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37 #include "residuetypes.h"
42 #include "gromacs/fileio/strdb.h"
43 #include "gromacs/utility/cstringutil.h"
44 #include "gromacs/utility/fatalerror.h"
45 #include "gromacs/utility/futil.h"
46 #include "gromacs/utility/smalloc.h"
48 const char gmx_residuetype_undefined
[] = "Other";
50 struct gmx_residuetype_t
58 gmx_residuetype_init(gmx_residuetype_t
**prt
)
62 char resname
[STRLEN
], restype
[STRLEN
], dum
[STRLEN
];
63 gmx_residuetype_t
*rt
;
72 db
= libopen("residuetypes.dat");
74 while (get_a_line(db
, line
, STRLEN
))
80 if (sscanf(line
, "%1000s %1000s %1000s", resname
, restype
, dum
) != 2)
82 gmx_fatal(FARGS
, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
84 gmx_residuetype_add(rt
, resname
, restype
);
94 gmx_residuetype_destroy(gmx_residuetype_t
*rt
)
98 for (i
= 0; i
< rt
->n
; i
++)
100 sfree(rt
->resname
[i
]);
101 sfree(rt
->restype
[i
]);
110 /* Return 0 if the name was found, otherwise -1.
111 * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
114 gmx_residuetype_get_type(gmx_residuetype_t
*rt
, const char * resname
, const char ** p_restype
)
119 for (i
= 0; i
< rt
->n
&& rc
; i
++)
121 rc
= gmx_strcasecmp(rt
->resname
[i
], resname
);
124 *p_restype
= (rc
== 0) ? rt
->restype
[i
-1] : gmx_residuetype_undefined
;
130 gmx_residuetype_add(gmx_residuetype_t
*rt
, const char *newresname
, const char *newrestype
)
133 const char * p_oldtype
;
135 found
= !gmx_residuetype_get_type(rt
, newresname
, &p_oldtype
);
137 if (found
&& gmx_strcasecmp(p_oldtype
, newrestype
))
139 fprintf(stderr
, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
140 newresname
, p_oldtype
, newrestype
);
145 srenew(rt
->resname
, rt
->n
+1);
146 srenew(rt
->restype
, rt
->n
+1);
147 rt
->resname
[rt
->n
] = gmx_strdup(newresname
);
148 rt
->restype
[rt
->n
] = gmx_strdup(newrestype
);
156 gmx_residuetype_get_alltypes(gmx_residuetype_t
*rt
,
157 const char *** p_typenames
,
161 const char ** my_typename
;
165 for (i
= 0; i
< rt
->n
; i
++)
167 const char *const p
= rt
->restype
[i
];
169 for (int j
= 0; j
< n
&& !bFound
; j
++)
171 assert(my_typename
!= NULL
);
172 bFound
= !gmx_strcasecmp(p
, my_typename
[j
]);
176 srenew(my_typename
, n
+1);
182 *p_typenames
= my_typename
;
188 gmx_residuetype_is_protein(gmx_residuetype_t
*rt
, const char *resnm
)
193 if (gmx_residuetype_get_type(rt
, resnm
, &p_type
) == 0 &&
194 gmx_strcasecmp(p_type
, "Protein") == 0)
206 gmx_residuetype_is_dna(gmx_residuetype_t
*rt
, const char *resnm
)
211 if (gmx_residuetype_get_type(rt
, resnm
, &p_type
) == 0 &&
212 gmx_strcasecmp(p_type
, "DNA") == 0)
224 gmx_residuetype_is_rna(gmx_residuetype_t
*rt
, const char *resnm
)
229 if (gmx_residuetype_get_type(rt
, resnm
, &p_type
) == 0 &&
230 gmx_strcasecmp(p_type
, "RNA") == 0)
241 /* Return the size of the arrays */
243 gmx_residuetype_get_size(gmx_residuetype_t
*rt
)
248 /* Search for a residuetype with name resnm within the
249 * gmx_residuetype database. Return the index if found,
253 gmx_residuetype_get_index(gmx_residuetype_t
*rt
, const char *resnm
)
258 for (i
= 0; i
< rt
->n
&& rc
; i
++)
260 rc
= gmx_strcasecmp(rt
->resname
[i
], resnm
);
263 return (0 == rc
) ? i
-1 : -1;
266 /* Return the name of the residuetype with the given index, or
267 * NULL if not found. */
269 gmx_residuetype_get_name(gmx_residuetype_t
*rt
, int index
)
271 if (index
>= 0 && index
< rt
->n
)
273 return rt
->resname
[index
];