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45 #include "fflibutil.h"
46 #include "hackblock.h"
49 #include "gromacs/fileio/strdb.h"
50 #include "gromacs/topology/residuetypes.h"
51 #include "gromacs/topology/symtab.h"
52 #include "gromacs/utility/cstringutil.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/futil.h"
55 #include "gromacs/utility/smalloc.h"
64 static void get_xlatoms(const char *fn, FILE *fp,
65 int *nptr, t_xlate_atom **xlptr)
67 char filebase[STRLEN];
69 char abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
74 fflib_filename_base(fn, filebase, STRLEN);
79 while (get_a_line(fp, line, STRLEN))
81 na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
82 /* Check if we are reading an old format file with the number of items
85 if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
91 gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'", fn, line);
95 xl[n].filebase = strdup(filebase);
97 /* Use wildcards... */
98 if (strcmp(rbuf, "*") != 0)
100 xl[n].res = strdup(rbuf);
107 /* Replace underscores in the string by spaces */
108 while ((_ptr = strchr(abuf, '_')) != 0)
113 xl[n].atom = strdup(abuf);
114 xl[n].replace = strdup(repbuf);
122 static void done_xlatom(int nxlate, t_xlate_atom *xlatom)
126 for (i = 0; (i < nxlate); i++)
128 sfree(xlatom[i].filebase);
129 if (xlatom[i].res != NULL)
131 sfree(xlatom[i].res);
133 sfree(xlatom[i].atom);
134 sfree(xlatom[i].replace);
139 void rename_atoms(const char *xlfile, const char *ffdir,
140 t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
141 gmx_bool bResname, gmx_residuetype_t *rt, gmx_bool bReorderNum,
145 int nxlate, a, i, resind;
146 t_xlate_atom *xlatom;
149 char c, *rnm, atombuf[32], *ptr0, *ptr1;
150 gmx_bool bReorderedNum, bRenamed, bMatch;
156 fp = libopen(xlfile);
157 get_xlatoms(xlfile, fp, &nxlate, &xlatom);
162 nf = fflib_search_file_end(ffdir, ".arn", FALSE, &f);
163 for (i = 0; i < nf; i++)
165 fp = fflib_open(f[i]);
166 get_xlatoms(f[i], fp, &nxlate, &xlatom);
173 for (a = 0; (a < atoms->nr); a++)
175 resind = atoms->atom[a].resind;
178 rnm = *(atoms->resinfo[resind].name);
182 rnm = *(atoms->resinfo[resind].rtp);
185 strcpy(atombuf, *(atoms->atomname[a]));
186 bReorderedNum = FALSE;
189 if (isdigit(atombuf[0]))
192 for (i = 0; ((size_t)i < strlen(atombuf)-1); i++)
194 atombuf[i] = atombuf[i+1];
197 bReorderedNum = TRUE;
201 for (i = 0; (i < nxlate) && !bRenamed; i++)
203 /* Check if the base file name of the rtp and arn entry match */
205 gmx_strcasecmp(restp[resind].filebase, xlatom[i].filebase) == 0)
207 /* Match the residue name */
208 bMatch = (xlatom[i].res == NULL ||
209 (gmx_strcasecmp("protein", xlatom[i].res) == 0 &&
210 gmx_residuetype_is_protein(rt, rnm)) ||
211 (gmx_strcasecmp("DNA", xlatom[i].res) == 0 &&
212 gmx_residuetype_is_dna(rt, rnm)) ||
213 (gmx_strcasecmp("RNA", xlatom[i].res) == 0 &&
214 gmx_residuetype_is_rna(rt, rnm)));
218 ptr1 = xlatom[i].res;
219 while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
220 (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
225 bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
227 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
229 /* We have a match. */
230 /* Don't free the old atomname,
231 * since it might be in the symtab.
233 ptr0 = strdup(xlatom[i].replace);
236 printf("Renaming atom '%s' in residue %d %s to '%s'\n",
238 atoms->resinfo[resind].nr,
239 *atoms->resinfo[resind].name,
242 atoms->atomname[a] = put_symtab(symtab, ptr0);
247 if (bReorderedNum && !bRenamed)
249 atoms->atomname[a] = put_symtab(symtab, atombuf);
253 done_xlatom(nxlate, xlatom);