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44 #include "gromacs/utility/cstringutil.h"
45 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/fileio/futil.h"
49 #include "fflibutil.h"
50 #include "hackblock.h"
51 #include "gmx_fatal.h"
54 #include "gromacs/fileio/strdb.h"
63 static void get_xlatoms(const char *fn, FILE *fp,
64 int *nptr, t_xlate_atom **xlptr)
66 char filebase[STRLEN];
68 char abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
73 fflib_filename_base(fn, filebase, STRLEN);
78 while (get_a_line(fp, line, STRLEN))
80 na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
81 /* Check if we are reading an old format file with the number of items
84 if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
90 gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'", fn, line);
94 xl[n].filebase = strdup(filebase);
96 /* Use wildcards... */
97 if (strcmp(rbuf, "*") != 0)
99 xl[n].res = strdup(rbuf);
106 /* Replace underscores in the string by spaces */
107 while ((_ptr = strchr(abuf, '_')) != 0)
112 xl[n].atom = strdup(abuf);
113 xl[n].replace = strdup(repbuf);
121 static void done_xlatom(int nxlate, t_xlate_atom *xlatom)
125 for (i = 0; (i < nxlate); i++)
127 sfree(xlatom[i].filebase);
128 if (xlatom[i].res != NULL)
130 sfree(xlatom[i].res);
132 sfree(xlatom[i].atom);
133 sfree(xlatom[i].replace);
138 void rename_atoms(const char *xlfile, const char *ffdir,
139 t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
140 gmx_bool bResname, gmx_residuetype_t rt, gmx_bool bReorderNum,
144 int nxlate, a, i, resind;
145 t_xlate_atom *xlatom;
148 char c, *rnm, atombuf[32], *ptr0, *ptr1;
149 gmx_bool bReorderedNum, bRenamed, bMatch;
150 gmx_bool bStartTerm, bEndTerm;
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;
177 bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind-1].chainnum;
178 bEndTerm = (resind >= atoms->nres-1) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind+1].chainnum;
182 rnm = *(atoms->resinfo[resind].name);
186 rnm = *(atoms->resinfo[resind].rtp);
189 strcpy(atombuf, *(atoms->atomname[a]));
190 bReorderedNum = FALSE;
193 if (isdigit(atombuf[0]))
196 for (i = 0; ((size_t)i < strlen(atombuf)-1); i++)
198 atombuf[i] = atombuf[i+1];
201 bReorderedNum = TRUE;
205 for (i = 0; (i < nxlate) && !bRenamed; i++)
207 /* Check if the base file name of the rtp and arn entry match */
209 gmx_strcasecmp(restp[resind].filebase, xlatom[i].filebase) == 0)
211 /* Match the residue name */
212 bMatch = (xlatom[i].res == NULL ||
213 (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0 &&
214 gmx_residuetype_is_protein(rt, rnm) && bStartTerm) ||
215 (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0 &&
216 gmx_residuetype_is_protein(rt, rnm) && bEndTerm) ||
217 (gmx_strcasecmp("protein", xlatom[i].res) == 0 &&
218 gmx_residuetype_is_protein(rt, rnm)) ||
219 (gmx_strcasecmp("DNA", xlatom[i].res) == 0 &&
220 gmx_residuetype_is_dna(rt, rnm)) ||
221 (gmx_strcasecmp("RNA", xlatom[i].res) == 0 &&
222 gmx_residuetype_is_rna(rt, rnm)));
226 ptr1 = xlatom[i].res;
227 while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
228 (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
233 bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
235 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
237 /* We have a match. */
238 /* Don't free the old atomname,
239 * since it might be in the symtab.
241 ptr0 = strdup(xlatom[i].replace);
244 printf("Renaming atom '%s' in residue %d %s to '%s'\n",
246 atoms->resinfo[resind].nr,
247 *atoms->resinfo[resind].name,
250 atoms->atomname[a] = put_symtab(symtab, ptr0);
255 if (bReorderedNum && !bRenamed)
257 atoms->atomname[a] = put_symtab(symtab, atombuf);
261 done_xlatom(nxlate, xlatom);