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