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 | * World.cpp
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26 | *
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27 | * Created on: Feb 3, 2010
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28 | * Author: crueger
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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 "World.hpp"
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39 |
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40 | #include <functional>
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41 |
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42 | #include "Actions/ActionTrait.hpp"
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43 | #include "Actions/ManipulateAtomsProcess.hpp"
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44 | #include "Atom/atom.hpp"
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45 | #include "Box.hpp"
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46 | #include "CodePatterns/Assert.hpp"
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47 | #include "config.hpp"
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48 | #include "Descriptors/AtomDescriptor.hpp"
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49 | #include "Descriptors/AtomDescriptor_impl.hpp"
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50 | #include "Descriptors/AtomIdDescriptor.hpp"
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51 | #include "Descriptors/AtomSelectionDescriptor.hpp"
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52 | #include "Descriptors/MoleculeDescriptor.hpp"
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53 | #include "Descriptors/MoleculeDescriptor_impl.hpp"
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54 | #include "Descriptors/MoleculeIdDescriptor.hpp"
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55 | #include "Descriptors/MoleculeSelectionDescriptor.hpp"
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56 | #include "Descriptors/SelectiveConstIterator_impl.hpp"
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57 | #include "Descriptors/SelectiveIterator_impl.hpp"
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58 | #include "Element/periodentafel.hpp"
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59 | #include "Fragmentation/Homology/HomologyContainer.hpp"
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60 | #include "Graph/BondGraph.hpp"
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61 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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62 | #include "Helpers/defs.hpp"
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63 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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64 | #include "LinkedCell/LinkedCell_Controller.hpp"
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65 | #include "LinkedCell/PointCloudAdaptor.hpp"
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66 | #include "molecule.hpp"
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67 | #include "Thermostats/ThermoStatContainer.hpp"
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68 | #include "WorldTime.hpp"
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69 |
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70 | #include "IdPool_impl.hpp"
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71 |
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72 | #include "CodePatterns/IteratorAdaptors.hpp"
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73 | #include "CodePatterns/Singleton_impl.hpp"
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74 | #include "CodePatterns/Observer/Channels.hpp"
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75 | #include "CodePatterns/Observer/ObservedContainer_impl.hpp"
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76 |
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77 | using namespace MoleCuilder;
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78 |
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79 | /******************************* Notifications ************************/
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80 |
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81 |
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82 | atom* World::_lastchangedatom = NULL;
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83 | atomId_t World::_lastchangedatomid = -1;
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84 | molecule* World::_lastchangedmol = NULL;
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85 | moleculeId_t World::_lastchangedmolid = -1;
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86 |
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87 | /******************************* getter and setter ************************/
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88 | periodentafel *&World::getPeriode()
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89 | {
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90 | return periode;
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91 | }
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92 |
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93 | BondGraph *&World::getBondGraph()
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94 | {
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95 | return BG;
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96 | }
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97 |
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98 | HomologyContainer &World::getHomologies()
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99 | {
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100 | return *homologies;
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101 | }
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102 |
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103 | void World::resetHomologies(HomologyContainer *&_homologies)
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104 | {
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105 | HomologyContainer *oldhomologies = homologies;
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106 |
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107 | // install new instance, resetting given pointer
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108 | homologies = _homologies;
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109 | _homologies = NULL;
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110 |
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111 | // delete old instance which also informs all observers
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112 | delete oldhomologies;
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113 | }
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114 |
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115 | void World::setBondGraph(BondGraph *_BG){
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116 | delete (BG);
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117 | BG = _BG;
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118 | }
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119 |
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120 | config *&World::getConfig(){
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121 | return configuration;
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122 | }
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123 |
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124 | // Atoms
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125 |
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126 | atom* World::getAtom(AtomDescriptor descriptor){
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127 | return descriptor.find();
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128 | }
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129 |
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130 | const atom* World::getAtom(AtomDescriptor descriptor) const{
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131 | return const_cast<const AtomDescriptor &>(descriptor).find();
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132 | }
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133 |
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134 | World::AtomComposite World::getAllAtoms(AtomDescriptor descriptor){
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135 | return descriptor.findAll();
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136 | }
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137 |
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138 | World::ConstAtomComposite World::getAllAtoms(AtomDescriptor descriptor) const {
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139 | return const_cast<const AtomDescriptor &>(descriptor).findAll();
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140 | }
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141 |
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142 | World::AtomComposite World::getAllAtoms(){
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143 | return getAllAtoms(AllAtoms());
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144 | }
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145 |
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146 | World::ConstAtomComposite World::getAllAtoms() const {
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147 | return getAllAtoms(AllAtoms());
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148 | }
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149 |
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150 | int World::numAtoms() const {
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151 | return atoms.size();
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152 | }
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153 |
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154 | // Molecules
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155 |
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156 | molecule *World::getMolecule(MoleculeDescriptor descriptor){
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157 | return descriptor.find();
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158 | }
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159 |
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160 | const molecule *World::getMolecule(MoleculeDescriptor descriptor) const {
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161 | return const_cast<const MoleculeDescriptor &>(descriptor).find();
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162 | }
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163 |
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164 | std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
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165 | return descriptor.findAll();
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166 | }
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167 |
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168 | std::vector<const molecule*> World::getAllMolecules(MoleculeDescriptor descriptor) const {
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169 | return const_cast<const MoleculeDescriptor &>(descriptor).findAll();
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170 | }
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171 |
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172 | std::vector<molecule*> World::getAllMolecules(){
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173 | return getAllMolecules(AllMolecules());
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174 | }
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175 |
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176 | std::vector<const molecule*> World::getAllMolecules() const {
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177 | return getAllMolecules(AllMolecules());
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178 | }
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179 |
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180 | int World::numMolecules() const {
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181 | return molecules.size();
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182 | }
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183 |
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184 | // system
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185 |
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186 | Box& World::getDomain() {
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187 | return *cell_size;
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188 | }
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189 |
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190 | void World::setDomain(const RealSpaceMatrix &mat){
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191 | OBSERVE;
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192 | *cell_size = mat;
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193 | }
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194 |
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195 | void World::setDomain(double * matrix)
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196 | {
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197 | OBSERVE;
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198 | RealSpaceMatrix M = ReturnFullMatrixforSymmetric(matrix);
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199 | cell_size->setM(M);
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200 | }
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201 |
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202 | LinkedCell::LinkedCell_View World::getLinkedCell(double distance)
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203 | {
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204 | ASSERT( distance >= 0,
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205 | "World::getLinkedCell() - distance is not positive.");
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206 | if (distance < 1.) {
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207 | ELOG(2, "Linked cell grid with length less than 1. is very memory-intense!");
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208 | distance = 1.;
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209 | }
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210 | // we have to grope past the ObservedContainer mechanism and transmorph the map
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211 | // into a traversable list for the adaptor
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212 | PointCloudAdaptor< AtomSet::set_t, MapValueIterator<AtomSet::set_t::iterator> > atomset(
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213 | &(atoms.getContent()),
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214 | std::string("WorldsAtoms"));
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215 | return LCcontroller->getView(distance, atomset);
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216 | }
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217 |
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218 | const unsigned World::getTime() const
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219 | {
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220 | return WorldTime::getTime();
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221 | }
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222 |
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223 | static bool areBondsPresent(const unsigned int _step)
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224 | {
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225 | bool status = false;
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226 |
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227 | for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
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228 | (!status) && (iter != const_cast<const World &>(World::getInstance()).atomEnd()); ++iter) {
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229 | const atom * const Walker = *iter;
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230 | status |= !Walker->getListOfBondsAtStep(_step).empty();
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231 | }
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232 |
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233 | return status;
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234 | }
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235 |
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236 | static bool areAtomsPresent(const unsigned int _step)
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237 | {
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238 | bool status = false;
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239 |
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240 | for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
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241 | (!status) && (iter != const_cast<const World &>(World::getInstance()).atomEnd()); ++iter) {
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242 | const atom * const Walker = *iter;
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243 | status |= (Walker->getTrajectorySize() >= _step);
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244 | }
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245 |
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246 | return status;
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247 | }
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248 |
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249 | static void copyBondgraph(const unsigned int _srcstep, const unsigned int _deststep)
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250 | {
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251 | // gather all bonds from _srcstep
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252 | std::set<bond *> SetOfBonds;
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253 | for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
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254 | iter != const_cast<const World &>(World::getInstance()).atomEnd(); ++iter) {
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255 | const atom * const Walker = *iter;
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256 | const BondList bonds = Walker->getListOfBondsAtStep(_srcstep);
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257 | BOOST_FOREACH( bond::ptr bondptr, bonds) {
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258 | SetOfBonds.insert(bondptr.get());
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259 | }
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260 | }
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261 | LOG(4, "DEBUG: We gathered " << SetOfBonds.size() << " bonds in total.");
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262 |
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263 | // copy bond to new time step
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264 | for (std::set<bond *>::const_iterator bonditer = SetOfBonds.begin();
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265 | bonditer != SetOfBonds.end(); ++bonditer) {
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266 | const atom * const Walker = (*bonditer)->leftatom;
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267 | const atom * const OtherWalker = (*bonditer)->rightatom;
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268 | bond::ptr const _bond =
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269 | const_cast<atom *>(Walker)->addBond(_deststep, const_cast<atom *>(OtherWalker));
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270 | _bond->setDegree((*bonditer)->getDegree());
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271 | }
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272 | }
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273 |
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274 | //static void copyAtoms(const unsigned int _srcstep, const unsigned int _deststep)
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275 | //{
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276 | // for (World::AtomIterator iter = World::getInstance().getAtomIter();
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277 | // iter != World::getInstance().atomEnd(); ++iter) {
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278 | // atom * const Walker = *iter;
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279 | // Walker->UpdateStep(_deststep);
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280 | // Walker->setPositionAtStep(_deststep, Walker->getPositionAtStep(_srcstep));
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281 | // Walker->setAtomicVelocityAtStep(_deststep, Walker->getAtomicVelocityAtStep(_srcstep));
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282 | // Walker->setAtomicForceAtStep(_deststep, Walker->getAtomicForceAtStep(_srcstep));
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283 | // }
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284 | //}
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285 |
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286 | void World::setTime(const unsigned int _step)
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287 | {
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288 | if (_step != WorldTime::getTime()) {
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289 | const unsigned int oldstep = WorldTime::getTime();
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290 |
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291 | // if (!areAtomsPresent(_step))
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292 | // copyAtoms(oldstep, _step);
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293 |
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294 | // 1. copy bond graph (such not each addBond causes GUI update)
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295 | if (!areBondsPresent(_step)) {
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296 | // AtomComposite Set = getAllAtoms();
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297 | // BG->cleanAdjacencyList(Set);
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298 | copyBondgraph(oldstep, _step);
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299 | }
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300 |
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301 | // 2. set new time
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302 | WorldTime::getInstance().setTime(_step);
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303 |
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304 | // 4. scan for connected subgraphs => molecules
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305 | DepthFirstSearchAnalysis DFS;
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306 | DFS();
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307 | DFS.UpdateMoleculeStructure();
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308 | }
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309 | }
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310 |
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311 | std::string World::getDefaultName() {
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312 | return defaultName;
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313 | }
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314 |
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315 | void World::setDefaultName(std::string name)
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316 | {
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317 | OBSERVE;
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318 | defaultName = name;
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319 | };
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320 |
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321 | class ThermoStatContainer * World::getThermostats()
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322 | {
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323 | return Thermostats;
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324 | }
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325 |
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326 |
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327 | int World::getExitFlag() {
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328 | return ExitFlag;
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329 | }
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330 |
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331 | void World::setExitFlag(int flag) {
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332 | if (ExitFlag < flag)
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333 | ExitFlag = flag;
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334 | }
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335 |
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336 | /******************** Methods to change World state *********************/
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337 |
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338 | molecule* World::createMolecule(){
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339 | OBSERVE;
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340 | molecule *mol = NULL;
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341 | mol = NewMolecule();
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342 | moleculeId_t id = moleculeIdPool.getNextId();
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343 | ASSERT(!molecules.count(id),"proposed id did not specify an unused ID");
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344 | mol->setId(id);
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345 | // store the molecule by ID
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346 | molecules[mol->getId()] = mol;
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347 | _lastchangedmol = mol;
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348 | _lastchangedmolid = mol->getId();
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349 | NOTIFY(MoleculeInserted);
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350 | return mol;
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351 | }
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352 |
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353 | molecule* World::recreateMolecule(const moleculeId_t &_id)
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354 | {
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355 | molecule *mol = NULL;
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356 | if (!molecules.count(_id)) {
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357 | OBSERVE;
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358 | mol = NewMolecule();
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359 | mol->setId(_id);
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360 | // store the molecule by ID
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361 | molecules[mol->getId()] = mol;
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362 | _lastchangedmol = mol;
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363 | _lastchangedmolid = mol->getId();
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364 | NOTIFY(MoleculeInserted);
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365 | }
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366 | return mol;
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367 | }
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368 |
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369 | void World::destroyMolecule(molecule* mol){
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370 | ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
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371 | destroyMolecule(mol->getId());
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372 | }
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373 |
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374 | void World::destroyMolecule(moleculeId_t id){
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375 | molecule *mol = molecules[id];
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376 | ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
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377 | // give notice about immediate removal
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378 | {
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379 | OBSERVE;
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380 | _lastchangedmol = mol;
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381 | _lastchangedmolid = mol->getId();
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382 | NOTIFY(MoleculeRemoved);
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383 | }
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384 | if (isMoleculeSelected(id)) {
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385 | selectedMolecules.erase(id);
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386 | NOTIFY(SelectionChanged);
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387 | }
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388 | DeleteMolecule(mol);
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389 | molecules.erase(id);
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390 | moleculeIdPool.releaseId(id);
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391 | }
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392 |
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393 | atom *World::createAtom(){
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394 | OBSERVE;
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395 | atomId_t id = atomIdPool.getNextId();
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396 | ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
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397 | atom *res = NewAtom(id);
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398 | res->setWorld(this);
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399 | // store the atom by ID
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400 | atoms[res->getId()] = res;
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401 | _lastchangedatom = res;
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402 | _lastchangedatomid = res->getId();
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403 | NOTIFY(AtomInserted);
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404 | return res;
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405 | }
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406 |
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407 | atom *World::recreateAtom(const atomId_t _id){
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408 | if (!atoms.count(_id)) {
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409 | OBSERVE;
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410 | atom *res = NewAtom(_id);
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411 | res->setWorld(this);
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412 | // store the atom by ID
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413 | atoms[res->getId()] = res;
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414 | _lastchangedatom = res;
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415 | _lastchangedatomid = res->getId();
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416 | NOTIFY(AtomInserted);
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417 | return res;
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418 | } else
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419 | return NULL;
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420 | }
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421 |
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422 |
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423 | int World::registerAtom(atom *atom){
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424 | OBSERVE;
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425 | atomId_t id = atomIdPool.getNextId();
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426 | atom->setId(id);
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427 | atom->setWorld(this);
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428 | atoms[atom->getId()] = atom;
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429 | _lastchangedatom = atom;
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430 | _lastchangedatomid = atom->getId();
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431 | NOTIFY(AtomInserted);
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432 | return atom->getId();
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433 | }
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434 |
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435 | void World::destroyAtom(atom* atom){
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436 | int id = atom->getId();
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437 | destroyAtom(id);
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438 | }
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439 |
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440 | void World::destroyAtom(atomId_t id) {
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441 | atom *atom = atoms[id];
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442 | ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
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443 | // give notice about immediate removal
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444 | {
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445 | OBSERVE;
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446 | _lastchangedatom = atom;
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447 | _lastchangedatomid = atom->getId();
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448 | NOTIFY(AtomRemoved);
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449 | }
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450 | // check if it's the last atom
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451 | molecule *_mol = const_cast<molecule *>(atom->getMolecule());
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452 | if ((_mol == NULL) || (_mol->getAtomCount() > 1))
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453 | _mol = NULL;
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454 | if (isAtomSelected(id)) {
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455 | selectedAtoms.erase(id);
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456 | NOTIFY(SelectionChanged);
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457 | }
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458 | DeleteAtom(atom);
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459 | atoms.erase(id);
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460 | atomIdPool.releaseId(id);
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461 | // remove molecule if empty
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462 | if (_mol != NULL)
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463 | destroyMolecule(_mol);
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464 | }
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465 |
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466 | bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
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467 | OBSERVE;
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468 | // in case this call did not originate from inside the atom, we redirect it,
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469 | // to also let it know that it has changed
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470 | if(!target){
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471 | target = atoms[oldId];
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472 | ASSERT(target,"Atom with that ID not found");
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473 | return target->changeId(newId);
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474 | }
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475 | else{
|
---|
476 | if(atomIdPool.reserveId(newId)){
|
---|
477 | atoms.erase(oldId);
|
---|
478 | atoms.insert(pair<atomId_t,atom*>(newId,target));
|
---|
479 | return true;
|
---|
480 | }
|
---|
481 | else{
|
---|
482 | return false;
|
---|
483 | }
|
---|
484 | }
|
---|
485 | }
|
---|
486 |
|
---|
487 | bool World::changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target){
|
---|
488 | OBSERVE;
|
---|
489 | // in case this call did not originate from inside the atom, we redirect it,
|
---|
490 | // to also let it know that it has changed
|
---|
491 | if(!target){
|
---|
492 | target = molecules[oldId];
|
---|
493 | ASSERT(target,"Molecule with that ID not found");
|
---|
494 | return target->changeId(newId);
|
---|
495 | }
|
---|
496 | else{
|
---|
497 | if(moleculeIdPool.reserveId(newId)){
|
---|
498 | molecules.erase(oldId);
|
---|
499 | molecules.insert(pair<moleculeId_t,molecule*>(newId,target));
|
---|
500 | return true;
|
---|
501 | }
|
---|
502 | else{
|
---|
503 | return false;
|
---|
504 | }
|
---|
505 | }
|
---|
506 | }
|
---|
507 |
|
---|
508 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
|
---|
509 | ActionTrait manipulateTrait(name);
|
---|
510 | return new ManipulateAtomsProcess(op, descr,manipulateTrait);
|
---|
511 | }
|
---|
512 |
|
---|
513 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
|
---|
514 | return manipulateAtoms(op,name,AllAtoms());
|
---|
515 | }
|
---|
516 |
|
---|
517 | /********************* Internal Change methods for double Callback and Observer mechanism ********/
|
---|
518 |
|
---|
519 | void World::doManipulate(ManipulateAtomsProcess *proc){
|
---|
520 | proc->signOn(this);
|
---|
521 | {
|
---|
522 | OBSERVE;
|
---|
523 | proc->doManipulate(this);
|
---|
524 | }
|
---|
525 | proc->signOff(this);
|
---|
526 | }
|
---|
527 | /******************************* Iterators ********************************/
|
---|
528 |
|
---|
529 | // external parts with observers
|
---|
530 |
|
---|
531 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor)
|
---|
532 |
|
---|
533 | CONSTRUCT_SELECTIVE_CONST_ITERATOR(atom*,World::AtomSet,AtomDescriptor)
|
---|
534 |
|
---|
535 | World::AtomIterator
|
---|
536 | World::getAtomIter(AtomDescriptor descr){
|
---|
537 | return AtomIterator(descr,atoms);
|
---|
538 | }
|
---|
539 |
|
---|
540 | World::AtomConstIterator
|
---|
541 | World::getAtomIter(AtomDescriptor descr) const{
|
---|
542 | return AtomConstIterator(descr,atoms);
|
---|
543 | }
|
---|
544 |
|
---|
545 | World::AtomIterator
|
---|
546 | World::getAtomIter(){
|
---|
547 | return AtomIterator(AllAtoms(),atoms);
|
---|
548 | }
|
---|
549 |
|
---|
550 | World::AtomConstIterator
|
---|
551 | World::getAtomIter() const{
|
---|
552 | return AtomConstIterator(AllAtoms(),atoms);
|
---|
553 | }
|
---|
554 |
|
---|
555 | World::AtomIterator
|
---|
556 | World::atomEnd(){
|
---|
557 | return AtomIterator(AllAtoms(),atoms,atoms.end());
|
---|
558 | }
|
---|
559 |
|
---|
560 | World::AtomConstIterator
|
---|
561 | World::atomEnd() const{
|
---|
562 | return AtomConstIterator(AllAtoms(),atoms,atoms.end());
|
---|
563 | }
|
---|
564 |
|
---|
565 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor)
|
---|
566 |
|
---|
567 | CONSTRUCT_SELECTIVE_CONST_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor)
|
---|
568 |
|
---|
569 | World::MoleculeIterator
|
---|
570 | World::getMoleculeIter(MoleculeDescriptor descr){
|
---|
571 | return MoleculeIterator(descr,molecules);
|
---|
572 | }
|
---|
573 |
|
---|
574 | World::MoleculeConstIterator
|
---|
575 | World::getMoleculeIter(MoleculeDescriptor descr) const{
|
---|
576 | return MoleculeConstIterator(descr,molecules);
|
---|
577 | }
|
---|
578 |
|
---|
579 | World::MoleculeIterator
|
---|
580 | World::getMoleculeIter(){
|
---|
581 | return MoleculeIterator(AllMolecules(),molecules);
|
---|
582 | }
|
---|
583 |
|
---|
584 | World::MoleculeConstIterator
|
---|
585 | World::getMoleculeIter() const{
|
---|
586 | return MoleculeConstIterator(AllMolecules(),molecules);
|
---|
587 | }
|
---|
588 |
|
---|
589 | World::MoleculeIterator
|
---|
590 | World::moleculeEnd(){
|
---|
591 | return MoleculeIterator(AllMolecules(),molecules,molecules.end());
|
---|
592 | }
|
---|
593 |
|
---|
594 | World::MoleculeConstIterator
|
---|
595 | World::moleculeEnd() const{
|
---|
596 | return MoleculeConstIterator(AllMolecules(),molecules,molecules.end());
|
---|
597 | }
|
---|
598 |
|
---|
599 | // Internal parts, without observers
|
---|
600 |
|
---|
601 | // Build the AtomIterator from template
|
---|
602 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet::set_t,AtomDescriptor);
|
---|
603 |
|
---|
604 |
|
---|
605 | World::internal_AtomIterator
|
---|
606 | World::getAtomIter_internal(AtomDescriptor descr){
|
---|
607 | return internal_AtomIterator(descr,atoms.getContent());
|
---|
608 | }
|
---|
609 |
|
---|
610 | World::internal_AtomIterator
|
---|
611 | World::atomEnd_internal(){
|
---|
612 | return internal_AtomIterator(AllAtoms(),atoms.getContent(),atoms.end_internal());
|
---|
613 | }
|
---|
614 |
|
---|
615 | // build the MoleculeIterator from template
|
---|
616 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet::set_t,MoleculeDescriptor);
|
---|
617 |
|
---|
618 | World::internal_MoleculeIterator World::getMoleculeIter_internal(MoleculeDescriptor descr){
|
---|
619 | return internal_MoleculeIterator(descr,molecules.getContent());
|
---|
620 | }
|
---|
621 |
|
---|
622 | World::internal_MoleculeIterator World::moleculeEnd_internal(){
|
---|
623 | return internal_MoleculeIterator(AllMolecules(),molecules.getContent(),molecules.end_internal());
|
---|
624 | }
|
---|
625 |
|
---|
626 | /************************** Selection of Atoms and molecules ******************/
|
---|
627 |
|
---|
628 | // translate type's selection member functions to overloaded with specific type
|
---|
629 |
|
---|
630 | template <class T>
|
---|
631 | void World::selectVectorOfInstances(const typename T::iterator _begin, const typename T::iterator _end)
|
---|
632 | {
|
---|
633 | std::for_each(_begin,_end,
|
---|
634 | boost::bind(&World::selectInstance<typename T::value_type::second_type>,
|
---|
635 | boost::bind(_take<typename T::value_type::second_type,typename T::value_type>::get, _1)));
|
---|
636 | }
|
---|
637 |
|
---|
638 | template <class T>
|
---|
639 | void World::unselectVectorOfInstances(const typename T::iterator _begin, const typename T::iterator _end)
|
---|
640 | {
|
---|
641 | std::for_each(_begin,_end,
|
---|
642 | boost::bind(&World::unselectInstance<typename T::value_type::second_type>,
|
---|
643 | boost::bind(_take<typename T::value_type::second_type,typename T::value_type>::get, _1)));
|
---|
644 | }
|
---|
645 |
|
---|
646 | // Atoms
|
---|
647 |
|
---|
648 | void World::clearAtomSelection(){
|
---|
649 | OBSERVE;
|
---|
650 | NOTIFY(SelectionChanged);
|
---|
651 | unselectVectorOfInstances<AtomSet>(selectedAtoms.begin(), selectedAtoms.end());
|
---|
652 | selectedAtoms.clear();
|
---|
653 | }
|
---|
654 |
|
---|
655 | void World::invertAtomSelection(){
|
---|
656 | // get all atoms not selected
|
---|
657 | AtomComposite invertedSelection(getAllAtoms());
|
---|
658 | bool (World::*predicate)(const atom*) const = &World::isSelected; // needed for type resolution of overloaded function
|
---|
659 | AtomComposite::iterator iter =
|
---|
660 | std::remove_if(invertedSelection.begin(), invertedSelection.end(),
|
---|
661 | std::bind1st(std::mem_fun(predicate), this));
|
---|
662 | invertedSelection.erase(iter, invertedSelection.end());
|
---|
663 | // apply new selection
|
---|
664 | unselectVectorOfInstances<AtomSet>(selectedAtoms.begin(), selectedAtoms.end());
|
---|
665 | selectedAtoms.clear();
|
---|
666 | void (World::*selector)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
|
---|
667 | std::for_each(invertedSelection.begin(),invertedSelection.end(),
|
---|
668 | std::bind1st(std::mem_fun(selector),this)); // func is select... see above
|
---|
669 | }
|
---|
670 |
|
---|
671 | void World::popAtomSelection(){
|
---|
672 | if (!selectedAtoms_Stack.empty()) {
|
---|
673 | OBSERVE;
|
---|
674 | NOTIFY(SelectionChanged);
|
---|
675 | const atomIdsVector_t atomids = selectedAtoms_Stack.top();
|
---|
676 | boost::function<void (const atomId_t)> IdSelector =
|
---|
677 | boost::bind(static_cast<void (World::*)(const atomId_t)>(&World::selectAtom), this, _1);
|
---|
678 | unselectVectorOfInstances<AtomSet>(selectedAtoms.begin(), selectedAtoms.end());
|
---|
679 | selectedAtoms.clear();
|
---|
680 | std::for_each(atomids.begin(),atomids.end(), IdSelector);
|
---|
681 | selectedAtoms_Stack.pop();
|
---|
682 | }
|
---|
683 | }
|
---|
684 |
|
---|
685 | void World::pushAtomSelection(){
|
---|
686 | OBSERVE;
|
---|
687 | NOTIFY(SelectionChanged);
|
---|
688 | atomIdsVector_t atomids(countSelectedAtoms(), (atomId_t)-1);
|
---|
689 | std::copy(
|
---|
690 | MapKeyIterator<AtomSelectionConstIterator>(beginAtomSelection()),
|
---|
691 | MapKeyIterator<AtomSelectionConstIterator>(endAtomSelection()),
|
---|
692 | atomids.begin());
|
---|
693 | selectedAtoms_Stack.push( atomids );
|
---|
694 | unselectVectorOfInstances<AtomSet>(selectedAtoms.begin(), selectedAtoms.end());
|
---|
695 | selectedAtoms.clear();
|
---|
696 | }
|
---|
697 |
|
---|
698 | void World::selectAtom(const atom *_atom){
|
---|
699 | OBSERVE;
|
---|
700 | NOTIFY(SelectionChanged);
|
---|
701 | // atom * is unchanged in this function, but we do store entity as changeable
|
---|
702 | ASSERT(_atom,"Invalid pointer in selection of atom");
|
---|
703 | selectAtom(_atom->getId());
|
---|
704 | }
|
---|
705 |
|
---|
706 | void World::selectAtom(const atomId_t id){
|
---|
707 | OBSERVE;
|
---|
708 | NOTIFY(SelectionChanged);
|
---|
709 | ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
|
---|
710 | selectedAtoms[id]=atoms[id];
|
---|
711 | atoms[id]->select();
|
---|
712 | }
|
---|
713 |
|
---|
714 | void World::selectAllAtoms(AtomDescriptor descr){
|
---|
715 | OBSERVE;
|
---|
716 | NOTIFY(SelectionChanged);
|
---|
717 | internal_AtomIterator begin = getAtomIter_internal(descr);
|
---|
718 | internal_AtomIterator end = atomEnd_internal();
|
---|
719 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
|
---|
720 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
|
---|
721 | }
|
---|
722 |
|
---|
723 | void World::selectAtomsOfMolecule(const molecule *_mol){
|
---|
724 | OBSERVE;
|
---|
725 | NOTIFY(SelectionChanged);
|
---|
726 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
|
---|
727 | // need to make it const to get the fast iterators
|
---|
728 | const molecule *mol = _mol;
|
---|
729 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
|
---|
730 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
|
---|
731 | }
|
---|
732 |
|
---|
733 | void World::selectAtomsOfMolecule(const moleculeId_t id){
|
---|
734 | OBSERVE;
|
---|
735 | NOTIFY(SelectionChanged);
|
---|
736 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
|
---|
737 | selectAtomsOfMolecule(molecules[id]);
|
---|
738 | }
|
---|
739 |
|
---|
740 | void World::unselectAtom(const atom *_atom){
|
---|
741 | OBSERVE;
|
---|
742 | NOTIFY(SelectionChanged);
|
---|
743 | ASSERT(_atom,"Invalid pointer in unselection of atom");
|
---|
744 | unselectAtom(_atom->getId());
|
---|
745 | }
|
---|
746 |
|
---|
747 | void World::unselectAtom(const atomId_t id){
|
---|
748 | OBSERVE;
|
---|
749 | NOTIFY(SelectionChanged);
|
---|
750 | ASSERT(atoms.count(id),"Atom Id unselected that was not in the world");
|
---|
751 | atoms[id]->unselect();
|
---|
752 | selectedAtoms.erase(id);
|
---|
753 | }
|
---|
754 |
|
---|
755 | void World::unselectAllAtoms(AtomDescriptor descr){
|
---|
756 | OBSERVE;
|
---|
757 | NOTIFY(SelectionChanged);
|
---|
758 | internal_AtomIterator begin = getAtomIter_internal(descr);
|
---|
759 | internal_AtomIterator end = atomEnd_internal();
|
---|
760 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
761 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
762 | }
|
---|
763 |
|
---|
764 | void World::unselectAtomsOfMolecule(const molecule *_mol){
|
---|
765 | OBSERVE;
|
---|
766 | NOTIFY(SelectionChanged);
|
---|
767 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
|
---|
768 | // need to make it const to get the fast iterators
|
---|
769 | const molecule *mol = _mol;
|
---|
770 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
771 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
772 | }
|
---|
773 |
|
---|
774 | void World::unselectAtomsOfMolecule(const moleculeId_t id){
|
---|
775 | OBSERVE;
|
---|
776 | NOTIFY(SelectionChanged);
|
---|
777 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
|
---|
778 | unselectAtomsOfMolecule(molecules[id]);
|
---|
779 | }
|
---|
780 |
|
---|
781 | size_t World::countSelectedAtoms() const {
|
---|
782 | size_t count = 0;
|
---|
783 | for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
|
---|
784 | count++;
|
---|
785 | return count;
|
---|
786 | }
|
---|
787 |
|
---|
788 | bool World::isSelected(const atom *_atom) const {
|
---|
789 | const bool status = isAtomSelected(_atom->getId());
|
---|
790 | ASSERT( status == _atom->selected,
|
---|
791 | "World::isSelected() - mismatch between selection state in atom "+
|
---|
792 | toString(_atom->getId())+" and World.");
|
---|
793 | return status;
|
---|
794 | }
|
---|
795 |
|
---|
796 | bool World::isAtomSelected(const atomId_t no) const {
|
---|
797 | return selectedAtoms.find(no) != selectedAtoms.end();
|
---|
798 | }
|
---|
799 |
|
---|
800 | std::vector<atom *> World::getSelectedAtoms() {
|
---|
801 | std::vector<atom *> returnAtoms;
|
---|
802 | std::transform(
|
---|
803 | selectedAtoms.begin(),
|
---|
804 | selectedAtoms.end(),
|
---|
805 | back_inserter(returnAtoms),
|
---|
806 | _take<atom*,World::AtomSet::value_type>::get);
|
---|
807 | return returnAtoms;
|
---|
808 | }
|
---|
809 |
|
---|
810 | std::vector<const atom *> World::getSelectedAtoms() const {
|
---|
811 | std::vector<const atom *> returnAtoms;
|
---|
812 | std::transform(
|
---|
813 | selectedAtoms.begin(),
|
---|
814 | selectedAtoms.end(),
|
---|
815 | back_inserter(returnAtoms),
|
---|
816 | _take<atom*,World::AtomSet::value_type>::get);
|
---|
817 | return returnAtoms;
|
---|
818 | }
|
---|
819 |
|
---|
820 | std::vector<atomId_t> World::getSelectedAtomIds() const {
|
---|
821 | std::vector<atomId_t> returnAtomIds;
|
---|
822 | std::transform(
|
---|
823 | selectedAtoms.begin(),
|
---|
824 | selectedAtoms.end(),
|
---|
825 | back_inserter(returnAtomIds),
|
---|
826 | _take<atom*,World::AtomSet::value_type>::getKey);
|
---|
827 | return returnAtomIds;
|
---|
828 | }
|
---|
829 |
|
---|
830 | // Molecules
|
---|
831 |
|
---|
832 | void World::clearMoleculeSelection(){
|
---|
833 | OBSERVE;
|
---|
834 | NOTIFY(SelectionChanged);
|
---|
835 | unselectVectorOfInstances<MoleculeSet>(selectedMolecules.begin(), selectedMolecules.end());
|
---|
836 | selectedMolecules.clear();
|
---|
837 | }
|
---|
838 |
|
---|
839 | void World::invertMoleculeSelection(){
|
---|
840 | // get all molecules not selected
|
---|
841 | typedef std::vector<molecule *> MoleculeVector_t;
|
---|
842 | MoleculeVector_t invertedSelection(getAllMolecules());
|
---|
843 | bool (World::*predicate)(const molecule*) const = &World::isSelected; // needed for type resolution of overloaded function
|
---|
844 | MoleculeVector_t::iterator iter =
|
---|
845 | std::remove_if(invertedSelection.begin(), invertedSelection.end(),
|
---|
846 | std::bind1st(std::mem_fun(predicate), this));
|
---|
847 | invertedSelection.erase(iter, invertedSelection.end());
|
---|
848 | // apply new selection
|
---|
849 | unselectVectorOfInstances<MoleculeSet>(selectedMolecules.begin(), selectedMolecules.end());
|
---|
850 | selectedMolecules.clear();
|
---|
851 | void (World::*selector)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
|
---|
852 | std::for_each(invertedSelection.begin(),invertedSelection.end(),
|
---|
853 | std::bind1st(std::mem_fun(selector),this)); // func is select... see above
|
---|
854 | }
|
---|
855 |
|
---|
856 | void World::popMoleculeSelection(){
|
---|
857 | if (!selectedMolecules_Stack.empty()) {
|
---|
858 | OBSERVE;
|
---|
859 | NOTIFY(SelectionChanged);
|
---|
860 | const moleculeIdsVector_t moleculeids = selectedMolecules_Stack.top();
|
---|
861 | boost::function<void (const moleculeId_t)> IdSelector =
|
---|
862 | boost::bind(static_cast<void (World::*)(const moleculeId_t)>(&World::selectMolecule), this, _1);
|
---|
863 | unselectVectorOfInstances<MoleculeSet>(selectedMolecules.begin(), selectedMolecules.end());
|
---|
864 | selectedMolecules.clear();
|
---|
865 | std::for_each(moleculeids.begin(),moleculeids.end(), IdSelector);
|
---|
866 | selectedMolecules_Stack.pop();
|
---|
867 | }
|
---|
868 | }
|
---|
869 |
|
---|
870 | void World::pushMoleculeSelection(){
|
---|
871 | OBSERVE;
|
---|
872 | NOTIFY(SelectionChanged);
|
---|
873 | moleculeIdsVector_t moleculeids(countSelectedMolecules(), (moleculeId_t)-1);
|
---|
874 | boost::function<moleculeId_t (const molecule*)> IdRetriever =
|
---|
875 | boost::bind(&molecule::getId, _1);
|
---|
876 | std::copy(
|
---|
877 | MapKeyIterator<MoleculeSelectionConstIterator>(beginMoleculeSelection()),
|
---|
878 | MapKeyIterator<MoleculeSelectionConstIterator>(endMoleculeSelection()),
|
---|
879 | moleculeids.begin());
|
---|
880 | selectedMolecules_Stack.push( moleculeids );
|
---|
881 | unselectVectorOfInstances<MoleculeSet>(selectedMolecules.begin(), selectedMolecules.end());
|
---|
882 | selectedMolecules.clear();
|
---|
883 | }
|
---|
884 |
|
---|
885 | void World::selectMolecule(const molecule *_mol){
|
---|
886 | OBSERVE;
|
---|
887 | NOTIFY(SelectionChanged);
|
---|
888 | // molecule * is unchanged in this function, but we do store entity as changeable
|
---|
889 | ASSERT(_mol,"Invalid pointer to molecule in selection");
|
---|
890 | selectMolecule(_mol->getId());
|
---|
891 | }
|
---|
892 |
|
---|
893 | void World::selectMolecule(const moleculeId_t id){
|
---|
894 | OBSERVE;
|
---|
895 | NOTIFY(SelectionChanged);
|
---|
896 | ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
|
---|
897 | molecules[id]->select();
|
---|
898 | selectedMolecules[id]=molecules[id];
|
---|
899 | }
|
---|
900 |
|
---|
901 | void World::selectAllMolecules(MoleculeDescriptor descr){
|
---|
902 | OBSERVE;
|
---|
903 | NOTIFY(SelectionChanged);
|
---|
904 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
905 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
906 | void (World::*func)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
|
---|
907 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
|
---|
908 | }
|
---|
909 |
|
---|
910 | void World::selectMoleculeOfAtom(const atom *_atom){
|
---|
911 | OBSERVE;
|
---|
912 | NOTIFY(SelectionChanged);
|
---|
913 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
914 | const molecule *mol=_atom->getMolecule();
|
---|
915 | // the atom might not be part of a molecule
|
---|
916 | if(mol){
|
---|
917 | selectMolecule(mol);
|
---|
918 | }
|
---|
919 | }
|
---|
920 |
|
---|
921 | void World::selectMoleculeOfAtom(const atomId_t id){
|
---|
922 | OBSERVE;
|
---|
923 | NOTIFY(SelectionChanged);
|
---|
924 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
925 | selectMoleculeOfAtom(atoms[id]);
|
---|
926 | }
|
---|
927 |
|
---|
928 | void World::unselectMolecule(const molecule *_mol){
|
---|
929 | OBSERVE;
|
---|
930 | NOTIFY(SelectionChanged);
|
---|
931 | ASSERT(_mol,"invalid pointer in unselection of molecule");
|
---|
932 | unselectMolecule(_mol->getId());
|
---|
933 | }
|
---|
934 |
|
---|
935 | void World::unselectMolecule(const moleculeId_t id){
|
---|
936 | OBSERVE;
|
---|
937 | NOTIFY(SelectionChanged);
|
---|
938 | ASSERT(molecules.count(id),"No such molecule with ID in unselection");
|
---|
939 | molecules[id]->unselect();
|
---|
940 | selectedMolecules.erase(id);
|
---|
941 | }
|
---|
942 |
|
---|
943 | void World::unselectAllMolecules(MoleculeDescriptor descr){
|
---|
944 | OBSERVE;
|
---|
945 | NOTIFY(SelectionChanged);
|
---|
946 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
947 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
948 | void (World::*func)(const molecule*) = &World::unselectMolecule; // needed for type resolution of overloaded function
|
---|
949 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
950 | }
|
---|
951 |
|
---|
952 | void World::unselectMoleculeOfAtom(const atom *_atom){
|
---|
953 | OBSERVE;
|
---|
954 | NOTIFY(SelectionChanged);
|
---|
955 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
956 | const molecule *mol=_atom->getMolecule();
|
---|
957 | // the atom might not be part of a molecule
|
---|
958 | if(mol){
|
---|
959 | unselectMolecule(mol);
|
---|
960 | }
|
---|
961 | }
|
---|
962 |
|
---|
963 | void World::unselectMoleculeOfAtom(const atomId_t id){
|
---|
964 | OBSERVE;
|
---|
965 | NOTIFY(SelectionChanged);
|
---|
966 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
967 | unselectMoleculeOfAtom(atoms[id]);
|
---|
968 | }
|
---|
969 |
|
---|
970 | size_t World::countSelectedMolecules() const {
|
---|
971 | size_t count = 0;
|
---|
972 | for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
|
---|
973 | count++;
|
---|
974 | return count;
|
---|
975 | }
|
---|
976 |
|
---|
977 | bool World::isSelected(const molecule *_mol) const {
|
---|
978 | const bool status = isMoleculeSelected(_mol->getId());
|
---|
979 | ASSERT( status == _mol->selected,
|
---|
980 | "World::isSelected() - mismatch in selection status between mol "+
|
---|
981 | toString(_mol->getId())+" and World.");
|
---|
982 | return status;
|
---|
983 | }
|
---|
984 |
|
---|
985 | bool World::isMoleculeSelected(const moleculeId_t no) const {
|
---|
986 | return selectedMolecules.find(no) != selectedMolecules.end();
|
---|
987 | }
|
---|
988 |
|
---|
989 | std::vector<molecule *> World::getSelectedMolecules() {
|
---|
990 | std::vector<molecule *> returnMolecules;
|
---|
991 | std::transform(
|
---|
992 | selectedMolecules.begin(),
|
---|
993 | selectedMolecules.end(),
|
---|
994 | back_inserter(returnMolecules),
|
---|
995 | _take<molecule*,World::MoleculeSet::value_type>::get);
|
---|
996 | return returnMolecules;
|
---|
997 | }
|
---|
998 |
|
---|
999 | std::vector<const molecule *> World::getSelectedMolecules() const {
|
---|
1000 | std::vector<const molecule *> returnMolecules;
|
---|
1001 | std::transform(
|
---|
1002 | selectedMolecules.begin(),
|
---|
1003 | selectedMolecules.end(),
|
---|
1004 | back_inserter(returnMolecules),
|
---|
1005 | _take<molecule*,World::MoleculeSet::value_type>::get);
|
---|
1006 | return returnMolecules;
|
---|
1007 | }
|
---|
1008 |
|
---|
1009 | std::vector<moleculeId_t> World::getSelectedMoleculeIds() const {
|
---|
1010 | std::vector<moleculeId_t> returnMoleculeIds;
|
---|
1011 | std::transform(
|
---|
1012 | selectedMolecules.begin(),
|
---|
1013 | selectedMolecules.end(),
|
---|
1014 | back_inserter(returnMoleculeIds),
|
---|
1015 | _take<molecule*,World::MoleculeSet::value_type>::getKey);
|
---|
1016 | return returnMoleculeIds;
|
---|
1017 | }
|
---|
1018 |
|
---|
1019 | /******************* Iterators over Selection *****************************/
|
---|
1020 | World::AtomSelectionIterator World::beginAtomSelection(){
|
---|
1021 | return selectedAtoms.begin();
|
---|
1022 | }
|
---|
1023 |
|
---|
1024 | World::AtomSelectionIterator World::endAtomSelection(){
|
---|
1025 | return selectedAtoms.end();
|
---|
1026 | }
|
---|
1027 |
|
---|
1028 | World::AtomSelectionConstIterator World::beginAtomSelection() const{
|
---|
1029 | return selectedAtoms.begin();
|
---|
1030 | }
|
---|
1031 |
|
---|
1032 | World::AtomSelectionConstIterator World::endAtomSelection() const{
|
---|
1033 | return selectedAtoms.end();
|
---|
1034 | }
|
---|
1035 |
|
---|
1036 |
|
---|
1037 | World::MoleculeSelectionIterator World::beginMoleculeSelection(){
|
---|
1038 | return selectedMolecules.begin();
|
---|
1039 | }
|
---|
1040 |
|
---|
1041 | World::MoleculeSelectionIterator World::endMoleculeSelection(){
|
---|
1042 | return selectedMolecules.end();
|
---|
1043 | }
|
---|
1044 |
|
---|
1045 | World::MoleculeSelectionConstIterator World::beginMoleculeSelection() const{
|
---|
1046 | return selectedMolecules.begin();
|
---|
1047 | }
|
---|
1048 |
|
---|
1049 | World::MoleculeSelectionConstIterator World::endMoleculeSelection() const{
|
---|
1050 | return selectedMolecules.end();
|
---|
1051 | }
|
---|
1052 |
|
---|
1053 | /******************************* Singleton Stuff **************************/
|
---|
1054 |
|
---|
1055 | World::World() :
|
---|
1056 | Observable("World"),
|
---|
1057 | BG(new BondGraph(true)), // assume Angstroem for the moment
|
---|
1058 | periode(new periodentafel(true)),
|
---|
1059 | configuration(new config),
|
---|
1060 | homologies(new HomologyContainer()),
|
---|
1061 | Thermostats(new ThermoStatContainer),
|
---|
1062 | ExitFlag(0),
|
---|
1063 | atoms(this),
|
---|
1064 | selectedAtoms(this),
|
---|
1065 | atomIdPool(0, 20, 100),
|
---|
1066 | molecules(this),
|
---|
1067 | selectedMolecules(this),
|
---|
1068 | moleculeIdPool(0, 20,100)
|
---|
1069 | {
|
---|
1070 | cell_size = new Box;
|
---|
1071 | RealSpaceMatrix domain;
|
---|
1072 | domain.at(0,0) = 20;
|
---|
1073 | domain.at(1,1) = 20;
|
---|
1074 | domain.at(2,2) = 20;
|
---|
1075 | cell_size->setM(domain);
|
---|
1076 | LCcontroller = new LinkedCell::LinkedCell_Controller(*cell_size);
|
---|
1077 | defaultName = "none";
|
---|
1078 | Channels *OurChannel = new Channels;
|
---|
1079 | Observable::insertNotificationChannel( std::make_pair( static_cast<Observable *>(this), OurChannel) );
|
---|
1080 | for (size_t type = 0; type < (size_t)NotificationType_MAX; ++type)
|
---|
1081 | OurChannel->addChannel(type);
|
---|
1082 | }
|
---|
1083 |
|
---|
1084 | World::~World()
|
---|
1085 | {
|
---|
1086 | delete LCcontroller;
|
---|
1087 | delete cell_size;
|
---|
1088 | MoleculeSet::iterator molIter;
|
---|
1089 | for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
|
---|
1090 | DeleteMolecule((*molIter).second);
|
---|
1091 | }
|
---|
1092 | molecules.clear();
|
---|
1093 | AtomSet::iterator atIter;
|
---|
1094 | for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
|
---|
1095 | DeleteAtom((*atIter).second);
|
---|
1096 | }
|
---|
1097 | atoms.clear();
|
---|
1098 |
|
---|
1099 | delete BG;
|
---|
1100 | delete periode;
|
---|
1101 | delete configuration;
|
---|
1102 | delete Thermostats;
|
---|
1103 | delete homologies;
|
---|
1104 | }
|
---|
1105 |
|
---|
1106 | // Explicit instantiation of the singleton mechanism at this point
|
---|
1107 |
|
---|
1108 | // moleculeId_t und atomId_t sind gleicher Basistyp, deswegen nur einen von beiden konstruieren
|
---|
1109 | CONSTRUCT_IDPOOL(atomId_t, uniqueId)
|
---|
1110 | CONSTRUCT_IDPOOL(moleculeId_t, continuousId)
|
---|
1111 |
|
---|
1112 | CONSTRUCT_SINGLETON(World)
|
---|
1113 |
|
---|
1114 | CONSTRUCT_OBSERVEDCONTAINER(World::AtomSTLSet, UnobservedIterator<World::AtomSTLSet> )
|
---|
1115 |
|
---|
1116 | CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet, UnobservedIterator<World::MoleculeSTLSet> )
|
---|