source: src/Actions/FragmentationAction/FragmentationAction.cpp@ e60558

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * Copyright (C)  2013 Frederik Heber. 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/>.
 */

/*
 * FragmentationAction.cpp
 *
 *  Created on: May 9, 2010
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "Atom/atom.hpp"
#include "CodePatterns/IteratorAdaptors.hpp"
#include "CodePatterns/Log.hpp"
#include "Descriptors/AtomSelectionDescriptor.hpp"
#include "Descriptors/MoleculeIdDescriptor.hpp"
#include "Fragmentation/AdaptivityMap.hpp"
#include "Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp"
#include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
#include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
#include "Fragmentation/Exporters/SaturatedBond.hpp"
#include "Fragmentation/Exporters/SaturatedFragment.hpp"
#include "Fragmentation/Exporters/SaturationDistanceMaximizer.hpp"
#include "Fragmentation/Fragmentation.hpp"
#include "Fragmentation/Graph.hpp"
#include "Fragmentation/HydrogenSaturation_enum.hpp"
#include "Fragmentation/Interfragmenter.hpp"
#include "Fragmentation/KeySetsContainer.hpp"
#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
#include "Graph/AdjacencyList.hpp"
#include "Graph/BondGraph.hpp"
#include "Graph/CyclicStructureAnalysis.hpp"
#include "Graph/DepthFirstSearchAnalysis.hpp"
#include "Helpers/defs.hpp"
#include "molecule.hpp"
#include "World.hpp"

#include <boost/shared_ptr.hpp>
#include <boost/filesystem.hpp>
#include <algorithm>
#include <iostream>
#include <map>
#include <string>
#include <vector>

#include "Actions/FragmentationAction/FragmentationAction.hpp"

using namespace MoleCuilder;

// and construct the stuff
#include "FragmentationAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */
ActionState::ptr FragmentationFragmentationAction::performCall() {
  clock_t start,end;
  int ExitFlag = -1;
  World &world = World::getInstance();

  // inform about used parameters
  LOG(0, "STATUS: Fragmenting molecular system with current connection matrix up to "
      << params.order.get() << " order. ");
  if (params.types.get().size() != 0)
    LOG(0, "STATUS: Fragment files begin with "
        << params.prefix.get() << " and are stored as: "
        << params.types.get() << "." << std::endl);

  // check for selected atoms
  if (world.beginAtomSelection() == world.endAtomSelection()) {
    STATUS("There are no atoms selected for fragmentation.");
    return Action::failure;
  }

  // go through all atoms, note down their molecules and group them
  typedef std::multimap<const molecule *, atom *> clusters_t;
  typedef std::vector<atomId_t> atomids_t;
  atomids_t atomids;
  clusters_t clusters;
  for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
      iter != world.endAtomSelection(); ++iter) {
    clusters.insert( std::make_pair(iter->second->getMolecule(), iter->second) );
    atomids.push_back(iter->second->getId());
  }
  {
    std::vector<const molecule *> molecules;
    molecules.insert( molecules.end(), MapKeyIterator<clusters_t::const_iterator>(clusters.begin()),
        MapKeyIterator<clusters_t::const_iterator>(clusters.end()) );
    molecules.erase( std::unique(molecules.begin(), molecules.end()), molecules.end() );
    LOG(1, "INFO: There are " << molecules.size()  << " molecules to consider.");
  }

  // parse in Adjacency file
  boost::shared_ptr<AdjacencyList> FileChecker;
  boost::filesystem::path filename(params.prefix.get() + std::string(ADJACENCYFILE));
  if (params.ParseStateFiles.get()) {
    if (boost::filesystem::exists(filename)
    && boost::filesystem::is_regular_file(filename)) {
      std::ifstream File;
      File.open(filename.string().c_str(), ios::out);
      FileChecker.reset(new AdjacencyList(File));
      File.close();
    } else {
      LOG(1, "INFO: Could not open default adjacency file " << filename.string() << ".");
      FileChecker.reset(new AdjacencyList);
    }
  } else
    FileChecker.reset(new AdjacencyList);

  // make sure bond degree is correct
  {
    BondGraph *BG = World::getInstance().getBondGraph();
    World::AtomComposite Set = World::getInstance().getAllAtoms(AtomsBySelection());
    // check whether bond graph is correct
    if (!BG->checkBondDegree(Set))
      BG->CorrectBondDegree(Set);
    else
      LOG(1, "INFO: Bond degrees all valid, not correcting.");
  }

  // we parse in the keysets from last time if present
  Graph StoredGraph;
  if (params.ParseStateFiles.get()) {
    StoredGraph.ParseKeySetFile(params.prefix.get());
    // check parsed graph against the set of atoms
    {
      AdaptivityMap *amap = StoredGraph.GraphToAdaptivityMap();
      bool status = true;
      for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
          iter != world.endAtomSelection(); ++iter) {
        const atomId_t atomid = iter->second->getId();
        // skip hydrogens in check if saturation is turned on
        if ((iter->second->getType()->getAtomicNumber() != 1)
            || (!params.DoSaturation.get())) {
          if (amap->count(atomid) == 0) {
            ELOG(1, "Atom #" << atomid << " not contained in KeySet file. ");
            status = false;
            break;
          }
        } else if (amap->count(atomid) != 0) {
          ELOG(1, "Atom #" << atomid << " in KeySet file is a hydrogen, but is now excluded. ");
          status = false;
          break;
        }
      }
      delete amap;

      if (!status) {
        ELOG(1, "KeySetsFile seems to contain leftover from an old fragmentation, hence not using file.");
        StoredGraph.clear();
      }
    }
  }

  start = clock();
  // go through all keys (i.e. all molecules)
  clusters_t::const_iterator advanceiter;
  Graph TotalGraph;
  int keysetcounter = 0;
  for (clusters_t::const_iterator iter = clusters.begin();
      iter != clusters.end();
      iter = advanceiter) {
    // get iterator to past last atom in this molecule
    const molecule * mol = iter->first;
    advanceiter = clusters.upper_bound(mol);

    // copy molecule's atoms' ids as parameters to Fragmentation's AtomMask
    std::vector<atomId_t> mols_atomids;
    std::transform(iter, advanceiter, std::back_inserter(mols_atomids),
        boost::bind( &atom::getNr,
            boost::bind( &clusters_t::value_type::second, _1 ))
    );
    LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
        << " atoms, out of " << mol->getAtomCount() << ".");
    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
    molecule * non_const_mol = World::getInstance().getMolecule(MoleculeById(mol->getId()));
    Fragmentation Fragmenter(non_const_mol, *FileChecker, treatment);

    // perform fragmentation
    LOG(0, std::endl << " ========== Fragmentation of molecule " << mol->getName() << " ========================= ");
    {
      Graph StoredLocalGraph(StoredGraph.getLocalGraph(mol));
      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph, params.ParseStateFiles.get());
      if ((ExitFlag == 2) && (tempFlag != 2))
        ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others
      if (ExitFlag == -1)
        ExitFlag = tempFlag; // if we are the first, we set the standard
    }
    if (TotalGraph.empty()) {
      TotalGraph = Fragmenter.getGraph();
      keysetcounter = TotalGraph.size();
    } else
      TotalGraph.InsertGraph(Fragmenter.getGraph(), keysetcounter);

  }
  // add full cycles if desired
  if (params.DoCyclesFull.get()) {
    // get the BackEdgeStack from somewhere
    DepthFirstSearchAnalysis DFS;
    DFS();
    std::deque<bond::ptr> BackEdgeStack = DFS.getBackEdgeStack();
    // then we analyse the cycles and get them
    CyclicStructureAnalysis CycleAnalysis(params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen);
    CycleAnalysis(&BackEdgeStack);
    CyclicStructureAnalysis::cycles_t cycles = CycleAnalysis.getAllCycles();
    // sort them according to KeySet::operator<()
    std::sort(cycles.begin(), cycles.end());
    // store all found cycles to file
    {
      boost::filesystem::path filename(params.prefix.get() + std::string(CYCLEKEYSETFILE));
      std::ofstream File;
      LOG(1, "INFO: Storing cycle keysets to " << filename.string() << ".");
      File.open(filename.string().c_str(), ios::out);
      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
          iter != cycles.end(); ++iter) {
        for (CyclicStructureAnalysis::cycle_t::const_iterator cycleiter = (*iter).begin();
            cycleiter != (*iter).end(); ++cycleiter) {
          File << *cycleiter << "\t";
        }
        File << "\n";
      }
      File.close();
    }
    // ... and to result container
    {
      KeySetsContainer cyclekeys;
      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
          iter != cycles.end(); ++iter) {
        const CyclicStructureAnalysis::cycle_t &cycle = *iter;
        const size_t order = cycle.size();
        KeySetsContainer::IntVector temp_cycle(cycle.begin(), cycle.end());
        cyclekeys.insert(temp_cycle, order);
      }
      FragmentationResultContainer::getInstance().addCycles(cyclekeys);
    }
    // Create graph and insert into TotalGraph
    LOG(0, "STATUS: Adding " << cycles.size() << " cycles.");
    {
      Graph CycleGraph;
      for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
          iter != cycles.end(); ++iter) {
        const CyclicStructureAnalysis::cycle_t &currentcycle = *iter;
        LOG(2, "INFO: Inserting cycle " << currentcycle << ".");
#ifndef NDEBUG
        std::pair< Graph::iterator, bool > inserter =
#endif
        CycleGraph.insert( std::make_pair(currentcycle, NumberValuePair(1,1.)) );
        ASSERT( inserter.second,
            "FragmentationFragmentationAction::performCall() - keyset "
            +toString(currentcycle)+" inserted twice into CycleGraph.");
      }
      TotalGraph.InsertGraph(CycleGraph, keysetcounter);
    }
  }

  LOG(0, "STATUS: There are " << TotalGraph.size() << " fragments.");

  {
    // remove OrderAtSite file
    std::string line;
    std::ofstream file;
    line = params.prefix.get() + ORDERATSITEFILE;
    file.open(line.c_str(), std::ofstream::out | std::ofstream::trunc);
    file << "";
    file.close();
  }

  // store graph internally
  AtomFragmentsMap &atomfragments = AtomFragmentsMap::getInstance();
  atomfragments.clear();
  atomfragments.insert(TotalGraph);

  // now add interfragments
  if (params.InterOrder.get() != 0) {
    LOG(0, "STATUS: Putting fragments together up to order "
        << params.InterOrder.get() << " and distance of "
        << params.distance.get() << ".");
    const enum HydrogenTreatment treatment =
        params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
    const double UpperBound = std::max(10., params.distance.get());
    Interfragmenter fragmenter;

    // check the largest Rcut that causes no additional inter-fragments
    const double Min_Rcut =
        fragmenter.findLargestCutoff(params.InterOrder.get(), UpperBound, treatment);

    // if we smear out electronic charges, warn when non-overlapping criterion does not hold
    if (params.InterOrder.get() < Min_Rcut)
      ELOG(2, "Inter-order is too low to cause any additional fragments.");

    // then add fragments
    fragmenter(TotalGraph, params.InterOrder.get(), params.distance.get(), treatment);

    LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
  }
  // TODO: When insert only adds and replaces if already present, no clear needed
  atomfragments.clear();
  atomfragments.insert(TotalGraph);

  // store keysets to file
  {
    TotalGraph.StoreKeySetFile(params.prefix.get());
  }

  // create global saturation positions map
  SaturatedFragment::GlobalSaturationPositions_t globalsaturationpositions;
  {
    // go through each atom
    for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
        iter != world.endAtomSelection(); ++iter) {
      const atom * const _atom = iter->second;

      // skip hydrogens if treated special
      const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
      if ((treatment == ExcludeHydrogen) && (_atom->getType()->getAtomicNumber() == 1)) {
        LOG(4, "DEBUG: Skipping hydrogen atom " << *_atom);
        continue;
      }

      // get the valence
      unsigned int NumberOfPoints = _atom->getElement().getNoValenceOrbitals();
      LOG(3, "DEBUG: There are " << NumberOfPoints
          << " places to fill in in total for this atom " << *_atom << ".");

      // check whether there are any bonds with degree larger than 1
      unsigned int SumOfDegrees = 0;
      bool PresentHigherBonds = false;
      const BondList &bondlist = _atom->getListOfBonds();
      for (BondList::const_iterator bonditer = bondlist.begin();
          bonditer != bondlist.end(); ++bonditer) {
        SumOfDegrees += (*bonditer)->getDegree();
        PresentHigherBonds |= (*bonditer)->getDegree() > 1;
      }

      // check whether there are alphas to maximize the hydrogens distances
      SaturationDistanceMaximizer::position_bins_t position_bins;
      {
        // gather all bonds and convert to SaturatedBonds
        SaturationDistanceMaximizer::PositionContainers_t CutBonds;
        for (BondList::const_iterator bonditer = bondlist.begin();
            bonditer != bondlist.end(); ++bonditer) {
          CutBonds.push_back(
              SaturatedBond::ptr(new SaturatedBond(*(bonditer->get()), *_atom) )
            );
        }
        SaturationDistanceMaximizer maximizer(CutBonds);
        if (PresentHigherBonds) {
          // then find best alphas
          maximizer();
        } else {
          // if no higher order bonds, we simply gather the scaled positions
        }
        position_bins = maximizer.getAllPositionBins();
        LOG(4, "DEBUG: Positions for atom " << *_atom << " are " << position_bins);
      }

      // convert into the desired entry in the map
      SaturatedFragment::SaturationsPositionsPerNeighbor_t positions_per_neighbor;
      {
        BondList::const_iterator bonditer = bondlist.begin();
        SaturationDistanceMaximizer::position_bins_t::const_iterator biniter =
            position_bins.begin();

        for (;bonditer != bondlist.end(); ++bonditer, ++biniter) {
          const atom * const OtherAtom = (*bonditer)->GetOtherAtom(_atom);
          std::pair<
              SaturatedFragment::SaturationsPositionsPerNeighbor_t::iterator,
              bool
              > inserter;
          // check whether we treat hydrogen special
          if ((treatment == ExcludeHydrogen) && (OtherAtom->getType()->getAtomicNumber() == 1)) {
            // if hydrogen, forget rescaled position and use original one
            inserter =
                positions_per_neighbor.insert(
                    std::make_pair(
                        OtherAtom->getId(),
                        SaturatedFragment::SaturationsPositions_t(
                            1, OtherAtom->getPosition() - _atom->getPosition())
                    )
                );
          } else {
            inserter =
                positions_per_neighbor.insert(
                    std::make_pair(
                        OtherAtom->getId(),
                        SaturatedFragment::SaturationsPositions_t(
                            biniter->begin(),
                            biniter->end())
                    )
                );
          }
          // if already pressent, add to this present list
          ASSERT (inserter.second,
              "FragmentationAction::performCall() - other atom "
              +toString(*OtherAtom)+" already present?");
        }
        // bonditer follows nicely
        ASSERT( biniter == position_bins.end(),
            "FragmentationAction::performCall() - biniter is out of step, it still points at bond "
            +toString(*biniter)+".");
      }
      // and insert
      globalsaturationpositions.insert(
          std::make_pair( _atom->getId(),
              positions_per_neighbor
          ));
    }
  }

  {
    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
    if (params.types.get().size() != 0) {
      // store molecule's fragment to file
      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
      exporter.setPrefix(params.prefix.get());
      exporter.setOutputTypes(params.types.get());
      if (!exporter())
        return Action::failure;
    } else {
      // store molecule's fragment in FragmentJobQueue
      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
      exporter.setLevel(params.level.get());
      exporter.setMaximumMeshWidth(params.max_meshwidth.get());
      if (!exporter())
        return Action::failure;
    }
    // add full keysets to present keysets in AtomFragmentsMap
    ExportGraph_ToAtomFragments exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
    if (!exporter())
      return Action::failure;
  }
  if (!AtomFragmentsMap::getInstance().checkCompleteness()) {
    ELOG(0, "Something went wrong with placing keysets in AtomFragmentsMap.");
    return Action::failure;
  }

  // store Adjacency to file
  {
    std::string filename = params.prefix.get() + ADJACENCYFILE;
    std::ofstream AdjacencyFile;
    AdjacencyFile.open(filename.c_str(), ios::out);
    AdjacencyList adjacency(atomids);
    adjacency.StoreToFile(AdjacencyFile);
    AdjacencyFile.close();
  }

  World::getInstance().setExitFlag(ExitFlag);
  end = clock();
  LOG(0, "STATUS: Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s.");

  return Action::success;
}

ActionState::ptr FragmentationFragmentationAction::performUndo(ActionState::ptr _state) {
  return Action::success;
}

ActionState::ptr FragmentationFragmentationAction::performRedo(ActionState::ptr _state){
  return Action::success;
}

bool FragmentationFragmentationAction::canUndo() {
  return true;
}

bool FragmentationFragmentationAction::shouldUndo() {
  return true;
}
/** =========== end of function ====================== */