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44 #include "gromacs/gmxpreprocess/fflibutil.h"
45 #include "gromacs/gmxpreprocess/hackblock.h"
46 #include "gromacs/topology/residuetypes.h"
47 #include "gromacs/topology/symtab.h"
48 #include "gromacs/utility/cstringutil.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/utility/futil.h"
51 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/utility/strdb.h"
61 static void get_xlatoms(const char *fn, FILE *fp,
62 int *nptr, t_xlate_atom **xlptr)
64 char filebase[STRLEN];
66 char abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
71 fflib_filename_base(fn, filebase, STRLEN);
76 while (get_a_line(fp, line, STRLEN))
78 na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
79 /* Check if we are reading an old format file with the number of items
82 if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
88 gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'", fn, line);
92 xl[n].filebase = gmx_strdup(filebase);
94 /* Use wildcards... */
95 if (strcmp(rbuf, "*") != 0)
97 xl[n].res = gmx_strdup(rbuf);
104 /* Replace underscores in the string by spaces */
105 while ((_ptr = strchr(abuf, '_')) != nullptr)
110 xl[n].atom = gmx_strdup(abuf);
111 xl[n].replace = gmx_strdup(repbuf);
119 static void done_xlatom(int nxlate, t_xlate_atom *xlatom)
123 for (i = 0; (i < nxlate); i++)
125 sfree(xlatom[i].filebase);
126 if (xlatom[i].res != nullptr)
128 sfree(xlatom[i].res);
130 sfree(xlatom[i].atom);
131 sfree(xlatom[i].replace);
136 void rename_atoms(const char *xlfile, const char *ffdir,
137 t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
138 bool bResname, gmx_residuetype_t *rt, bool bReorderNum,
142 int nxlate, a, i, resind;
143 t_xlate_atom *xlatom;
146 char c, *rnm, atombuf[32], *ptr0, *ptr1;
147 bool bReorderedNum, bRenamed, bMatch;
148 bool bStartTerm, bEndTerm;
152 if (xlfile != nullptr)
154 fp = libopen(xlfile);
155 get_xlatoms(xlfile, fp, &nxlate, &xlatom);
160 nf = fflib_search_file_end(ffdir, ".arn", FALSE, &f);
161 for (i = 0; i < nf; i++)
163 fp = fflib_open(f[i]);
164 get_xlatoms(f[i], fp, &nxlate, &xlatom);
171 for (a = 0; (a < atoms->nr); a++)
173 resind = atoms->atom[a].resind;
175 bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind-1].chainnum;
176 bEndTerm = (resind >= atoms->nres-1) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind+1].chainnum;
180 rnm = *(atoms->resinfo[resind].name);
184 rnm = *(atoms->resinfo[resind].rtp);
187 strcpy(atombuf, *(atoms->atomname[a]));
188 bReorderedNum = FALSE;
191 if (isdigit(atombuf[0]))
194 for (i = 0; (static_cast<size_t>(i) < strlen(atombuf)-1); i++)
196 atombuf[i] = atombuf[i+1];
199 bReorderedNum = TRUE;
203 for (i = 0; (i < nxlate) && !bRenamed; i++)
205 /* Check if the base file name of the rtp and arn entry match */
206 if (restp == nullptr ||
207 gmx_strcasecmp(restp[resind].filebase, xlatom[i].filebase) == 0)
209 /* Match the residue name */
210 bMatch = (xlatom[i].res == nullptr ||
211 (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0 &&
212 gmx_residuetype_is_protein(rt, rnm) && bStartTerm) ||
213 (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0 &&
214 gmx_residuetype_is_protein(rt, rnm) && bEndTerm) ||
215 (gmx_strcasecmp("protein", xlatom[i].res) == 0 &&
216 gmx_residuetype_is_protein(rt, rnm)) ||
217 (gmx_strcasecmp("DNA", xlatom[i].res) == 0 &&
218 gmx_residuetype_is_dna(rt, rnm)) ||
219 (gmx_strcasecmp("RNA", xlatom[i].res) == 0 &&
220 gmx_residuetype_is_rna(rt, rnm)));
224 ptr1 = xlatom[i].res;
225 while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
226 (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
231 bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
233 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
235 /* We have a match. */
236 /* Don't free the old atomname,
237 * since it might be in the symtab.
239 ptr0 = gmx_strdup(xlatom[i].replace);
242 printf("Renaming atom '%s' in residue %d %s to '%s'\n",
244 atoms->resinfo[resind].nr,
245 *atoms->resinfo[resind].name,
248 atoms->atomname[a] = put_symtab(symtab, ptr0);
253 if (bReorderedNum && !bRenamed)
255 atoms->atomname[a] = put_symtab(symtab, atombuf);
259 done_xlatom(nxlate, xlatom);