2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2010,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
35 #include "gromacs/topology/residuetypes.h"
40 #include "gromacs/fileio/strdb.h"
41 #include "gromacs/utility/cstringutil.h"
42 #include "gromacs/utility/fatalerror.h"
43 #include "gromacs/utility/futil.h"
44 #include "gromacs/utility/smalloc.h"
46 const char gmx_residuetype_undefined[] = "Other";
48 struct gmx_residuetype_t
56 gmx_residuetype_init(gmx_residuetype_t **prt)
60 char resname[STRLEN], restype[STRLEN], dum[STRLEN];
61 gmx_residuetype_t *rt;
70 db = libopen("residuetypes.dat");
72 while (get_a_line(db, line, STRLEN))
78 if (sscanf(line, "%1000s %1000s %1000s", resname, restype, dum) != 2)
80 gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
82 gmx_residuetype_add(rt, resname, restype);
92 gmx_residuetype_destroy(gmx_residuetype_t *rt)
96 for (i = 0; i < rt->n; i++)
98 sfree(rt->resname[i]);
99 sfree(rt->restype[i]);
108 /* Return 0 if the name was found, otherwise -1.
109 * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
112 gmx_residuetype_get_type(gmx_residuetype_t *rt, const char * resname, const char ** p_restype)
117 for (i = 0; i < rt->n && rc; i++)
119 rc = gmx_strcasecmp(rt->resname[i], resname);
122 *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
128 gmx_residuetype_add(gmx_residuetype_t *rt, const char *newresname, const char *newrestype)
131 const char * p_oldtype;
133 found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
135 if (found && gmx_strcasecmp(p_oldtype, newrestype))
137 fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
138 newresname, p_oldtype, newrestype);
143 srenew(rt->resname, rt->n+1);
144 srenew(rt->restype, rt->n+1);
145 rt->resname[rt->n] = gmx_strdup(newresname);
146 rt->restype[rt->n] = gmx_strdup(newrestype);
154 gmx_residuetype_get_alltypes(gmx_residuetype_t *rt,
155 const char *** p_typenames,
159 const char ** my_typename;
163 for (i = 0; i < rt->n; i++)
165 const char *const p = rt->restype[i];
167 for (int j = 0; j < n && !bFound; j++)
169 assert(my_typename != NULL);
170 bFound = !gmx_strcasecmp(p, my_typename[j]);
174 srenew(my_typename, n+1);
180 *p_typenames = my_typename;
186 gmx_residuetype_is_protein(gmx_residuetype_t *rt, const char *resnm)
191 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
192 gmx_strcasecmp(p_type, "Protein") == 0)
204 gmx_residuetype_is_dna(gmx_residuetype_t *rt, const char *resnm)
209 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
210 gmx_strcasecmp(p_type, "DNA") == 0)
222 gmx_residuetype_is_rna(gmx_residuetype_t *rt, const char *resnm)
227 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
228 gmx_strcasecmp(p_type, "RNA") == 0)
239 /* Return the size of the arrays */
241 gmx_residuetype_get_size(gmx_residuetype_t *rt)
246 /* Search for a residuetype with name resnm within the
247 * gmx_residuetype database. Return the index if found,
251 gmx_residuetype_get_index(gmx_residuetype_t *rt, const char *resnm)
256 for (i = 0; i < rt->n && rc; i++)
258 rc = gmx_strcasecmp(rt->resname[i], resnm);
261 return (0 == rc) ? i-1 : -1;
264 /* Return the name of the residuetype with the given index, or
265 * NULL if not found. */
267 gmx_residuetype_get_name(gmx_residuetype_t *rt, int index)
269 if (index >= 0 && index < rt->n)
271 return rt->resname[index];