source: src/Actions/FragmentationAction/AddSelectedAtomsAsFragmentAction.cpp

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2025 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/>.
 */

/*
 * AddSelectedAtomsAsFragmentAction.cpp
 *
 *  Created on: Nov 20, 2025
 *      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/AddSelectedAtomsAsFragmentAction.hpp"

using namespace MoleCuilder;

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

  // inform about used parameters
  LOG(0, "STATUS: Adding currently selected atoms as one fragment ");
  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 storing as a single fragment.");
    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 among the selected atoms to consider.");
  }

  // 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);

    /**
     * The "cluster" sorts the atoms into one set per molecule (from lower_bound to upper_bound
     * as \a *mol is same key for all these atoms). 
     * Hence, we just need to convert this set of atoms into a KeySet and turn it into a Graph.
     */
    KeySet mols_atomids;
    std::transform(iter, advanceiter, std::inserter(mols_atomids, mols_atomids.end()),
        boost::bind( &atom::getId,
            boost::bind( &clusters_t::value_type::second, _1 ))
    );
    Graph MoleculeGraph;
    MoleculeGraph.insert( make_pair(mols_atomids, NumberValuePair(1, 1.)) );

    if (TotalGraph.empty()) {
      TotalGraph = MoleculeGraph;
      keysetcounter = TotalGraph.size();
    } else
      TotalGraph.InsertGraph(MoleculeGraph, 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);

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

  {
    const enum HydrogenSaturation saturation = DontSaturate;
    const enum HydrogenTreatment treatment = IncludeHydrogen;
    const SaturatedFragment::GlobalSaturationPositions_t empty_globalsaturationpositions;
    if (params.types.get().size() != 0) {
      // store molecule's fragment to file
      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, empty_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, empty_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, empty_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();
  }

  return Action::success;
}

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

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

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

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