[6afd46] | 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2017 Frederik Heber. All rights reserved.
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| 5 | *
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| 6 | *
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| 7 | * This file is part of MoleCuilder.
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| 8 | *
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| 9 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 10 | * it under the terms of the GNU General Public License as published by
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| 11 | * the Free Software Foundation, either version 2 of the License, or
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| 12 | * (at your option) any later version.
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| 13 | *
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| 14 | * MoleCuilder is distributed in the hope that it will be useful,
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| 15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 17 | * GNU General Public License for more details.
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| 18 | *
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| 19 | * You should have received a copy of the GNU General Public License
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| 20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 21 | */
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| 22 |
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| 23 | /*
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| 24 | * BoostGraphCreator.cpp
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| 25 | *
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| 26 | * Created on: May 17, 2017
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| 27 | * Author: heber
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| 28 | */
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| 29 |
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| 30 |
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| 31 | // include config.h
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| 32 | #ifdef HAVE_CONFIG_H
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| 33 | #include <config.h>
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| 34 | #endif
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| 35 |
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| 36 | //#include "CodePatterns/MemDebug.hpp"
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| 37 |
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| 38 | #include "BoostGraphCreator.hpp"
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| 39 |
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| 40 | #include <algorithm>
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| 41 | #include <iterator>
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| 42 |
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| 43 | #include "CodePatterns/Assert.hpp"
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| 44 | #include "CodePatterns/Log.hpp"
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| 45 |
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| 46 | #include "Atom/atom.hpp"
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| 47 | #include "Bond/bond.hpp"
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| 48 | #include "molecule.hpp"
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| 49 |
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| 50 | void BoostGraphCreator::createFromMolecule(
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| 51 | const molecule &_mol,
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| 52 | const predicate_t &_pred)
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| 53 | {
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| 54 | createFromRange<molecule::const_iterator>(_mol.begin(), _mol.end(), _mol.getAtomCount(), _pred);
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| 55 | }
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| 56 |
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| 57 | static bool predicateAnd(
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| 58 | const BoostGraphCreator::predicate_t &_pred1,
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| 59 | const BoostGraphCreator::predicate_t &_pred2,
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| 60 | const bond &_bond)
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| 61 | { return (_pred1(_bond) && _pred2(_bond)); }
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| 62 |
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| 63 | static atomId_t getAtomId(
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| 64 | const atom *_atom
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| 65 | )
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| 66 | { return _atom->getId(); }
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| 67 |
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| 68 | static bool inSetPredicate(
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| 69 | const std::vector<atomId_t> &_atomids,
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| 70 | const bond &_bond)
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| 71 | {
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| 72 | const atomId_t leftid = _bond.leftatom->getId();
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| 73 | const atomId_t rightid = _bond.rightatom->getId();
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| 74 | return std::binary_search(_atomids.begin(), _atomids.end(), leftid)
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| 75 | && std::binary_search(_atomids.begin(), _atomids.end(), rightid);
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| 76 | }
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| 77 |
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| 78 | void BoostGraphCreator::createFromAtoms(
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| 79 | const std::vector<atom *> &_atoms,
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| 80 | const predicate_t &_pred)
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| 81 | {
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| 82 | // sort makes binary_search possible
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| 83 | std::vector<atomId_t> atomids;
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| 84 | std::transform(_atoms.begin(), _atoms.end(),
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| 85 | std::back_inserter(atomids), getAtomId);
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| 86 | ASSERT( _atoms.size() == atomids.size(),
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[6e5907] | 87 | "BoostGraphCreator::createFromAtom() - atomids "
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| 88 | +toString(atomids.size())+" and atoms "+toString(_atoms.size())
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| 89 | +" differ in size?");
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[6afd46] | 90 | std::sort(atomids.begin(), atomids.end());
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| 91 | const predicate_t predicate = boost::bind(inSetPredicate, boost::ref(atomids), _1);
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| 92 | createFromRange<std::vector<atom *>::const_iterator>(
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| 93 | const_cast<const std::vector<atom *> &>(_atoms).begin(),
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| 94 | const_cast<const std::vector<atom *> &>(_atoms).end(),
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| 95 | _atoms.size(),
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| 96 | boost::bind(predicateAnd, _pred, predicate, _1));
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| 97 | }
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| 98 |
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[6e5907] | 99 | BoostGraphCreator::nodeId_t BoostGraphCreator::getNodeId(
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| 100 | const atomId_t &_atomid) const
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| 101 | {
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| 102 | atomids_nodeids_t::const_iterator iter =
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| 103 | atomids_nodeids.find(_atomid);
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| 104 | return (iter == atomids_nodeids.end()) ? (nodeId_t)-1 : iter->second;
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| 105 | }
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| 106 |
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[6afd46] | 107 | template <typename iterator>
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| 108 | void BoostGraphCreator::createFromRange(
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| 109 | const iterator &_begin,
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| 110 | const iterator &_end,
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| 111 | const size_t &_no_nodes,
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| 112 | const predicate_t &_pred
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[6e5907] | 113 | )
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| 114 | {
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| 115 | graph = UndirectedGraph();
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| 116 |
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| 117 | // add vertices
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| 118 | for(iterator iter = _begin; iter != _end; ++iter) {
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| 119 | const atomId_t atomid = (*iter)->getId();
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| 120 | Vertex v = boost::add_vertex(atomid, graph);
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| 121 | const atomId_t vertexname = boost::get(boost::get(boost::vertex_name, graph), v);
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| 122 | const nodeId_t vertexindex = boost::get(boost::get(boost::vertex_index, graph), v);
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| 123 | LOG(2, "DEBUG: Adding node " << vertexindex << " associated to atom #" << vertexname);
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| 124 | ASSERT( vertexname == atomid,
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| 125 | "BoostGraphCreator::createFromRange() - atomid "+toString(atomid)
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| 126 | +" is not name of vertex "+toString(vertexname)+".");
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| 127 | atomids_nodeids.insert( std::make_pair(vertexname, vertexindex) );
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| 128 | }
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| 129 |
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| 130 | // add edges
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[6afd46] | 131 | for(iterator iter = _begin; iter != _end; ++iter) {
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[6e5907] | 132 | LOG(2, "DEBUG: Looking at atom " << (*iter)->getId());
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[6afd46] | 133 | const BondList& ListOfBonds = (*iter)->getListOfBonds();
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| 134 | for(BondList::const_iterator bonditer = ListOfBonds.begin();
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| 135 | bonditer != ListOfBonds.end(); ++bonditer) {
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[6e5907] | 136 | LOG(2, "DEBUG: Looking at bond " << *(*bonditer));
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[6afd46] | 137 | const atomId_t leftid = (*bonditer)->leftatom->getId();
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[6e5907] | 138 | const nodeId_t leftnodeid = getNodeId(leftid);
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[6afd46] | 139 | const atomId_t rightid = (*bonditer)->rightatom->getId();
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[6e5907] | 140 | const nodeId_t rightnodeid = getNodeId(rightid);
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[6afd46] | 141 | // only pick each bond once and evaluate predicate
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| 142 | if ((leftid == (*iter)->getId())
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| 143 | && (_pred(**bonditer))) {
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[6e5907] | 144 | LOG(3, "DEBUG: ADDING edge " << leftnodeid << " <-> " << rightnodeid);
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| 145 | boost::add_edge(leftnodeid, rightnodeid, graph);
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[6afd46] | 146 | } else {
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[6e5907] | 147 | LOG(3, "DEBUG: Discarding edge " << leftnodeid << " <-> " << rightnodeid);
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[6afd46] | 148 | }
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| 149 | }
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| 150 | }
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| 151 | LOG(2, "DEBUG: We have " << getNumVertices() << " nodes and " << getNumEdges()
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| 152 | << " edges in the molecule graph.");
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| 153 | }
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| 154 |
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| 155 |
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