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-              r22b786
+              r8652a30
     const enum HydrogenTreatment _treatment,
     const enum HydrogenSaturation _saturation) :
+                ExportGraph(_graph),
+                BondFragments(World::getPointer()),
+                treatment(_treatment),
+                saturation(_saturation)
+                ExportGraph(_graph, _treatment, _saturation)
 {}
 …
  */
 ExportGraph_ToFiles::~ExportGraph_ToFiles()
+{
+  // remove all create molecules again from the World including their atoms
+  for (MoleculeList::iterator iter = BondFragments.ListOfMolecules.begin();
+      !BondFragments.ListOfMolecules.empty();
+      iter = BondFragments.ListOfMolecules.begin()) {
+    // remove copied atoms and molecule again
+    molecule *mol = *iter;
+    mol->removeAtomsinMolecule();
+    World::getInstance().destroyMolecule(mol);
+    BondFragments.ListOfMolecules.erase(iter);
+  }
+}
+{}
 /** Actual implementation of the export to files function.
 …
 void ExportGraph_ToFiles::operator()()
+{
+  if (BondFragments.ListOfMolecules.size() == 0)
+    prepareMolecule();
+  ExportGraph::operator()();
   // ===== 9. Save fragments' configuration and keyset files et al to disk ===
 …
+}
-/** Internal helper to create from each keyset a molecule
+ *
- */
-void ExportGraph_ToFiles::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_ToFiles::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_ToFiles::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_ToFiles::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)->BondDegree);
-//            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)->BondDegree);
+          }
-          //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
+        }
+      }
-    } 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 8652a30 for src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

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src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

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