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 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /** \file molecules.cpp
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9 | *
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10 | * Functions for the class molecule.
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11 | *
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12 | */
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13 |
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14 | // include config.h
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15 | #ifdef HAVE_CONFIG_H
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16 | #include <config.h>
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17 | #endif
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18 |
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19 | #include "CodePatterns/MemDebug.hpp"
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20 |
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21 | #include <cstring>
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22 | #include <boost/bind.hpp>
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23 | #include <boost/foreach.hpp>
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24 |
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25 | #include <gsl/gsl_inline.h>
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26 | #include <gsl/gsl_heapsort.h>
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27 |
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28 | #include "molecule.hpp"
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29 |
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30 | #include "Atom/atom.hpp"
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31 | #include "Bond/bond.hpp"
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32 | #include "Box.hpp"
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33 | #include "CodePatterns/enumeration.hpp"
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34 | #include "CodePatterns/Log.hpp"
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35 | #include "config.hpp"
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36 | #include "Descriptors/AtomIdDescriptor.hpp"
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37 | #include "Element/element.hpp"
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38 | #include "Graph/BondGraph.hpp"
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39 | #include "LinearAlgebra/Exceptions.hpp"
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40 | #include "LinearAlgebra/leastsquaremin.hpp"
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41 | #include "LinearAlgebra/Plane.hpp"
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42 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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43 | #include "LinearAlgebra/Vector.hpp"
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44 | #include "LinkedCell/linkedcell.hpp"
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45 | #include "IdPool_impl.hpp"
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46 | #include "Shapes/BaseShapes.hpp"
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47 | #include "Tesselation/tesselation.hpp"
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48 | #include "World.hpp"
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49 | #include "WorldTime.hpp"
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50 |
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51 |
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52 | /************************************* Functions for class molecule *********************************/
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53 |
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54 | /** Constructor of class molecule.
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55 | * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
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56 | */
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57 | molecule::molecule() :
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58 | Observable("molecule"),
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59 | MDSteps(0),
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60 | NoNonBonds(0),
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61 | NoCyclicBonds(0),
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62 | ActiveFlag(false),
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63 | IndexNr(-1),
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64 | NoNonHydrogen(this,boost::bind(&molecule::doCountNoNonHydrogen,this),"NoNonHydrogen"),
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65 | BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
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66 | atomIdPool(1, 20, 100),
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67 | last_atom(0)
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68 | {
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69 | // add specific channels
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70 | Channels *OurChannel = new Channels;
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71 | NotificationChannels.insert( std::make_pair( this, OurChannel) );
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72 | for (size_t type = 0; type < (size_t)NotificationType_MAX; ++type)
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73 | OurChannel->addChannel(type);
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74 |
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75 | strcpy(name,World::getInstance().getDefaultName().c_str());
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76 | };
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77 |
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78 | molecule *NewMolecule(){
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79 | return new molecule();
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80 | }
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81 |
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82 | /** Destructor of class molecule.
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83 | * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
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84 | */
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85 | molecule::~molecule()
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86 | {
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87 | CleanupMolecule();
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88 | };
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89 |
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90 |
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91 | void DeleteMolecule(molecule *mol){
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92 | delete mol;
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93 | }
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94 |
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95 | // getter and setter
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96 | const std::string molecule::getName() const{
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97 | return std::string(name);
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98 | }
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99 |
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100 | int molecule::getAtomCount() const{
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101 | return atomIds.size();
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102 | }
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103 |
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104 | size_t molecule::getNoNonHydrogen() const{
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105 | return *NoNonHydrogen;
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106 | }
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107 |
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108 | int molecule::getBondCount() const{
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109 | return *BondCount;
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110 | }
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111 |
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112 | void molecule::setName(const std::string _name){
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113 | OBSERVE;
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114 | NOTIFY(MoleculeNameChanged);
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115 | cout << "Set name of molecule " << getId() << " to " << _name << endl;
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116 | strncpy(name,_name.c_str(),MAXSTRINGSIZE);
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117 | }
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118 |
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119 | bool molecule::changeAtomNr(int oldNr, int newNr, atom* target){
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120 | OBSERVE;
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121 | if(atomIdPool.reserveId(newNr)){
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122 | NOTIFY(AtomNrChanged);
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123 | if (oldNr != -1) // -1 is reserved and indicates no number
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124 | atomIdPool.releaseId(oldNr);
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125 | ASSERT (target,
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126 | "molecule::changeAtomNr() - given target is NULL, cannot set Nr or name.");
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127 | target->setNr(newNr);
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128 | setAtomName(target);
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129 | return true;
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130 | } else{
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131 | return false;
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132 | }
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133 | }
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134 |
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135 | bool molecule::changeId(moleculeId_t newId){
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136 | // first we move ourselves in the world
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137 | // the world lets us know if that succeeded
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138 | if(World::getInstance().changeMoleculeId(id,newId,this)){
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139 | id = newId;
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140 | return true;
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141 | }
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142 | else{
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143 | return false;
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144 | }
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145 | }
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146 |
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147 |
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148 | moleculeId_t molecule::getId() const {
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149 | return id;
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150 | }
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151 |
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152 | void molecule::setId(moleculeId_t _id){
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153 | id =_id;
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154 | }
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155 |
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156 | const Formula &molecule::getFormula() const {
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157 | return formula;
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158 | }
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159 |
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160 | unsigned int molecule::getElementCount() const{
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161 | return formula.getElementCount();
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162 | }
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163 |
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164 | bool molecule::hasElement(const element *element) const{
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165 | return formula.hasElement(element);
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166 | }
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167 |
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168 | bool molecule::hasElement(atomicNumber_t Z) const{
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169 | return formula.hasElement(Z);
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170 | }
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171 |
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172 | bool molecule::hasElement(const string &shorthand) const{
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173 | return formula.hasElement(shorthand);
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174 | }
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175 |
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176 | /************************** Access to the List of Atoms ****************/
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177 |
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178 | molecule::const_iterator molecule::erase( const_iterator loc )
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179 | {
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180 | OBSERVE;
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181 | NOTIFY(AtomRemoved);
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182 | const_iterator iter = loc;
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183 | ++iter;
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184 | atom * const _atom = const_cast<atom *>(*loc);
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185 | atomIds.erase( _atom->getId() );
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186 | {
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187 | NOTIFY(AtomNrChanged);
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188 | atomIdPool.releaseId(_atom->getNr());
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189 | _atom->setNr(-1);
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190 | }
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191 | formula-=_atom->getType();
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192 | _atom->removeFromMolecule();
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193 | return iter;
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194 | }
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195 |
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196 | molecule::const_iterator molecule::erase( atom * key )
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197 | {
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198 | OBSERVE;
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199 | NOTIFY(AtomRemoved);
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200 | const_iterator iter = find(key);
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201 | if (iter != end()){
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202 | ++iter;
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203 | atomIds.erase( key->getId() );
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204 | {
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205 | NOTIFY(AtomNrChanged);
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206 | atomIdPool.releaseId(key->getNr());
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207 | key->setNr(-1);
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208 | }
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209 | formula-=key->getType();
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210 | key->removeFromMolecule();
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211 | }
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212 | return iter;
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213 | }
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214 |
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215 | pair<molecule::iterator,bool> molecule::insert ( atom * const key )
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216 | {
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217 | OBSERVE;
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218 | NOTIFY(AtomInserted);
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219 | std::pair<iterator,bool> res = atomIds.insert(key->getId());
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220 | if (res.second) { // push atom if went well
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221 | NOTIFY(AtomNrChanged);
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222 | key->setNr(atomIdPool.getNextId());
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223 | setAtomName(key);
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224 | formula+=key->getType();
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225 | return res;
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226 | } else {
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227 | return pair<iterator,bool>(end(),res.second);
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228 | }
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229 | }
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230 |
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231 | void molecule::setAtomName(atom *_atom) const
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232 | {
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233 | std::stringstream sstr;
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234 | sstr << _atom->getType()->getSymbol() << _atom->getNr();
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235 | _atom->setName(sstr.str());
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236 | }
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237 |
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238 | World::AtomComposite molecule::getAtomSet() const
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239 | {
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240 | World::AtomComposite vector_of_atoms;
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241 | for (molecule::iterator iter = begin(); iter != end(); ++iter)
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242 | vector_of_atoms.push_back(*iter);
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243 | return vector_of_atoms;
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244 | }
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245 |
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246 | /** Adds given atom \a *pointer from molecule list.
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247 | * 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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248 | * \param *pointer allocated and set atom
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249 | * \return true - succeeded, false - atom not found in list
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250 | */
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251 | bool molecule::AddAtom(atom *pointer)
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252 | {
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253 | if (pointer != NULL) {
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254 | insert(pointer);
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255 | pointer->setMolecule(this);
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256 | }
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257 | return true;
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258 | };
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259 |
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260 | /** Adds a copy of the given atom \a *pointer from molecule list.
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261 | * Increases molecule::last_atom and gives last number to added atom.
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262 | * \param *pointer allocated and set atom
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263 | * \return pointer to the newly added atom
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264 | */
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265 | atom * molecule::AddCopyAtom(atom *pointer)
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266 | {
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267 | atom *retval = NULL;
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268 | if (pointer != NULL) {
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269 | atom *walker = pointer->clone();
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270 | walker->setName(pointer->getName());
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271 | walker->setNr(last_atom++); // increase number within molecule
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272 | insert(walker);
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273 | walker->setMolecule(this);
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274 | retval=walker;
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275 | }
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276 | return retval;
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277 | };
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278 |
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279 | /** Adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
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280 | * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
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281 | * a different scheme when adding \a *replacement atom for the given one.
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282 | * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
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283 | * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
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284 | * *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
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285 | * The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
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286 | * replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
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287 | * element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
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288 | * hydrogens forming this angle with *origin.
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289 | * -# 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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290 | * 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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291 | * determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
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292 | * We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
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293 | * \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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294 | * \f]
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295 | * vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
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296 | * the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
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297 | * 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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298 | * the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
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299 | * \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
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300 | * \f]
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301 | * as the coordination of all three atoms in the coordinate system of these three vectors:
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302 | * \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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303 | *
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304 | * \param *out output stream for debugging
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305 | * \param *Bond pointer to bond between \a *origin and \a *replacement
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306 | * \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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307 | * \param *origin pointer to atom which acts as the origin for scaling the added hydrogen to correct bond length
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308 | * \param *replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
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309 | * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
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310 | * \return number of atoms added, if < bond::BondDegree then something went wrong
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311 | * \todo double and triple bonds splitting (always use the tetraeder angle!)
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312 | */
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313 | bool molecule::AddHydrogenReplacementAtom(bond *TopBond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem)
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314 | {
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315 | // Info info(__func__);
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316 | bool AllWentWell = true; // flag gathering the boolean return value of molecule::AddAtom and other functions, as return value on exit
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317 | double bondlength; // bond length of the bond to be replaced/cut
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318 | double bondangle; // bond angle of the bond to be replaced/cut
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319 | double BondRescale; // rescale value for the hydrogen bond length
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320 | bond *FirstBond = NULL, *SecondBond = NULL; // Other bonds in double bond case to determine "other" plane
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321 | atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
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322 | double b,l,d,f,g, alpha, factors[NDIM]; // hold temporary values in triple bond case for coordination determination
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323 | Vector Orthovector1, Orthovector2; // temporary vectors in coordination construction
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324 | Vector InBondvector; // vector in direction of *Bond
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325 | const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
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326 | bond *Binder = NULL;
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327 |
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328 | // create vector in direction of bond
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329 | InBondvector = TopReplacement->getPosition() - TopOrigin->getPosition();
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330 | bondlength = InBondvector.Norm();
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331 |
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332 | // is greater than typical bond distance? Then we have to correct periodically
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333 | // the problem is not the H being out of the box, but InBondvector have the wrong direction
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334 | // due to TopReplacement or Origin being on the wrong side!
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335 | const BondGraph * const BG = World::getInstance().getBondGraph();
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336 | const range<double> MinMaxBondDistance(
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337 | BG->getMinMaxDistance(TopOrigin,TopReplacement));
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338 | if (!MinMaxBondDistance.isInRange(bondlength)) {
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339 | // LOG(4, "InBondvector is: " << InBondvector << ".");
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340 | Orthovector1.Zero();
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341 | for (int i=NDIM;i--;) {
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342 | l = TopReplacement->at(i) - TopOrigin->at(i);
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343 | if (fabs(l) > MinMaxBondDistance.last) { // is component greater than bond distance (check against min not useful here)
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344 | Orthovector1[i] = (l < 0) ? -1. : +1.;
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345 | } // (signs are correct, was tested!)
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346 | }
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347 | Orthovector1 *= matrix;
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348 | InBondvector -= Orthovector1; // subtract just the additional translation
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349 | bondlength = InBondvector.Norm();
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350 | // LOG(4, "INFO: Corrected InBondvector is now: " << InBondvector << ".");
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351 | } // periodic correction finished
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352 |
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353 | InBondvector.Normalize();
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354 | // get typical bond length and store as scale factor for later
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355 | ASSERT(TopOrigin->getType() != NULL, "AddHydrogenReplacementAtom: element of TopOrigin is not given.");
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356 | BondRescale = TopOrigin->getType()->getHBondDistance(TopBond->BondDegree-1);
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357 | if (BondRescale == -1) {
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358 | ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!");
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359 | return false;
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360 | BondRescale = bondlength;
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361 | } else {
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362 | if (!IsAngstroem)
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363 | BondRescale /= (1.*AtomicLengthToAngstroem);
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364 | }
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365 |
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366 | // discern single, double and triple bonds
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367 | switch(TopBond->BondDegree) {
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368 | case 1:
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369 | FirstOtherAtom = World::getInstance().createAtom(); // new atom
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370 | FirstOtherAtom->setType(1); // element is Hydrogen
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371 | FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
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372 | FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
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373 | if (TopReplacement->getType()->getAtomicNumber() == 1) { // neither rescale nor replace if it's already hydrogen
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374 | FirstOtherAtom->father = TopReplacement;
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375 | BondRescale = bondlength;
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376 | } else {
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377 | FirstOtherAtom->father = NULL; // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
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378 | }
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379 | InBondvector *= BondRescale; // rescale the distance vector to Hydrogen bond length
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380 | FirstOtherAtom->setPosition(TopOrigin->getPosition() + InBondvector); // set coordination to origin and add distance vector to replacement atom
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381 | AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
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382 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
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383 | Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
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384 | Binder->Cyclic = false;
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385 | Binder->Type = GraphEdge::TreeEdge;
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386 | break;
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387 | case 2:
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388 | {
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389 | // determine two other bonds (warning if there are more than two other) plus valence sanity check
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390 | const BondList& ListOfBonds = TopOrigin->getListOfBonds();
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391 | for (BondList::const_iterator Runner = ListOfBonds.begin();
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392 | Runner != ListOfBonds.end();
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393 | ++Runner) {
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394 | if ((*Runner) != TopBond) {
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395 | if (FirstBond == NULL) {
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396 | FirstBond = (*Runner);
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397 | FirstOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
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398 | } else if (SecondBond == NULL) {
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399 | SecondBond = (*Runner);
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400 | SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
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401 | } else {
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402 | ELOG(2, "Detected more than four bonds for atom " << TopOrigin->getName());
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403 | }
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404 | }
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405 | }
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406 | }
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407 | 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)
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408 | SecondBond = TopBond;
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409 | SecondOtherAtom = TopReplacement;
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410 | }
|
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411 | if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
|
---|
412 | // 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.");
|
---|
413 |
|
---|
414 | // determine the plane of these two with the *origin
|
---|
415 | try {
|
---|
416 | Orthovector1 = Plane(TopOrigin->getPosition(), FirstOtherAtom->getPosition(), SecondOtherAtom->getPosition()).getNormal();
|
---|
417 | }
|
---|
418 | catch(LinearDependenceException &excp){
|
---|
419 | LOG(0, boost::diagnostic_information(excp));
|
---|
420 | // TODO: figure out what to do with the Orthovector in this case
|
---|
421 | AllWentWell = false;
|
---|
422 | }
|
---|
423 | } else {
|
---|
424 | Orthovector1.GetOneNormalVector(InBondvector);
|
---|
425 | }
|
---|
426 | //LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
427 | // orthogonal vector and bond vector between origin and replacement form the new plane
|
---|
428 | Orthovector1.MakeNormalTo(InBondvector);
|
---|
429 | Orthovector1.Normalize();
|
---|
430 | //LOG(3, "ReScaleCheck: " << Orthovector1.Norm() << " and " << InBondvector.Norm() << ".");
|
---|
431 |
|
---|
432 | // create the two Hydrogens ...
|
---|
433 | FirstOtherAtom = World::getInstance().createAtom();
|
---|
434 | SecondOtherAtom = World::getInstance().createAtom();
|
---|
435 | FirstOtherAtom->setType(1);
|
---|
436 | SecondOtherAtom->setType(1);
|
---|
437 | FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
438 | FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
439 | SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
440 | SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
441 | FirstOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
442 | SecondOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
443 | bondangle = TopOrigin->getType()->getHBondAngle(1);
|
---|
444 | if (bondangle == -1) {
|
---|
445 | ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!");
|
---|
446 | return false;
|
---|
447 | bondangle = 0;
|
---|
448 | }
|
---|
449 | bondangle *= M_PI/180./2.;
|
---|
450 | // LOG(3, "INFO: ReScaleCheck: InBondvector " << InBondvector << ", " << Orthovector1 << ".");
|
---|
451 | // LOG(3, "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle));
|
---|
452 | FirstOtherAtom->Zero();
|
---|
453 | SecondOtherAtom->Zero();
|
---|
454 | for(int i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondvector is bondangle = 0 direction)
|
---|
455 | FirstOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (sin(bondangle)));
|
---|
456 | SecondOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (-sin(bondangle)));
|
---|
457 | }
|
---|
458 | FirstOtherAtom->Scale(BondRescale); // rescale by correct BondDistance
|
---|
459 | SecondOtherAtom->Scale(BondRescale);
|
---|
460 | //LOG(3, "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << ".");
|
---|
461 | *FirstOtherAtom += TopOrigin->getPosition();
|
---|
462 | *SecondOtherAtom += TopOrigin->getPosition();
|
---|
463 | // ... and add to molecule
|
---|
464 | AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
|
---|
465 | AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
|
---|
466 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
467 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
468 | Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
|
---|
469 | Binder->Cyclic = false;
|
---|
470 | Binder->Type = GraphEdge::TreeEdge;
|
---|
471 | Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
|
---|
472 | Binder->Cyclic = false;
|
---|
473 | Binder->Type = GraphEdge::TreeEdge;
|
---|
474 | break;
|
---|
475 | case 3:
|
---|
476 | // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
|
---|
477 | FirstOtherAtom = World::getInstance().createAtom();
|
---|
478 | SecondOtherAtom = World::getInstance().createAtom();
|
---|
479 | ThirdOtherAtom = World::getInstance().createAtom();
|
---|
480 | FirstOtherAtom->setType(1);
|
---|
481 | SecondOtherAtom->setType(1);
|
---|
482 | ThirdOtherAtom->setType(1);
|
---|
483 | FirstOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
484 | FirstOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
485 | SecondOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
486 | SecondOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
487 | ThirdOtherAtom->setAtomicVelocity(TopReplacement->getAtomicVelocity()); // copy velocity
|
---|
488 | ThirdOtherAtom->setFixedIon(TopReplacement->getFixedIon());
|
---|
489 | FirstOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
490 | SecondOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
491 | ThirdOtherAtom->father = NULL; // we are just an added hydrogen with no father
|
---|
492 |
|
---|
493 | // we need to vectors orthonormal the InBondvector
|
---|
494 | AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(InBondvector);
|
---|
495 | // LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
496 | try{
|
---|
497 | Orthovector2 = Plane(InBondvector, Orthovector1,0).getNormal();
|
---|
498 | }
|
---|
499 | catch(LinearDependenceException &excp) {
|
---|
500 | LOG(0, boost::diagnostic_information(excp));
|
---|
501 | AllWentWell = false;
|
---|
502 | }
|
---|
503 | // LOG(3, "INFO: Orthovector2: " << Orthovector2 << ".")
|
---|
504 |
|
---|
505 | // create correct coordination for the three atoms
|
---|
506 | alpha = (TopOrigin->getType()->getHBondAngle(2))/180.*M_PI/2.; // retrieve triple bond angle from database
|
---|
507 | l = BondRescale; // desired bond length
|
---|
508 | b = 2.*l*sin(alpha); // base length of isosceles triangle
|
---|
509 | d = l*sqrt(cos(alpha)*cos(alpha) - sin(alpha)*sin(alpha)/3.); // length for InBondvector
|
---|
510 | f = b/sqrt(3.); // length for Orthvector1
|
---|
511 | g = b/2.; // length for Orthvector2
|
---|
512 | // LOG(3, "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", ");
|
---|
513 | // 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));
|
---|
514 | factors[0] = d;
|
---|
515 | factors[1] = f;
|
---|
516 | factors[2] = 0.;
|
---|
517 | FirstOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
518 | factors[1] = -0.5*f;
|
---|
519 | factors[2] = g;
|
---|
520 | SecondOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
521 | factors[2] = -g;
|
---|
522 | ThirdOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
523 |
|
---|
524 | // rescale each to correct BondDistance
|
---|
525 | // FirstOtherAtom->x.Scale(&BondRescale);
|
---|
526 | // SecondOtherAtom->x.Scale(&BondRescale);
|
---|
527 | // ThirdOtherAtom->x.Scale(&BondRescale);
|
---|
528 |
|
---|
529 | // and relative to *origin atom
|
---|
530 | *FirstOtherAtom += TopOrigin->getPosition();
|
---|
531 | *SecondOtherAtom += TopOrigin->getPosition();
|
---|
532 | *ThirdOtherAtom += TopOrigin->getPosition();
|
---|
533 |
|
---|
534 | // ... and add to molecule
|
---|
535 | AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
|
---|
536 | AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
|
---|
537 | AllWentWell = AllWentWell && AddAtom(ThirdOtherAtom);
|
---|
538 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
539 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
540 | // LOG(4, "INFO: Added " << *ThirdOtherAtom << " at: " << ThirdOtherAtom->x << ".");
|
---|
541 | Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
|
---|
542 | Binder->Cyclic = false;
|
---|
543 | Binder->Type = GraphEdge::TreeEdge;
|
---|
544 | Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
|
---|
545 | Binder->Cyclic = false;
|
---|
546 | Binder->Type = GraphEdge::TreeEdge;
|
---|
547 | Binder = AddBond(BottomOrigin, ThirdOtherAtom, 1);
|
---|
548 | Binder->Cyclic = false;
|
---|
549 | Binder->Type = GraphEdge::TreeEdge;
|
---|
550 | break;
|
---|
551 | default:
|
---|
552 | ELOG(1, "BondDegree does not state single, double or triple bond!");
|
---|
553 | AllWentWell = false;
|
---|
554 | break;
|
---|
555 | }
|
---|
556 |
|
---|
557 | return AllWentWell;
|
---|
558 | };
|
---|
559 |
|
---|
560 | /** Creates a copy of this molecule.
|
---|
561 | * \param offset translation Vector for the new molecule relative to old one
|
---|
562 | * \return copy of molecule
|
---|
563 | */
|
---|
564 | molecule *molecule::CopyMolecule(const Vector &offset) const
|
---|
565 | {
|
---|
566 | molecule *copy = World::getInstance().createMolecule();
|
---|
567 |
|
---|
568 | // copy all atoms
|
---|
569 | std::map< const atom *, atom *> FatherFinder;
|
---|
570 | for (iterator iter = begin(); iter != end(); ++iter) {
|
---|
571 | atom * const copy_atom = copy->AddCopyAtom(*iter);
|
---|
572 | copy_atom->setPosition(copy_atom->getPosition() + offset);
|
---|
573 | FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
|
---|
574 | }
|
---|
575 |
|
---|
576 | // copy all bonds
|
---|
577 | for(const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
|
---|
578 | const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
|
---|
579 | for(BondList::const_iterator BondRunner = ListOfBonds.begin();
|
---|
580 | BondRunner != ListOfBonds.end();
|
---|
581 | ++BondRunner)
|
---|
582 | if ((*BondRunner)->leftatom == *AtomRunner) {
|
---|
583 | bond *Binder = (*BondRunner);
|
---|
584 | // get the pendant atoms of current bond in the copy molecule
|
---|
585 | ASSERT(FatherFinder.count(Binder->leftatom),
|
---|
586 | "molecule::CopyMolecule() - No copy of original left atom "
|
---|
587 | +toString(Binder->leftatom)+" for bond copy found");
|
---|
588 | ASSERT(FatherFinder.count(Binder->rightatom),
|
---|
589 | "molecule::CopyMolecule() - No copy of original right atom "
|
---|
590 | +toString(Binder->rightatom)+" for bond copy found");
|
---|
591 | atom * const LeftAtom = FatherFinder[Binder->leftatom];
|
---|
592 | atom * const RightAtom = FatherFinder[Binder->rightatom];
|
---|
593 |
|
---|
594 | bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
|
---|
595 | NewBond->Cyclic = Binder->Cyclic;
|
---|
596 | if (Binder->Cyclic)
|
---|
597 | copy->NoCyclicBonds++;
|
---|
598 | NewBond->Type = Binder->Type;
|
---|
599 | }
|
---|
600 | }
|
---|
601 | // correct fathers
|
---|
602 | //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
|
---|
603 |
|
---|
604 | return copy;
|
---|
605 | };
|
---|
606 |
|
---|
607 |
|
---|
608 | /** Destroys all atoms inside this molecule.
|
---|
609 | */
|
---|
610 | void molecule::removeAtomsinMolecule()
|
---|
611 | {
|
---|
612 | // remove each atom from world
|
---|
613 | for(iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
|
---|
614 | World::getInstance().destroyAtom(*AtomRunner);
|
---|
615 | };
|
---|
616 |
|
---|
617 |
|
---|
618 | /**
|
---|
619 | * Copies all atoms of a molecule which are within the defined parallelepiped.
|
---|
620 | *
|
---|
621 | * @param offest for the origin of the parallelepiped
|
---|
622 | * @param three vectors forming the matrix that defines the shape of the parallelpiped
|
---|
623 | */
|
---|
624 | molecule* molecule::CopyMoleculeFromSubRegion(const Shape ®ion) const {
|
---|
625 | molecule *copy = World::getInstance().createMolecule();
|
---|
626 |
|
---|
627 | // copy all atoms
|
---|
628 | std::map< const atom *, atom *> FatherFinder;
|
---|
629 | for (iterator iter = begin(); iter != end(); ++iter) {
|
---|
630 | if((*iter)->IsInShape(region)){
|
---|
631 | atom * const copy_atom = copy->AddCopyAtom(*iter);
|
---|
632 | FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
|
---|
633 | }
|
---|
634 | }
|
---|
635 |
|
---|
636 | // copy all bonds
|
---|
637 | for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
|
---|
638 | const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
|
---|
639 | for(BondList::const_iterator BondRunner = ListOfBonds.begin();
|
---|
640 | BondRunner != ListOfBonds.end();
|
---|
641 | ++BondRunner)
|
---|
642 | if ((*BondRunner)->leftatom == *AtomRunner) {
|
---|
643 | bond *Binder = (*BondRunner);
|
---|
644 | if ((FatherFinder.count(Binder->leftatom))
|
---|
645 | && (FatherFinder.count(Binder->rightatom))) {
|
---|
646 | // if copy present, then it must be from subregion
|
---|
647 | atom * const LeftAtom = FatherFinder[Binder->leftatom];
|
---|
648 | atom * const RightAtom = FatherFinder[Binder->rightatom];
|
---|
649 |
|
---|
650 | bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
|
---|
651 | NewBond->Cyclic = Binder->Cyclic;
|
---|
652 | if (Binder->Cyclic)
|
---|
653 | copy->NoCyclicBonds++;
|
---|
654 | NewBond->Type = Binder->Type;
|
---|
655 | }
|
---|
656 | }
|
---|
657 | }
|
---|
658 | // correct fathers
|
---|
659 | //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
|
---|
660 |
|
---|
661 | //TODO: copy->BuildInducedSubgraph(this);
|
---|
662 |
|
---|
663 | return copy;
|
---|
664 | }
|
---|
665 |
|
---|
666 | /** Adds a bond to a the molecule specified by two atoms, \a *first and \a *second.
|
---|
667 | * Also updates molecule::BondCount and molecule::NoNonBonds.
|
---|
668 | * \param *first first atom in bond
|
---|
669 | * \param *second atom in bond
|
---|
670 | * \return pointer to bond or NULL on failure
|
---|
671 | */
|
---|
672 | bond * molecule::AddBond(atom *atom1, atom *atom2, int degree)
|
---|
673 | {
|
---|
674 | bond *Binder = NULL;
|
---|
675 |
|
---|
676 | // some checks to make sure we are able to create the bond
|
---|
677 | ASSERT(atom1,
|
---|
678 | "molecule::AddBond() - First atom "+toString(atom1)
|
---|
679 | +" is not a invalid pointer");
|
---|
680 | ASSERT(atom2,
|
---|
681 | "molecule::AddBond() - Second atom "+toString(atom2)
|
---|
682 | +" is not a invalid pointer");
|
---|
683 | ASSERT(isInMolecule(atom1),
|
---|
684 | "molecule::AddBond() - First atom "+toString(atom1)
|
---|
685 | +" is not part of molecule");
|
---|
686 | ASSERT(isInMolecule(atom2),
|
---|
687 | "molecule::AddBond() - Second atom "+toString(atom2)
|
---|
688 | +" is not part of molecule");
|
---|
689 |
|
---|
690 | Binder = new bond(atom1, atom2, degree);
|
---|
691 | atom1->RegisterBond(WorldTime::getTime(), Binder);
|
---|
692 | atom2->RegisterBond(WorldTime::getTime(), Binder);
|
---|
693 | if ((atom1->getType() != NULL)
|
---|
694 | && (atom1->getType()->getAtomicNumber() != 1)
|
---|
695 | && (atom2->getType() != NULL)
|
---|
696 | && (atom2->getType()->getAtomicNumber() != 1))
|
---|
697 | NoNonBonds++;
|
---|
698 |
|
---|
699 | return Binder;
|
---|
700 | };
|
---|
701 |
|
---|
702 | /** Remove bond from bond chain list and from the both atom::ListOfBonds.
|
---|
703 | * Bond::~Bond takes care of bond removal
|
---|
704 | * \param *pointer bond pointer
|
---|
705 | * \return true - bound found and removed, false - bond not found/removed
|
---|
706 | */
|
---|
707 | bool molecule::RemoveBond(bond *pointer)
|
---|
708 | {
|
---|
709 | //ELOG(1, "molecule::RemoveBond: Function not implemented yet.");
|
---|
710 | delete(pointer);
|
---|
711 | return true;
|
---|
712 | };
|
---|
713 |
|
---|
714 | /** Remove every bond from bond chain list that atom \a *BondPartner is a constituent of.
|
---|
715 | * \todo Function not implemented yet
|
---|
716 | * \param *BondPartner atom to be removed
|
---|
717 | * \return true - bounds found and removed, false - bonds not found/removed
|
---|
718 | */
|
---|
719 | bool molecule::RemoveBonds(atom *BondPartner)
|
---|
720 | {
|
---|
721 | //ELOG(1, "molecule::RemoveBond: Function not implemented yet.");
|
---|
722 | BondPartner->removeAllBonds();
|
---|
723 | return false;
|
---|
724 | };
|
---|
725 |
|
---|
726 | /** Set molecule::name from the basename without suffix in the given \a *filename.
|
---|
727 | * \param *filename filename
|
---|
728 | */
|
---|
729 | void molecule::SetNameFromFilename(const char *filename)
|
---|
730 | {
|
---|
731 | OBSERVE;
|
---|
732 | int length = 0;
|
---|
733 | const char *molname = strrchr(filename, '/');
|
---|
734 | if (molname != NULL)
|
---|
735 | molname += sizeof(char); // search for filename without dirs
|
---|
736 | else
|
---|
737 | molname = filename; // contains no slashes
|
---|
738 | const char *endname = strchr(molname, '.');
|
---|
739 | if ((endname == NULL) || (endname < molname))
|
---|
740 | length = strlen(molname);
|
---|
741 | else
|
---|
742 | length = strlen(molname) - strlen(endname);
|
---|
743 | cout << "Set name of molecule " << getId() << " to " << molname << endl;
|
---|
744 | strncpy(name, molname, length);
|
---|
745 | name[length]='\0';
|
---|
746 | };
|
---|
747 |
|
---|
748 | /** Sets the molecule::cell_size to the components of \a *dim (rectangular box)
|
---|
749 | * \param *dim vector class
|
---|
750 | */
|
---|
751 | void molecule::SetBoxDimension(Vector *dim)
|
---|
752 | {
|
---|
753 | RealSpaceMatrix domain;
|
---|
754 | for(int i =0; i<NDIM;++i)
|
---|
755 | domain.at(i,i) = dim->at(i);
|
---|
756 | World::getInstance().setDomain(domain);
|
---|
757 | };
|
---|
758 |
|
---|
759 | /** Removes atom from molecule list and removes all of its bonds.
|
---|
760 | * \param *pointer atom to be removed
|
---|
761 | * \return true - succeeded, false - atom not found in list
|
---|
762 | */
|
---|
763 | bool molecule::RemoveAtom(atom *pointer)
|
---|
764 | {
|
---|
765 | ASSERT(pointer, "Null pointer passed to molecule::RemoveAtom().");
|
---|
766 | RemoveBonds(pointer);
|
---|
767 | pointer->removeFromMolecule();
|
---|
768 | return true;
|
---|
769 | };
|
---|
770 |
|
---|
771 | /** Removes atom from molecule list, but does not delete it.
|
---|
772 | * \param *pointer atom to be removed
|
---|
773 | * \return true - succeeded, false - atom not found in list
|
---|
774 | */
|
---|
775 | bool molecule::UnlinkAtom(atom *pointer)
|
---|
776 | {
|
---|
777 | if (pointer == NULL)
|
---|
778 | return false;
|
---|
779 | pointer->removeFromMolecule();
|
---|
780 | return true;
|
---|
781 | };
|
---|
782 |
|
---|
783 | /** Removes every atom from molecule list.
|
---|
784 | * \return true - succeeded, false - atom not found in list
|
---|
785 | */
|
---|
786 | bool molecule::CleanupMolecule()
|
---|
787 | {
|
---|
788 | for (molecule::iterator iter = begin(); !empty(); iter = begin())
|
---|
789 | (*iter)->removeFromMolecule();
|
---|
790 | return empty();
|
---|
791 | };
|
---|
792 |
|
---|
793 | /** Finds an atom specified by its continuous number.
|
---|
794 | * \param Nr number of atom withim molecule
|
---|
795 | * \return pointer to atom or NULL
|
---|
796 | */
|
---|
797 | atom * molecule::FindAtom(int Nr) const
|
---|
798 | {
|
---|
799 | molecule::iterator iter = begin();
|
---|
800 | for (; iter != end(); ++iter)
|
---|
801 | if ((*iter)->getNr() == Nr)
|
---|
802 | break;
|
---|
803 | if (iter != end()) {
|
---|
804 | //LOG(0, "Found Atom Nr. " << walker->getNr());
|
---|
805 | return (*iter);
|
---|
806 | } else {
|
---|
807 | ELOG(1, "Atom not found in molecule " << getName() << "'s list.");
|
---|
808 | return NULL;
|
---|
809 | }
|
---|
810 | }
|
---|
811 |
|
---|
812 | /** Checks whether the given atom is a member of this molecule.
|
---|
813 | *
|
---|
814 | * We make use here of molecule::atomIds to get a result on
|
---|
815 | *
|
---|
816 | * @param _atom atom to check
|
---|
817 | * @return true - is member, false - is not
|
---|
818 | */
|
---|
819 | bool molecule::isInMolecule(const atom * const _atom)
|
---|
820 | {
|
---|
821 | ASSERT(_atom->getMolecule() == this,
|
---|
822 | "molecule::isInMolecule() - atom is not designated to be in molecule '"
|
---|
823 | +toString(this->getName())+"'.");
|
---|
824 | molecule::const_iterator iter = atomIds.find(_atom->getId());
|
---|
825 | return (iter != atomIds.end());
|
---|
826 | }
|
---|
827 |
|
---|
828 | /** Asks for atom number, and checks whether in list.
|
---|
829 | * \param *text question before entering
|
---|
830 | */
|
---|
831 | atom * molecule::AskAtom(std::string text)
|
---|
832 | {
|
---|
833 | int No;
|
---|
834 | atom *ion = NULL;
|
---|
835 | do {
|
---|
836 | //std::cout << "============Atom list==========================" << std::endl;
|
---|
837 | //mol->Output((ofstream *)&cout);
|
---|
838 | //std::cout << "===============================================" << std::endl;
|
---|
839 | std::cout << text;
|
---|
840 | cin >> No;
|
---|
841 | ion = this->FindAtom(No);
|
---|
842 | } while (ion == NULL);
|
---|
843 | return ion;
|
---|
844 | };
|
---|
845 |
|
---|
846 | /** Checks if given coordinates are within cell volume.
|
---|
847 | * \param *x array of coordinates
|
---|
848 | * \return true - is within, false - out of cell
|
---|
849 | */
|
---|
850 | bool molecule::CheckBounds(const Vector *x) const
|
---|
851 | {
|
---|
852 | const RealSpaceMatrix &domain = World::getInstance().getDomain().getM();
|
---|
853 | bool result = true;
|
---|
854 | for (int i=0;i<NDIM;i++) {
|
---|
855 | result = result && ((x->at(i) >= 0) && (x->at(i) < domain.at(i,i)));
|
---|
856 | }
|
---|
857 | //return result;
|
---|
858 | return true; /// probably not gonna use the check no more
|
---|
859 | };
|
---|
860 |
|
---|
861 | /** Prints molecule to *out.
|
---|
862 | * \param *out output stream
|
---|
863 | */
|
---|
864 | bool molecule::Output(ostream * const output) const
|
---|
865 | {
|
---|
866 | if (output == NULL) {
|
---|
867 | return false;
|
---|
868 | } else {
|
---|
869 | int AtomNo[MAX_ELEMENTS];
|
---|
870 | memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
|
---|
871 | enumeration<const element*> elementLookup = formula.enumerateElements();
|
---|
872 | *output << "#Ion_TypeNr._Nr.R[0] R[1] R[2] MoveType (0 MoveIon, 1 FixedIon)" << endl;
|
---|
873 | for_each(begin(),end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
|
---|
874 | return true;
|
---|
875 | }
|
---|
876 | };
|
---|
877 |
|
---|
878 | /** Outputs contents of each atom::ListOfBonds.
|
---|
879 | * \param *out output stream
|
---|
880 | */
|
---|
881 | void molecule::OutputListOfBonds() const
|
---|
882 | {
|
---|
883 | std::stringstream output;
|
---|
884 | LOG(2, "From Contents of ListOfBonds, all atoms:");
|
---|
885 | for (molecule::const_iterator iter = begin();
|
---|
886 | iter != end();
|
---|
887 | ++iter) {
|
---|
888 | (*iter)->OutputBondOfAtom(output);
|
---|
889 | output << std::endl << "\t\t";
|
---|
890 | }
|
---|
891 | LOG(2, output.str());
|
---|
892 | }
|
---|
893 |
|
---|
894 | /** Brings molecule::AtomCount and atom::*Name up-to-date.
|
---|
895 | * \param *out output stream for debugging
|
---|
896 | */
|
---|
897 | size_t molecule::doCountNoNonHydrogen() const
|
---|
898 | {
|
---|
899 | int temp = 0;
|
---|
900 | // go through atoms and look for new ones
|
---|
901 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
|
---|
902 | if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
|
---|
903 | ++temp;
|
---|
904 | return temp;
|
---|
905 | };
|
---|
906 |
|
---|
907 | /** Counts the number of present bonds.
|
---|
908 | * \return number of bonds
|
---|
909 | */
|
---|
910 | int molecule::doCountBonds() const
|
---|
911 | {
|
---|
912 | unsigned int counter = 0;
|
---|
913 | for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
|
---|
914 | const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
|
---|
915 | for(BondList::const_iterator BondRunner = ListOfBonds.begin();
|
---|
916 | BondRunner != ListOfBonds.end();
|
---|
917 | ++BondRunner)
|
---|
918 | if ((*BondRunner)->leftatom == *AtomRunner)
|
---|
919 | counter++;
|
---|
920 | }
|
---|
921 | return counter;
|
---|
922 | }
|
---|
923 |
|
---|
924 |
|
---|
925 | /** Returns an index map for two father-son-molecules.
|
---|
926 | * The map tells which atom in this molecule corresponds to which one in the other molecul with their fathers.
|
---|
927 | * \param *out output stream for debugging
|
---|
928 | * \param *OtherMolecule corresponding molecule with fathers
|
---|
929 | * \return allocated map of size molecule::AtomCount with map
|
---|
930 | * \todo make this with a good sort O(n), not O(n^2)
|
---|
931 | */
|
---|
932 | int * molecule::GetFatherSonAtomicMap(molecule *OtherMolecule)
|
---|
933 | {
|
---|
934 | LOG(3, "Begin of GetFatherAtomicMap.");
|
---|
935 | int *AtomicMap = new int[getAtomCount()];
|
---|
936 | for (int i=getAtomCount();i--;)
|
---|
937 | AtomicMap[i] = -1;
|
---|
938 | if (OtherMolecule == this) { // same molecule
|
---|
939 | for (int i=getAtomCount();i--;) // no need as -1 means already that there is trivial correspondence
|
---|
940 | AtomicMap[i] = i;
|
---|
941 | LOG(4, "Map is trivial.");
|
---|
942 | } else {
|
---|
943 | std::stringstream output;
|
---|
944 | output << "Map is ";
|
---|
945 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
946 | if ((*iter)->father == NULL) {
|
---|
947 | AtomicMap[(*iter)->getNr()] = -2;
|
---|
948 | } else {
|
---|
949 | for (molecule::const_iterator runner = OtherMolecule->begin(); runner != OtherMolecule->end(); ++runner) {
|
---|
950 | //for (int i=0;i<AtomCount;i++) { // search atom
|
---|
951 | //for (int j=0;j<OtherMolecule->getAtomCount();j++) {
|
---|
952 | //LOG(4, "Comparing father " << (*iter)->father << " with the other one " << (*runner)->father << ".");
|
---|
953 | if ((*iter)->father == (*runner))
|
---|
954 | AtomicMap[(*iter)->getNr()] = (*runner)->getNr();
|
---|
955 | }
|
---|
956 | }
|
---|
957 | output << AtomicMap[(*iter)->getNr()] << "\t";
|
---|
958 | }
|
---|
959 | LOG(4, output.str());
|
---|
960 | }
|
---|
961 | LOG(3, "End of GetFatherAtomicMap.");
|
---|
962 | return AtomicMap;
|
---|
963 | };
|
---|
964 |
|
---|
965 |
|
---|
966 | void molecule::flipActiveFlag(){
|
---|
967 | ActiveFlag = !ActiveFlag;
|
---|
968 | }
|
---|
969 |
|
---|
970 | Shape molecule::getBoundingShape() const
|
---|
971 | {
|
---|
972 | // get center and radius
|
---|
973 | Vector center;
|
---|
974 | double radius = 0.;
|
---|
975 | {
|
---|
976 | center.Zero();
|
---|
977 | for(const_iterator iter = begin(); iter != end(); ++iter)
|
---|
978 | center += (*iter)->getPosition();
|
---|
979 | center *= 1./(double)size();
|
---|
980 | for(const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
981 | const Vector &position = (*iter)->getPosition();
|
---|
982 | const double temp_distance = position.DistanceSquared(center);
|
---|
983 | if (temp_distance > radius)
|
---|
984 | radius = temp_distance;
|
---|
985 | }
|
---|
986 | }
|
---|
987 | // convert radius to true value and add some small boundary
|
---|
988 | radius = sqrt(radius) + 1e+6*std::numeric_limits<double>::epsilon();
|
---|
989 | LOG(1, "INFO: The " << size() << " atoms of the molecule are contained in a sphere at "
|
---|
990 | << center << " with radius " << radius << ".");
|
---|
991 |
|
---|
992 | Shape BoundingShape(Sphere(center, radius));
|
---|
993 | LOG(1, "INFO: Created sphere at " << BoundingShape.getCenter() << " and radius "
|
---|
994 | << BoundingShape.getRadius() << ".");
|
---|
995 | return BoundingShape;
|
---|
996 | }
|
---|
997 |
|
---|
998 | // construct idpool
|
---|
999 | CONSTRUCT_IDPOOL(atomId_t, continuousId)
|
---|
1000 |
|
---|