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 | /** \file molecules.cpp
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25 | *
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26 | * Functions for the class molecule.
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27 | *
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28 | */
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | #include "CodePatterns/MemDebug.hpp"
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36 |
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37 | #include <algorithm>
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38 | #include <boost/assign.hpp>
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39 | #include <boost/bind.hpp>
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40 | #include <boost/foreach.hpp>
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41 | #include <cstring>
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42 |
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43 | #include <gsl/gsl_inline.h>
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44 | #include <gsl/gsl_heapsort.h>
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45 |
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46 | #include "molecule.hpp"
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47 |
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48 | #include "Atom/atom.hpp"
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49 | #include "Bond/bond.hpp"
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50 | #include "Box.hpp"
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51 | #include "CodePatterns/enumeration.hpp"
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52 | #include "CodePatterns/Log.hpp"
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53 | #include "CodePatterns/Observer/Observable.hpp"
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54 | #include "CodePatterns/Observer/Notification.hpp"
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55 | #include "config.hpp"
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56 | #include "Descriptors/AtomIdDescriptor.hpp"
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57 | #include "Element/element.hpp"
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58 | #include "Graph/BondGraph.hpp"
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59 | #include "LinearAlgebra/Exceptions.hpp"
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60 | #include "LinearAlgebra/leastsquaremin.hpp"
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61 | #include "LinearAlgebra/Plane.hpp"
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62 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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63 | #include "LinearAlgebra/Vector.hpp"
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64 | #include "LinkedCell/linkedcell.hpp"
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65 | #include "MoleculeObserver.hpp"
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66 | #include "IdPool_impl.hpp"
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67 | #include "Shapes/BaseShapes.hpp"
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68 | #include "Tesselation/tesselation.hpp"
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69 | #include "World.hpp"
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70 | #include "WorldTime.hpp"
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71 |
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72 | using namespace boost::assign;
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73 |
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74 | // static entities
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75 | static Observable::channels_t getAtomPositionsChannels()
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76 | {
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77 | Observable::channels_t channels;
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78 | channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
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79 | return channels;
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80 | }
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81 |
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82 | /************************************* Functions for class molecule *********************************/
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83 |
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84 | /** Constructor of class molecule.
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85 | * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
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86 | */
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87 | molecule::molecule() :
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88 | Observable("molecule"),
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89 | MDSteps(0),
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90 | NoNonBonds(0),
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91 | NoCyclicBonds(0),
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92 | ActiveFlag(false),
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93 | IndexNr(-1),
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94 | NoNonHydrogen(0),
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95 | BondCount(0),
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96 | atomIdPool(1, 20, 100),
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97 | BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
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98 | _lastchangedatomid(-1),
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99 | last_atom(0),
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100 | molcenter(zeroVec),
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101 | selected(false)
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102 | {
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103 | // add specific channels
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104 | Channels *OurChannel = new Channels;
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105 | Observable::insertNotificationChannel( std::make_pair( static_cast<Observable *>(this), OurChannel) );
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106 | for (size_t type = 0; type < (size_t)NotificationType_MAX; ++type)
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107 | OurChannel->addChannel(type);
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108 |
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109 | // cannot initialize in initializer body as then channels have not been setup yet
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110 | BoundingBox.reset(
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111 | new Cacheable<BoundingBoxInfo>(
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112 | this, boost::bind(&molecule::updateBoundingBox, this), "molecule_BoundingBox", getAtomPositionsChannels()));
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113 | MoleculeCenter.reset(
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114 | new Cacheable<Vector>(
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115 | this, boost::bind(&molecule::updateMoleculeCenter, this), "molecule_center", getAtomPositionsChannels()));
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116 |
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117 | strcpy(name,World::getInstance().getDefaultName().c_str());
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118 |
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119 | // inform MoleculeObserver about new molecule
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120 | MoleculeObserver::getInstance().Inserted(this);
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121 | }
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122 |
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123 | molecule *NewMolecule(){
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124 | return new molecule();
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125 | }
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126 |
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127 | /** Destructor of class molecule.
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128 | * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
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129 | */
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130 | molecule::~molecule()
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131 | {
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132 | CleanupMolecule();
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133 |
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134 | // inform MoleculeObserver about removed molecule
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135 | MoleculeObserver::getInstance().Removed(this);
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136 | };
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137 |
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138 |
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139 | void DeleteMolecule(molecule *mol){
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140 | delete mol;
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141 | }
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142 |
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143 | // getter and setter
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144 | const std::string molecule::getName() const{
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145 | return std::string(name);
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146 | }
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147 |
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148 | int molecule::getAtomCount() const{
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149 | return atomIds.size();
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150 | }
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151 |
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152 | void molecule::setName(const std::string _name){
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153 | OBSERVE;
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154 | NOTIFY(MoleculeNameChanged);
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155 | cout << "Set name of molecule " << getId() << " to " << _name << endl;
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156 | strncpy(name,_name.c_str(),MAXSTRINGSIZE);
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157 | }
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158 |
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159 | void molecule::InsertLocalToGlobalId(atom * const pointer)
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160 | {
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161 | #ifndef NDEBUG
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162 | std::pair< LocalToGlobalId_t::iterator, bool > inserter =
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163 | #endif
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164 | LocalToGlobalId.insert( std::make_pair(pointer->getNr(), pointer) );
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165 | ASSERT( inserter.second,
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166 | "molecule::AddAtom() - local number "+toString(pointer->getNr())+" appears twice.");
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167 | }
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168 |
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169 | bool molecule::changeAtomNr(int oldNr, int newNr, atom* target){
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170 | OBSERVE;
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171 | if(atomIdPool.reserveId(newNr)){
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172 | NOTIFY(AtomNrChanged);
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173 | if (oldNr != -1) // -1 is reserved and indicates no number
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174 | atomIdPool.releaseId(oldNr);
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175 | LocalToGlobalId.erase(oldNr);
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176 | ASSERT (target,
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177 | "molecule::changeAtomNr() - given target is NULL, cannot set Nr or name.");
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178 | target->setNr(newNr);
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179 | _lastchangedatomid = target->getId();
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180 | InsertLocalToGlobalId(target);
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181 | setAtomName(target);
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182 | return true;
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183 | } else{
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184 | return false;
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185 | }
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186 | }
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187 |
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188 | bool molecule::changeAtomId(int oldId, int newId)
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189 | {
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190 | OBSERVE;
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191 | if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
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192 | return false;
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193 | atomIds.erase( oldId );
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194 | atomIds.insert( newId );
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195 | // also update BoundingBoxSweepingAxis
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196 | for (int i=0;i<NDIM;++i) {
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197 | AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(oldId);
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198 | ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
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199 | "molecule::changeAtomId() - could not find atom "+toString(oldId)
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200 | +" in BoundingBoxSweepingAxis.");
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201 | const double component = iter->second;
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202 | BoundingBoxSweepingAxis[i].left.erase(iter);
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203 | BoundingBoxSweepingAxis[i].left.insert( std::make_pair(newId, component) );
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204 | }
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205 | return true;
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206 | }
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207 |
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208 | bool molecule::changeId(moleculeId_t newId){
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209 | // first we move ourselves in the world
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210 | // the world lets us know if that succeeded
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211 | if(World::getInstance().changeMoleculeId(id,newId,this)){
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212 | OBSERVE;
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213 | NOTIFY(IndexChanged);
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214 | id = newId;
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215 | return true;
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216 | }
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217 | else{
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218 | return false;
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219 | }
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220 | }
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221 |
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222 |
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223 | moleculeId_t molecule::getId() const {
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224 | return id;
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225 | }
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226 |
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227 | void molecule::setId(moleculeId_t _id){
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228 | id =_id;
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229 | }
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230 |
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231 | const Formula &molecule::getFormula() const {
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232 | return formula;
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233 | }
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234 |
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235 | unsigned int molecule::getElementCount() const{
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236 | return formula.getElementCount();
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237 | }
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238 |
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239 | bool molecule::hasElement(const element *element) const{
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240 | return formula.hasElement(element);
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241 | }
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242 |
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243 | bool molecule::hasElement(atomicNumber_t Z) const{
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244 | return formula.hasElement(Z);
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245 | }
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246 |
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247 | bool molecule::hasElement(const string &shorthand) const{
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248 | return formula.hasElement(shorthand);
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249 | }
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250 |
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251 | /************************** Access to the List of Atoms ****************/
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252 |
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253 | molecule::const_iterator molecule::erase( const_iterator loc )
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254 | {
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255 | OBSERVE;
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256 | const_iterator iter = loc;
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257 | ++iter;
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258 | atom * const _atom = const_cast<atom *>(*loc);
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259 | {
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260 | _lastchangedatomid = _atom->getId();
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261 | NOTIFY(AtomRemoved);
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262 | }
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263 | atomIds.erase( _atom->getId() );
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264 | {
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265 | BoundingBoxInfo oldinfo = updateBoundingBox();
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266 | for (int i=0;i<NDIM;++i)
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267 | BoundingBoxSweepingAxis[i].left.erase( _atom->getId() );
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268 | BoundingBoxInfo newinfo = updateBoundingBox();
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269 | if (oldinfo != newinfo)
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270 | NOTIFY(BoundingBoxChanged);
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271 | }
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272 | {
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273 | molcenter -= _atom->getPosition();
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274 | }
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275 | {
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276 | NOTIFY(AtomNrChanged);
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277 | atomIdPool.releaseId(_atom->getNr());
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278 | LocalToGlobalId.erase(_atom->getNr());
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279 | _atom->setNr(-1);
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280 | }
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281 | _atom->removeFromMolecule();
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282 | return iter;
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283 | }
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284 |
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285 | molecule::const_iterator molecule::erase( atom * key )
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286 | {
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287 | const_iterator iter = const_cast<const molecule &>(*this).find(key);
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288 | if (iter != const_cast<const molecule &>(*this).end())
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289 | return erase(iter);
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290 | else
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291 | return iter;
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292 | }
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293 |
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294 | pair<molecule::iterator,bool> molecule::insert ( atom * const key )
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295 | {
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296 | OBSERVE;
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297 | NOTIFY(AtomInserted);
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298 | _lastchangedatomid = key->getId();
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299 | std::pair<iterator,bool> res = atomIds.insert(key->getId());
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300 | if (res.second) { // push atom if went well
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301 | {
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302 | BoundingBoxInfo oldinfo = updateBoundingBox();
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303 | for (int i=0;i<NDIM;++i)
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304 | BoundingBoxSweepingAxis[i].left.insert( std::make_pair(key->getId(), key->getPosition()[i]));
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305 | BoundingBoxInfo newinfo = updateBoundingBox();
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306 | if (oldinfo != newinfo)
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307 | NOTIFY(BoundingBoxChanged);
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308 | }
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309 | {
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310 | molcenter += key->getPosition();
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311 | }
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312 | NOTIFY(AtomNrChanged);
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313 | key->setNr(atomIdPool.getNextId());
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314 | InsertLocalToGlobalId(key);
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315 | setAtomName(key);
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316 | return res;
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317 | } else {
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318 | return pair<iterator,bool>(end(),res.second);
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319 | }
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320 | }
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321 |
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322 | void molecule::setAtomName(atom *_atom) const
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323 | {
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324 | std::stringstream sstr;
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325 | sstr << _atom->getType()->getSymbol() << _atom->getNr();
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326 | _atom->setName(sstr.str());
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327 | }
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328 |
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329 | World::AtomComposite molecule::getAtomSet()
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330 | {
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331 | World::AtomComposite vector_of_atoms;
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332 | for (molecule::iterator iter = begin(); iter != end(); ++iter)
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333 | vector_of_atoms.push_back(*iter);
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334 | return vector_of_atoms;
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335 | }
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336 |
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337 | World::ConstAtomComposite molecule::getAtomSet() const
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338 | {
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339 | World::ConstAtomComposite vector_of_atoms;
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340 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
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341 | vector_of_atoms.push_back(*iter);
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342 | return vector_of_atoms;
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343 | }
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344 |
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345 | /** Adds given atom \a *pointer from molecule list.
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346 | * Increases molecule::last_atom and gives last number to added atom and names it according to its element::abbrev and molecule::AtomCount
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347 | * \param *pointer allocated and set atom
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348 | * \return true - succeeded, false - atom not found in list
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349 | */
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350 | bool molecule::AddAtom(atom *pointer)
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351 | {
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352 | if (pointer != NULL) {
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353 | // molecule::insert() is called by setMolecule()
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354 | pointer->setMolecule(this);
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355 | }
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356 | return true;
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357 | };
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358 |
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359 | /** Adds a copy of the given atom \a *pointer from molecule list.
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360 | * Increases molecule::last_atom and gives last number to added atom.
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361 | * \param *pointer allocated and set atom
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362 | * \return pointer to the newly added atom
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363 | */
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364 | atom * molecule::AddCopyAtom(atom *pointer)
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365 | {
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366 | atom *retval = NULL;
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367 | if (pointer != NULL) {
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368 | atom *walker = pointer->clone();
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369 | AddAtom(walker);
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370 | retval=walker;
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371 | }
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372 | return retval;
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373 | };
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374 |
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375 | /** Adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
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376 | * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
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377 | * a different scheme when adding \a *replacement atom for the given one.
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378 | * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
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379 | * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
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380 | * *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
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381 | * The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
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382 | * replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
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383 | * element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
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384 | * hydrogens forming this angle with *origin.
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385 | * -# Triple Bond: The idea is to set up a tetraoid (C1-H1-H2-H3) (however the lengths \f$b\f$ of the sides of the base
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386 | * triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
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387 | * determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
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388 | * We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
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389 | * \f[ h = l \cdot \cos{\left (\frac{\alpha}{2} \right )} \qquad b = 2l \cdot \sin{\left (\frac{\alpha}{2} \right)} \quad \rightarrow \quad d = l \cdot \sqrt{\cos^2{\left (\frac{\alpha}{2} \right)}-\frac{1}{3}\cdot\sin^2{\left (\frac{\alpha}{2}\right )}}
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390 | * \f]
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391 | * vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
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392 | * the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
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393 | * The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
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394 | * the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
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395 | * \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
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396 | * \f]
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397 | * as the coordination of all three atoms in the coordinate system of these three vectors:
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398 | * \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
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399 | *
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400 | * \param *out output stream for debugging
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401 | * \param *Bond pointer to bond between \a *origin and \a *replacement
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402 | * \param *TopOrigin son of \a *origin of upper level molecule (the atom added to this molecule as a copy of \a *origin)
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403 | * \param *origin pointer to atom which acts as the origin for scaling the added hydrogen to correct bond length
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404 | * \param *replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
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405 | * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
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406 | * \return number of atoms added, if < bond::BondDegree then something went wrong
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407 | * \todo double and triple bonds splitting (always use the tetraeder angle!)
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408 | */
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409 | //bool molecule::AddHydrogenReplacementAtom(bond::ptr TopBond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem)
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410 | //{
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411 | //// Info info(__func__);
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412 | // bool AllWentWell = true; // flag gathering the boolean return value of molecule::AddAtom and other functions, as return value on exit
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413 | // double bondlength; // bond length of the bond to be replaced/cut
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414 | // double bondangle; // bond angle of the bond to be replaced/cut
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415 | // double BondRescale; // rescale value for the hydrogen bond length
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416 | // bond::ptr FirstBond;
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417 | // bond::ptr SecondBond; // Other bonds in double bond case to determine "other" plane
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418 | // atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
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419 | // double b,l,d,f,g, alpha, factors[NDIM]; // hold temporary values in triple bond case for coordination determination
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420 | // Vector Orthovector1, Orthovector2; // temporary vectors in coordination construction
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421 | // Vector InBondvector; // vector in direction of *Bond
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422 | // const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
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423 | // bond::ptr Binder;
|
---|
424 | //
|
---|
425 | // // create vector in direction of bond
|
---|
426 | // InBondvector = TopReplacement->getPosition() - TopOrigin->getPosition();
|
---|
427 | // bondlength = InBondvector.Norm();
|
---|
428 | //
|
---|
429 | // // is greater than typical bond distance? Then we have to correct periodically
|
---|
430 | // // the problem is not the H being out of the box, but InBondvector have the wrong direction
|
---|
431 | // // due to TopReplacement or Origin being on the wrong side!
|
---|
432 | // const BondGraph * const BG = World::getInstance().getBondGraph();
|
---|
433 | // const range<double> MinMaxBondDistance(
|
---|
434 | // BG->getMinMaxDistance(TopOrigin,TopReplacement));
|
---|
435 | // if (!MinMaxBondDistance.isInRange(bondlength)) {
|
---|
436 | //// LOG(4, "InBondvector is: " << InBondvector << ".");
|
---|
437 | // Orthovector1.Zero();
|
---|
438 | // for (int i=NDIM;i--;) {
|
---|
439 | // l = TopReplacement->at(i) - TopOrigin->at(i);
|
---|
440 | // if (fabs(l) > MinMaxBondDistance.last) { // is component greater than bond distance (check against min not useful here)
|
---|
441 | // Orthovector1[i] = (l < 0) ? -1. : +1.;
|
---|
442 | // } // (signs are correct, was tested!)
|
---|
443 | // }
|
---|
444 | // Orthovector1 *= matrix;
|
---|
445 | // InBondvector -= Orthovector1; // subtract just the additional translation
|
---|
446 | // bondlength = InBondvector.Norm();
|
---|
447 | //// LOG(4, "INFO: Corrected InBondvector is now: " << InBondvector << ".");
|
---|
448 | // } // periodic correction finished
|
---|
449 | //
|
---|
450 | // InBondvector.Normalize();
|
---|
451 | // // get typical bond length and store as scale factor for later
|
---|
452 | // ASSERT(TopOrigin->getType() != NULL, "AddHydrogenReplacementAtom: element of TopOrigin is not given.");
|
---|
453 | // BondRescale = TopOrigin->getType()->getHBondDistance(TopBond->getDegree()-1);
|
---|
454 | // if (BondRescale == -1) {
|
---|
455 | // ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->getDegree() << "!");
|
---|
456 | // return false;
|
---|
457 | // BondRescale = bondlength;
|
---|
458 | // } else {
|
---|
459 | // if (!IsAngstroem)
|
---|
460 | // BondRescale /= (1.*AtomicLengthToAngstroem);
|
---|
461 | // }
|
---|
462 | //
|
---|
463 | // // discern single, double and triple bonds
|
---|
464 | // switch(TopBond->getDegree()) {
|
---|
465 | // case 1:
|
---|
466 | // FirstOtherAtom = World::getInstance().createAtom(); // new atom
|
---|
467 | // FirstOtherAtom->setType(1); // element is Hydrogen
|
---|
468 | // FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
469 | // FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
470 | // if (TopReplacement->getType()->getAtomicNumber() == 1) { // neither rescale nor replace if it's already hydrogen
|
---|
471 | // FirstOtherAtom->father = TopReplacement;
|
---|
472 | // BondRescale = bondlength;
|
---|
473 | // } else {
|
---|
474 | // FirstOtherAtom->father = NULL; // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
|
---|
475 | // }
|
---|
476 | // InBondvector *= BondRescale; // rescale the distance vector to Hydrogen bond length
|
---|
477 | // FirstOtherAtom->setPosition(TopOrigin->getPosition() + InBondvector); // set coordination to origin and add distance vector to replacement atom
|
---|
478 | // AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
|
---|
479 | //// LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
480 | // Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
|
---|
481 | // Binder->Cyclic = false;
|
---|
482 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
483 | // break;
|
---|
484 | // case 2:
|
---|
485 | // {
|
---|
486 | // // determine two other bonds (warning if there are more than two other) plus valence sanity check
|
---|
487 | // const BondList& ListOfBonds = TopOrigin->getListOfBonds();
|
---|
488 | // for (BondList::const_iterator Runner = ListOfBonds.begin();
|
---|
489 | // Runner != ListOfBonds.end();
|
---|
490 | // ++Runner) {
|
---|
491 | // if ((*Runner) != TopBond) {
|
---|
492 | // if (FirstBond == NULL) {
|
---|
493 | // FirstBond = (*Runner);
|
---|
494 | // FirstOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
|
---|
495 | // } else if (SecondBond == NULL) {
|
---|
496 | // SecondBond = (*Runner);
|
---|
497 | // SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
|
---|
498 | // } else {
|
---|
499 | // ELOG(2, "Detected more than four bonds for atom " << TopOrigin->getName());
|
---|
500 | // }
|
---|
501 | // }
|
---|
502 | // }
|
---|
503 | // }
|
---|
504 | // if (SecondOtherAtom == NULL) { // then we have an atom with valence four, but only 3 bonds: one to replace and one which is TopBond (third is FirstBond)
|
---|
505 | // SecondBond = TopBond;
|
---|
506 | // SecondOtherAtom = TopReplacement;
|
---|
507 | // }
|
---|
508 | // if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
|
---|
509 | //// LOG(3, "Regarding the double bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << TopOrigin->Name << " to determine orthogonal plane.");
|
---|
510 | //
|
---|
511 | // // determine the plane of these two with the *origin
|
---|
512 | // try {
|
---|
513 | // Orthovector1 = Plane(TopOrigin->getPosition(), FirstOtherAtom->getPosition(), SecondOtherAtom->getPosition()).getNormal();
|
---|
514 | // }
|
---|
515 | // catch(LinearDependenceException &excp){
|
---|
516 | // LOG(0, boost::diagnostic_information(excp));
|
---|
517 | // // TODO: figure out what to do with the Orthovector in this case
|
---|
518 | // AllWentWell = false;
|
---|
519 | // }
|
---|
520 | // } else {
|
---|
521 | // Orthovector1.GetOneNormalVector(InBondvector);
|
---|
522 | // }
|
---|
523 | // //LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
524 | // // orthogonal vector and bond vector between origin and replacement form the new plane
|
---|
525 | // Orthovector1.MakeNormalTo(InBondvector);
|
---|
526 | // Orthovector1.Normalize();
|
---|
527 | // //LOG(3, "ReScaleCheck: " << Orthovector1.Norm() << " and " << InBondvector.Norm() << ".");
|
---|
528 | //
|
---|
529 | // // create the two Hydrogens ...
|
---|
530 | // FirstOtherAtom = World::getInstance().createAtom();
|
---|
531 | // SecondOtherAtom = World::getInstance().createAtom();
|
---|
532 | // FirstOtherAtom->setType(1);
|
---|
533 | // SecondOtherAtom->setType(1);
|
---|
534 | // FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
535 | // FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
536 | // SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
537 | // SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
538 | // FirstOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
539 | // SecondOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
540 | // bondangle = TopOrigin->getType()->getHBondAngle(1);
|
---|
541 | // if (bondangle == -1) {
|
---|
542 | // ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->getDegree() << "!");
|
---|
543 | // return false;
|
---|
544 | // bondangle = 0;
|
---|
545 | // }
|
---|
546 | // bondangle *= M_PI/180./2.;
|
---|
547 | //// LOG(3, "INFO: ReScaleCheck: InBondvector " << InBondvector << ", " << Orthovector1 << ".");
|
---|
548 | //// LOG(3, "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle));
|
---|
549 | // FirstOtherAtom->Zero();
|
---|
550 | // SecondOtherAtom->Zero();
|
---|
551 | // for(int i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondvector is bondangle = 0 direction)
|
---|
552 | // FirstOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (sin(bondangle)));
|
---|
553 | // SecondOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (-sin(bondangle)));
|
---|
554 | // }
|
---|
555 | // FirstOtherAtom->Scale(BondRescale); // rescale by correct BondDistance
|
---|
556 | // SecondOtherAtom->Scale(BondRescale);
|
---|
557 | // //LOG(3, "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << ".");
|
---|
558 | // *FirstOtherAtom += TopOrigin->getPosition();
|
---|
559 | // *SecondOtherAtom += TopOrigin->getPosition();
|
---|
560 | // // ... and add to molecule
|
---|
561 | // AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
|
---|
562 | // AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
|
---|
563 | //// LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
564 | //// LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
565 | // Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
|
---|
566 | // Binder->Cyclic = false;
|
---|
567 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
568 | // Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
|
---|
569 | // Binder->Cyclic = false;
|
---|
570 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
571 | // break;
|
---|
572 | // case 3:
|
---|
573 | // // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
|
---|
574 | // FirstOtherAtom = World::getInstance().createAtom();
|
---|
575 | // SecondOtherAtom = World::getInstance().createAtom();
|
---|
576 | // ThirdOtherAtom = World::getInstance().createAtom();
|
---|
577 | // FirstOtherAtom->setType(1);
|
---|
578 | // SecondOtherAtom->setType(1);
|
---|
579 | // ThirdOtherAtom->setType(1);
|
---|
580 | // FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
581 | // FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
582 | // SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
583 | // SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
584 | // ThirdOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
585 | // ThirdOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
586 | // FirstOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
587 | // SecondOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
588 | // ThirdOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
589 | //
|
---|
590 | // // we need to vectors orthonormal the InBondvector
|
---|
591 | // AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(InBondvector);
|
---|
592 | //// LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
593 | // try{
|
---|
594 | // Orthovector2 = Plane(InBondvector, Orthovector1,0).getNormal();
|
---|
595 | // }
|
---|
596 | // catch(LinearDependenceException &excp) {
|
---|
597 | // LOG(0, boost::diagnostic_information(excp));
|
---|
598 | // AllWentWell = false;
|
---|
599 | // }
|
---|
600 | //// LOG(3, "INFO: Orthovector2: " << Orthovector2 << ".")
|
---|
601 | //
|
---|
602 | // // create correct coordination for the three atoms
|
---|
603 | // alpha = (TopOrigin->getType()->getHBondAngle(2))/180.*M_PI/2.; // retrieve triple bond angle from database
|
---|
604 | // l = BondRescale; // desired bond length
|
---|
605 | // b = 2.*l*sin(alpha); // base length of isosceles triangle
|
---|
606 | // d = l*sqrt(cos(alpha)*cos(alpha) - sin(alpha)*sin(alpha)/3.); // length for InBondvector
|
---|
607 | // f = b/sqrt(3.); // length for Orthvector1
|
---|
608 | // g = b/2.; // length for Orthvector2
|
---|
609 | //// LOG(3, "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", ");
|
---|
610 | //// LOG(3, "The three Bond lengths: " << sqrt(d*d+f*f) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g));
|
---|
611 | // factors[0] = d;
|
---|
612 | // factors[1] = f;
|
---|
613 | // factors[2] = 0.;
|
---|
614 | // FirstOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
615 | // factors[1] = -0.5*f;
|
---|
616 | // factors[2] = g;
|
---|
617 | // SecondOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
618 | // factors[2] = -g;
|
---|
619 | // ThirdOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
620 | //
|
---|
621 | // // rescale each to correct BondDistance
|
---|
622 | //// FirstOtherAtom->x.Scale(&BondRescale);
|
---|
623 | //// SecondOtherAtom->x.Scale(&BondRescale);
|
---|
624 | //// ThirdOtherAtom->x.Scale(&BondRescale);
|
---|
625 | //
|
---|
626 | // // and relative to *origin atom
|
---|
627 | // *FirstOtherAtom += TopOrigin->getPosition();
|
---|
628 | // *SecondOtherAtom += TopOrigin->getPosition();
|
---|
629 | // *ThirdOtherAtom += TopOrigin->getPosition();
|
---|
630 | //
|
---|
631 | // // ... and add to molecule
|
---|
632 | // AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
|
---|
633 | // AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
|
---|
634 | // AllWentWell = AllWentWell && AddAtom(ThirdOtherAtom);
|
---|
635 | //// LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
636 | //// LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
637 | //// LOG(4, "INFO: Added " << *ThirdOtherAtom << " at: " << ThirdOtherAtom->x << ".");
|
---|
638 | // Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
|
---|
639 | // Binder->Cyclic = false;
|
---|
640 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
641 | // Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
|
---|
642 | // Binder->Cyclic = false;
|
---|
643 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
644 | // Binder = AddBond(BottomOrigin, ThirdOtherAtom, 1);
|
---|
645 | // Binder->Cyclic = false;
|
---|
646 | // Binder->Type = GraphEdge::TreeEdge;
|
---|
647 | // break;
|
---|
648 | // default:
|
---|
649 | // ELOG(1, "BondDegree does not state single, double or triple bond!");
|
---|
650 | // AllWentWell = false;
|
---|
651 | // break;
|
---|
652 | // }
|
---|
653 | //
|
---|
654 | // return AllWentWell;
|
---|
655 | //};
|
---|
656 |
|
---|
657 | /** Creates a copy of this molecule.
|
---|
658 | * \param offset translation Vector for the new molecule relative to old one
|
---|
659 | * \return copy of molecule
|
---|
660 | */
|
---|
661 | molecule *molecule::CopyMolecule(const Vector &offset)
|
---|
662 | {
|
---|
663 | molecule *copy = World::getInstance().createMolecule();
|
---|
664 |
|
---|
665 | // copy all atoms
|
---|
666 | std::map< const atom *, atom *> FatherFinder;
|
---|
667 | for (iterator iter = begin(); iter != end(); ++iter) {
|
---|
668 | atom * const copy_atom = copy->AddCopyAtom(*iter);
|
---|
669 | copy_atom->setPosition(copy_atom->getPosition() + offset);
|
---|
670 | FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
|
---|
671 | }
|
---|
672 |
|
---|
673 | // copy all bonds
|
---|
674 | for(const_iterator AtomRunner = const_cast<const molecule &>(*this).begin();
|
---|
675 | AtomRunner != const_cast<const molecule &>(*this).end();
|
---|
676 | ++AtomRunner) {
|
---|
677 | const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
|
---|
678 | for(BondList::const_iterator BondRunner = ListOfBonds.begin();
|
---|
679 | BondRunner != ListOfBonds.end();
|
---|
680 | ++BondRunner)
|
---|
681 | if ((*BondRunner)->leftatom == *AtomRunner) {
|
---|
682 | bond::ptr Binder = (*BondRunner);
|
---|
683 | // get the pendant atoms of current bond in the copy molecule
|
---|
684 | ASSERT(FatherFinder.count(Binder->leftatom),
|
---|
685 | "molecule::CopyMolecule() - No copy of original left atom "
|
---|
686 | +toString(Binder->leftatom)+" for bond copy found");
|
---|
687 | ASSERT(FatherFinder.count(Binder->rightatom),
|
---|
688 | "molecule::CopyMolecule() - No copy of original right atom "
|
---|
689 | +toString(Binder->rightatom)+" for bond copy found");
|
---|
690 | atom * const LeftAtom = FatherFinder[Binder->leftatom];
|
---|
691 | atom * const RightAtom = FatherFinder[Binder->rightatom];
|
---|
692 |
|
---|
693 | bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->getDegree());
|
---|
694 | NewBond->Cyclic = Binder->Cyclic;
|
---|
695 | if (Binder->Cyclic)
|
---|
696 | copy->NoCyclicBonds++;
|
---|
697 | NewBond->Type = Binder->Type;
|
---|
698 | }
|
---|
699 | }
|
---|
700 | // correct fathers
|
---|
701 | //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
|
---|
702 |
|
---|
703 | return copy;
|
---|
704 | };
|
---|
705 |
|
---|
706 |
|
---|
707 | /** Destroys all atoms inside this molecule.
|
---|
708 | */
|
---|
709 | void removeAtomsinMolecule(molecule *&_mol)
|
---|
710 | {
|
---|
711 | // copy list of atoms from molecule as it will be changed
|
---|
712 | std::vector<atom *> atoms;
|
---|
713 | atoms.resize(_mol->getAtomCount(), NULL);
|
---|
714 | std::copy(_mol->begin(), _mol->end(), atoms.begin());
|
---|
715 | // remove each atom from world
|
---|
716 | for(std::vector<atom *>::iterator AtomRunner = atoms.begin();
|
---|
717 | AtomRunner != atoms.end(); ++AtomRunner)
|
---|
718 | World::getInstance().destroyAtom(*AtomRunner);
|
---|
719 | // make sure that pointer os not usable
|
---|
720 | _mol = NULL;
|
---|
721 | };
|
---|
722 |
|
---|
723 |
|
---|
724 | /**
|
---|
725 | * Copies all atoms of a molecule which are within the defined parallelepiped.
|
---|
726 | *
|
---|
727 | * @param offest for the origin of the parallelepiped
|
---|
728 | * @param three vectors forming the matrix that defines the shape of the parallelpiped
|
---|
729 | */
|
---|
730 | molecule* molecule::CopyMoleculeFromSubRegion(const Shape ®ion) {
|
---|
731 | molecule *copy = World::getInstance().createMolecule();
|
---|
732 |
|
---|
733 | // copy all atoms
|
---|
734 | std::map< const atom *, atom *> FatherFinder;
|
---|
735 | for (iterator iter = begin(); iter != end(); ++iter) {
|
---|
736 | if (region.isInside((*iter)->getPosition())) {
|
---|
737 | atom * const copy_atom = copy->AddCopyAtom(*iter);
|
---|
738 | FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
|
---|
739 | }
|
---|
740 | }
|
---|
741 |
|
---|
742 | // copy all bonds
|
---|
743 | for(molecule::const_iterator AtomRunner = const_cast<const molecule &>(*this).begin();
|
---|
744 | AtomRunner != const_cast<const molecule &>(*this).end();
|
---|
745 | ++AtomRunner) {
|
---|
746 | const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
|
---|
747 | for(BondList::const_iterator BondRunner = ListOfBonds.begin();
|
---|
748 | BondRunner != ListOfBonds.end();
|
---|
749 | ++BondRunner)
|
---|
750 | if ((*BondRunner)->leftatom == *AtomRunner) {
|
---|
751 | bond::ptr Binder = (*BondRunner);
|
---|
752 | if ((FatherFinder.count(Binder->leftatom))
|
---|
753 | && (FatherFinder.count(Binder->rightatom))) {
|
---|
754 | // if copy present, then it must be from subregion
|
---|
755 | atom * const LeftAtom = FatherFinder[Binder->leftatom];
|
---|
756 | atom * const RightAtom = FatherFinder[Binder->rightatom];
|
---|
757 |
|
---|
758 | bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->getDegree());
|
---|
759 | NewBond->Cyclic = Binder->Cyclic;
|
---|
760 | if (Binder->Cyclic)
|
---|
761 | copy->NoCyclicBonds++;
|
---|
762 | NewBond->Type = Binder->Type;
|
---|
763 | }
|
---|
764 | }
|
---|
765 | }
|
---|
766 | // correct fathers
|
---|
767 | //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
|
---|
768 |
|
---|
769 | //TODO: copy->BuildInducedSubgraph(this);
|
---|
770 |
|
---|
771 | return copy;
|
---|
772 | }
|
---|
773 |
|
---|
774 | /** Adds a bond to a the molecule specified by two atoms, \a *first and \a *second.
|
---|
775 | * Also updates molecule::BondCount and molecule::NoNonBonds.
|
---|
776 | * \param *first first atom in bond
|
---|
777 | * \param *second atom in bond
|
---|
778 | * \return pointer to bond or NULL on failure
|
---|
779 | */
|
---|
780 | bond::ptr molecule::AddBond(atom *atom1, atom *atom2, int degree)
|
---|
781 | {
|
---|
782 | bond::ptr Binder;
|
---|
783 |
|
---|
784 | // some checks to make sure we are able to create the bond
|
---|
785 | ASSERT(atom1,
|
---|
786 | "molecule::AddBond() - First atom "+toString(atom1)
|
---|
787 | +" is not a invalid pointer");
|
---|
788 | ASSERT(atom2,
|
---|
789 | "molecule::AddBond() - Second atom "+toString(atom2)
|
---|
790 | +" is not a invalid pointer");
|
---|
791 | ASSERT(isInMolecule(atom1),
|
---|
792 | "molecule::AddBond() - First atom "+toString(atom1)
|
---|
793 | +" is not part of molecule");
|
---|
794 | ASSERT(isInMolecule(atom2),
|
---|
795 | "molecule::AddBond() - Second atom "+toString(atom2)
|
---|
796 | +" is not part of molecule");
|
---|
797 |
|
---|
798 | Binder.reset(new bond(atom1, atom2, degree));
|
---|
799 | atom1->RegisterBond(WorldTime::getTime(), Binder);
|
---|
800 | atom2->RegisterBond(WorldTime::getTime(), Binder);
|
---|
801 | if ((atom1->getType() != NULL)
|
---|
802 | && (atom1->getType()->getAtomicNumber() != 1)
|
---|
803 | && (atom2->getType() != NULL)
|
---|
804 | && (atom2->getType()->getAtomicNumber() != 1))
|
---|
805 | NoNonBonds++;
|
---|
806 |
|
---|
807 | return Binder;
|
---|
808 | };
|
---|
809 |
|
---|
810 | /** Set molecule::name from the basename without suffix in the given \a *filename.
|
---|
811 | * \param *filename filename
|
---|
812 | */
|
---|
813 | void molecule::SetNameFromFilename(const char *filename)
|
---|
814 | {
|
---|
815 | OBSERVE;
|
---|
816 | NOTIFY(MoleculeNameChanged);
|
---|
817 | int length = 0;
|
---|
818 | const char *molname = strrchr(filename, '/');
|
---|
819 | if (molname != NULL)
|
---|
820 | molname += sizeof(char); // search for filename without dirs
|
---|
821 | else
|
---|
822 | molname = filename; // contains no slashes
|
---|
823 | const char *endname = strchr(molname, '.');
|
---|
824 | if ((endname == NULL) || (endname < molname))
|
---|
825 | length = strlen(molname);
|
---|
826 | else
|
---|
827 | length = strlen(molname) - strlen(endname);
|
---|
828 | cout << "Set name of molecule " << getId() << " to " << molname << endl;
|
---|
829 | strncpy(name, molname, length);
|
---|
830 | name[length]='\0';
|
---|
831 | };
|
---|
832 |
|
---|
833 | /** Removes atom from molecule list, but does not delete it.
|
---|
834 | * \param *pointer atom to be removed
|
---|
835 | * \return true - succeeded, false - atom not found in list
|
---|
836 | */
|
---|
837 | bool molecule::UnlinkAtom(atom *pointer)
|
---|
838 | {
|
---|
839 | if (pointer == NULL)
|
---|
840 | return false;
|
---|
841 | pointer->removeFromMolecule();
|
---|
842 | return true;
|
---|
843 | };
|
---|
844 |
|
---|
845 | /** Removes every atom from molecule list.
|
---|
846 | * \return true - succeeded, false - atom not found in list
|
---|
847 | */
|
---|
848 | bool molecule::CleanupMolecule()
|
---|
849 | {
|
---|
850 | for (molecule::iterator iter = begin(); !empty(); iter = begin())
|
---|
851 | (*iter)->removeFromMolecule();
|
---|
852 | return empty();
|
---|
853 | };
|
---|
854 |
|
---|
855 | /** Finds an atom specified by its continuous number.
|
---|
856 | * \param Nr number of atom withim molecule
|
---|
857 | * \return pointer to atom or NULL
|
---|
858 | */
|
---|
859 | atom * molecule::FindAtom(int Nr) const
|
---|
860 | {
|
---|
861 | LocalToGlobalId_t::const_iterator iter = LocalToGlobalId.find(Nr);
|
---|
862 | if (iter != LocalToGlobalId.end()) {
|
---|
863 | //LOG(0, "Found Atom Nr. " << walker->getNr());
|
---|
864 | return iter->second;
|
---|
865 | } else {
|
---|
866 | ELOG(1, "Atom with Nr " << Nr << " not found in molecule " << getName() << "'s list.");
|
---|
867 | return NULL;
|
---|
868 | }
|
---|
869 | }
|
---|
870 |
|
---|
871 | /** Checks whether the given atom is a member of this molecule.
|
---|
872 | *
|
---|
873 | * We make use here of molecule::atomIds to get a result on
|
---|
874 | *
|
---|
875 | * @param _atom atom to check
|
---|
876 | * @return true - is member, false - is not
|
---|
877 | */
|
---|
878 | bool molecule::isInMolecule(const atom * const _atom) const
|
---|
879 | {
|
---|
880 | ASSERT(_atom->getMolecule() == this,
|
---|
881 | "molecule::isInMolecule() - atom is not designated to be in molecule '"
|
---|
882 | +toString(this->getName())+"'.");
|
---|
883 | molecule::const_iterator iter = atomIds.find(_atom->getId());
|
---|
884 | return (iter != atomIds.end());
|
---|
885 | }
|
---|
886 |
|
---|
887 | /** Asks for atom number, and checks whether in list.
|
---|
888 | * \param *text question before entering
|
---|
889 | */
|
---|
890 | atom * molecule::AskAtom(std::string text)
|
---|
891 | {
|
---|
892 | int No;
|
---|
893 | atom *ion = NULL;
|
---|
894 | do {
|
---|
895 | //std::cout << "============Atom list==========================" << std::endl;
|
---|
896 | //mol->Output((ofstream *)&cout);
|
---|
897 | //std::cout << "===============================================" << std::endl;
|
---|
898 | std::cout << text;
|
---|
899 | cin >> No;
|
---|
900 | ion = this->FindAtom(No);
|
---|
901 | } while (ion == NULL);
|
---|
902 | return ion;
|
---|
903 | };
|
---|
904 |
|
---|
905 | /** Checks if given coordinates are within cell volume.
|
---|
906 | * \param *x array of coordinates
|
---|
907 | * \return true - is within, false - out of cell
|
---|
908 | */
|
---|
909 | bool molecule::CheckBounds(const Vector *x) const
|
---|
910 | {
|
---|
911 | const RealSpaceMatrix &domain = World::getInstance().getDomain().getM();
|
---|
912 | bool result = true;
|
---|
913 | for (int i=0;i<NDIM;i++) {
|
---|
914 | result = result && ((x->at(i) >= 0) && (x->at(i) < domain.at(i,i)));
|
---|
915 | }
|
---|
916 | //return result;
|
---|
917 | return true; /// probably not gonna use the check no more
|
---|
918 | };
|
---|
919 |
|
---|
920 | /** Prints molecule to *out.
|
---|
921 | * \param *out output stream
|
---|
922 | */
|
---|
923 | bool molecule::Output(ostream * const output) const
|
---|
924 | {
|
---|
925 | if (output == NULL) {
|
---|
926 | return false;
|
---|
927 | } else {
|
---|
928 | int AtomNo[MAX_ELEMENTS];
|
---|
929 | memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
|
---|
930 | enumeration<const element*> elementLookup = formula.enumerateElements();
|
---|
931 | *output << "#Ion_TypeNr._Nr.R[0] R[1] R[2] MoveType (0 MoveIon, 1 FixedIon)" << endl;
|
---|
932 | for_each(begin(),end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
|
---|
933 | return true;
|
---|
934 | }
|
---|
935 | };
|
---|
936 |
|
---|
937 | /** Outputs contents of each atom::ListOfBonds.
|
---|
938 | * \param *out output stream
|
---|
939 | */
|
---|
940 | void molecule::OutputListOfBonds() const
|
---|
941 | {
|
---|
942 | std::stringstream output;
|
---|
943 | LOG(2, "From Contents of ListOfBonds, all atoms:");
|
---|
944 | for (molecule::const_iterator iter = begin();
|
---|
945 | iter != end();
|
---|
946 | ++iter) {
|
---|
947 | (*iter)->OutputBondOfAtom(output);
|
---|
948 | output << std::endl << "\t\t";
|
---|
949 | }
|
---|
950 | LOG(2, output.str());
|
---|
951 | }
|
---|
952 |
|
---|
953 | /** Returns an index map for two father-son-molecules.
|
---|
954 | * The map tells which atom in this molecule corresponds to which one in the other molecul with their fathers.
|
---|
955 | * \param *out output stream for debugging
|
---|
956 | * \param *OtherMolecule corresponding molecule with fathers
|
---|
957 | * \return allocated map of size molecule::AtomCount with map
|
---|
958 | * \todo make this with a good sort O(n), not O(n^2)
|
---|
959 | */
|
---|
960 | int * molecule::GetFatherSonAtomicMap(const molecule * const OtherMolecule)
|
---|
961 | {
|
---|
962 | LOG(3, "Begin of GetFatherAtomicMap.");
|
---|
963 | int *AtomicMap = new int[getAtomCount()];
|
---|
964 | for (int i=getAtomCount();i--;)
|
---|
965 | AtomicMap[i] = -1;
|
---|
966 | if (OtherMolecule == this) { // same molecule
|
---|
967 | for (int i=getAtomCount();i--;) // no need as -1 means already that there is trivial correspondence
|
---|
968 | AtomicMap[i] = i;
|
---|
969 | LOG(4, "Map is trivial.");
|
---|
970 | } else {
|
---|
971 | std::stringstream output;
|
---|
972 | output << "Map is ";
|
---|
973 | for (molecule::const_iterator iter = const_cast<const molecule &>(*this).begin();
|
---|
974 | iter != const_cast<const molecule &>(*this).end();
|
---|
975 | ++iter) {
|
---|
976 | if ((*iter)->getFather() == NULL) {
|
---|
977 | AtomicMap[(*iter)->getNr()] = -2;
|
---|
978 | } else {
|
---|
979 | for (molecule::const_iterator runner = OtherMolecule->begin(); runner != OtherMolecule->end(); ++runner) {
|
---|
980 | //for (int i=0;i<AtomCount;i++) { // search atom
|
---|
981 | //for (int j=0;j<OtherMolecule->getAtomCount();j++) {
|
---|
982 | //LOG(4, "Comparing father " << (*iter)->getFather() << " with the other one " << (*runner)->getFather() << ".");
|
---|
983 | if ((*iter)->getFather() == (*runner))
|
---|
984 | AtomicMap[(*iter)->getNr()] = (*runner)->getNr();
|
---|
985 | }
|
---|
986 | }
|
---|
987 | output << AtomicMap[(*iter)->getNr()] << "\t";
|
---|
988 | }
|
---|
989 | LOG(4, output.str());
|
---|
990 | }
|
---|
991 | LOG(3, "End of GetFatherAtomicMap.");
|
---|
992 | return AtomicMap;
|
---|
993 | };
|
---|
994 |
|
---|
995 |
|
---|
996 | void molecule::flipActiveFlag(){
|
---|
997 | ActiveFlag = !ActiveFlag;
|
---|
998 | }
|
---|
999 |
|
---|
1000 | Shape molecule::getBoundingShape(const double scale) const
|
---|
1001 | {
|
---|
1002 | // create Sphere around every atom
|
---|
1003 | if (empty())
|
---|
1004 | return Nowhere();
|
---|
1005 | const_iterator iter = begin();
|
---|
1006 | const Vector center = (*iter)->getPosition();
|
---|
1007 | const double vdWRadius = (*iter)->getElement().getVanDerWaalsRadius();
|
---|
1008 | Shape BoundingShape = Sphere(center, vdWRadius*scale);
|
---|
1009 | for(++iter; iter != end(); ++iter) {
|
---|
1010 | const Vector center = (*iter)->getPosition();
|
---|
1011 | const double vdWRadius = (*iter)->getElement().getVanDerWaalsRadius();
|
---|
1012 | if (vdWRadius*scale != 0.)
|
---|
1013 | BoundingShape = Sphere(center, vdWRadius*scale) || BoundingShape;
|
---|
1014 | }
|
---|
1015 | return BoundingShape;
|
---|
1016 | }
|
---|
1017 |
|
---|
1018 | Shape molecule::getBoundingSphere(const double boundary) const
|
---|
1019 | {
|
---|
1020 | // get center and radius
|
---|
1021 | Vector center;
|
---|
1022 | double radius = 0.;
|
---|
1023 | {
|
---|
1024 | center.Zero();
|
---|
1025 | for(const_iterator iter = begin(); iter != end(); ++iter)
|
---|
1026 | center += (*iter)->getPosition();
|
---|
1027 | if (begin() != end())
|
---|
1028 | center *= 1./(double)size();
|
---|
1029 | for(const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
1030 | const Vector &position = (*iter)->getPosition();
|
---|
1031 | const double temp_distance = position.DistanceSquared(center);
|
---|
1032 | if (temp_distance > radius)
|
---|
1033 | radius = temp_distance;
|
---|
1034 | }
|
---|
1035 | }
|
---|
1036 | // convert radius to true value and add some small boundary
|
---|
1037 | radius = sqrt(radius) + boundary + 1e+6*std::numeric_limits<double>::epsilon();
|
---|
1038 | LOG(1, "INFO: The " << size() << " atoms of the molecule are contained in a sphere at "
|
---|
1039 | << center << " with radius " << radius << ".");
|
---|
1040 |
|
---|
1041 | // TODO: When we do not use a Sphere here anymore, then FillRegularGridAction will
|
---|
1042 | // will not work as it expects a sphere due to possible random rotations.
|
---|
1043 | Shape BoundingShape(Sphere(center, radius));
|
---|
1044 | LOG(1, "INFO: Created sphere at " << BoundingShape.getCenter() << " and radius "
|
---|
1045 | << BoundingShape.getRadius() << ".");
|
---|
1046 | return BoundingShape;
|
---|
1047 | }
|
---|
1048 |
|
---|
1049 | molecule::BoundingBoxInfo molecule::updateBoundingBox() const
|
---|
1050 | {
|
---|
1051 | BoundingBoxInfo info;
|
---|
1052 | Vector min = zeroVec;
|
---|
1053 | Vector max = zeroVec;
|
---|
1054 | for (int i=0;i<NDIM;++i) {
|
---|
1055 | if (!BoundingBoxSweepingAxis[i].right.empty()) {
|
---|
1056 | min[i] = BoundingBoxSweepingAxis[i].right.begin()->first;
|
---|
1057 | max[i] = BoundingBoxSweepingAxis[i].right.rbegin()->first;
|
---|
1058 | }
|
---|
1059 | }
|
---|
1060 | info.radius = (.5*(max-min)).Norm();
|
---|
1061 | info.position = .5*(max+min);
|
---|
1062 | return info;
|
---|
1063 | }
|
---|
1064 |
|
---|
1065 | Vector molecule::updateMoleculeCenter() const
|
---|
1066 | {
|
---|
1067 | return (1./(double)getAtomCount())*molcenter;
|
---|
1068 | }
|
---|
1069 |
|
---|
1070 | molecule::BoundingBoxInfo molecule::getBoundingBox() const
|
---|
1071 | {
|
---|
1072 | return **BoundingBox;
|
---|
1073 | }
|
---|
1074 |
|
---|
1075 | Vector molecule::getMoleculeCenter() const
|
---|
1076 | {
|
---|
1077 | return **MoleculeCenter;
|
---|
1078 | }
|
---|
1079 |
|
---|
1080 | void molecule::update(Observable *publisher)
|
---|
1081 | {
|
---|
1082 | ASSERT(0, "molecule::update() - did not sign on for any general updates.");
|
---|
1083 | }
|
---|
1084 |
|
---|
1085 | void molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
|
---|
1086 | {
|
---|
1087 | const atom * const _atom = dynamic_cast<atom *>(publisher);
|
---|
1088 | if ((_atom != NULL) && containsAtom(_atom)) {
|
---|
1089 | #ifdef LOG_OBSERVER
|
---|
1090 | observerLog().addMessage() << "++ Update of Observer "<< observerLog().getName(static_cast<Observer *>(this))
|
---|
1091 | << " received notification from atom " << _atom->getId() << " for channel "
|
---|
1092 | << notification->getChannelNo() << ".";
|
---|
1093 | #endif
|
---|
1094 | switch (notification->getChannelNo()) {
|
---|
1095 | case AtomObservable::PositionChanged:
|
---|
1096 | {
|
---|
1097 | // emit others about one of our atoms moved
|
---|
1098 | _lastchangedatomid = _atom->getId();
|
---|
1099 | // update entry in map and also molecule center
|
---|
1100 | BoundingBoxInfo oldinfo = updateBoundingBox();
|
---|
1101 | for (int i=0;i<NDIM;++i) {
|
---|
1102 | AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(_atom->getId());
|
---|
1103 | ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
|
---|
1104 | "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
|
---|
1105 | +" in BoundingBoxSweepingAxis.");
|
---|
1106 | molcenter[i] -= iter->second;
|
---|
1107 | BoundingBoxSweepingAxis[i].left.erase(iter);
|
---|
1108 | const Vector &position = _atom->getPosition();
|
---|
1109 | BoundingBoxSweepingAxis[i].left.insert(
|
---|
1110 | std::make_pair(_atom->getId(), position[i]) );
|
---|
1111 | molcenter[i] += position[i];
|
---|
1112 | }
|
---|
1113 | BoundingBoxInfo newinfo = updateBoundingBox();
|
---|
1114 | OBSERVE;
|
---|
1115 | NOTIFY(AtomMoved);
|
---|
1116 | NOTIFY(MoleculeCenterChanged);
|
---|
1117 | if (oldinfo != newinfo)
|
---|
1118 | NOTIFY(BoundingBoxChanged);
|
---|
1119 | break;
|
---|
1120 | }
|
---|
1121 | case AtomObservable::ElementChanged:
|
---|
1122 | {
|
---|
1123 | // emit others about one of our atoms moved
|
---|
1124 | _lastchangedatomid = _atom->getId();
|
---|
1125 | OBSERVE;
|
---|
1126 | NOTIFY(FormulaChanged);
|
---|
1127 | const ElementPerAtom_t::iterator iter = ElementPerAtom.find(_lastchangedatomid);
|
---|
1128 | ASSERT( iter != ElementPerAtom.end(),
|
---|
1129 | "molecule::recieveNotification() - atom "
|
---|
1130 | +toString(_atom->getId()+" is not contained in ElementsPerAtom."));
|
---|
1131 | formula -= iter->second;
|
---|
1132 | if (iter->second == (atomicNumber_t)1) // was a hydrogen ?
|
---|
1133 | --NoNonHydrogen;
|
---|
1134 | iter->second = _atom->getElementNo();
|
---|
1135 | formula += iter->second;
|
---|
1136 | if (iter->second == (atomicNumber_t)1) // is a hydrogen ?
|
---|
1137 | ++NoNonHydrogen;
|
---|
1138 | break;
|
---|
1139 | }
|
---|
1140 | case AtomObservable::BondsAdded:
|
---|
1141 | case AtomObservable::BondsRemoved:
|
---|
1142 | {
|
---|
1143 | // emit others about one of our atoms moved
|
---|
1144 | _lastchangedatomid = _atom->getId();
|
---|
1145 | const BondCountsPerAtom_t::iterator iter = BondCountsPerAtom.find(_lastchangedatomid);
|
---|
1146 | ASSERT( iter != BondCountsPerAtom.end(),
|
---|
1147 | "molecule::recieveNotification() - atom "
|
---|
1148 | +toString(_atom->getId()+" is not contained in BondCountsPerAtom."));
|
---|
1149 | BondCount -= iter->second;
|
---|
1150 | iter->second = _atom->getListOfBonds().size();
|
---|
1151 | BondCount += iter->second;
|
---|
1152 | break;
|
---|
1153 | }
|
---|
1154 | default:
|
---|
1155 | ASSERT( 0, "molecule::recieveNotification() - we did not sign up for channel "
|
---|
1156 | +toString(notification->getChannelNo()));
|
---|
1157 | break;
|
---|
1158 | }
|
---|
1159 | }
|
---|
1160 | }
|
---|
1161 |
|
---|
1162 | void molecule::subjectKilled(Observable *publisher)
|
---|
1163 | {
|
---|
1164 | // do nothing, atom does it all
|
---|
1165 | }
|
---|
1166 |
|
---|
1167 | void molecule::select()
|
---|
1168 | {
|
---|
1169 | OBSERVE;
|
---|
1170 | selected = true;
|
---|
1171 | NOTIFY(SelectionChanged);
|
---|
1172 | }
|
---|
1173 |
|
---|
1174 | void molecule::unselect()
|
---|
1175 | {
|
---|
1176 | OBSERVE;
|
---|
1177 | selected = false;
|
---|
1178 | NOTIFY(SelectionChanged);
|
---|
1179 | }
|
---|
1180 |
|
---|
1181 | void molecule::associateAtomWithMolecule(atom *_atom)
|
---|
1182 | {
|
---|
1183 | _atom->signOn(this, AtomObservable::PositionChanged);
|
---|
1184 | _atom->signOn(this, AtomObservable::ElementChanged);
|
---|
1185 | _atom->signOn(this, AtomObservable::BondsAdded);
|
---|
1186 | _atom->signOn(this, AtomObservable::BondsRemoved);
|
---|
1187 | insert(_atom);
|
---|
1188 | {
|
---|
1189 | const size_t atom_bondcount = _atom->getListOfBonds().size();
|
---|
1190 | #ifndef NDEBUG
|
---|
1191 | const std::pair<BondCountsPerAtom_t::iterator, bool> inserter =
|
---|
1192 | #endif
|
---|
1193 | BondCountsPerAtom.insert( std::make_pair(_atom->getId(), atom_bondcount) );
|
---|
1194 | ASSERT( inserter.second,
|
---|
1195 | "molecule::associateAtomWithMolecule() - atom "
|
---|
1196 | +toString(_atom->getId()+" already in BondCountsPerAtom."));
|
---|
1197 | BondCount += atom_bondcount;
|
---|
1198 | }
|
---|
1199 | {
|
---|
1200 | OBSERVE;
|
---|
1201 | const int atom_elementno = _atom->getElementNo();
|
---|
1202 | #ifndef NDEBUG
|
---|
1203 | const std::pair<ElementPerAtom_t::iterator, bool> inserter =
|
---|
1204 | #endif
|
---|
1205 | ElementPerAtom.insert( std::make_pair(_atom->getId(), atom_elementno) );
|
---|
1206 | ASSERT( inserter.second,
|
---|
1207 | "molecule::associateAtomWithMolecule() - atom "
|
---|
1208 | +toString(_atom->getId()+" already in ElementPerAtom."));
|
---|
1209 | formula += atom_elementno;
|
---|
1210 | NOTIFY(FormulaChanged);
|
---|
1211 | }
|
---|
1212 | }
|
---|
1213 |
|
---|
1214 | void molecule::disassociateAtomWithMolecule(atom *_atom)
|
---|
1215 | {
|
---|
1216 | _atom->signOff(this, AtomObservable::PositionChanged);
|
---|
1217 | _atom->signOff(this, AtomObservable::ElementChanged);
|
---|
1218 | _atom->signOff(this, AtomObservable::BondsAdded);
|
---|
1219 | _atom->signOff(this, AtomObservable::BondsRemoved);
|
---|
1220 | erase(_atom);
|
---|
1221 | {
|
---|
1222 | const BondCountsPerAtom_t::iterator iter = BondCountsPerAtom.find(_atom->getId());
|
---|
1223 | ASSERT( iter != BondCountsPerAtom.end(),
|
---|
1224 | "molecule::disassociateAtomWithMolecule() - atom "
|
---|
1225 | +toString(_atom->getId()+" is not contained in BondCountsPerAtom."));
|
---|
1226 | BondCount -= iter->second;
|
---|
1227 | BondCountsPerAtom.erase(iter);
|
---|
1228 | }
|
---|
1229 | {
|
---|
1230 | OBSERVE;
|
---|
1231 | const ElementPerAtom_t::iterator iter = ElementPerAtom.find(_atom->getId());
|
---|
1232 | ASSERT( iter != ElementPerAtom.end(),
|
---|
1233 | "molecule::disassociateAtomWithMolecule() - atom "
|
---|
1234 | +toString(_atom->getId()+" is not contained in ElementPerAtom."));
|
---|
1235 | formula -= iter->second;
|
---|
1236 | ElementPerAtom.erase(iter);
|
---|
1237 | NOTIFY(FormulaChanged);
|
---|
1238 | }
|
---|
1239 | }
|
---|
1240 |
|
---|
1241 | // construct idpool
|
---|
1242 | CONSTRUCT_IDPOOL(atomId_t, continuousId)
|
---|
1243 |
|
---|