/* * Project: MoleCuilder * Description: creates and alters molecular systems * Copyright (C) 2012 University of Bonn. All rights reserved. * Please see the COPYING file or "Copyright notice" in builder.cpp for details. * * * 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 . */ /* * HomologyGraph_getFromKeyset.cpp * * Created on: Sep 25, 2012 * Author: heber */ // include config.h #ifdef HAVE_CONFIG_H #include #endif #include "CodePatterns/MemDebug.hpp" #include "Fragmentation/Homology/HomologyGraph.hpp" #include "CodePatterns/Log.hpp" #include "Atom/atom.hpp" #include "Bond/bond.hpp" #include "Descriptors/AtomIdDescriptor.hpp" #include "Fragmentation/KeySet.hpp" #include "Fragmentation/Summation/IndexSet.hpp" #include "World.hpp" // we have placed these functions into an extra module to allow compiling the // unit tests which do no require them against dummy units which do not pull // in all the cludder of World, atom, molecule, and so on ... template void addNodeToMap(S &_map, std::pair< U, size_t> _pair) { std::pair inserter = _map.insert( _pair ); if (!inserter.second) inserter.first->second += _pair.second; } template const HomologyGraph::nodes_t getNodesFromSet(const std::set &keyset) { HomologyGraph::nodes_t nodes; for (typename std::set::const_iterator iter = keyset.begin(); iter != keyset.end(); ++iter) { // LOG(2, "DEBUG: Current global id is " << *iter << "."); const atom * const Walker = const_cast(World::getInstance()). getAtom(AtomById(*iter)); if (Walker != NULL) { size_t NoBonds = 0; const BondList& ListOfBonds = Walker->getListOfBonds(); for (BondList::const_iterator bonditer = ListOfBonds.begin(); bonditer != ListOfBonds.end(); ++bonditer) { const atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker); if (keyset.count(OtherWalker->getId())) ++NoBonds; else { // add as many bonds as saturation hydrogens NoBonds += (*bonditer)->getDegree(); // add a saturation node for each, too // LOG(1, "DEBUG: Adding saturation node " << *Walker << "."); addNodeToMap(nodes, std::make_pair(FragmentNode(1, 1), (size_t)1) ); } } // LOG(1, "DEBUG: Adding node " << *Walker << " with element " // << Walker->getElementNo() << " and " << NoBonds << " bonds."); addNodeToMap(nodes, std::make_pair(FragmentNode(Walker->getElementNo(), NoBonds), (size_t)1) ); } else { ELOG(3, "Skipping id " << *iter << ", is not associated with any atom."); } } return nodes; } template const HomologyGraph::edges_t getEdgesFromSet(const std::set &keyset) { HomologyGraph::edges_t edges; for (typename std::set::const_iterator iter = keyset.begin(); iter != keyset.end(); ++iter) { // LOG(2, "DEBUG: Current global id is " << *iter << "."); const atom * const Walker = const_cast(World::getInstance()). getAtom(AtomById(*iter)); if (Walker != NULL) { const BondList& ListOfBonds = Walker->getListOfBonds(); for (BondList::const_iterator bonditer = ListOfBonds.begin(); bonditer != ListOfBonds.end(); ++bonditer) { const atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker); // LOG(1, "DEBUG: Neighbor is " << OtherWalker->getId() << "."); if (keyset.count(OtherWalker->getId())) { if (Walker->getId() < OtherWalker->getId()) { // LOG(1, "DEBUG: Adding edge " << Walker->getId() << " and " << OtherWalker->getId() << "."); addNodeToMap(edges, std::make_pair(FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()), (size_t)1) ); } } else { // also add edge for each saturation hydrogen const size_t bonddegree = (*bonditer)->getDegree(); // LOG(1, "DEBUG: Adding " << bonddegree << " saturation edge(s) " << Walker->getId() << " and " << OtherWalker->getId() << "."); addNodeToMap(edges, std::make_pair(FragmentEdge( Walker->getElementNo(), 1), bonddegree) ); } } } else { ELOG(3, "Skipping id " << *iter << ", is not associated with any atom."); } } return edges; } namespace detail { const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset) { return getNodesFromSet(keyset); } const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset) { return getNodesFromSet(keyset); } const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset) { return getEdgesFromSet(keyset); } const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset) { return getEdgesFromSet(keyset); } }; /* namespace detail */