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-              r22b786
+              r8652a30
 #include "ExportGraph.hpp"
+#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "Bond/bond.hpp"
+#include "Element/element.hpp"
+#include "Fragmentation/Graph.hpp"
+#include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/SortIndex.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
+#include "molecule.hpp"
+#include "MoleculeListClass.hpp"
+#include "World.hpp"
 /** Constructor for class ExportGraph.
+ *
  * @param _graph
  */
+ExportGraph::ExportGraph(const Graph &_graph) :
+        TotalGraph(_graph)
+{
+ExportGraph::ExportGraph(
+  const Graph &_graph,
+  const enum HydrogenTreatment _treatment,
+  const enum HydrogenSaturation _saturation) :
+  TotalGraph(_graph),
+  BondFragments(World::getPointer()),
+  treatment(_treatment),
+  saturation(_saturation)
+{
+}
 …
  */
 ExportGraph::~ExportGraph()
+{}
+{
+  // 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);
+  }
+}
+void ExportGraph::operator()()
+{
+  if (BondFragments.ListOfMolecules.size() == 0)
+    prepareMolecule();
+}
+/** 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)->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.cpp

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src/Fragmentation/Exporters/ExportGraph.cpp

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