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) 2013 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * SaturatedFragment.cpp
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26 | *
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27 | * Created on: Mar 3, 2013
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28 | * Author: heber
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29 | */
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30 |
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31 | // include config.h
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32 | #ifdef HAVE_CONFIG_H
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33 | #include <config.h>
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34 | #endif
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35 |
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36 | #include "CodePatterns/MemDebug.hpp"
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37 |
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38 | #include "SaturatedFragment.hpp"
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39 |
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40 | #include <cmath>
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41 | #include <iostream>
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42 |
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43 | #include "CodePatterns/Assert.hpp"
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44 | #include "CodePatterns/Log.hpp"
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45 |
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46 | #include "LinearAlgebra/Exceptions.hpp"
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47 | #include "LinearAlgebra/Plane.hpp"
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48 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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49 | #include "LinearAlgebra/Vector.hpp"
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50 |
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51 | #include "Atom/atom.hpp"
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52 | #include "Bond/bond.hpp"
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53 | #include "config.hpp"
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54 | #include "Descriptors/AtomIdDescriptor.hpp"
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55 | #include "Fragmentation/Exporters/HydrogenPool.hpp"
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56 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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57 | #include "Graph/BondGraph.hpp"
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58 | #include "World.hpp"
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59 |
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60 | SaturatedFragment::SaturatedFragment(
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61 | const KeySet &_set,
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62 | KeySetsInUse_t &_container,
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63 | HydrogenPool &_hydrogens,
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64 | const enum HydrogenTreatment _treatment,
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65 | const enum HydrogenSaturation _saturation,
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66 | const GlobalSaturationPositions_t &_globalsaturationpositions) :
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67 | container(_container),
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68 | set(_set),
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69 | hydrogens(_hydrogens),
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70 | FullMolecule(set),
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71 | treatment(_treatment),
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72 | saturation(_saturation)
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73 | {
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74 | // add to in-use container
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75 | ASSERT( container.find(set) == container.end(),
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76 | "SaturatedFragment::SaturatedFragment() - the set "
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77 | +toString(set)+" is already marked as in use.");
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78 | container.insert(set);
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79 |
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80 | // prepare saturation hydrogens, either using global information
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81 | // or if not given, local information (created in the function)
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82 | if (_globalsaturationpositions.empty())
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83 | saturate();
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84 | else
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85 | saturate(_globalsaturationpositions);
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86 | }
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87 |
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88 | SaturatedFragment::~SaturatedFragment()
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89 | {
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90 | // release all saturation hydrogens if present
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91 | for (KeySet::iterator iter = SaturationHydrogens.begin();
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92 | !SaturationHydrogens.empty();
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93 | iter = SaturationHydrogens.begin()) {
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94 | hydrogens.releaseHydrogen(*iter);
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95 | SaturationHydrogens.erase(iter);
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96 | }
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97 |
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98 | // remove ourselves from in-use container
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99 | KeySetsInUse_t::iterator iter = container.find(set);
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100 | ASSERT( container.find(set) != container.end(),
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101 | "SaturatedFragment::SaturatedFragment() - the set "
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102 | +toString(set)+" is not marked as in use.");
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103 | container.erase(iter);
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104 | }
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105 |
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106 | typedef std::vector<atom *> atoms_t;
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107 |
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108 | atoms_t gatherAllAtoms(const KeySet &_FullMolecule)
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109 | {
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110 | atoms_t atoms;
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111 | for (KeySet::const_iterator iter = _FullMolecule.begin();
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112 | iter != _FullMolecule.end();
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113 | ++iter) {
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114 | atom * const Walker = World::getInstance().getAtom(AtomById(*iter));
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115 | ASSERT( Walker != NULL,
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116 | "gatherAllAtoms() - id "
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117 | +toString(*iter)+" is unknown to World.");
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118 | atoms.push_back(Walker);
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119 | }
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120 |
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121 | return atoms;
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122 | }
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123 |
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124 | typedef std::map<atom *, BondList > CutBonds_t;
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125 |
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126 | CutBonds_t gatherCutBonds(
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127 | const atoms_t &_atoms,
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128 | const KeySet &_set,
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129 | const enum HydrogenTreatment _treatment)
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130 | {
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131 | // bool LonelyFlag = false;
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132 | CutBonds_t CutBonds;
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133 | for (atoms_t::const_iterator iter = _atoms.begin();
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134 | iter != _atoms.end();
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135 | ++iter) {
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136 | atom * const Walker = *iter;
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137 |
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138 | // go through all bonds
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139 | const BondList& ListOfBonds = Walker->getListOfBonds();
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140 | for (BondList::const_iterator BondRunner = ListOfBonds.begin();
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141 | BondRunner != ListOfBonds.end();
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142 | ++BondRunner) {
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143 | atom * const OtherWalker = (*BondRunner)->GetOtherAtom(Walker);
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144 | // if other atom is in key set or is a specially treated hydrogen
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145 | if (_set.find(OtherWalker->getId()) != _set.end()) {
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146 | LOG(4, "DEBUG: Walker " << *Walker << " is bound to " << *OtherWalker << ".");
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147 | } else if ((_treatment == ExcludeHydrogen)
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148 | && (OtherWalker->getElementNo() == (atomicNumber_t)1)) {
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149 | LOG(4, "DEBUG: Walker " << *Walker << " is bound to specially treated hydrogen " <<
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150 | *OtherWalker << ".");
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151 | } else {
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152 | LOG(4, "DEBUG: Walker " << *Walker << " is bound to "
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153 | << *OtherWalker << ", who is not in this fragment molecule.");
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154 | if (CutBonds.count(Walker) == 0)
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155 | CutBonds.insert( std::make_pair(Walker, BondList() ));
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156 | CutBonds[Walker].push_back(*BondRunner);
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157 | }
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158 | }
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159 | }
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160 |
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161 | return CutBonds;
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162 | }
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163 |
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164 | typedef std::vector<atomId_t> atomids_t;
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165 |
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166 | atomids_t gatherPresentExcludedHydrogens(
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167 | const atoms_t &_atoms,
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168 | const KeySet &_set,
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169 | const enum HydrogenTreatment _treatment)
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170 | {
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171 | // bool LonelyFlag = false;
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172 | atomids_t ExcludedHydrogens;
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173 | for (atoms_t::const_iterator iter = _atoms.begin();
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174 | iter != _atoms.end();
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175 | ++iter) {
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176 | atom * const Walker = *iter;
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177 |
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178 | // go through all bonds
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179 | const BondList& ListOfBonds = Walker->getListOfBonds();
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180 | for (BondList::const_iterator BondRunner = ListOfBonds.begin();
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181 | BondRunner != ListOfBonds.end();
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182 | ++BondRunner) {
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183 | atom * const OtherWalker = (*BondRunner)->GetOtherAtom(Walker);
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184 | // if other atom is in key set or is a specially treated hydrogen
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185 | if (_set.find(OtherWalker->getId()) != _set.end()) {
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186 | LOG(6, "DEBUG: OtherWalker " << *OtherWalker << " is in set already.");
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187 | } else if ((_treatment == ExcludeHydrogen)
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188 | && (OtherWalker->getElementNo() == (atomicNumber_t)1)) {
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189 | LOG(5, "DEBUG: Adding excluded hydrogen OtherWalker " << *OtherWalker << ".");
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190 | ExcludedHydrogens.push_back(OtherWalker->getId());
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191 | } else {
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192 | LOG(6, "DEBUG: OtherWalker " << *Walker << " is not in this fragment molecule and no hydrogen.");
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193 | }
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194 | }
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195 | }
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196 |
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197 | return ExcludedHydrogens;
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198 | }
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199 |
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200 | void SaturatedFragment::saturate()
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201 | {
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202 | // so far, we just have a set of keys. Hence, convert to atom refs
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203 | // and gather all atoms in a vector
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204 | std::vector<atom *> atoms = gatherAllAtoms(FullMolecule);
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205 |
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206 | // go through each atom of the fragment and gather all cut bonds in list
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207 | CutBonds_t CutBonds = gatherCutBonds(atoms, set, treatment);
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208 |
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209 | // add excluded hydrogens to FullMolecule if treated specially
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210 | if (treatment == ExcludeHydrogen) {
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211 | atomids_t ExcludedHydrogens = gatherPresentExcludedHydrogens(atoms, set, treatment);
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212 | FullMolecule.insert(ExcludedHydrogens.begin(), ExcludedHydrogens.end());
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213 | }
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214 |
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215 | // go through all cut bonds and replace with a hydrogen
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216 | for (CutBonds_t::const_iterator atomiter = CutBonds.begin();
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217 | atomiter != CutBonds.end(); ++atomiter) {
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218 | atom * const Walker = atomiter->first;
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219 | if (!saturateAtom(Walker, atomiter->second))
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220 | exit(1);
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221 | }
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222 | }
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223 |
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224 | void SaturatedFragment::saturate(
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225 | const GlobalSaturationPositions_t &_globalsaturationpositions)
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226 | {
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227 | // so far, we just have a set of keys. Hence, convert to atom refs
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228 | // and gather all atoms in a vector
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229 | std::vector<atom *> atoms = gatherAllAtoms(FullMolecule);
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230 |
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231 | // go through each atom of the fragment and gather all cut bonds in list
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232 | CutBonds_t CutBonds = gatherCutBonds(atoms, set, treatment);
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233 |
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234 | // add excluded hydrogens to FullMolecule if treated specially
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235 | if (treatment == ExcludeHydrogen) {
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236 | atomids_t ExcludedHydrogens = gatherPresentExcludedHydrogens(atoms, set, treatment);
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237 | FullMolecule.insert(ExcludedHydrogens.begin(), ExcludedHydrogens.end());
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238 | }
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239 |
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240 | // go through all cut bonds and replace with a hydrogen
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241 | if (saturation == DoSaturate) {
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242 | for (CutBonds_t::const_iterator atomiter = CutBonds.begin();
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243 | atomiter != CutBonds.end(); ++atomiter) {
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244 | atom * const Walker = atomiter->first;
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245 | LOG(4, "DEBUG: We are now saturating dangling bonds of " << *Walker);
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246 |
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247 | // gather set of positions for this atom from global map
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248 | GlobalSaturationPositions_t::const_iterator mapiter =
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249 | _globalsaturationpositions.find(Walker->getId());
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250 | ASSERT( mapiter != _globalsaturationpositions.end(),
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251 | "SaturatedFragment::saturate() - no global information for "
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252 | +toString(*Walker));
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253 | const SaturationsPositionsPerNeighbor_t &saturationpositions =
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254 | mapiter->second;
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255 |
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256 | // go through all cut bonds for this atom
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257 | for (BondList::const_iterator bonditer = atomiter->second.begin();
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258 | bonditer != atomiter->second.end(); ++bonditer) {
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259 | atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
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260 |
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261 | // get positions from global map
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262 | SaturationsPositionsPerNeighbor_t::const_iterator positionsiter =
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263 | saturationpositions.find(OtherWalker->getId());
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264 | ASSERT(positionsiter != saturationpositions.end(),
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265 | "SaturatedFragment::saturate() - no information on bond neighbor "
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266 | +toString(*OtherWalker)+" to atom "+toString(*Walker));
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267 | ASSERT(!positionsiter->second.empty(),
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268 | "SaturatedFragment::saturate() - no positions for saturating bond to"
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269 | +toString(*OtherWalker)+" to atom "+toString(*Walker));
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270 |
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271 | // // get typical bond distance from elements database
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272 | // double BondDistance = Walker->getType()->getHBondDistance(positionsiter->second.size()-1);
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273 | // if (BondDistance < 0.) {
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274 | // ELOG(2, "saturateAtoms() - no typical hydrogen bond distance of degree "
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275 | // +toString(positionsiter->second.size())+" for element "
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276 | // +toString(Walker->getType()->getName()));
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277 | // // try bond degree 1 distance
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278 | // BondDistance = Walker->getType()->getHBondDistance(1-1);
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279 | // if (BondDistance < 0.) {
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280 | // ELOG(1, "saturateAtoms() - no typical hydrogen bond distance for element "
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281 | // +toString(Walker->getType()->getName()));
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282 | // BondDistance = 1.;
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283 | // }
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284 | // }
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285 |
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286 | // place hydrogen at each point
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287 | LOG(4, "DEBUG: Places to saturate for atom " << *OtherWalker
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288 | << " are " << positionsiter->second);
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289 | atom * const father = Walker;
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290 | for (SaturationsPositions_t::const_iterator positer = positionsiter->second.begin();
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291 | positer != positionsiter->second.end(); ++positer) {
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292 | const atom& hydrogen =
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293 | setHydrogenReplacement(Walker, *positer, 1., father);
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294 | FullMolecule.insert(hydrogen.getId());
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295 | }
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296 | }
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297 | }
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298 | } else
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299 | LOG(3, "INFO: We are not saturating cut bonds.");
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300 | }
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301 |
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302 | const atom& SaturatedFragment::setHydrogenReplacement(
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303 | const atom * const _OwnerAtom,
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304 | const Vector &_position,
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305 | const double _distance,
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306 | atom * const _father)
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307 | {
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308 | atom * const _atom = hydrogens.leaseHydrogen(); // new atom
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309 | _atom->setPosition( _OwnerAtom->getPosition() + _distance * _position );
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310 | // always set as fixed ion (not moving during molecular dynamics simulation)
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311 | _atom->setFixedIon(true);
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312 | // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
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313 | _atom->father = _father;
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314 | SaturationHydrogens.insert(_atom->getId());
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315 |
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316 | return *_atom;
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317 | }
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318 |
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319 | bool SaturatedFragment::saturateAtom(
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320 | atom * const _atom,
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321 | const BondList &_cutbonds)
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322 | {
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323 | // go through each bond and replace
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324 | for (BondList::const_iterator bonditer = _cutbonds.begin();
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325 | bonditer != _cutbonds.end(); ++bonditer) {
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326 | atom * const OtherWalker = (*bonditer)->GetOtherAtom(_atom);
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327 | if (!AddHydrogenReplacementAtom(
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328 | (*bonditer),
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329 | _atom,
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330 | OtherWalker,
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331 | World::getInstance().getConfig()->IsAngstroem == 1))
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332 | return false;
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333 | }
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334 | return true;
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335 | }
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336 |
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337 | bool SaturatedFragment::OutputConfig(
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338 | std::ostream &out,
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339 | const ParserTypes _type) const
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340 | {
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341 | // gather all atoms in a vector
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342 | std::vector<atom *> atoms;
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343 | for (KeySet::const_iterator iter = FullMolecule.begin();
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344 | iter != FullMolecule.end();
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345 | ++iter) {
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346 | atom * const Walker = World::getInstance().getAtom(AtomById(*iter));
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347 | ASSERT( Walker != NULL,
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348 | "SaturatedFragment::OutputConfig() - id "
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349 | +toString(*iter)+" is unknown to World.");
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350 | atoms.push_back(Walker);
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351 | }
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352 |
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353 | // TODO: ScanForPeriodicCorrection() is missing so far!
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354 | // note however that this is not straight-forward for the following reasons:
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355 | // - we do not copy all atoms anymore, hence we are forced to shift the real
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356 | // atoms hither and back again
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357 | // - we use a long-range potential that supports periodic boundary conditions.
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358 | // Hence, there we would like the original configuration (split through the
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359 | // the periodic boundaries). Otherwise, we would have to shift (and probably
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360 | // interpolate) the potential with OBCs applying.
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361 |
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362 | // list atoms in fragment for debugging
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363 | {
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364 | std::stringstream output;
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365 | output << "INFO: Contained atoms: ";
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366 | for (std::vector<atom *>::const_iterator iter = atoms.begin();
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367 | iter != atoms.end(); ++iter) {
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368 | output << (*iter)->getName() << " ";
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369 | }
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370 | LOG(3, output.str());
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371 | }
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372 |
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373 | // store to stream via FragmentParser
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374 | const bool intermediateResult =
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375 | FormatParserStorage::getInstance().save(
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376 | out,
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377 | FormatParserStorage::getInstance().getSuffixFromType(_type),
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378 | atoms);
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379 |
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380 | return intermediateResult;
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381 | }
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382 |
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383 | atom * const SaturatedFragment::getHydrogenReplacement(atom * const replacement)
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384 | {
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385 | atom * const _atom = hydrogens.leaseHydrogen(); // new atom
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386 | _atom->setAtomicVelocity(replacement->getAtomicVelocity()); // copy velocity
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387 | _atom->setFixedIon(replacement->getFixedIon());
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388 | // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
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389 | _atom->father = replacement;
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390 | SaturationHydrogens.insert(_atom->getId());
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391 | return _atom;
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392 | }
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393 |
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394 | bool SaturatedFragment::AddHydrogenReplacementAtom(
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395 | bond::ptr TopBond,
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396 | atom *Origin,
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397 | atom *Replacement,
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398 | bool IsAngstroem)
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399 | {
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400 | // Info info(__func__);
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401 | bool AllWentWell = true; // flag gathering the boolean return value of molecule::AddAtom and other functions, as return value on exit
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402 | double bondlength; // bond length of the bond to be replaced/cut
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403 | double bondangle; // bond angle of the bond to be replaced/cut
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404 | double BondRescale; // rescale value for the hydrogen bond length
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405 | bond::ptr FirstBond;
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406 | bond::ptr SecondBond; // Other bonds in double bond case to determine "other" plane
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407 | atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
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408 | double b,l,d,f,g, alpha, factors[NDIM]; // hold temporary values in triple bond case for coordination determination
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409 | Vector Orthovector1, Orthovector2; // temporary vectors in coordination construction
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410 | Vector InBondvector; // vector in direction of *Bond
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411 | const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
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412 | bond::ptr Binder;
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413 |
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414 | // create vector in direction of bond
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415 | InBondvector = Replacement->getPosition() - Origin->getPosition();
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416 | bondlength = InBondvector.Norm();
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417 |
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418 | // is greater than typical bond distance? Then we have to correct periodically
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419 | // the problem is not the H being out of the box, but InBondvector have the wrong direction
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420 | // due to Replacement or Origin being on the wrong side!
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421 | const BondGraph * const BG = World::getInstance().getBondGraph();
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422 | const range<double> MinMaxBondDistance(
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423 | BG->getMinMaxDistance(Origin,Replacement));
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424 | if (!MinMaxBondDistance.isInRange(bondlength)) {
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425 | // LOG(4, "InBondvector is: " << InBondvector << ".");
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426 | Orthovector1.Zero();
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427 | for (int i=NDIM;i--;) {
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428 | l = Replacement->at(i) - Origin->at(i);
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429 | if (fabs(l) > MinMaxBondDistance.last) { // is component greater than bond distance (check against min not useful here)
|
---|
430 | Orthovector1[i] = (l < 0) ? -1. : +1.;
|
---|
431 | } // (signs are correct, was tested!)
|
---|
432 | }
|
---|
433 | Orthovector1 *= matrix;
|
---|
434 | InBondvector -= Orthovector1; // subtract just the additional translation
|
---|
435 | bondlength = InBondvector.Norm();
|
---|
436 | // LOG(4, "INFO: Corrected InBondvector is now: " << InBondvector << ".");
|
---|
437 | } // periodic correction finished
|
---|
438 |
|
---|
439 | InBondvector.Normalize();
|
---|
440 | // get typical bond length and store as scale factor for later
|
---|
441 | ASSERT(Origin->getType() != NULL,
|
---|
442 | "SaturatedFragment::AddHydrogenReplacementAtom() - element of Origin is not given.");
|
---|
443 | BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree()-1);
|
---|
444 | if (BondRescale == -1) {
|
---|
445 | ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
|
---|
446 | BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree());
|
---|
447 | if (BondRescale == -1) {
|
---|
448 | ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of any degree!");
|
---|
449 | return false;
|
---|
450 | BondRescale = bondlength;
|
---|
451 | }
|
---|
452 | } else {
|
---|
453 | if (!IsAngstroem)
|
---|
454 | BondRescale /= (1.*AtomicLengthToAngstroem);
|
---|
455 | }
|
---|
456 |
|
---|
457 | // discern single, double and triple bonds
|
---|
458 | switch(TopBond->getDegree()) {
|
---|
459 | case 1:
|
---|
460 | // check whether replacement has been an excluded hydrogen
|
---|
461 | if (Replacement->getType()->getAtomicNumber() == HydrogenPool::HYDROGEN) { // neither rescale nor replace if it's already hydrogen
|
---|
462 | FirstOtherAtom = Replacement;
|
---|
463 | BondRescale = bondlength;
|
---|
464 | } else {
|
---|
465 | FirstOtherAtom = getHydrogenReplacement(Replacement);
|
---|
466 | InBondvector *= BondRescale; // rescale the distance vector to Hydrogen bond length
|
---|
467 | FirstOtherAtom->setPosition(Origin->getPosition() + InBondvector); // set coordination to origin and add distance vector to replacement atom
|
---|
468 | }
|
---|
469 | FullMolecule.insert(FirstOtherAtom->getId());
|
---|
470 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
471 | break;
|
---|
472 | case 2:
|
---|
473 | {
|
---|
474 | // determine two other bonds (warning if there are more than two other) plus valence sanity check
|
---|
475 | const BondList& ListOfBonds = Origin->getListOfBonds();
|
---|
476 | for (BondList::const_iterator Runner = ListOfBonds.begin();
|
---|
477 | Runner != ListOfBonds.end();
|
---|
478 | ++Runner) {
|
---|
479 | if ((*Runner) != TopBond) {
|
---|
480 | if (FirstBond == NULL) {
|
---|
481 | FirstBond = (*Runner);
|
---|
482 | FirstOtherAtom = (*Runner)->GetOtherAtom(Origin);
|
---|
483 | } else if (SecondBond == NULL) {
|
---|
484 | SecondBond = (*Runner);
|
---|
485 | SecondOtherAtom = (*Runner)->GetOtherAtom(Origin);
|
---|
486 | } else {
|
---|
487 | ELOG(2, "Detected more than four bonds for atom " << Origin->getName());
|
---|
488 | }
|
---|
489 | }
|
---|
490 | }
|
---|
491 | }
|
---|
492 | 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)
|
---|
493 | SecondBond = TopBond;
|
---|
494 | SecondOtherAtom = Replacement;
|
---|
495 | }
|
---|
496 | if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
|
---|
497 | // LOG(3, "Regarding the double bond (" << Origin->Name << "<->" << Replacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << Origin->Name << " to determine orthogonal plane.");
|
---|
498 |
|
---|
499 | // determine the plane of these two with the *origin
|
---|
500 | try {
|
---|
501 | Orthovector1 = Plane(Origin->getPosition(), FirstOtherAtom->getPosition(), SecondOtherAtom->getPosition()).getNormal();
|
---|
502 | }
|
---|
503 | catch(LinearDependenceException &excp){
|
---|
504 | LOG(0, boost::diagnostic_information(excp));
|
---|
505 | // TODO: figure out what to do with the Orthovector in this case
|
---|
506 | AllWentWell = false;
|
---|
507 | }
|
---|
508 | } else {
|
---|
509 | Orthovector1.GetOneNormalVector(InBondvector);
|
---|
510 | }
|
---|
511 | //LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
512 | // orthogonal vector and bond vector between origin and replacement form the new plane
|
---|
513 | Orthovector1.MakeNormalTo(InBondvector);
|
---|
514 | Orthovector1.Normalize();
|
---|
515 | //LOG(3, "ReScaleCheck: " << Orthovector1.Norm() << " and " << InBondvector.Norm() << ".");
|
---|
516 |
|
---|
517 | // create the two Hydrogens ...
|
---|
518 | FirstOtherAtom = getHydrogenReplacement(Replacement);
|
---|
519 | SecondOtherAtom = getHydrogenReplacement(Replacement);
|
---|
520 | FullMolecule.insert(FirstOtherAtom->getId());
|
---|
521 | FullMolecule.insert(SecondOtherAtom->getId());
|
---|
522 | bondangle = Origin->getType()->getHBondAngle(1);
|
---|
523 | if (bondangle == -1) {
|
---|
524 | ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
|
---|
525 | return false;
|
---|
526 | bondangle = 0;
|
---|
527 | }
|
---|
528 | bondangle *= M_PI/180./2.;
|
---|
529 | // LOG(3, "INFO: ReScaleCheck: InBondvector " << InBondvector << ", " << Orthovector1 << ".");
|
---|
530 | // LOG(3, "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle));
|
---|
531 | FirstOtherAtom->Zero();
|
---|
532 | SecondOtherAtom->Zero();
|
---|
533 | for(int i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondvector is bondangle = 0 direction)
|
---|
534 | FirstOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (sin(bondangle)));
|
---|
535 | SecondOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (-sin(bondangle)));
|
---|
536 | }
|
---|
537 | FirstOtherAtom->Scale(BondRescale); // rescale by correct BondDistance
|
---|
538 | SecondOtherAtom->Scale(BondRescale);
|
---|
539 | //LOG(3, "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << ".");
|
---|
540 | *FirstOtherAtom += Origin->getPosition();
|
---|
541 | *SecondOtherAtom += Origin->getPosition();
|
---|
542 | // ... and add to molecule
|
---|
543 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
544 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
545 | break;
|
---|
546 | case 3:
|
---|
547 | // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
|
---|
548 | FirstOtherAtom = getHydrogenReplacement(Replacement);
|
---|
549 | SecondOtherAtom = getHydrogenReplacement(Replacement);
|
---|
550 | ThirdOtherAtom = getHydrogenReplacement(Replacement);
|
---|
551 | FullMolecule.insert(FirstOtherAtom->getId());
|
---|
552 | FullMolecule.insert(SecondOtherAtom->getId());
|
---|
553 | FullMolecule.insert(ThirdOtherAtom->getId());
|
---|
554 |
|
---|
555 | // we need to vectors orthonormal the InBondvector
|
---|
556 | AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(InBondvector);
|
---|
557 | // LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
|
---|
558 | try{
|
---|
559 | Orthovector2 = Plane(InBondvector, Orthovector1,0).getNormal();
|
---|
560 | }
|
---|
561 | catch(LinearDependenceException &excp) {
|
---|
562 | LOG(0, boost::diagnostic_information(excp));
|
---|
563 | AllWentWell = false;
|
---|
564 | }
|
---|
565 | // LOG(3, "INFO: Orthovector2: " << Orthovector2 << ".")
|
---|
566 |
|
---|
567 | // create correct coordination for the three atoms
|
---|
568 | alpha = (Origin->getType()->getHBondAngle(2))/180.*M_PI/2.; // retrieve triple bond angle from database
|
---|
569 | l = BondRescale; // desired bond length
|
---|
570 | b = 2.*l*sin(alpha); // base length of isosceles triangle
|
---|
571 | d = l*sqrt(cos(alpha)*cos(alpha) - sin(alpha)*sin(alpha)/3.); // length for InBondvector
|
---|
572 | f = b/sqrt(3.); // length for Orthvector1
|
---|
573 | g = b/2.; // length for Orthvector2
|
---|
574 | // LOG(3, "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", ");
|
---|
575 | // 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));
|
---|
576 | factors[0] = d;
|
---|
577 | factors[1] = f;
|
---|
578 | factors[2] = 0.;
|
---|
579 | FirstOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
580 | factors[1] = -0.5*f;
|
---|
581 | factors[2] = g;
|
---|
582 | SecondOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
583 | factors[2] = -g;
|
---|
584 | ThirdOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
|
---|
585 |
|
---|
586 | // rescale each to correct BondDistance
|
---|
587 | // FirstOtherAtom->x.Scale(&BondRescale);
|
---|
588 | // SecondOtherAtom->x.Scale(&BondRescale);
|
---|
589 | // ThirdOtherAtom->x.Scale(&BondRescale);
|
---|
590 |
|
---|
591 | // and relative to *origin atom
|
---|
592 | *FirstOtherAtom += Origin->getPosition();
|
---|
593 | *SecondOtherAtom += Origin->getPosition();
|
---|
594 | *ThirdOtherAtom += Origin->getPosition();
|
---|
595 |
|
---|
596 | // ... and add to molecule
|
---|
597 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
|
---|
598 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
|
---|
599 | // LOG(4, "INFO: Added " << *ThirdOtherAtom << " at: " << ThirdOtherAtom->x << ".");
|
---|
600 | break;
|
---|
601 | default:
|
---|
602 | ELOG(1, "BondDegree does not state single, double or triple bond!");
|
---|
603 | AllWentWell = false;
|
---|
604 | break;
|
---|
605 | }
|
---|
606 |
|
---|
607 | return AllWentWell;
|
---|
608 | };
|
---|