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) 2010-2012 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * FragmentationAction.cpp
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26 | *
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27 | * Created on: May 9, 2010
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28 | * Author: heber
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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 "Atom/atom.hpp"
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39 | #include "CodePatterns/IteratorAdaptors.hpp"
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40 | #include "CodePatterns/Log.hpp"
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41 | #include "Descriptors/AtomSelectionDescriptor.hpp"
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42 | #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
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43 | #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
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44 | #include "Fragmentation/Exporters/SaturatedBond.hpp"
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45 | #include "Fragmentation/Exporters/SaturatedFragment.hpp"
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46 | #include "Fragmentation/Exporters/SaturationDistanceMaximizer.hpp"
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47 | #include "Fragmentation/Fragmentation.hpp"
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48 | #include "Fragmentation/Graph.hpp"
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49 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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50 | #include "Fragmentation/Interfragmenter.hpp"
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51 | #include "Fragmentation/KeySetsContainer.hpp"
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52 | #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
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53 | #include "Graph/AdjacencyList.hpp"
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54 | #include "Graph/BondGraph.hpp"
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55 | #include "Graph/CyclicStructureAnalysis.hpp"
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56 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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57 | #include "Helpers/defs.hpp"
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58 | #include "molecule.hpp"
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59 | #include "World.hpp"
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60 |
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61 | #include <boost/shared_ptr.hpp>
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62 | #include <boost/filesystem.hpp>
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63 | #include <algorithm>
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64 | #include <iostream>
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65 | #include <map>
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66 | #include <string>
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67 | #include <vector>
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68 |
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69 | #include "Actions/FragmentationAction/FragmentationAction.hpp"
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70 |
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71 | using namespace MoleCuilder;
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72 |
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73 | // and construct the stuff
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74 | #include "FragmentationAction.def"
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75 | #include "Action_impl_pre.hpp"
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76 | /** =========== define the function ====================== */
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77 | ActionState::ptr FragmentationFragmentationAction::performCall() {
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78 | clock_t start,end;
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79 | int ExitFlag = -1;
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80 | World &world = World::getInstance();
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81 |
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82 | // inform about used parameters
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83 | LOG(0, "STATUS: Fragmenting molecular system with current connection matrix up to "
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84 | << params.order.get() << " order. ");
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85 | if (params.types.get().size() != 0)
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86 | LOG(0, "STATUS: Fragment files begin with "
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87 | << params.prefix.get() << " and are stored as: "
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88 | << params.types.get() << "." << std::endl);
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89 |
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90 | // check for selected atoms
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91 | if (world.beginAtomSelection() == world.endAtomSelection()) {
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92 | STATUS("There are no atoms selected for fragmentation.");
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93 | return Action::failure;
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94 | }
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95 |
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96 | // go through all atoms, note down their molecules and group them
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97 | typedef std::multimap<molecule *, atom *> clusters_t;
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98 | typedef std::vector<atomId_t> atomids_t;
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99 | atomids_t atomids;
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100 | clusters_t clusters;
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101 | for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
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102 | iter != world.endAtomSelection(); ++iter) {
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103 | clusters.insert( std::make_pair(iter->second->getMolecule(), iter->second) );
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104 | atomids.push_back(iter->second->getId());
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105 | }
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106 | {
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107 | std::vector<molecule *> molecules;
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108 | molecules.insert( molecules.end(), MapKeyIterator<clusters_t::const_iterator>(clusters.begin()),
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109 | MapKeyIterator<clusters_t::const_iterator>(clusters.end()) );
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110 | molecules.erase( std::unique(molecules.begin(), molecules.end()), molecules.end() );
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111 | LOG(1, "INFO: There are " << molecules.size() << " molecules to consider.");
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112 | }
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113 |
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114 | // parse in Adjacency file
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115 | boost::shared_ptr<AdjacencyList> FileChecker;
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116 | boost::filesystem::path filename(params.prefix.get() + std::string(ADJACENCYFILE));
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117 | if (boost::filesystem::exists(filename) && boost::filesystem::is_regular_file(filename)) {
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118 | std::ifstream File;
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119 | File.open(filename.string().c_str(), ios::out);
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120 | FileChecker.reset(new AdjacencyList(File));
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121 | File.close();
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122 | } else {
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123 | LOG(1, "INFO: Could not open default adjacency file " << filename.string() << ".");
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124 | FileChecker.reset(new AdjacencyList);
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125 | }
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126 |
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127 | // make sure bond degree is correct
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128 | {
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129 | BondGraph *BG = World::getInstance().getBondGraph();
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130 | World::AtomComposite Set = World::getInstance().getAllAtoms(AtomsBySelection());
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131 | BG->CorrectBondDegree(Set);
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132 | }
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133 |
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134 | // we parse in the keysets from last time if present
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135 | Graph StoredGraph;
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136 | StoredGraph.ParseKeySetFile(params.prefix.get());
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137 |
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138 | start = clock();
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139 | // go through all keys (i.e. all molecules)
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140 | clusters_t::const_iterator advanceiter;
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141 | Graph TotalGraph;
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142 | int keysetcounter = 0;
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143 | for (clusters_t::const_iterator iter = clusters.begin();
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144 | iter != clusters.end();
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145 | iter = advanceiter) {
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146 | // get iterator to past last atom in this molecule
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147 | molecule * mol = iter->first;
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148 | advanceiter = clusters.upper_bound(mol);
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149 |
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150 | // copy molecule's atoms' ids as parameters to Fragmentation's AtomMask
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151 | std::vector<atomId_t> mols_atomids;
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152 | std::transform(iter, advanceiter, std::back_inserter(mols_atomids),
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153 | boost::bind( &atom::getNr,
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154 | boost::bind( &clusters_t::value_type::second, _1 ))
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155 | );
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156 | LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol)
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157 | << " atoms, out of " << mol->getAtomCount() << ".");
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158 | const enum HydrogenTreatment treatment = params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
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159 | Fragmentation Fragmenter(mol, *FileChecker, treatment);
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160 |
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161 | // perform fragmentation
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162 | LOG(0, std::endl << " ========== Fragmentation of molecule " << mol->getName() << " ========================= ");
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163 | {
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164 | Graph StoredLocalGraph(StoredGraph.getLocalGraph(mol));
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165 | const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph);
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166 | if ((ExitFlag == 2) && (tempFlag != 2))
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167 | ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others
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168 | if (ExitFlag == -1)
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169 | ExitFlag = tempFlag; // if we are the first, we set the standard
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170 | }
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171 | if (TotalGraph.empty()) {
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172 | TotalGraph = Fragmenter.getGraph();
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173 | keysetcounter = TotalGraph.size();
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174 | } else
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175 | TotalGraph.InsertGraph(Fragmenter.getGraph(), keysetcounter);
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176 |
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177 | }
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178 | // add full cycles if desired
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179 | if (params.DoCyclesFull.get()) {
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180 | // get the BackEdgeStack from somewhere
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181 | DepthFirstSearchAnalysis DFS;
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182 | DFS();
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183 | std::deque<bond::ptr> BackEdgeStack = DFS.getBackEdgeStack();
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184 | // then we analyse the cycles and get them
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185 | CyclicStructureAnalysis CycleAnalysis(params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen);
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186 | CycleAnalysis(&BackEdgeStack);
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187 | CyclicStructureAnalysis::cycles_t cycles = CycleAnalysis.getAllCycles();
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188 | // sort them according to KeySet::operator<()
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189 | std::sort(cycles.begin(), cycles.end());
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190 | // store all found cycles to file
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191 | {
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192 | boost::filesystem::path filename(params.prefix.get() + std::string(CYCLEKEYSETFILE));
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193 | std::ofstream File;
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194 | LOG(1, "INFO: Storing cycle keysets to " << filename.string() << ".");
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195 | File.open(filename.string().c_str(), ios::out);
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196 | for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
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197 | iter != cycles.end(); ++iter) {
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198 | for (CyclicStructureAnalysis::cycle_t::const_iterator cycleiter = (*iter).begin();
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199 | cycleiter != (*iter).end(); ++cycleiter) {
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200 | File << *cycleiter << "\t";
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201 | }
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202 | File << "\n";
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203 | }
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204 | File.close();
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205 | }
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206 | // ... and to result container
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207 | {
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208 | KeySetsContainer cyclekeys;
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209 | for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
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210 | iter != cycles.end(); ++iter) {
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211 | const CyclicStructureAnalysis::cycle_t &cycle = *iter;
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212 | const size_t order = cycle.size();
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213 | KeySetsContainer::IntVector temp_cycle(cycle.begin(), cycle.end());
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214 | cyclekeys.insert(temp_cycle, order);
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215 | }
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216 | FragmentationResultContainer::getInstance().addCycles(cyclekeys);
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217 | }
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218 | // Create graph and insert into TotalGraph
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219 | LOG(0, "STATUS: Adding " << cycles.size() << " cycles.");
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220 | {
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221 | Graph CycleGraph;
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222 | for (CyclicStructureAnalysis::cycles_t::const_iterator iter = cycles.begin();
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223 | iter != cycles.end(); ++iter) {
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224 | const CyclicStructureAnalysis::cycle_t ¤tcycle = *iter;
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225 | LOG(2, "INFO: Inserting cycle " << currentcycle << ".");
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226 | #ifndef NDEBUG
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227 | std::pair< Graph::iterator, bool > inserter =
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228 | #endif
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229 | CycleGraph.insert( std::make_pair(currentcycle, NumberValuePair(1,1.)) );
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230 | ASSERT( inserter.second,
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231 | "FragmentationFragmentationAction::performCall() - keyset "
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232 | +toString(currentcycle)+" inserted twice into CycleGraph.");
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233 | }
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234 | TotalGraph.InsertGraph(CycleGraph, keysetcounter);
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235 | }
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236 | }
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237 |
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238 | LOG(0, "STATUS: There are " << TotalGraph.size() << " fragments.");
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239 |
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240 | {
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241 | // remove OrderAtSite file
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242 | std::string line;
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243 | std::ofstream file;
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244 | line = params.prefix.get() + ORDERATSITEFILE;
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245 | file.open(line.c_str(), std::ofstream::out | std::ofstream::trunc);
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246 | file << "";
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247 | file.close();
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248 | }
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249 |
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250 | // now add interfragments
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251 | if (params.InterOrder.get() != 0) {
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252 | LOG(0, "STATUS: Putting fragments together up to order "
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253 | << params.InterOrder.get() << " and distance of "
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254 | << params.distance.get() << ".");
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255 | Interfragmenter fragmenter(TotalGraph);
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256 | const enum HydrogenTreatment treatment = params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
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257 | fragmenter(params.InterOrder.get(), params.distance.get(), treatment);
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258 | LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
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259 | }
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260 |
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261 | // store keysets to file
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262 | {
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263 | TotalGraph.StoreKeySetFile(params.prefix.get());
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264 | }
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265 |
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266 | // create global saturation positions map
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267 | SaturatedFragment::GlobalSaturationPositions_t globalsaturationpositions;
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268 | {
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269 | // go through each atom
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270 | for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
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271 | iter != world.endAtomSelection(); ++iter) {
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272 | const atom * const _atom = iter->second;
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273 |
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274 | // skip hydrogens if treated special
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275 | const enum HydrogenTreatment treatment = params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
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276 | if ((treatment == ExcludeHydrogen) && (_atom->getType()->getAtomicNumber() == 1)) {
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277 | LOG(4, "DEBUG: Skipping hydrogen atom " << *_atom);
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278 | continue;
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279 | }
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280 |
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281 | // get the valence
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282 | unsigned int NumberOfPoints = _atom->getElement().getNoValenceOrbitals();
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283 | LOG(3, "DEBUG: There are " << NumberOfPoints
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284 | << " places to fill in in total for this atom " << *_atom << ".");
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285 |
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286 | // check whether there are any bonds with degree larger than 1
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287 | unsigned int SumOfDegrees = 0;
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288 | bool PresentHigherBonds = false;
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289 | const BondList &bondlist = _atom->getListOfBonds();
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290 | for (BondList::const_iterator bonditer = bondlist.begin();
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291 | bonditer != bondlist.end(); ++bonditer) {
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292 | SumOfDegrees += (*bonditer)->getDegree();
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293 | PresentHigherBonds |= (*bonditer)->getDegree() > 1;
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294 | }
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295 |
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296 | // check whether there are alphas to maximize the hydrogens distances
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297 | SaturationDistanceMaximizer::position_bins_t position_bins;
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298 | {
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299 | // gather all bonds and convert to SaturatedBonds
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300 | SaturationDistanceMaximizer::PositionContainers_t CutBonds;
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301 | for (BondList::const_iterator bonditer = bondlist.begin();
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302 | bonditer != bondlist.end(); ++bonditer) {
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303 | CutBonds.push_back(
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304 | SaturatedBond::ptr(new SaturatedBond(*(bonditer->get()), *_atom) )
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305 | );
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306 | }
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307 | SaturationDistanceMaximizer maximizer(CutBonds);
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308 | if (PresentHigherBonds) {
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309 | // then find best alphas
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310 | maximizer();
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311 | } else {
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312 | // if no higher order bonds, we simply gather the scaled positions
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313 | }
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314 | position_bins = maximizer.getAllPositionBins();
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315 | LOG(4, "DEBUG: Positions for atom " << *_atom << " are " << position_bins);
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316 | }
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317 |
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318 | // convert into the desired entry in the map
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319 | SaturatedFragment::SaturationsPositionsPerNeighbor_t positions_per_neighbor;
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320 | {
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321 | BondList::const_iterator bonditer = bondlist.begin();
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322 | SaturationDistanceMaximizer::position_bins_t::const_iterator biniter =
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323 | position_bins.begin();
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324 |
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325 | for (;bonditer != bondlist.end(); ++bonditer, ++biniter) {
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326 | const atom * const OtherAtom = (*bonditer)->GetOtherAtom(_atom);
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327 | std::pair<
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328 | SaturatedFragment::SaturationsPositionsPerNeighbor_t::iterator,
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329 | bool
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330 | > inserter;
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331 | // check whether we treat hydrogen special
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332 | if ((treatment == ExcludeHydrogen) && (OtherAtom->getType()->getAtomicNumber() == 1)) {
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333 | // if hydrogen, forget rescaled position and use original one
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334 | inserter =
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335 | positions_per_neighbor.insert(
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336 | std::make_pair(
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337 | OtherAtom->getId(),
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338 | SaturatedFragment::SaturationsPositions_t(
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339 | 1, OtherAtom->getPosition() - _atom->getPosition())
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340 | )
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341 | );
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342 | } else {
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343 | inserter =
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344 | positions_per_neighbor.insert(
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345 | std::make_pair(
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346 | OtherAtom->getId(),
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347 | SaturatedFragment::SaturationsPositions_t(
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348 | biniter->begin(),
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349 | biniter->end())
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350 | )
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351 | );
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352 | }
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353 | // if already pressent, add to this present list
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354 | ASSERT (inserter.second,
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355 | "FragmentationAction::performCall() - other atom "
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356 | +toString(*OtherAtom)+" already present?");
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357 | }
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358 | // bonditer follows nicely
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359 | ASSERT( biniter == position_bins.end(),
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360 | "FragmentationAction::performCall() - biniter is out of step, it still points at bond "
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361 | +toString(*biniter)+".");
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362 | }
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363 | // and insert
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364 | globalsaturationpositions.insert(
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365 | std::make_pair( _atom->getId(),
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366 | positions_per_neighbor
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367 | ));
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368 | }
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369 | }
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370 |
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371 | {
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372 | const enum HydrogenSaturation saturation = params.DoSaturation.get() ? DoSaturate : DontSaturate;
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373 | const enum HydrogenTreatment treatment = params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
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374 | if (params.types.get().size() != 0) {
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375 | // store molecule's fragment to file
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376 | ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
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377 | exporter.setPrefix(params.prefix.get());
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378 | exporter.setOutputTypes(params.types.get());
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379 | exporter();
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380 | } else {
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381 | // store molecule's fragment in FragmentJobQueue
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382 | ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
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383 | exporter.setLevel(params.level.get());
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384 | exporter();
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385 | }
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386 | }
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387 |
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388 | // store Adjacency to file
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389 | {
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390 | std::string filename = params.prefix.get() + ADJACENCYFILE;
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391 | std::ofstream AdjacencyFile;
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392 | AdjacencyFile.open(filename.c_str(), ios::out);
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393 | AdjacencyList adjacency(atomids);
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394 | adjacency.StoreToFile(AdjacencyFile);
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395 | AdjacencyFile.close();
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396 | }
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397 |
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398 | World::getInstance().setExitFlag(ExitFlag);
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399 | end = clock();
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400 | LOG(0, "STATUS: Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s.");
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401 |
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402 | return Action::success;
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403 | }
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404 |
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405 | ActionState::ptr FragmentationFragmentationAction::performUndo(ActionState::ptr _state) {
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406 | return Action::success;
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407 | }
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408 |
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409 | ActionState::ptr FragmentationFragmentationAction::performRedo(ActionState::ptr _state){
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410 | return Action::success;
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411 | }
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412 |
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413 | bool FragmentationFragmentationAction::canUndo() {
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414 | return true;
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415 | }
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416 |
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417 | bool FragmentationFragmentationAction::shouldUndo() {
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418 | return true;
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419 | }
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420 | /** =========== end of function ====================== */
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