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Revision 819 by tim, Fri Dec 16 21:52:50 2005 UTC vs.
Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC

# Line 2 | Line 2 | Copyright (C) 1998-2001 by OpenEye Scientific Software
2   data.cpp - Global data and resource file parsers.
3  
4   Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5 < Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
5 > Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
6  
7   This file is part of the Open Babel project.
8   For more information, see <http://openbabel.sourceforge.net/>
# Line 41 | Line 41 | namespace OpenBabel
41   namespace OpenBabel
42   {
43  
44 < OBElementTable   etab;
45 < OBTypeTable      ttab;
46 < OBIsotopeTable   isotab;
47 < OBResidueData    resdat;
44 >  OBElementTable   etab;
45 >  OBTypeTable      ttab;
46 >  OBIsotopeTable   isotab;
47 >  OBResidueData    resdat;
48  
49 < /** \class OBElementTable
50 <    \brief Periodic Table of the Elements
49 >  /** \class OBElementTable
50 >      \brief Periodic Table of the Elements
51  
52 <    Translating element data is a common task given that many file
53 <  formats give either element symbol or atomic number information, but
54 <  not both. The OBElementTable class facilitates conversion between
55 <  textual and numeric element information. An instance of the
56 <  OBElementTable class (etab) is declared as external in data.cpp. Source
57 <  files that include the header file mol.h automatically have an extern
58 <  definition to etab. The following code sample demonstrates the use
59 <  of the OBElementTable class:
60 < \code
61 < cout << "The symbol for element 6 is " << etab.GetSymbol(6) << endl;
62 < cout << "The atomic number for Sulfur is " << etab.GetAtomicNum(16) << endl;
63 < cout << "The van der Waal radius for Nitrogen is " << etab.GetVdwRad(7);
64 < \endcode
52 >      Translating element data is a common task given that many file
53 >      formats give either element symbol or atomic number information, but
54 >      not both. The OBElementTable class facilitates conversion between
55 >      textual and numeric element information. An instance of the
56 >      OBElementTable class (etab) is declared as external in data.cpp. Source
57 >      files that include the header file mol.h automatically have an extern
58 >      definition to etab. The following code sample demonstrates the use
59 >      of the OBElementTable class:
60 >      \code
61 >      cout << "The symbol for element 6 is " << etab.GetSymbol(6) << endl;
62 >      cout << "The atomic number for Sulfur is " << etab.GetAtomicNum(16) << endl;
63 >      cout << "The van der Waal radius for Nitrogen is " << etab.GetVdwRad(7);
64 >      \endcode
65  
66 <  Stored information in the OBElementTable includes elemental:
67 <   - symbols
68 <   - covalent radii
69 <   - van der Waal radii
70 <   - expected maximum bonding valence
71 <   - molar mass (by IUPAC recommended atomic masses)
72 <   - electronegativity
73 <   - ionization potential
74 <   - electron affinity
75 <   - RGB colors for visualization programs
76 <   - names (by IUPAC recommendation)
77 < */
66 >      Stored information in the OBElementTable includes elemental:
67 >      - symbols
68 >      - covalent radii
69 >      - van der Waal radii
70 >      - expected maximum bonding valence
71 >      - molar mass (by IUPAC recommended atomic masses)
72 >      - electronegativity
73 >      - ionization potential
74 >      - electron affinity
75 >      - RGB colors for visualization programs
76 >      - names (by IUPAC recommendation)
77 >  */
78  
79 < OBElementTable::OBElementTable()
80 < {
79 >  OBElementTable::OBElementTable()
80 >  {
81      _init = false;
82 <    STR_DEFINE(_dir, FRC_PATH);
82 >    STR_DEFINE(_dir, FRC_PATH );
83      _envvar = "FORCE_PARAM_PATH";
84      _filename = "element.txt";
85      _subdir = "data";
86      _dataptr = ElementData;
87 < }
87 >  }
88  
89 < OBElementTable::~OBElementTable()
90 < {
89 >  OBElementTable::~OBElementTable()
90 >  {
91      vector<OBElement*>::iterator i;
92      for (i = _element.begin();i != _element.end();i++)
93 <        delete *i;
94 < }
93 >      delete *i;
94 >  }
95  
96 < void OBElementTable::ParseLine(const char *buffer)
97 < {
96 >  void OBElementTable::ParseLine(const char *buffer)
97 >  {
98      int num,maxbonds;
99      char symbol[5];
100 <    char name[BUFF_SIZE];
100 >    char name[256];
101      double Rcov,Rvdw,mass, elNeg, ionize, elAffin;
102      double red, green, blue;
103  
104      if (buffer[0] != '#') // skip comment line (at the top)
105 <    {
106 <      sscanf(buffer,"%d %s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %s",
107 <             &num,
108 <             symbol,
109 <             &Rcov,
110 <             &Rvdw,
111 <             &maxbonds,
112 <             &mass,
113 <             &elNeg,
114 <             &ionize,
115 <             &elAffin,
116 <             &red,
117 <             &green,
118 <             &blue,
119 <             name);
105 >      {
106 >        sscanf(buffer,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s",
107 >               &num,
108 >               symbol,
109 >               &Rcov,
110 >               &Rvdw,
111 >               &maxbonds,
112 >               &mass,
113 >               &elNeg,
114 >               &ionize,
115 >               &elAffin,
116 >               &red,
117 >               &green,
118 >               &blue,
119 >               name);
120  
121 <      OBElement *ele = new OBElement(num,symbol,Rcov,Rvdw,maxbonds,mass,elNeg,
122 <                                     ionize, elAffin, red, green, blue, name);
123 <      _element.push_back(ele);
124 <    }
125 < }
121 >        OBElement *ele = new OBElement(num,symbol,Rcov,Rvdw,maxbonds,mass,elNeg,
122 >                                       ionize, elAffin, red, green, blue, name);
123 >        _element.push_back(ele);
124 >      }
125 >  }
126  
127 < unsigned int OBElementTable::GetNumberOfElements()
128 < {
127 >  unsigned int OBElementTable::GetNumberOfElements()
128 >  {
129      if (!_init)
130 <        Init();
130 >      Init();
131      
132      return _element.size();
133 < }
133 >  }
134  
135 < char *OBElementTable::GetSymbol(int atomicnum)
136 < {
135 >  char *OBElementTable::GetSymbol(int atomicnum)
136 >  {
137      if (!_init)
138 <        Init();
138 >      Init();
139  
140      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
141 <        return("\0");
141 >      return("\0");
142  
143      return(_element[atomicnum]->GetSymbol());
144 < }
144 >  }
145  
146 < int OBElementTable::GetMaxBonds(int atomicnum)
147 < {
146 >  int OBElementTable::GetMaxBonds(int atomicnum)
147 >  {
148      if (!_init)
149 <        Init();
149 >      Init();
150  
151      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
152 <        return(0);
152 >      return(0);
153  
154      return(_element[atomicnum]->GetMaxBonds());
155 < }
155 >  }
156  
157 < double OBElementTable::GetElectroNeg(int atomicnum)
158 < {
157 >  double OBElementTable::GetElectroNeg(int atomicnum)
158 >  {
159      if (!_init)
160 <        Init();
160 >      Init();
161  
162      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
163 <        return(0.0);
163 >      return(0.0);
164  
165      return(_element[atomicnum]->GetElectroNeg());
166 < }
166 >  }
167  
168 < double OBElementTable::GetIonization(int atomicnum)
169 < {
168 >  double OBElementTable::GetIonization(int atomicnum)
169 >  {
170      if (!_init)
171 <        Init();
171 >      Init();
172  
173      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
174 <        return(0.0);
174 >      return(0.0);
175  
176      return(_element[atomicnum]->GetIonization());
177 < }
177 >  }
178  
179  
180 < double OBElementTable::GetElectronAffinity(int atomicnum)
181 < {
180 >  double OBElementTable::GetElectronAffinity(int atomicnum)
181 >  {
182      if (!_init)
183 <        Init();
183 >      Init();
184  
185      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
186 <        return(0.0);
186 >      return(0.0);
187  
188      return(_element[atomicnum]->GetElectronAffinity());
189 < }
189 >  }
190  
191 < vector<double> OBElementTable::GetRGB(int atomicnum)
192 < {
191 >  vector<double> OBElementTable::GetRGB(int atomicnum)
192 >  {
193      if (!_init)
194 <        Init();
194 >      Init();
195  
196      vector <double> colors;
197      colors.reserve(3);
198      
199      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
200        {
201 <        colors.push_back(0.0f);
202 <        colors.push_back(0.0f);
203 <        colors.push_back(0.0f);
201 >        colors.push_back(0.0f);
202 >        colors.push_back(0.0f);
203 >        colors.push_back(0.0f);
204          return(colors);
205        }
206  
# Line 209 | Line 209 | vector<double> OBElementTable::GetRGB(int atomicnum)
209      colors.push_back(_element[atomicnum]->GetBlue());
210  
211      return (colors);
212 < }
212 >  }
213  
214 < string OBElementTable::GetName(int atomicnum)
215 < {
214 >  string OBElementTable::GetName(int atomicnum)
215 >  {
216      if (!_init)
217 <        Init();
217 >      Init();
218  
219      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
220 <        return("Unknown");
220 >      return("Unknown");
221  
222      return(_element[atomicnum]->GetName());
223 < }
223 >  }
224  
225 < double OBElementTable::GetVdwRad(int atomicnum)
226 < {
225 >  double OBElementTable::GetVdwRad(int atomicnum)
226 >  {
227      if (!_init)
228 <        Init();
228 >      Init();
229  
230      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
231 <        return(0.0);
231 >      return(0.0);
232  
233      return(_element[atomicnum]->GetVdwRad());
234 < }
234 >  }
235  
236 < double OBElementTable::CorrectedBondRad(int atomicnum, int hyb)
237 < {
236 >  double OBElementTable::CorrectedBondRad(int atomicnum, int hyb)
237 >  {
238      double rad;
239      if (!_init)
240 <        Init();
240 >      Init();
241  
242      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
243 <        return(1.0);
243 >      return(1.0);
244  
245      rad = _element[atomicnum]->GetCovalentRad();
246  
247      if (hyb == 2)
248 <        rad *= 0.95;
248 >      rad *= 0.95;
249      else if (hyb == 1)
250 <        rad *= 0.90;
250 >      rad *= 0.90;
251  
252      return(rad);
253 < }
253 >  }
254  
255 < double OBElementTable::CorrectedVdwRad(int atomicnum, int hyb)
256 < {
255 >  double OBElementTable::CorrectedVdwRad(int atomicnum, int hyb)
256 >  {
257      double rad;
258      if (!_init)
259 <        Init();
259 >      Init();
260  
261      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
262 <        return(1.95);
262 >      return(1.95);
263  
264      rad = _element[atomicnum]->GetVdwRad();
265  
266      if (hyb == 2)
267 <        rad *= 0.95;
267 >      rad *= 0.95;
268      else if (hyb == 1)
269 <        rad *= 0.90;
269 >      rad *= 0.90;
270  
271      return(rad);
272 < }
272 >  }
273  
274 < double OBElementTable::GetCovalentRad(int atomicnum)
275 < {
274 >  double OBElementTable::GetCovalentRad(int atomicnum)
275 >  {
276      if (!_init)
277 <        Init();
277 >      Init();
278  
279      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
280 <        return(0.0);
280 >      return(0.0);
281  
282      return(_element[atomicnum]->GetCovalentRad());
283 < }
283 >  }
284  
285 < double OBElementTable::GetMass(int atomicnum)
286 < {
285 >  double OBElementTable::GetMass(int atomicnum)
286 >  {
287      if (!_init)
288 <        Init();
288 >      Init();
289  
290      if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
291 <        return(0.0);
291 >      return(0.0);
292  
293      return(_element[atomicnum]->GetMass());
294 < }
294 >  }
295  
296 < int OBElementTable::GetAtomicNum(const char *sym)
297 < {
298 <  int temp;
299 <  return GetAtomicNum(sym, temp);
300 < }
296 >  int OBElementTable::GetAtomicNum(const char *sym)
297 >  {
298 >    int temp;
299 >    return GetAtomicNum(sym, temp);
300 >  }
301  
302 < int OBElementTable::GetAtomicNum(const char *sym, int &iso)
303 < {
302 >  int OBElementTable::GetAtomicNum(const char *sym, int &iso)
303 >  {
304      if (!_init)
305 <        Init();
305 >      Init();
306  
307      vector<OBElement*>::iterator i;
308      for (i = _element.begin();i != _element.end();i++)
309 <        if (!strncasecmp(sym,(*i)->GetSymbol(),2))
310 <            return((*i)->GetAtomicNum());
309 >      if (!strncasecmp(sym,(*i)->GetSymbol(),2))
310 >        return((*i)->GetAtomicNum());
311      if (strcasecmp(sym, "D") == 0)
312 <    {
312 >      {
313          iso = 2;
314          return(1);
315 <    }
315 >      }
316      else if (strcasecmp(sym, "T") == 0)
317 <    {
317 >      {
318          iso = 3;
319          return(1);
320 <    }
321 <                else
322 <                        iso = 0;
320 >      }
321 >    else
322 >      iso = 0;
323      return(0);
324 < }
324 >  }
325  
326 < /** \class OBIsotopeTable
327 <    \brief Table of atomic isotope masses
326 >  /** \class OBIsotopeTable
327 >      \brief Table of atomic isotope masses
328  
329 < */
329 >  */
330  
331 < OBIsotopeTable::OBIsotopeTable()
332 < {
331 >  OBIsotopeTable::OBIsotopeTable()
332 >  {
333      _init = false;
334 <    STR_DEFINE(_dir, FRC_PATH);
334 >    STR_DEFINE(_dir, FRC_PATH );
335      _envvar = "FORCE_PARAM_PATH";
336      _filename = "isotope.txt";
337      _subdir = "data";
338      _dataptr = IsotopeData;
339 < }
339 >  }
340  
341 < void OBIsotopeTable::ParseLine(const char *buffer)
342 < {
341 >  void OBIsotopeTable::ParseLine(const char *buffer)
342 >  {
343      unsigned int atomicNum;
344      unsigned int i;
345      vector<string> vs;
# Line 348 | Line 348 | void OBIsotopeTable::ParseLine(const char *buffer)
348      vector <pair <unsigned int, double> > row;
349  
350      if (buffer[0] != '#') // skip comment line (at the top)
351 <    {
351 >      {
352          tokenize(vs,buffer);
353          if (vs.size() > 3) // atomic number, 0, most abundant mass (...)
354 <        {
354 >          {
355              atomicNum = atoi(vs[0].c_str());
356              for (i = 1; i < vs.size() - 1; i += 2) // make sure i+1 still exists
357 <            {
357 >              {
358                  entry.first = atoi(vs[i].c_str()); // isotope
359                  entry.second = atof(vs[i + 1].c_str()); // exact mass
360                  row.push_back(entry);
361 <            }
361 >              }
362              _isotopes.push_back(row);
363 <        }
364 <        else
365 <          obErrorLog.ThrowError(__func__, " Could not parse line in isotope table isotope.txt", obInfo);
366 <    }
367 < }
363 >          }
364 >        else
365 >          obErrorLog.ThrowError(__func__, " Could not parse line in isotope table isotope.txt", obInfo);
366 >      }
367 >  }
368  
369 < double  OBIsotopeTable::GetExactMass(const unsigned int ele,
370 <                                    const unsigned int isotope)
371 < {
369 >  double        OBIsotopeTable::GetExactMass(const unsigned int ele,
370 >                                             const unsigned int isotope)
371 >  {
372      if (!_init)
373 <        Init();
373 >      Init();
374  
375      if (ele > _isotopes.size())
376 <        return 0.0;
376 >      return 0.0;
377  
378      unsigned int iso;
379      for (iso = 0; iso < _isotopes[ele].size(); iso++)
380 <        if (isotope == _isotopes[ele][iso].first)
381 <            return _isotopes[ele][iso].second;
380 >      if (isotope == _isotopes[ele][iso].first)
381 >        return _isotopes[ele][iso].second;
382  
383      return 0.0;
384 < }
384 >  }
385  
386 < /** \class OBTypeTable
387 <    \brief Atom Type Translation Table
386 >  /** \class OBTypeTable
387 >      \brief Atom Type Translation Table
388  
389 < Molecular file formats frequently store information about atoms in an
390 < atom type field. Some formats store only the element for each atom,
391 < while others include hybridization and local environments, such as the
392 < Sybyl mol2 atom type field. The OBTypeTable class acts as a translation
393 < table to convert atom types between a number of different molecular
394 < file formats. The constructor for OBTypeTable automatically reads the
395 < text file types.txt. Just as OBElementTable, an instance of
396 < OBTypeTable (ttab) is declared external in data.cpp and is referenced as
397 < extern OBTypeTable ttab in mol.h.  The following code demonstrates how
398 < to use the OBTypeTable class to translate the internal representation
399 < of atom types in an OBMol Internal to Sybyl Mol2 atom types.
389 >      Molecular file formats frequently store information about atoms in an
390 >      atom type field. Some formats store only the element for each atom,
391 >      while others include hybridization and local environments, such as the
392 >      Sybyl mol2 atom type field. The OBTypeTable class acts as a translation
393 >      table to convert atom types between a number of different molecular
394 >      file formats. The constructor for OBTypeTable automatically reads the
395 >      text file types.txt. Just as OBElementTable, an instance of
396 >      OBTypeTable (ttab) is declared external in data.cpp and is referenced as
397 >      extern OBTypeTable ttab in mol.h.  The following code demonstrates how
398 >      to use the OBTypeTable class to translate the internal representation
399 >      of atom types in an OBMol Internal to Sybyl Mol2 atom types.
400  
401 < \code
402 < ttab.SetFromType("INT");
403 < ttab.SetToType("SYB");
404 < OBAtom *atom;
405 < vector<OBAtom*>::iterator i;
406 < string src,dst;
407 < for (atom = mol.BeginAtom(i);atom;atom = mol.EndAtom(i))
408 < {
409 < src = atom->GetType();
410 < ttab.Translate(dst,src);
411 < cout << "atom number " << atom->GetIdx() << "has mol2 type " << dst << endl;
412 < }
413 < \endcode
401 >      \code
402 >      ttab.SetFromType("INT");
403 >      ttab.SetToType("SYB");
404 >      OBAtom *atom;
405 >      vector<OBAtom*>::iterator i;
406 >      string src,dst;
407 >      for (atom = mol.BeginAtom(i);atom;atom = mol.EndAtom(i))
408 >      {
409 >      src = atom->GetType();
410 >      ttab.Translate(dst,src);
411 >      cout << "atom number " << atom->GetIdx() << "has mol2 type " << dst << endl;
412 >      }
413 >      \endcode
414  
415 < Current atom types include (defined in the top line of the data file types.txt):
416 < - INT (Open Babel internal codes)
417 < - ATN (atomic numbers)
418 < - HYB (hybridization)
419 < - MMD
420 < - MM2 (MM2 force field)
421 < - XYZ (element symbols from XYZ file format)
422 < - ALC (Alchemy file)
423 < - HAD
424 < - MCML
425 < - C3D (Chem3D)
426 < - SYB (Sybyl mol2)
427 < - MOL
428 < - MAP
429 < - DRE
430 < - XED (XED format)
431 < - DOK (Dock)
432 < - M3D
433 < */
415 >      Current atom types include (defined in the top line of the data file types.txt):
416 >      - INT (Open Babel internal codes)
417 >      - ATN (atomic numbers)
418 >      - HYB (hybridization)
419 >      - MMD
420 >      - MM2 (MM2 force field)
421 >      - XYZ (element symbols from XYZ file format)
422 >      - ALC (Alchemy file)
423 >      - HAD
424 >      - MCML
425 >      - C3D (Chem3D)
426 >      - SYB (Sybyl mol2)
427 >      - MOL
428 >      - MAP
429 >      - DRE
430 >      - XED (XED format)
431 >      - DOK (Dock)
432 >      - M3D
433 >  */
434  
435 < OBTypeTable::OBTypeTable()
436 < {
435 >  OBTypeTable::OBTypeTable()
436 >  {
437      _init = false;
438 <    STR_DEFINE(_dir, FRC_PATH);
438 >    STR_DEFINE(_dir, FRC_PATH );
439      _envvar = "FORCE_PARAM_PATH";
440      _filename = "types.txt";
441      _subdir = "data";
442      _dataptr = TypesData;
443      _linecount = 0;
444      _from = _to = -1;
445 < }
445 >  }
446  
447 < void OBTypeTable::ParseLine(const char *buffer)
448 < {
447 >  void OBTypeTable::ParseLine(const char *buffer)
448 >  {
449      if (buffer[0] == '#')
450 <        return; // just a comment line
450 >      return; // just a comment line
451  
452      if (_linecount == 0)
453 <        sscanf(buffer,"%d%d",&_nrows,&_ncols);
453 >      sscanf(buffer,"%d%d",&_nrows,&_ncols);
454      else if (_linecount == 1)
455 <        tokenize(_colnames,buffer);
455 >      tokenize(_colnames,buffer);
456      else
457 <    {
457 >      {
458          vector<string> vc;
459          tokenize(vc,buffer);
460          if (vc.size() == (unsigned)_ncols)
461 <            _table.push_back(vc);
462 <        else
463 <          {
464 <            stringstream errorMsg;
465 <            errorMsg << " Could not parse line in type translation table types.txt -- incorect number of columns";
466 <            errorMsg << " found " << vc.size() << " expected " << _ncols << ".";
467 <            obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
468 <          }
469 <    }
461 >          _table.push_back(vc);
462 >        else
463 >          {
464 >            stringstream errorMsg;
465 >            errorMsg << " Could not parse line in type translation table types.txt -- incorect number of columns";
466 >            errorMsg << " found " << vc.size() << " expected " << _ncols << ".";
467 >            obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
468 >          }
469 >      }
470      _linecount++;
471 < }
471 >  }
472  
473 < bool OBTypeTable::SetFromType(const char* from)
474 < {
473 >  bool OBTypeTable::SetFromType(const char* from)
474 >  {
475      if (!_init)
476 <        Init();
476 >      Init();
477  
478      string tmp = from;
479  
480      unsigned int i;
481      for (i = 0;i < _colnames.size();i++)
482 <        if (tmp == _colnames[i])
482 >      if (tmp == _colnames[i])
483          {
484 <            _from = i;
485 <            return(true);
484 >          _from = i;
485 >          return(true);
486          }
487  
488      obErrorLog.ThrowError(__func__, "Requested type column not found", obInfo);
489  
490      return(false);
491 < }
491 >  }
492  
493 < bool OBTypeTable::SetToType(const char* to)
494 < {
493 >  bool OBTypeTable::SetToType(const char* to)
494 >  {
495      if (!_init)
496 <        Init();
496 >      Init();
497  
498      string tmp = to;
499  
500      unsigned int i;
501      for (i = 0;i < _colnames.size();i++)
502 <        if (tmp == _colnames[i])
502 >      if (tmp == _colnames[i])
503          {
504 <            _to = i;
505 <            return(true);
504 >          _to = i;
505 >          return(true);
506          }
507  
508      obErrorLog.ThrowError(__func__, "Requested type column not found", obInfo);
509  
510      return(false);
511 < }
511 >  }
512  
513 < bool OBTypeTable::Translate(char *to, const char *from)
514 < {
513 >  //! Translates atom types (to, from), checking for size of destination
514 >  //!  string and null-terminating as needed
515 >  //! \deprecated Because there is no guarantee on the length of an atom type
516 >  //!  you should consider using std::string instead
517 >  bool OBTypeTable::Translate(char *to, const char *from)
518 >  {
519      if (!_init)
520 <        Init();
520 >      Init();
521  
522      bool rval;
523      string sto,sfrom;
524      sfrom = from;
525      rval = Translate(sto,sfrom);
526 <    strcpy(to,(char*)sto.c_str());
526 >    strncpy(to,(char*)sto.c_str(), sizeof(to) - 1);
527 >    to[sizeof(to) - 1] = '\0';
528  
529      return(rval);
530 < }
530 >  }
531  
532 < bool OBTypeTable::Translate(string &to, const string &from)
533 < {
532 >  bool OBTypeTable::Translate(string &to, const string &from)
533 >  {
534      if (!_init)
535 <        Init();
535 >      Init();
536  
537      if (from == "")
538 <        return(false);
538 >      return(false);
539  
540      if (_from >= 0 && _to >= 0 &&
541 <        _from < _table.size() && _to < _table.size())
541 >        _from < _table.size() && _to < _table.size())
542        {
543 <        vector<vector<string> >::iterator i;
544 <        for (i = _table.begin();i != _table.end();i++)
545 <          if ((signed)(*i).size() > _from &&  (*i)[_from] == from)
546 <            {
547 <              to = (*i)[_to];
548 <              return(true);
549 <            }
543 >        vector<vector<string> >::iterator i;
544 >        for (i = _table.begin();i != _table.end();i++)
545 >          if ((signed)(*i).size() > _from &&  (*i)[_from] == from)
546 >            {
547 >              to = (*i)[_to];
548 >              return(true);
549 >            }
550        }
551  
552      // Throw an error, copy the string and return false
553      obErrorLog.ThrowError(__func__, "Cannot perform atom type translation: table cannot find requested types.", obWarning);
554      to = from;
555      return(false);
556 < }
556 >  }
557  
558 < std::string OBTypeTable::GetFromType()
559 < {
558 >  std::string OBTypeTable::GetFromType()
559 >  {
560      if (!_init)
561 <        Init();
561 >      Init();
562  
563      if (_from > 0 && _from < _table.size())
564        return( _colnames[_from] );
565      else
566        return( _colnames[0] );
567 < }
567 >  }
568  
569 < std::string OBTypeTable::GetToType()
570 < {
569 >  std::string OBTypeTable::GetToType()
570 >  {
571      if (!_init)
572 <        Init();
572 >      Init();
573  
574      if (_to > 0 && _to < _table.size())
575        return( _colnames[_to] );
576      else
577        return( _colnames[0] );
578 < }
578 >  }
579  
580 < void Toupper(string &s)
581 < {
580 >  void Toupper(string &s)
581 >  {
582      unsigned int i;
583      for (i = 0;i < s.size();i++)
584 <        s[i] = toupper(s[i]);
585 < }
584 >      s[i] = toupper(s[i]);
585 >  }
586  
587 < void Tolower(string &s)
588 < {
587 >  void Tolower(string &s)
588 >  {
589      unsigned int i;
590      for (i = 0;i < s.size();i++)
591 <        s[i] = tolower(s[i]);
592 < }
591 >      s[i] = tolower(s[i]);
592 >  }
593  
594 < ///////////////////////////////////////////////////////////////////////
595 < OBResidueData::OBResidueData()
596 < {
594 >  ///////////////////////////////////////////////////////////////////////
595 >  OBResidueData::OBResidueData()
596 >  {
597      _init = false;
598 <    STR_DEFINE(_dir, FRC_PATH);
598 >    STR_DEFINE(_dir, FRC_PATH );
599      _envvar = "FORCE_PARAM_PATH";
600      _filename = "resdata.txt";
601      _subdir = "data";
602      _dataptr = ResidueData;
603 < }
603 >  }
604  
605 < bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv)
606 < {
605 >  bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv)
606 >  {
607 >    if (!_init)
608 >      Init();
609 >
610      OBAtom *a1,*a2;
611      OBResidue *r1,*r2;
612      vector<OBNodeBase*>::iterator i,j;
# Line 609 | Line 617 | bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &b
617      string rname = "";
618      //assign residue bonds
619      for (a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
620 <    {
620 >      {
621          r1 = a1->GetResidue();
622          if (skipres && r1->GetNum() == skipres)
623 <            continue;
623 >          continue;
624  
625          if (r1->GetName() != rname)
626 <        {
626 >          {
627              skipres = SetResName(r1->GetName()) ? 0 : r1->GetNum();
628              rname = r1->GetName();
629 <        }
629 >          }
630          //assign bonds for each atom
631          for (j=i,a2 = mol.NextAtom(j);a2;a2 = mol.NextAtom(j))
632 <        {
632 >          {
633              r2 = a2->GetResidue();
634              if (r1->GetNum() != r2->GetNum())
635 <                break;
635 >              break;
636              if (r1->GetName() != r2->GetName())
637 <                break;
637 >              break;
638  
639              if ((bo = LookupBO(r1->GetAtomID(a1),r2->GetAtomID(a2))))
640 <            {
640 >              {
641                  v = a1->GetVector() - a2->GetVector();
642                  if (v.length_2() < 3.5) //check by distance
643 <                    mol.AddBond(a1->GetIdx(),a2->GetIdx(),bo);
644 <            }
645 <        }
646 <    }
643 >                  mol.AddBond(a1->GetIdx(),a2->GetIdx(),bo);
644 >              }
645 >          }
646 >      }
647  
648      int hyb;
649      string type;
650  
651      //types and hybridization
652 +    rname = ""; // name of current residue
653 +    skipres = 0; // don't skip any residues right now
654      for (a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
655 <    {
655 >      {
656          if (a1->IsOxygen() && !a1->GetValence())
657 <        {
657 >          {
658              a1->SetType("O3");
659              continue;
660 <        }
651 <
660 >          }
661          if (a1->IsHydrogen())
662 <        {
662 >          {
663              a1->SetType("H");
664              continue;
665 <        }
665 >          }
666  
658 –        r1 = a1->GetResidue();
659 –        if (skipres && r1->GetNum() == skipres)
660 –            continue;
661 –
662 –        if (r1->GetName() != rname)
663 –        {
664 –            skipres = SetResName(r1->GetName()) ? 0 : r1->GetNum();
665 –            rname = r1->GetName();
666 –        }
667 –
667          //***valence rule for O-
668          if (a1->IsOxygen() && a1->GetValence() == 1)
669 <        {
669 >          {
670              OBBond *bond;
671              bond = (OBBond*)*(a1->BeginBonds());
672              if (bond->GetBO() == 2)
673 <            {
673 >              {
674                  a1->SetType("O2");
675                  a1->SetHyb(2);
676 <            }
677 <            if (bond->GetBO() == 1)
678 <            {
676 >              }
677 >            else if (bond->GetBO() == 1)
678 >              {
679                  a1->SetType("O-");
680                  a1->SetHyb(3);
681                  a1->SetFormalCharge(-1);
682 <            }
683 <        }
684 <        else
685 <            if (LookupType(r1->GetAtomID(a1),type,hyb))
686 <            {
687 <                a1->SetType(type);
688 <                a1->SetHyb(hyb);
690 <            }
691 <            else // try to figure it out by bond order ???
692 <            {}
693 <    }
682 >              }
683 >            continue;
684 >          }
685 >        
686 >        r1 = a1->GetResidue();
687 >        if (skipres && r1->GetNum() == skipres)
688 >          continue;
689  
690 +        if (r1->GetName() != rname)
691 +          {
692 +            // if SetResName fails, skip this residue
693 +            skipres = SetResName(r1->GetName()) ? 0 : r1->GetNum();
694 +            rname = r1->GetName();
695 +          }
696 +
697 +        if (LookupType(r1->GetAtomID(a1),type,hyb))
698 +          {
699 +            a1->SetType(type);
700 +            a1->SetHyb(hyb);
701 +          }
702 +        else // try to figure it out by bond order ???
703 +          {}
704 +      }
705 +
706      return(true);
707 < }
707 >  }
708  
709 < void OBResidueData::ParseLine(const char *buffer)
710 < {
709 >  void OBResidueData::ParseLine(const char *buffer)
710 >  {
711      int bo;
712      string s;
713      vector<string> vs;
714  
715      if (buffer[0] == '#')
716 <        return;
716 >      return;
717  
718      tokenize(vs,buffer);
719      if (!vs.empty())
720 <    {
720 >      {
721          if (vs[0] == "BOND")
722 <        {
722 >          {
723              s = (vs[1] < vs[2]) ? vs[1] + " " + vs[2] :
724 <                vs[2] + " " + vs[1];
724 >              vs[2] + " " + vs[1];
725              bo = atoi(vs[3].c_str());
726              _vtmp.push_back(pair<string,int> (s,bo));
727 <        }
727 >          }
728  
729          if (vs[0] == "ATOM" && vs.size() == 4)
730 <        {
730 >          {
731              _vatmtmp.push_back(vs[1]);
732              _vatmtmp.push_back(vs[2]);
733              _vatmtmp.push_back(vs[3]);
734 <        }
734 >          }
735  
736          if (vs[0] == "RES")
737 <            _resname.push_back(vs[1]);
737 >          _resname.push_back(vs[1]);
738  
739          if (vs[0]== "END")
740 <        {
740 >          {
741              _resatoms.push_back(_vatmtmp);
742              _resbonds.push_back(_vtmp);
743              _vtmp.clear();
744              _vatmtmp.clear();
745 <        }
746 <    }
747 < }
745 >          }
746 >      }
747 >  }
748  
749 < bool OBResidueData::SetResName(const string &s)
750 < {
749 >  bool OBResidueData::SetResName(const string &s)
750 >  {
751 >    if (!_init)
752 >      Init();
753 >
754      unsigned int i;
755 +
756      for (i = 0;i < _resname.size();i++)
757 <        if (_resname[i] == s)
757 >      if (_resname[i] == s)
758          {
759 <            _resnum = i;
760 <            return(true);
759 >          _resnum = i;
760 >          return(true);
761          }
762  
763      _resnum = -1;
764      return(false);
765 < }
765 >  }
766  
767 < int OBResidueData::LookupBO(const string &s)
768 < {
767 >  int OBResidueData::LookupBO(const string &s)
768 >  {
769      if (_resnum == -1)
770 <        return(0);
770 >      return(0);
771  
772      unsigned int i;
773      for (i = 0;i < _resbonds[_resnum].size();i++)
774 <        if (_resbonds[_resnum][i].first == s)
775 <            return(_resbonds[_resnum][i].second);
774 >      if (_resbonds[_resnum][i].first == s)
775 >        return(_resbonds[_resnum][i].second);
776  
777      return(0);
778 < }
778 >  }
779  
780 < int OBResidueData::LookupBO(const string &s1, const string &s2)
781 < {
780 >  int OBResidueData::LookupBO(const string &s1, const string &s2)
781 >  {
782      if (_resnum == -1)
783 <        return(0);
783 >      return(0);
784      string s;
785  
786      s = (s1 < s2) ? s1 + " " + s2 : s2 + " " + s1;
787  
788      unsigned int i;
789      for (i = 0;i < _resbonds[_resnum].size();i++)
790 <        if (_resbonds[_resnum][i].first == s)
791 <            return(_resbonds[_resnum][i].second);
790 >      if (_resbonds[_resnum][i].first == s)
791 >        return(_resbonds[_resnum][i].second);
792  
793      return(0);
794 < }
794 >  }
795  
796 < bool OBResidueData::LookupType(const string &atmid,string &type,int &hyb)
797 < {
796 >  bool OBResidueData::LookupType(const string &atmid,string &type,int &hyb)
797 >  {
798      if (_resnum == -1)
799 <        return(false);
799 >      return(false);
800  
801      string s;
802      vector<string>::iterator i;
803  
804      for (i = _resatoms[_resnum].begin();i != _resatoms[_resnum].end();i+=3)
805 <        if (atmid == *i)
805 >      if (atmid == *i)
806          {
807 <            i++;
808 <            type = *i;
809 <            i++;
810 <            hyb = atoi((*i).c_str());
811 <            return(true);
807 >          i++;
808 >          type = *i;
809 >          i++;
810 >          hyb = atoi((*i).c_str());
811 >          return(true);
812          }
813  
814      return(false);
815 < }
815 >  }
816  
817 < void OBGlobalDataBase::Init()
818 < {
817 >  void OBGlobalDataBase::Init()
818 >  {
819      if (_init)
820 <        return;
820 >      return;
821      _init = true;
822  
823 <    char buffer[BUFF_SIZE],subbuffer[BUFF_SIZE];
823 >    string buffer, subbuffer;
824      ifstream ifs1, ifs2, ifs3, ifs4, *ifsP;
825      // First, look for an environment variable
826      if (getenv(_envvar.c_str()) != NULL)
827 <    {
828 <        strcpy(buffer,getenv(_envvar.c_str()));
829 <        strcat(buffer,FILE_SEP_CHAR);
827 >      {
828 >        buffer = getenv(_envvar.c_str());
829 >        buffer += FILE_SEP_CHAR;
830  
831          if (!_subdir.empty())
832 <        {
833 <            strcpy(subbuffer,buffer);
834 <            strcat(subbuffer,_subdir.c_str());
835 <            strcat(subbuffer,FILE_SEP_CHAR);
836 <        }
832 >          {
833 >            subbuffer = buffer;
834 >            subbuffer += _subdir;
835 >            subbuffer += FILE_SEP_CHAR;
836 >          }
837  
838 <        strcat(buffer,(char*)_filename.c_str());
839 <        strcat(subbuffer,(char*)_filename.c_str());
838 >        buffer += _filename;
839 >        subbuffer += _filename;
840  
841 <        ifs1.open(subbuffer);
841 >        ifs1.open(subbuffer.c_str());
842          ifsP= &ifs1;
843          if (!(*ifsP))
844 <        {
845 <            ifs2.open(buffer);
844 >          {
845 >            ifs2.open(buffer.c_str());
846              ifsP = &ifs2;
847 <        }
848 <    }
847 >          }
848 >      }
849      // Then, check the configured data directory
850      else // if (!(*ifsP))
851 <    {
852 <        strcpy(buffer,_dir.c_str());
853 <        strcat(buffer,FILE_SEP_CHAR);
851 >      {
852 >        buffer = _dir;
853 >        buffer += FILE_SEP_CHAR;
854  
855 <        strcpy(subbuffer,buffer);
856 <        strcat(subbuffer,BABEL_VERSION);
857 <        strcat(subbuffer,FILE_SEP_CHAR);
843 <        strcat(subbuffer,(char*)_filename.c_str());
855 >        subbuffer = buffer;
856 >        subbuffer += BABEL_VERSION;
857 >        subbuffer += FILE_SEP_CHAR;
858  
859 <        strcat(buffer,(char*)_filename.c_str());
859 >        subbuffer += _filename;
860 >        buffer += _filename;
861  
862 <        ifs3.open(subbuffer);
862 >        ifs3.open(subbuffer.c_str());
863          ifsP= &ifs3;
864          if (!(*ifsP))
865 <        {
866 <            ifs4.open(buffer);
865 >          {
866 >            ifs4.open(buffer.c_str());
867              ifsP = &ifs4;
868 <        }
869 <    }
868 >          }
869 >      }
870  
871 +    char charBuffer[BUFF_SIZE];
872      if ((*ifsP))
873 <    {
874 <        while(ifsP->getline(buffer,BUFF_SIZE))
875 <            ParseLine(buffer);
876 <    }
873 >      {
874 >        while(ifsP->getline(charBuffer,BUFF_SIZE))
875 >          ParseLine(charBuffer);
876 >      }
877  
878      else
879 <        // If all else fails, use the compiled in values
880 <        if (_dataptr)
879 >      // If all else fails, use the compiled in values
880 >      if (_dataptr)
881          {
882 <            const char *p1,*p2;
883 <            for (p1 = p2 = _dataptr;*p2 != '\0';p2++)
884 <                if (*p2 == '\n')
885 <                {
886 <                    strncpy(buffer, p1, (p2 - p1));
887 <                    buffer[(p2 - p1)] = '\0';
888 <                    ParseLine(buffer);
889 <                    p1 = ++p2;
890 <                }
882 >          const char *p1,*p2;
883 >          for (p1 = p2 = _dataptr;*p2 != '\0';p2++)
884 >            if (*p2 == '\n')
885 >              {
886 >                strncpy(charBuffer, p1, (p2 - p1));
887 >                charBuffer[(p2 - p1)] = '\0';
888 >                ParseLine(charBuffer);
889 >                p1 = ++p2;
890 >              }
891          }
892 <        else
892 >      else
893          {
894 <            string s = "Unable to open data file '";
895 <            s += _filename;
896 <            s += "'";
897 <            obErrorLog.ThrowError(__func__, s, obWarning);
894 >          string s = "Unable to open data file '";
895 >          s += _filename;
896 >          s += "'";
897 >          obErrorLog.ThrowError(__func__, s, obWarning);
898          }
899  
900      if (ifs1)
901 <        ifs1.close();
901 >      ifs1.close();
902      if (ifs2)
903 <        ifs2.close();
903 >      ifs2.close();
904      if (ifs3)
905 <        ifs3.close();
905 >      ifs3.close();
906      if (ifs4)
907 <        ifs4.close();
907 >      ifs4.close();
908  
909      if (GetSize() == 0)
910        {
911 <            string s = "Cannot initialize database '";
912 <            s += _filename;
913 <            s += "' which may cause further errors.";
914 <      obErrorLog.ThrowError(__func__, "Cannot initialize database", obWarning);
911 >        string s = "Cannot initialize database '";
912 >        s += _filename;
913 >        s += "' which may cause further errors.";
914 >        obErrorLog.ThrowError(__func__, "Cannot initialize database", obWarning);
915        }
916        
917 < }
917 >  }
918  
919   } // end namespace OpenBabel
920  

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