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 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /*
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9 | * SubgraphDissectionAction.cpp
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10 | *
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11 | * Created on: May 9, 2010
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12 | * Author: heber
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13 | */
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | #include "CodePatterns/MemDebug.hpp"
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21 |
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22 | #include "Descriptors/AtomIdDescriptor.hpp"
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23 | #include "Descriptors/MoleculeDescriptor.hpp"
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24 |
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25 | #include "atom.hpp"
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26 | #include "Bond/bond.hpp"
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27 | #include "config.hpp"
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28 | #include "CodePatterns/Log.hpp"
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29 | #include "CodePatterns/Verbose.hpp"
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30 | #include "Graph/BondGraph.hpp"
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31 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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32 | #include "molecule.hpp"
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33 | #include "World.hpp"
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34 |
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35 | #include <iostream>
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36 | #include <string>
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37 |
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38 | typedef std::map< moleculeId_t, std::vector<atomId_t> > MolAtomList;
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39 | typedef std::map< atomId_t, atomId_t > AtomAtomList;
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40 |
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41 | #include "Actions/GraphAction/SubgraphDissectionAction.hpp"
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42 |
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43 | using namespace MoleCuilder;
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44 |
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45 | // and construct the stuff
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46 | #include "SubgraphDissectionAction.def"
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47 | #include "Action_impl_pre.hpp"
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48 | /** =========== define the function ====================== */
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49 | Action::state_ptr GraphSubgraphDissectionAction::performCall() {
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50 | // obtain information
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51 | getParametersfromValueStorage();
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52 |
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53 |
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54 | // first create stuff for undo state
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55 | LOG(0, "STATUS: Creating undo state.");
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56 | MolAtomList moleculelist;
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57 | vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
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58 | for (vector<molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
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59 | std::vector<atomId_t> atomlist;
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60 | atomlist.resize((*moliter)->size());
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61 | for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
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62 | atomlist.push_back((*atomiter)->getId());
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63 | }
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64 | moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
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65 | }
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66 | GraphSubgraphDissectionState *UndoState = new GraphSubgraphDissectionState(moleculelist, params);
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67 |
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68 | // 0a. remove all present molecules
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69 | LOG(0, "STATUS: Removing all present molecules.");
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70 | MoleculeListClass *molecules = World::getInstance().getMolecules();
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71 | for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
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72 | molecules->erase(*MolRunner);
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73 | World::getInstance().destroyMolecule(*MolRunner);
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74 | }
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75 |
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76 | // 1. create the bond structure of the single molecule
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77 | LOG(0, "STATUS: (Re-)constructing adjacency.");
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78 | BondGraph *BG = World::getInstance().getBondGraph();
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79 | World::AtomComposite Set = World::getInstance().getAllAtoms();
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80 | BG->CreateAdjacency(Set);
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81 |
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82 | // 2. scan for connected subgraphs
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83 | DepthFirstSearchAnalysis DFS;
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84 | DFS();
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85 | DFS.UpdateMoleculeStructure();
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86 | if (!World::getInstance().numMolecules()) {
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87 | //World::getInstance().destroyMolecule(mol);
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88 | DoeLog(1) && (eLog()<< Verbose(1) << "There are no molecules." << endl);
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89 | return Action::failure;
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90 | }
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91 |
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92 | DoLog(1) && (Log() << Verbose(1) << "I scanned " << World::getInstance().numMolecules() << " molecules." << endl);
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93 |
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94 | return Action::state_ptr(UndoState);
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95 | }
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96 |
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97 | Action::state_ptr GraphSubgraphDissectionAction::performUndo(Action::state_ptr _state) {
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98 | GraphSubgraphDissectionState *state = assert_cast<GraphSubgraphDissectionState*>(_state.get());
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99 |
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100 | {
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101 | // remove all present molecules
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102 | MoleculeListClass *molecules = World::getInstance().getMolecules();
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103 | vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
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104 | for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
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105 | molecules->erase(*MolRunner);
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106 | World::getInstance().destroyMolecule(*MolRunner);
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107 | }
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108 | }
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109 |
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110 | {
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111 | // construct the old state
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112 | MoleculeListClass *molecules = World::getInstance().getMolecules();
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113 | molecule *mol = NULL;
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114 | for (MolAtomList::const_iterator iter = state->moleculelist.begin(); iter != state->moleculelist.end(); ++iter) {
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115 | mol = World::getInstance().createMolecule();
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116 | if (mol->getId() != (*iter).first)
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117 | World::getInstance().changeMoleculeId(mol->getId(), (*iter).first);
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118 | for (std::vector<atomId_t>::const_iterator atomiter = (*iter).second.begin(); atomiter != (*iter).second.end(); ++atomiter) {
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119 | atom *Walker = World::getInstance().getAtom(AtomById(*atomiter));
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120 | mol->AddAtom(Walker);
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121 | }
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122 | molecules->insert(mol);
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123 | }
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124 | }
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125 |
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126 | return Action::state_ptr(_state);
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127 | }
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128 |
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129 | Action::state_ptr GraphSubgraphDissectionAction::performRedo(Action::state_ptr _state){
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130 | return performCall();
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131 | }
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132 |
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133 | bool GraphSubgraphDissectionAction::canUndo() {
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134 | return true;
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135 | }
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136 |
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137 | bool GraphSubgraphDissectionAction::shouldUndo() {
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138 | return true;
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139 | }
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140 | /** =========== end of function ====================== */
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