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-              r9fd44f
+              r06804b
+}
 /** Internal helper to create from each keyset a molecule
+ *
  */
 void ExportGraph::prepareMolecule()
+{
   size_t count = 0;
   for(Graph::const_iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
     KeySet test = (*runner).first;
     LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
         << (*runner).second.second << ".");
     BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
     ++count;
+  }
   LOG(1, "INFO: " << count << "/" << BondFragments.ListOfMolecules.size()
       << " fragments generated from the keysets.");
+}
 /** Stores a fragment from \a KeySet into \a molecule.
  * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
  * molecule and adds missing hydrogen where bonds were cut.
  * \param &Leaflet pointer to KeySet structure
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
  * \return pointer to constructed molecule
  */
 molecule * ExportGraph::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
+{
   Info info(__func__);
   ListOfLocalAtoms_t SonList;
   molecule *Leaf = World::getInstance().createMolecule();
   StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
   // create the bonds between all: Make it an induced subgraph and add hydrogen
 //  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
   CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
   //Leaflet->Leaf->ScanForPeriodicCorrection(out);
   return Leaf;
+}
 /** Initializes some value for putting fragment of \a *mol into \a *Leaf.
  * \param *Leaf fragment molecule
  * \param &Leaflet pointer to KeySet structure
  * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
  * \return number of atoms in fragment
  */
 int ExportGraph::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+{
   atom *FatherOfRunner = NULL;
   // first create the minimal set of atoms from the KeySet
   World &world = World::getInstance();
   int size = 0;
   for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
     FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
     SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
     size++;
+  }
   return size;
+}
 /** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
  * \param *Leaf fragment molecule
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
  * \param SonList list which atom of \a *Leaf is another atom's son
  */
 void ExportGraph::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+{
   bool LonelyFlag = false;
   atom *OtherFather = NULL;
   atom *FatherOfRunner = NULL;
   // we increment the iter just before skipping the hydrogen
   // as we use AddBond, we cannot have a const_iterator here
   for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
     LonelyFlag = true;
     FatherOfRunner = (*iter)->father;
     ASSERT(FatherOfRunner,"Atom without father found");
     if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
       // create all bonds
       const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
       for (BondList::const_iterator BondRunner = ListOfBonds.begin();
           BondRunner != ListOfBonds.end();
           ++BondRunner) {
         OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
         if (SonList.find(OtherFather->getNr()) != SonList.end()) {
 //          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
 //              << " is bound to " << *OtherFather << ", whose son is "
 //              << *SonList[OtherFather->getNr()] << ".");
           if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
             std::stringstream output;
 //            output << "ACCEPT: Adding Bond: "
             output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
 //            LOG(3, output.str());
             //NumBonds[(*iter)->getNr()]++;
           } else {
 //            LOG(3, "REJECY: Not adding bond, labels in wrong order.");
+          }
           LonelyFlag = false;
         } else {
 //          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
 //              << " is bound to " << *OtherFather << ", who has no son in this fragment molecule.");
           if (saturation == DoSaturate) {
 //          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
             if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
               exit(1);
           } else if ((treatment == ExcludeHydrogen) && (OtherFather->getElementNo() == (atomicNumber_t)1)) {
             // just copy the atom if it's a hydrogen
             atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
             Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
+          }
           //NumBonds[(*iter)->getNr()] += Binder->getDegree();
+        }
+      }
     } else {
       ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
+    }
     if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
       LOG(0, **iter << "has got bonds only to hydrogens!");
+    }
     ++iter;
     if (saturation == DoSaturate) {
       while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
         iter++;
+      }
+    }
+  }
+}
+///** Internal helper to create from each keyset a molecule
+// *
+// */
+//void ExportGraph::prepareMolecule()
+//{
+//  size_t count = 0;
+//  for(Graph::const_iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
+//    KeySet test = (*runner).first;
+//    LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
+//        << (*runner).second.second << ".");
+//    BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
+//    ++count;
+//  }
+//  LOG(1, "INFO: " << count << "/" << BondFragments.ListOfMolecules.size()
+//      << " fragments generated from the keysets.");
+//}
+//
+///** Stores a fragment from \a KeySet into \a molecule.
+// * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
+// * molecule and adds missing hydrogen where bonds were cut.
+// * \param &Leaflet pointer to KeySet structure
+// * \param IsAngstroem whether we have Ansgtroem or bohrradius
+// * \return pointer to constructed molecule
+// */
+//molecule * ExportGraph::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
+//{
+//  Info info(__func__);
+//  ListOfLocalAtoms_t SonList;
+//  molecule *Leaf = World::getInstance().createMolecule();
+//
+//  StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
+//  // create the bonds between all: Make it an induced subgraph and add hydrogen
+////  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
+//  CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
+//
+//  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
+//  return Leaf;
+//}
+//
+///** Initializes some value for putting fragment of \a *mol into \a *Leaf.
+// * \param *Leaf fragment molecule
+// * \param &Leaflet pointer to KeySet structure
+// * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
+// * \return number of atoms in fragment
+// */
+//int ExportGraph::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+//{
+//  atom *FatherOfRunner = NULL;
+//
+//  // first create the minimal set of atoms from the KeySet
+//  World &world = World::getInstance();
+//  int size = 0;
+//  for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
+//    FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
+//    SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
+//    size++;
+//  }
+//  return size;
+//}
+//
+///** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
+// * \param *Leaf fragment molecule
+// * \param IsAngstroem whether we have Ansgtroem or bohrradius
+// * \param SonList list which atom of \a *Leaf is another atom's son
+// */
+//void ExportGraph::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+//{
+//  bool LonelyFlag = false;
+//  atom *OtherFather = NULL;
+//  atom *FatherOfRunner = NULL;
+//
+//  // we increment the iter just before skipping the hydrogen
+//  // as we use AddBond, we cannot have a const_iterator here
+//  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
+//    LonelyFlag = true;
+//    FatherOfRunner = (*iter)->father;
+//    ASSERT(FatherOfRunner,"Atom without father found");
+//    if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
+//      // create all bonds
+//      const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
+//      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+//          BondRunner != ListOfBonds.end();
+//          ++BondRunner) {
+//        OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
+//        if (SonList.find(OtherFather->getNr()) != SonList.end()) {
+////          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
+////              << " is bound to " << *OtherFather << ", whose son is "
+////              << *SonList[OtherFather->getNr()] << ".");
+//          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
+//            std::stringstream output;
+////            output << "ACCEPT: Adding Bond: "
+//            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
+////            LOG(3, output.str());
+//            //NumBonds[(*iter)->getNr()]++;
+//          } else {
+////            LOG(3, "REJECY: Not adding bond, labels in wrong order.");
+//          }
+//          LonelyFlag = false;
+//        } else {
+////          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
+////              << " is bound to " << *OtherFather << ", who has no son in this fragment molecule.");
+//          if (saturation == DoSaturate) {
+////          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
+//            if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
+//              exit(1);
+//          } else if ((treatment == ExcludeHydrogen) && (OtherFather->getElementNo() == (atomicNumber_t)1)) {
+//            // just copy the atom if it's a hydrogen
+//            atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
+//            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
+//          }
+//          //NumBonds[(*iter)->getNr()] += Binder->getDegree();
+//        }
+//      }
+//    } else {
+//      ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
+//    }
+//    if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
+//      LOG(0, **iter << "has got bonds only to hydrogens!");
+//    }
+//    ++iter;
+//    if (saturation == DoSaturate) {
+//      while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
+//        iter++;
+//      }
+//    }
+//  }
+//}

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Changeset 06804b for src/Fragmentation/Exporters/ExportGraph.cpp

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src/Fragmentation/Exporters/ExportGraph.cpp

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