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38 #include "gmxpre.h"
39
40 #include "atomprop.h"
41
42 #include <cctype>
43 #include <cmath>
44 #include <cstdio>
45 #include <cstring>
46
47 #include <algorithm>
48 #include <memory>
49
50 #include "gromacs/math/functions.h"
51 #include "gromacs/math/utilities.h"
52 #include "gromacs/topology/residuetypes.h"
53 #include "gromacs/utility/cstringutil.h"
54 #include "gromacs/utility/fatalerror.h"
55 #include "gromacs/utility/futil.h"
56 #include "gromacs/utility/pleasecite.h"
57 #include "gromacs/utility/programcontext.h"
58 #include "gromacs/utility/smalloc.h"
59 #include "gromacs/utility/strdb.h"
60
61 /* NOTFOUND should be smallest, others larger in increasing priority */
62 enum
63 {
64 NOTFOUND = -4,
65 WILDCARD,
66 WILDPROT,
67 PROTEIN
68 };
69
70 //! Basic entries in AtomProperty.
71 struct BaseEntry
72 {
73 //! Default constructor.
BaseEntryBaseEntry74 BaseEntry(const std::string& aName, const std::string& rName) :
75 atomName(aName),
76 residueName(rName),
77 isAvailable(false),
78 value(0.0)
79 {
80 }
81 //! Name for atom.
82 std::string atomName;
83 //! Name for residue.
84 std::string residueName;
85 //! Is property available.
86 bool isAvailable;
87 //! Value set for property.
88 real value;
89 };
90
91 //! Conglomeration of atom property entries.
92 struct AtomProperty
93 {
94 //! Has property been set.
95 bool isSet = false;
96 //! Database the property is coming from.
97 std::string db;
98 //! Default value for property.
99 double def = 0.0;
100 //! Basic entries for properties.
101 std::vector<BaseEntry> entry;
102 };
103
104 //! Implementation detail type for Atomproperties.
105 class AtomProperties::Impl
106 {
107 public:
108 //! Should user be warned about error.
109 bool bWarned = false;
110 //! Should user be warned about vdW not found.
111 bool bWarnVDW = false;
112 //! The different atom properties.
113 AtomProperty prop[epropNR];
114 //! The residue types.
115 ResidueType restype;
116 };
117
118 /*! \brief
119 * Find number of matching characters in entry.
120 *
121 * If not all characters are matching, return NOTFOUND.
122 * If the length of the database entry is different from the search,
123 * also return NOTFOUND.
124 *
125 * \param[in] search Entry to compare to database.
126 * \param[in] database Name of the database entry to compare to.
127 * \returns Number of matching characters or NOTFOUND.
128 */
compareToDatabase(const std::string & search,const std::string & database)129 static int compareToDatabase(const std::string& search, const std::string& database)
130 {
131 if (database.length() > search.length())
132 {
133 return NOTFOUND;
134 }
135 size_t matches = 0;
136 for (size_t i = 0; i < database.length(); i++)
137 {
138 if (search[i] == database[i])
139 {
140 matches++;
141 }
142 }
143 if (matches == database.length())
144 {
145 return matches;
146 }
147 else
148 {
149 return NOTFOUND;
150 }
151 }
152
153 /*! \brief
154 * Finds the index for the property being searched.
155 *
156 * \param[in] ap Property to search for.
157 * \param[in] restype Residuetypes in database.
158 * \param[in] residueName The name of the residue to look for.
159 * \param[in] atomName The name of the atom to look for.
160 * \param[in] bExact Do we have the correct match.
161 * \returns The index for the property.
162 */
findPropertyIndex(AtomProperty * ap,ResidueType * restype,const std::string & residueName,const std::string & atomName,gmx_bool * bExact)163 static int findPropertyIndex(AtomProperty* ap,
164 ResidueType* restype,
165 const std::string& residueName,
166 const std::string& atomName,
167 gmx_bool* bExact)
168 {
169 int j = NOTFOUND;
170
171 bool bProtein = restype->namedResidueHasType(residueName, "Protein");
172 bool bProtWild = residueName == "AAA";
173 int malen = NOTFOUND;
174 int mrlen = NOTFOUND;
175 for (size_t i = 0; (i < ap->entry.size()); i++)
176 {
177 int rlen = compareToDatabase(residueName, ap->entry[i].residueName);
178 if (rlen == NOTFOUND)
179 {
180 if ((ap->entry[i].residueName == "*") || (ap->entry[i].residueName == "???"))
181 {
182 rlen = WILDCARD;
183 }
184 else if (ap->entry[i].residueName == "AAA")
185 {
186 rlen = WILDPROT;
187 }
188 }
189 int alen = compareToDatabase(atomName, ap->entry[i].atomName);
190 if ((alen > NOTFOUND) && (rlen > NOTFOUND))
191 {
192 if (((alen > malen) && (rlen >= mrlen)) || ((rlen > mrlen) && (alen >= malen)))
193 {
194 malen = alen;
195 mrlen = rlen;
196 j = i;
197 }
198 }
199 }
200
201 *bExact = ((malen == static_cast<long int>(atomName.length()))
202 && ((mrlen == static_cast<long int>(residueName.length())) || ((mrlen == WILDPROT) && bProtWild)
203 || ((mrlen == WILDCARD) && !bProtein && !bProtWild)));
204
205 if (debug)
206 {
207 fprintf(debug, "searching residue: %4s atom: %4s\n", residueName.c_str(), atomName.c_str());
208 if (j == NOTFOUND)
209 {
210 fprintf(debug, " not successful\n");
211 }
212 else
213 {
214 fprintf(debug, " match: %4s %4s\n", ap->entry[j].residueName.c_str(),
215 ap->entry[j].atomName.c_str());
216 }
217 }
218 return j;
219 }
220
221 /*! \brief
222 * Add new property to list.
223 *
224 * \param[in] ap Atomproperty to add.
225 * \param[in] restype Residue type database to use.
226 * \param[in] residueName Name of the residue.
227 * \param[in] atomName Name of the atom.
228 * \param[in] propValue Value of property.
229 * \param[in] line Where to add property.
230 */
addProperty(AtomProperty * ap,ResidueType * restype,const std::string & residueName,const std::string & atomName,real propValue,int line)231 static void addProperty(AtomProperty* ap,
232 ResidueType* restype,
233 const std::string& residueName,
234 const std::string& atomName,
235 real propValue,
236 int line)
237 {
238 bool bExact;
239 int j = findPropertyIndex(ap, restype, residueName, atomName, &bExact);
240
241 if (!bExact)
242 {
243 ap->entry.emplace_back(BaseEntry(atomName, residueName));
244
245 j = ap->entry.size() - 1;
246 }
247 if (ap->entry[j].isAvailable)
248 {
249 if (ap->entry[j].value == propValue)
250 {
251 fprintf(stderr, "Warning double identical entries for %s %s %g on line %d in file %s\n",
252 residueName.c_str(), atomName.c_str(), propValue, line, ap->db.c_str());
253 }
254 else
255 {
256 fprintf(stderr,
257 "Warning double different entries %s %s %g and %g on line %d in file %s\n"
258 "Using last entry (%g)\n",
259 residueName.c_str(), atomName.c_str(), propValue, ap->entry[j].value, line,
260 ap->db.c_str(), propValue);
261 ap->entry[j].value = propValue;
262 }
263 }
264 else
265 {
266 ap->entry[j].isAvailable = TRUE;
267 ap->entry[j].value = propValue;
268 }
269 }
270
271 /*! \brief
272 * Read property value into structure.
273 *
274 * \param[in] ap Atomproperty to be read in.
275 * \param[in] restype Library of residue types.
276 * \param[in] factor Scaling factor for property.
277 */
readProperty(AtomProperty * ap,ResidueType * restype,double factor)278 static void readProperty(AtomProperty* ap, ResidueType* restype, double factor)
279 {
280 char line[STRLEN], resnm[32], atomnm[32];
281
282 gmx::FilePtr fp = gmx::openLibraryFile(ap->db);
283 int line_no = 0;
284 while (get_a_line(fp.get(), line, STRLEN))
285 {
286 line_no++;
287 double pp;
288 if (sscanf(line, "%31s %31s %20lf", resnm, atomnm, &pp) == 3)
289 {
290 pp *= factor;
291 addProperty(ap, restype, resnm, atomnm, pp, line_no);
292 }
293 else
294 {
295 fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n", ap->db.c_str(), line_no);
296 }
297 }
298 ap->isSet = TRUE;
299 }
300
301 /*! \brief
302 * Set value for properties.
303 *
304 * \param[in] ap Atomproperty to set.
305 * \param[in] restype Library of residue types.
306 * \param[in] eprop Which property to set.
307 * \param[in] haveBeenWarned If we already set a warning before
308 * \returns True of warning should be printed.
309 */
setProperties(AtomProperty * ap,ResidueType * restype,int eprop,bool haveBeenWarned)310 static bool setProperties(AtomProperty* ap, ResidueType* restype, int eprop, bool haveBeenWarned)
311 {
312 const char* fns[epropNR] = { "atommass.dat", "vdwradii.dat", "dgsolv.dat", "electroneg.dat",
313 "elements.dat" };
314 double fac[epropNR] = { 1.0, 1.0, 418.4, 1.0, 1.0 };
315 double def[epropNR] = { 12.011, 0.14, 0.0, 2.2, -1 };
316
317 bool printWarning = false;
318 if (!ap->isSet)
319 {
320 ap->db = fns[eprop];
321 ap->def = def[eprop];
322 readProperty(ap, restype, fac[eprop]);
323
324 if (debug)
325 {
326 fprintf(debug, "Entries in %s: %zu\n", ap->db.c_str(), ap->entry.size());
327 }
328
329 if ((!haveBeenWarned && (eprop == epropMass)) || (eprop == epropVDW))
330 {
331 printWarning = true;
332 }
333 }
334 return printWarning;
335 }
336
AtomProperties()337 AtomProperties::AtomProperties() : impl_(new Impl) {}
338
~AtomProperties()339 AtomProperties::~AtomProperties() {}
340
prop(int eprop)341 AtomProperty* AtomProperties::prop(int eprop)
342 {
343 return &impl_->prop[eprop];
344 }
345
restype()346 ResidueType* AtomProperties::restype()
347 {
348 return &impl_->restype;
349 }
350
351 //! Print warning that vdW radii and masses are guessed.
printWarning()352 static void printWarning()
353 {
354 printf("\n"
355 "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n"
356 " based on residue and atom names, since they could not be\n"
357 " definitively assigned from the information in your input\n"
358 " files. These guessed numbers might deviate from the mass\n"
359 " and radius of the atom type. Please check the output\n"
360 " files if necessary.\n\n");
361 }
362
printvdwWarning(FILE * fp)363 static void printvdwWarning(FILE* fp)
364 {
365 if (nullptr != fp)
366 {
367 fprintf(fp, "NOTE: From version 5.0 %s uses the Van der Waals radii\n",
368 gmx::getProgramContext().displayName());
369 fprintf(fp, "from the source below. This means the results may be different\n");
370 fprintf(fp, "compared to previous GROMACS versions.\n");
371 please_cite(fp, "Bondi1964a");
372 }
373 }
374
setAtomProperty(int eprop,const std::string & residueName,const std::string & atomName,real * value)375 bool AtomProperties::setAtomProperty(int eprop,
376 const std::string& residueName,
377 const std::string& atomName,
378 real* value)
379 {
380 int j;
381 std::string tmpAtomName, tmpResidueName;
382 gmx_bool bExact;
383
384 if (setProperties(prop(eprop), restype(), eprop, impl_->bWarned))
385 {
386 printWarning();
387 impl_->bWarned = true;
388 }
389 if (isdigit(atomName[0]))
390 {
391 /* put digit after atomname */
392 tmpAtomName.append(atomName.substr(1));
393 tmpAtomName.append(1, atomName[0]);
394 }
395 else
396 {
397 tmpAtomName = atomName;
398 }
399 j = findPropertyIndex(&(impl_->prop[eprop]), &impl_->restype, residueName, tmpAtomName, &bExact);
400
401 if (eprop == epropVDW && !impl_->bWarnVDW)
402 {
403 printvdwWarning(stdout);
404 impl_->bWarnVDW = true;
405 }
406 if (j >= 0)
407 {
408 *value = impl_->prop[eprop].entry[j].value;
409 return true;
410 }
411 else
412 {
413 *value = impl_->prop[eprop].def;
414 return false;
415 }
416 }
417
418
elementFromAtomNumber(int atomNumber)419 std::string AtomProperties::elementFromAtomNumber(int atomNumber)
420 {
421 if (setProperties(prop(epropElement), restype(), epropElement, impl_->bWarned))
422 {
423 printWarning();
424 impl_->bWarned = true;
425 }
426 for (const auto& e : prop(epropElement)->entry)
427 {
428 if (std::round(e.value) == atomNumber)
429 {
430 return e.atomName;
431 }
432 }
433 return "";
434 }
435
atomNumberFromElement(const char * element)436 int AtomProperties::atomNumberFromElement(const char* element)
437 {
438 if (setProperties(prop(epropElement), restype(), epropElement, impl_->bWarned))
439 {
440 printWarning();
441 impl_->bWarned = true;
442 }
443 for (const auto& e : prop(epropElement)->entry)
444 {
445 if (gmx_strcasecmp(e.atomName.c_str(), element) == 0)
446 {
447 return gmx::roundToInt(e.value);
448 }
449 }
450 return -1;
451 }
452