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38 #include "gmxpre.h"
39
40 #include "xlate.h"
41
42 #include <cctype>
43 #include <cstring>
44
45 #include <string>
46 #include <vector>
47
48 #include "gromacs/gmxpreprocess/fflibutil.h"
49 #include "gromacs/gmxpreprocess/grompp_impl.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"
56 #include "gromacs/utility/strdb.h"
57
58 #include "hackblock.h"
59
60 typedef struct
61 {
62 char* filebase;
63 char* res;
64 char* atom;
65 char* replace;
66 } t_xlate_atom;
67
get_xlatoms(const std::string & filename,FILE * fp,int * nptr,t_xlate_atom ** xlptr)68 static void get_xlatoms(const std::string& filename, FILE* fp, int* nptr, t_xlate_atom** xlptr)
69 {
70 char filebase[STRLEN];
71 char line[STRLEN];
72 char abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
73 char* _ptr;
74 int n, na, idum;
75 t_xlate_atom* xl;
76
77 fflib_filename_base(filename.c_str(), filebase, STRLEN);
78
79 n = *nptr;
80 xl = *xlptr;
81
82 while (get_a_line(fp, line, STRLEN))
83 {
84 na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
85 /* Check if we are reading an old format file with the number of items
86 * on the first line.
87 */
88 if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
89 {
90 continue;
91 }
92 if (na != 3)
93 {
94 gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'",
95 filename.c_str(), line);
96 }
97
98 srenew(xl, n + 1);
99 xl[n].filebase = gmx_strdup(filebase);
100
101 /* Use wildcards... */
102 if (strcmp(rbuf, "*") != 0)
103 {
104 xl[n].res = gmx_strdup(rbuf);
105 }
106 else
107 {
108 xl[n].res = nullptr;
109 }
110
111 /* Replace underscores in the string by spaces */
112 while ((_ptr = strchr(abuf, '_')) != nullptr)
113 {
114 *_ptr = ' ';
115 }
116
117 xl[n].atom = gmx_strdup(abuf);
118 xl[n].replace = gmx_strdup(repbuf);
119 n++;
120 }
121
122 *nptr = n;
123 *xlptr = xl;
124 }
125
done_xlatom(int nxlate,t_xlate_atom * xlatom)126 static void done_xlatom(int nxlate, t_xlate_atom* xlatom)
127 {
128 int i;
129
130 for (i = 0; (i < nxlate); i++)
131 {
132 sfree(xlatom[i].filebase);
133 if (xlatom[i].res != nullptr)
134 {
135 sfree(xlatom[i].res);
136 }
137 sfree(xlatom[i].atom);
138 sfree(xlatom[i].replace);
139 }
140 sfree(xlatom);
141 }
142
rename_atoms(const char * xlfile,const char * ffdir,t_atoms * atoms,t_symtab * symtab,gmx::ArrayRef<const PreprocessResidue> localPpResidue,bool bResname,ResidueType * rt,bool bReorderNum,bool bVerbose)143 void rename_atoms(const char* xlfile,
144 const char* ffdir,
145 t_atoms* atoms,
146 t_symtab* symtab,
147 gmx::ArrayRef<const PreprocessResidue> localPpResidue,
148 bool bResname,
149 ResidueType* rt,
150 bool bReorderNum,
151 bool bVerbose)
152 {
153 int nxlate, a, i, resind;
154 t_xlate_atom* xlatom;
155 char c, *rnm, atombuf[32];
156 bool bReorderedNum, bRenamed, bMatch;
157 bool bStartTerm, bEndTerm;
158
159 nxlate = 0;
160 xlatom = nullptr;
161 if (xlfile != nullptr)
162 {
163 gmx::FilePtr fp = gmx::openLibraryFile(xlfile);
164 get_xlatoms(xlfile, fp.get(), &nxlate, &xlatom);
165 }
166 else
167 {
168 std::vector<std::string> fns = fflib_search_file_end(ffdir, ".arn", FALSE);
169 for (const auto& filename : fns)
170 {
171 FILE* fp = fflib_open(filename);
172 get_xlatoms(filename, fp, &nxlate, &xlatom);
173 gmx_ffclose(fp);
174 }
175 }
176
177 for (a = 0; (a < atoms->nr); a++)
178 {
179 resind = atoms->atom[a].resind;
180
181 bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind - 1].chainnum;
182 bEndTerm = (resind >= atoms->nres - 1)
183 || atoms->resinfo[resind].chainnum != atoms->resinfo[resind + 1].chainnum;
184
185 if (bResname)
186 {
187 rnm = *(atoms->resinfo[resind].name);
188 }
189 else
190 {
191 rnm = *(atoms->resinfo[resind].rtp);
192 }
193
194 strcpy(atombuf, *(atoms->atomname[a]));
195 bReorderedNum = FALSE;
196 if (bReorderNum)
197 {
198 if (isdigit(atombuf[0]))
199 {
200 c = atombuf[0];
201 for (i = 0; (static_cast<size_t>(i) < strlen(atombuf) - 1); i++)
202 {
203 atombuf[i] = atombuf[i + 1];
204 }
205 atombuf[i] = c;
206 bReorderedNum = TRUE;
207 }
208 }
209 bRenamed = FALSE;
210 for (i = 0; (i < nxlate) && !bRenamed; i++)
211 {
212 /* Check if the base file name of the rtp and arn entry match */
213 if (localPpResidue.empty()
214 || gmx::equalCaseInsensitive(localPpResidue[resind].filebase, xlatom[i].filebase))
215 {
216 /* Match the residue name */
217 bMatch = (xlatom[i].res == nullptr
218 || (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0
219 && rt->namedResidueHasType(rnm, "Protein") && bStartTerm)
220 || (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0
221 && rt->namedResidueHasType(rnm, "Protein") && bEndTerm)
222 || (gmx_strcasecmp("protein", xlatom[i].res) == 0
223 && rt->namedResidueHasType(rnm, "Protein"))
224 || (gmx_strcasecmp("DNA", xlatom[i].res) == 0
225 && rt->namedResidueHasType(rnm, "DNA"))
226 || (gmx_strcasecmp("RNA", xlatom[i].res) == 0
227 && rt->namedResidueHasType(rnm, "RNA")));
228 if (!bMatch)
229 {
230 const char* ptr0 = rnm;
231 const char* ptr1 = xlatom[i].res;
232 while (ptr0[0] != '\0' && ptr1[0] != '\0' && (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
233 {
234 ptr0++;
235 ptr1++;
236 }
237 bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
238 }
239 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
240 {
241 /* We have a match. */
242 /* Don't free the old atomname,
243 * since it might be in the symtab.
244 */
245 const char* ptr0 = xlatom[i].replace;
246 if (bVerbose)
247 {
248 printf("Renaming atom '%s' in residue %d %s to '%s'\n", *atoms->atomname[a],
249 atoms->resinfo[resind].nr, *atoms->resinfo[resind].name, ptr0);
250 }
251 atoms->atomname[a] = put_symtab(symtab, ptr0);
252 bRenamed = TRUE;
253 }
254 }
255 }
256 if (bReorderedNum && !bRenamed)
257 {
258 atoms->atomname[a] = put_symtab(symtab, atombuf);
259 }
260 }
261
262 done_xlatom(nxlate, xlatom);
263 }
264