source: src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp@ dbcc47

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 *
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * ExportGraph_ToFiles.cpp
 *
 *  Created on: 08.03.2012
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "ExportGraph_ToFiles.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 "Parser/FormatParserStorage.hpp"
#include "World.hpp"

/** Constructor for class ExportGraph_ToFiles.
 *
 * @param _graph instance of Graph containing keyset of each fragment
 * @param _treatment whether to always add already present hydrogens or not
 * @param _saturation whether to saturate dangling bonds with hydrogen or not
 */
ExportGraph_ToFiles::ExportGraph_ToFiles(
    const Graph &_graph,
    const enum HydrogenTreatment _treatment,
    const enum HydrogenSaturation _saturation) :
                ExportGraph(_graph),
                BondFragments(World::getPointer()),
                treatment(_treatment),
                saturation(_saturation)
{}

/** Destructor of class ExportGraph_ToFiles.
 *
 * We free all created molecules again and also removed their copied atoms.
 */
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();

  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
  LOG(1, "Writing " << BondFragments.ListOfMolecules.size() << " possible bond fragmentation configs");
  bool write_status = true;
  for (std::vector<std::string>::const_iterator iter = typelist.begin();
      iter != typelist.end();
      ++iter) {
    LOG(2, "INFO: Writing bond fragments for type " << (*iter) << ".");
    write_status = write_status
    && BondFragments.OutputConfigForListOfFragments(
        prefix,
        FormatParserStorage::getInstance().getTypeFromName(*iter));
  }
  if (write_status)
    LOG(1, "All configs written.");
  else
    LOG(1, "Some config writing failed.");

  // store force index reference file
  {
    SortIndex_t SortIndex;
    BondFragments.StoreForcesFile(prefix, SortIndex);
  }

  // store keysets file
  TotalGraph.StoreKeySetFile(prefix);

  // store Hydrogen saturation correction file
  BondFragments.AddHydrogenCorrection(prefix);

  // restore orbital and Stop values
  //CalculateOrbitals(*configuration);
}

/** 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++;
      }
    }
  }
}