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root/group/trunk/OOPSE-4/src/applications/atom2md/oopseformat.cpp
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Comparing trunk/OOPSE-4/src/applications/atom2md/oopseformat.cpp (file contents):
Revision 3319 by gezelter, Wed Jan 23 03:45:33 2008 UTC vs.
Revision 3424 by gezelter, Tue Jul 1 13:28:23 2008 UTC

# Line 16 | Line 16 | GNU General Public License for more details.
16  
17   #include <openbabel/babelconfig.h>
18   #include <openbabel/obmolecformat.h>
19 + #include <openbabel/obiter.h>
20 + #include <openbabel/mol.h>
21 + #include <openbabel/chains.h>
22   #include <fstream>
23  
24 + #include "utils/StringUtils.hpp"
25 +
26   using namespace std;
27   namespace OpenBabel
28   {
# Line 55 | Line 60 | namespace OpenBabel
60  
61    private:
62      bool AreSameFragments(OBMol& mol, vector<int>& frag1, vector<int>& frag2);
63 <    void findAngles(OBMol& mol);
63 >    //void findAngles(OBMol& mol);
64      OBMol* createMolFromFragment(OBMol& mol, vector<int>& fragment);
65      void WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os, OBMol& mol, vector<int>& indices);
66    };
# Line 119 | Line 124 | namespace OpenBabel
124        }
125      
126      string OutputFileName = pConv->GetInFilename();
127 <    unsigned int pos = OutputFileName.rfind(".");
128 <    if(pos==string::npos)
124 <      OutputFileName += ".md";
125 <    else
127 >    size_t pos = OutputFileName.rfind(".");
128 >    if(pos!=string::npos)
129        OutputFileName = OutputFileName.substr(0, pos) + ".md";      
130 +    else
131 +      OutputFileName += ".md";
132 +
133      ofstream ofs(OutputFileName.c_str());
134      if(!ofs)
135        {
# Line 174 | Line 180 | namespace OpenBabel
180        return (t1.second == t2.second) && ( (t1.first == t2.first && t1.third == t2.third) || (t1.first == t2.third && t1.third == t2.first));
181      }
182    };
183 <  
184 <  void OOPSEFormat::findAngles(OBMol& mol) {
185 <    /*
183 >
184 >  /*  
185 >    void OOPSEFormat::findAngles(OBMol& mol) {
186 >
187      //if already has data return
188      if(mol.HasData(OBGenericDataType::AngleData))
189      return;
# Line 213 | Line 220 | namespace OpenBabel
220          angle.SetAtoms(i->first, i->second, i->second);
221          angles->SetData(angle);
222      }
223 <    */
223 >
224    }
225 +  */
226    
227    OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol, vector<int>& fragment) {
228      
229      OBMol* newMol = new OBMol();
230 +    OBChainsParser* chainParser = new OBChainsParser();
231      newMol->ReserveAtoms(fragment.size());
232      newMol->BeginModify();
233      for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i) {
# Line 227 | Line 236 | namespace OpenBabel
236      }
237      newMol->EndModify();
238      newMol->ConnectTheDots();
239 <    findAngles(*newMol);
239 >    newMol->PerceiveBondOrders();
240 >    newMol->FindAngles();
241      newMol->FindTorsions();
242 +    //chainParser->PerceiveChains(*newMol, false);
243 +
244      return newMol;
245    }
246    
# Line 236 | Line 248 | namespace OpenBabel
248      std::string indentLevel1("  ");
249      std::string indentLevel2("    ");
250      std::string molPrefix("MolName");
251 +    std::string resName;
252      unsigned int i;
253      const int BUFFLEN = 1024;
254      char buffer[BUFFLEN];
255      string str, str1;
256 +    OBAtom *a, *b, *c, *d;    
257 +    OBChainsParser* chainParser = new OBChainsParser();
258 +    OBResidue *r;
259 +    int resKey;
260 +    char type_name[10];
261 +    char *element_name;
262 +    int res_num;
263      
264 <    
264 >    std::cerr << "yo\n";
265      os << "<OOPSE version=4>" << endl;
266      os << "  <MetaData>" << endl << endl;
267      
268      for(i = 0; i < mols.size(); ++i) {
269        OBMol* pmol = mols[i];
270 <      
270 >      std::cerr << "yo1\n";
271        pmol->ConnectTheDots();
272        pmol->PerceiveBondOrders();
273 +      chainParser->PerceiveChains(*pmol, false);
274        //pmol->FindSSSR();
275        //pmol->SetAromaticPerceived();
276        //pmol->Kekulize();
# Line 259 | Line 280 | namespace OpenBabel
280        sprintf(buffer, "%d", i);
281        os << indentLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";
282        
283 +
284        //atom
285 +      
286        int ai = 0;
287 +      FOR_RESIDUES_OF_MOL(res, *pmol) {
288 +
289 +        std::cerr << "found residue" << res->GetName() << "\n";
290 +      }
291 +      
292 + //       FOR_RESIDUES_OF_MOL(res, *pmol) {
293 +        
294 + //      resName = res->GetName();
295 + //      resKey = res->GetResKey();
296 +
297 +        
298 +
299 + //      std::cerr << "found residue " << resName << "\n";
300 + //      std::cerr << "  num = " << res->GetNum() << "\n";
301 + //      std::cerr << "  numAtoms = " << res->GetNumAtoms() << "\n";
302 + //      std::cerr << "  num = " << res->GetNum() << "\n";
303 + //      std::cerr << "  chain = " << res->GetChain() << "\n";
304 + //      std::cerr << "  chainnum = " << res->GetChainNum() << "\n";
305 + //      std::cerr << "  idx = " << res->GetIdx() << "\n";
306 + //      std::cerr << "  key = " << res->GetResKey() << "\n";
307 +
308 +
309 + //      FOR_ATOMS_OF_RESIDUE(atom, &*res) {
310 + //        str = atom->GetType();
311 + //        ttab.SetFromType("INT");
312 + //        ttab.SetToType("INT");
313 + //        ttab.Translate(str1,str);
314 + //        os << indentLevel1 << "atom[" << ai << "] {\n";
315 + //        os << indentLevel2 << "type = " << "\"" << resName << "-" << str1 << "\"" << ";\n";
316 + //        os << indentLevel1 << "}\n";
317 + //        atomMap[&(*atom)] = ai++;
318 + //      }        
319 + //      os << "\n";
320 +        
321 + //       }      
322 +
323 +      ai = 0;
324        FOR_ATOMS_OF_MOL(atom, *pmol ) {
325          str = atom->GetType();
326 <        ttab.SetFromType("INT");
327 <        ttab.SetToType("INT");
328 <        ttab.Translate(str1,str);
329 <        os << indentLevel1 << "atom[" << ai << "] {\n";
330 <        // os << indentLevel2 << "type = " << "\"" << etab.GetSymbol(atom->GetAtomicNum()) << "\"" << ";\n";
331 <        os << indentLevel2 << "type = " << "\"" << str1 << "\"" << ";\n";
332 <        os << indentLevel1 << "}\n";
326 >        r = atom->GetResidue();
327 >        
328 >        if (r == NULL)
329 >          resName = "NULL";
330 >        else
331 >          resName = r->GetName();
332 >                
333 >        if (resName.compare("NULL") ==0 || resName.compare("LIG") == 0 || resName.compare("UNK") == 0) {
334 >          // Either couldn't find a residue at all or couldn't find a reasonable
335 >          // residue name to use.  We'll punt and use OpenBabel's internal atom typing:
336 >          ttab.SetFromType("INT");
337 >          ttab.SetToType("INT");
338 >          ttab.Translate(str1,str);
339 >        } else {
340 >                
341 >
342 >          if (resName.compare("HOH") == 0) {
343 >            // HOH is a special residue name for water, and the standard atom types
344 >            // are OW and HW, so just append W to the string for the atom type:
345 >            ttab.SetFromType("INT");
346 >            ttab.SetToType("XYZ");
347 >            ttab.Translate(str1,str);
348 >            str1 += "W";
349 >          } else {
350 >
351 >            std::cerr << "found residue " << resName << "\n";
352 >
353 >            // If we know what residue we've got, the specific atom name can
354 >            // be used to help specify partial charges.
355 >
356 >            str = r->GetAtomID(&*atom);
357 >            size_t startpos = str.find_first_not_of(" ");
358 >            size_t endpos = str.find_last_not_of(" ");
359 >            str = str.substr( startpos, endpos-startpos+1 );
360 >            str1 = resName + "-" + str;
361 >          }
362 >
363 >        }
364 >
365 > //         os << indentLevel1 << "atom[" << ai << "] {\n";
366 > //         os << indentLevel2 << "type = " << "\"" << str1 << "\"" << ";\n";
367 > //         os << indentLevel1 << "}\n";
368 >        os << "atom[" << ai << "] { ";
369 >        os << "type = " << "\"" << str1 << "\"" << "; ";
370 >        os << "}\n";
371          atomMap[&(*atom)] = ai++;
372        }        
373        os << "\n";
374        
375        //bond
376        FOR_BONDS_OF_MOL(bond, *pmol ) {
377 <        os << indentLevel1 << "bond {\n";
378 <        os << indentLevel2 << "members(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
379 <        os << indentLevel1 << "}\n";
380 <      }  
377 > //         os << indentLevel1 << "bond {\n";
378 > //         os << indentLevel2 << "members(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
379 > //         os << indentLevel1 << "}\n";
380 >        os << "bond { ";
381 >        os << "members(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << "); ";
382 >        os << "}\n";
383 >      }
384 >
385 >      FOR_ANGLES_OF_MOL(angle, *pmol) {
386 >
387 >        // OpenBabel's getAtoms returns the 3 atom pointer for the
388 >        // angle with the vertex first.  These need to be reordered
389 >        // for vertex-second ordering for OOPSE.
390 >
391 >         b = pmol->GetAtom((*angle)[0] + 1);
392 >         a = pmol->GetAtom((*angle)[1] + 1);
393 >         c = pmol->GetAtom((*angle)[2] + 1);
394 >
395 > //       os << indentLevel1 << "bend {\n";
396 > //       os << indentLevel2 << "members(" << atomMap[a] <<  ", " << atomMap[b] << ", " << atomMap[c] << ");\n";
397 > //       os << indentLevel1 << "}\n";
398 >         os << "bend { ";
399 >         os << "members(" << atomMap[a] <<  ", " << atomMap[b] << ", " << atomMap[c] << "); ";
400 >         os << "}\n";
401 >      }
402 >
403 >      FOR_TORSIONS_OF_MOL(torsion, *pmol) {
404 >
405 >        // OpenBabel's getAtoms returns the 3 atom pointer for the
406 >        // angle with the vertex first.  These need to be reordered
407 >        // for vertex-second ordering for OOPSE.
408 >
409 >         a = pmol->GetAtom((*torsion)[0] + 1);
410 >         b = pmol->GetAtom((*torsion)[1] + 1);
411 >         c = pmol->GetAtom((*torsion)[2] + 1);
412 >         d = pmol->GetAtom((*torsion)[3] + 1);
413 >
414 > //         os << indentLevel1 << "torsion {\n";
415 > //         os << indentLevel2 << "members(" << atomMap[a] <<  ", " << atomMap[b] << ", " << atomMap[c] << ", " << atomMap[d] << ");\n";
416 > //         os << indentLevel1 << "}\n";
417 >
418 >        os << "torsion { ";
419 >        os << "members(" << atomMap[a] <<  ", " << atomMap[b] << ", " << atomMap[c] << ", " << atomMap[d] << "); ";
420 >        os << "}\n";
421 >      }
422 >
423        /*
424        //bend
425        OBGenericData* pGenericData = pmol->GetData(OBGenericDataType::AngleData);

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