
);
160 t_blocka
*new_blocka(void);
161 /* allocate new block */
164 void write_index(const char *outf
, t_blocka
*b
, char **gnames
);
165 /* Writes index blocks to outf (writes an indexfile) */
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 */
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.
179 int find_group(char s
[], int ngrps
, char **grpname
);
186 #endif /* _index_h */