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root/OpenMD/trunk/src/openbabel/oopseformat.cpp
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Comparing trunk/src/openbabel/oopseformat.cpp (file contents):
Revision 746 by tim, Wed Nov 16 21:22:51 2005 UTC vs.
Revision 759 by tim, Fri Nov 18 20:17:38 2005 UTC

# Line 14 | Line 14 | GNU General Public License for more details.
14   ***********************************************************************/
15  
16   #include "oopseformat.hpp"
17 + #include <fstream>
18   namespace OpenBabel
19   {
20  
# Line 65 | Line 66 | bool OOPSEFormat::WriteMolecule(OBBase* pOb, OBConvers
66          numMols.push_back((*i).size());
67      }
68  
69 <    WriteMDFile(mdMols, numMols);    
69 >    string OutputFileName = pConv->GetInFilename();
70 >    unsigned int pos = OutputFileName.rfind(".");
71 >    if(pos==string::npos)
72 >        OutputFileName += ".md";
73 >    else
74 >        OutputFileName = OutputFileName.substr(0, pos) + ".md";      
75 >    ofstream ofs(OutputFileName.c_str());
76 >    if(!ofs)
77 >    {
78 >         cerr << "Cannot write to " << OutputFileName <<endl;
79 >         return false;
80 >    }
81 >                
82 >    WriteMDFile(mdMols, numMols, ofs);    
83  
84      for(vector<OBMol*>::iterator  i = mdMols.begin(); i != mdMols.end(); ++i)
85      {
# Line 163 | Line 177 | OBMol* OOPSEFormat::createMolFromFragment(OBMol& mol,
177      newMol->FindTorsions();
178      return newMol;
179   }
180 < void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols)
180 > void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vector<int> numMols, ostream& os)
181   {
182      std::string identLevel1("\t");
183      std::string identLevel2("\t\t");
184      std::string molPrefix("MolName");
171 –    ostream& ofs = std::cout;
185      const int BUFFLEN = 1024;
186      char buffer[BUFFLEN];
187      
# Line 176 | Line 189 | void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vec
189      {
190          OBMol* pmol = mols[i];
191          map<OBAtom*, int> atomMap;
192 <        ofs << "molecule {\n";
192 >        os << "molecule {\n";
193          sprintf(buffer, "%d", i);
194 <        ofs << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";
194 >        os << identLevel1 << "name = " << "\"" << molPrefix << buffer << "\"" << ";\n";
195  
196          
197          //atom
185 –        ofs << identLevel1 << "nAtoms = " << pmol->NumAtoms() << ";\n";
198          int ai = 0;
199          FOR_ATOMS_OF_MOL(atom, *pmol ) {
200 <            ofs << identLevel1 << "atom[" << ai << "] {\n";
201 <            ofs << identLevel2 << "type = " << "\"" << atom->GetType() << "\"" << ";\n";
202 <            ofs << identLevel2 << "position(" << atom->GetX() << ", " << atom->GetY() << ", " << atom->GetZ() << ");\n";
191 <            ofs << identLevel1 << "}\n";
200 >            os << identLevel1 << "atom[" << ai << "] {\n";
201 >            os << identLevel2 << "type = " << "\"" << atom->GetType() << "\"" << ";\n";
202 >            os << identLevel1 << "}\n";
203              atomMap[&(*atom)] = ai++;
204          }        
205 +        os << "\n";
206  
207          //bond
196 –        ofs << identLevel1 << "nBonds = " << pmol->NumBonds() << ";\n";
197 –        int bi = 0;
208          FOR_BONDS_OF_MOL(bond, *pmol ) {
209 <            ofs << identLevel1 << "bond[" << bi++ << "] {\n";
210 <            ofs << identLevel2 << "member(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
211 <            ofs << identLevel1 << "}\n";
209 >            os << identLevel1 << "bond {\n";
210 >            os << identLevel2 << "members(" << atomMap[bond->GetBeginAtom()] <<  ", " << atomMap[bond->GetEndAtom()] << ");\n";
211 >            os << identLevel1 << "}\n";
212          }  
213          /*
214          //bend
# Line 206 | Line 216 | void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vec
216          OBAngleData* pAngleData = dynamic_cast<OBAngleData*>(pGenericData);
217          vector<OBAngle> angles = pAngleData->GetData();
218  
219 <        ofs << identLevel1 << "nBends = " << angles.size() << ";\n";        
219 >        os << identLevel1 << "nBends = " << angles.size() << ";\n";        
220          int bendIndex = 0;
221          for (vector<OBAngle>::iterator ti = angles.begin(); ti != angles.end(); ++ti)
222          {
223              triple<OBAtom*, OBAtom*, OBAtom*> bendAtoms = ti->getAtoms();
224 <            ofs << identLevel1 << "bend[" << bendIndex++ << "] {\n";
225 <            ofs << identLevel2 << "member(" << atomMap[bendAtoms.first] <<  ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
226 <            ofs << identLevel1 << "}\n";            
224 >            os << identLevel1 << "bend[" << bendIndex++ << "] {\n";
225 >            os << identLevel2 << "member(" << atomMap[bendAtoms.first] <<  ", " << atomMap[bendAtoms.second] << atomMap[bendAtoms.third] <<");\n";
226 >            os << identLevel1 << "}\n";            
227          }
228          
229          //torsion
# Line 227 | Line 237 | void OOPSEFormat::WriteMDFile(vector<OBMol*> mols, vec
237              torsionArray.insert(torsionArray.end(), tmpTorsions.begin(), tmpTorsions.end());            
238          }
239  
240 <        ofs << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n";
240 >        os << identLevel1 << "nTorsions = " << torsionArray.size() << ";\n";
241          int torsionIndex = 0;
242          for (vector<quad<OBAtom*,OBAtom*,OBAtom*,OBAtom*> >::iterator ti = torsionArray.begin(); ti != torsionArray.end(); ++ti)
243          {
244 <            ofs << identLevel1 << "torsion[" << torsionIndex++ << "] {\n";
245 <            ofs << identLevel2 << "member(" << atomMap[ti->first] <<  ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n";
246 <            ofs << identLevel1 << "}\n";          
244 >            os << identLevel1 << "torsion[" << torsionIndex++ << "] {\n";
245 >            os << identLevel2 << "member(" << atomMap[ti->first] <<  ", " << atomMap[ti->second] <<", " << atomMap[ti->third] <<", " << atomMap[ti->forth] << ");\n";
246 >            os << identLevel1 << "}\n";          
247          }
248          */
249 <        ofs << "}\n";
249 >        os << "}\n";
250 >        os << "\n";
251 >
252      }
253  
254 <    ofs << "nComponents = " << mols.size() << ";\n";
254 >    os << "\n";
255 >    os << "nComponents = " << mols.size() << ";\n";
256      
257      for(unsigned int i =0; i < mols.size(); ++i)
258      {
259 <        ofs << "component{\n";
259 >        os << "component{\n";
260          sprintf(buffer, "%d", i);
261 <        ofs << "type = " << molPrefix << buffer << ";\n";
262 <        ofs << "nMol = " << numMols[i]<< ";\n";
263 <        ofs << "}\n";
261 >        os << "type = " << molPrefix << buffer << ";\n";
262 >        os << "nMol = " << numMols[i]<< ";\n";
263 >        os << "}\n";
264      }
265   }
266   void OOPSEFormat::WriteINFile(OBMol& mol, ostream& ofs, vector<int>& indices)

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