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44 #include "gromacs/fileio/strdb.h"
45 #include "gromacs/gmxpreprocess/fflibutil.h"
46 #include "gromacs/gmxpreprocess/hackblock.h"
47 #include "gromacs/legacyheaders/typedefs.h"
48 #include "gromacs/topology/residuetypes.h"
49 #include "gromacs/topology/symtab.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/fatalerror.h"
52 #include "gromacs/utility/futil.h"
53 #include "gromacs/utility/smalloc.h"
62 static void get_xlatoms(const char *fn, FILE *fp,
63 int *nptr, t_xlate_atom **xlptr)
65 char filebase[STRLEN];
67 char abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
72 fflib_filename_base(fn, filebase, STRLEN);
77 while (get_a_line(fp, line, STRLEN))
79 na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
80 /* Check if we are reading an old format file with the number of items
83 if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
89 gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'", fn, line);
93 xl[n].filebase = gmx_strdup(filebase);
95 /* Use wildcards... */
96 if (strcmp(rbuf, "*") != 0)
98 xl[n].res = gmx_strdup(rbuf);
105 /* Replace underscores in the string by spaces */
106 while ((_ptr = strchr(abuf, '_')) != 0)
111 xl[n].atom = gmx_strdup(abuf);
112 xl[n].replace = gmx_strdup(repbuf);
120 static void done_xlatom(int nxlate, t_xlate_atom *xlatom)
124 for (i = 0; (i < nxlate); i++)
126 sfree(xlatom[i].filebase);
127 if (xlatom[i].res != NULL)
129 sfree(xlatom[i].res);
131 sfree(xlatom[i].atom);
132 sfree(xlatom[i].replace);
137 void rename_atoms(const char *xlfile, const char *ffdir,
138 t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
139 gmx_bool bResname, gmx_residuetype_t *rt, gmx_bool bReorderNum,
143 int nxlate, a, i, resind;
144 t_xlate_atom *xlatom;
147 char c, *rnm, atombuf[32], *ptr0, *ptr1;
148 gmx_bool bReorderedNum, bRenamed, bMatch;
149 gmx_bool bStartTerm, bEndTerm;
155 fp = libopen(xlfile);
156 get_xlatoms(xlfile, fp, &nxlate, &xlatom);
161 nf = fflib_search_file_end(ffdir, ".arn", FALSE, &f);
162 for (i = 0; i < nf; i++)
164 fp = fflib_open(f[i]);
165 get_xlatoms(f[i], fp, &nxlate, &xlatom);
172 for (a = 0; (a < atoms->nr); a++)
174 resind = atoms->atom[a].resind;
176 bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind-1].chainnum;
177 bEndTerm = (resind >= atoms->nres-1) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind+1].chainnum;
181 rnm = *(atoms->resinfo[resind].name);
185 rnm = *(atoms->resinfo[resind].rtp);
188 strcpy(atombuf, *(atoms->atomname[a]));
189 bReorderedNum = FALSE;
192 if (isdigit(atombuf[0]))
195 for (i = 0; ((size_t)i < strlen(atombuf)-1); i++)
197 atombuf[i] = atombuf[i+1];
200 bReorderedNum = TRUE;
204 for (i = 0; (i < nxlate) && !bRenamed; i++)
206 /* Check if the base file name of the rtp and arn entry match */
208 gmx_strcasecmp(restp[resind].filebase, xlatom[i].filebase) == 0)
210 /* Match the residue name */
211 bMatch = (xlatom[i].res == NULL ||
212 (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0 &&
213 gmx_residuetype_is_protein(rt, rnm) && bStartTerm) ||
214 (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0 &&
215 gmx_residuetype_is_protein(rt, rnm) && bEndTerm) ||
216 (gmx_strcasecmp("protein", xlatom[i].res) == 0 &&
217 gmx_residuetype_is_protein(rt, rnm)) ||
218 (gmx_strcasecmp("DNA", xlatom[i].res) == 0 &&
219 gmx_residuetype_is_dna(rt, rnm)) ||
220 (gmx_strcasecmp("RNA", xlatom[i].res) == 0 &&
221 gmx_residuetype_is_rna(rt, rnm)));
225 ptr1 = xlatom[i].res;
226 while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
227 (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
232 bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
234 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
236 /* We have a match. */
237 /* Don't free the old atomname,
238 * since it might be in the symtab.
240 ptr0 = gmx_strdup(xlatom[i].replace);
243 printf("Renaming atom '%s' in residue %d %s to '%s'\n",
245 atoms->resinfo[resind].nr,
246 *atoms->resinfo[resind].name,
249 atoms->atomname[a] = put_symtab(symtab, ptr0);
254 if (bReorderedNum && !bRenamed)
256 atoms->atomname[a] = put_symtab(symtab, atombuf);
260 done_xlatom(nxlate, xlatom);