1 | /*
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2 | * bondgraph.cpp
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3 | *
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4 | * Created on: Oct 29, 2009
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5 | * Author: heber
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6 | */
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7 |
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8 | #include <iostream>
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9 |
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10 | #include "atom.hpp"
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11 | #include "bond.hpp"
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12 | #include "bondgraph.hpp"
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13 | #include "element.hpp"
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14 | #include "info.hpp"
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15 | #include "log.hpp"
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16 | #include "molecule.hpp"
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17 | #include "parser.hpp"
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18 | #include "periodentafel.hpp"
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19 | #include "vector.hpp"
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20 |
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21 | /** Constructor of class BondGraph.
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22 | * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
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23 | */
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24 | BondGraph::BondGraph(bool IsA) : BondLengthMatrix(NULL), max_distance(0), IsAngstroem(IsA)
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25 | {
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26 | };
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27 |
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28 | /** Destructor of class BondGraph.
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29 | */
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30 | BondGraph::~BondGraph()
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31 | {
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32 | if (BondLengthMatrix != NULL) {
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33 | delete(BondLengthMatrix);
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34 | }
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35 | };
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36 |
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37 | /** Parses the bond lengths in a given file and puts them int a matrix form.
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38 | * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
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39 | * but only if parsing is successful. Otherwise variable is left as NULL.
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40 | * \param *out output stream for debugging
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41 | * \param filename file with bond lengths to parse
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42 | * \return true - success in parsing file, false - failed to parse the file
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43 | */
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44 | bool BondGraph::LoadBondLengthTable(const string &filename)
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45 | {
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46 | Info FunctionInfo(__func__);
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47 | bool status = true;
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48 | MatrixContainer *TempContainer = NULL;
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49 |
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50 | // allocate MatrixContainer
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51 | if (BondLengthMatrix != NULL) {
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52 | DoLog(1) && (Log() << Verbose(1) << "MatrixContainer for Bond length already present, removing." << endl);
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53 | delete(BondLengthMatrix);
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54 | }
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55 | TempContainer = new MatrixContainer;
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56 |
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57 | // parse in matrix
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58 | if ((status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0))) {
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59 | DoLog(1) && (Log() << Verbose(1) << "Parsing bond length matrix successful." << endl);
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60 | } else {
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61 | DoeLog(1) && (eLog()<< Verbose(1) << "Parsing bond length matrix failed." << endl);
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62 | }
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63 |
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64 | // find greatest distance
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65 | max_distance=0;
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66 | if (status) {
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67 | for(int i=0;i<TempContainer->RowCounter[0];i++)
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68 | for(int j=i;j<TempContainer->ColumnCounter[0];j++)
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69 | if (TempContainer->Matrix[0][i][j] > max_distance)
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70 | max_distance = TempContainer->Matrix[0][i][j];
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71 | }
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72 |
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73 | if (status) // set to not NULL only if matrix was parsed
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74 | BondLengthMatrix = TempContainer;
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75 | else {
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76 | BondLengthMatrix = NULL;
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77 | delete(TempContainer);
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78 | }
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79 | return status;
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80 | };
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81 |
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82 | /** Parses the bond lengths in a given file and puts them int a matrix form.
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83 | * \param *out output stream for debugging
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84 | * \param *mol molecule with atoms
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85 | * \return true - success, false - failed to construct bond structure
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86 | */
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87 | bool BondGraph::ConstructBondGraph(molecule * const mol)
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88 | {
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89 | Info FunctionInfo(__func__);
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90 | bool status = true;
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91 |
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92 | if (mol->empty()) // only construct if molecule is not empty
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93 | return false;
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94 |
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95 | if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
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96 | SetMaxDistanceToMaxOfCovalentRadii(mol);
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97 | mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
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98 | } else
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99 | mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
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100 |
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101 | return status;
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102 | };
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103 |
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104 | /** Returns the entry for a given index pair.
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105 | * \param firstelement index/atom number of first element (row index)
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106 | * \param secondelement index/atom number of second element (column index)
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107 | * \note matrix is of course symmetric.
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108 | */
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109 | double BondGraph::GetBondLength(int firstZ, int secondZ)
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110 | {
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111 | if (BondLengthMatrix == NULL)
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112 | return( -1. );
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113 | else
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114 | return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
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115 | };
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116 |
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117 | /** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
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118 | * \param *out output stream for debugging
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119 | * \param *mol molecule with all atoms and their respective elements.
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120 | */
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121 | double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol)
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122 | {
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123 | Info FunctionInfo(__func__);
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124 | max_distance = 0.;
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125 |
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126 | for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
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127 | if ((*iter)->type->CovalentRadius > max_distance)
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128 | max_distance = (*iter)->type->CovalentRadius;
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129 | }
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130 | max_distance *= 2.;
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131 |
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132 | return max_distance;
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133 | };
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134 |
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135 | /** Returns bond criterion for given pair based on covalent radius.
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136 | * \param *Walker first BondedParticle
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137 | * \param *OtherWalker second BondedParticle
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138 | * \param &MinDistance lower bond bound on return
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139 | * \param &MaxDistance upper bond bound on return
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140 | * \param IsAngstroem whether units are in angstroem or bohr radii
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141 | */
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142 | void BondGraph::CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
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143 | {
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144 | MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;
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145 | MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
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146 | MaxDistance = MinDistance + BONDTHRESHOLD;
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147 | MinDistance -= BONDTHRESHOLD;
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148 | };
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149 |
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150 | /** Returns bond criterion for given pair based on a bond length matrix.
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151 | * The matrix should be contained in \a this BondGraph and contain an element-
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152 | * to-element length.
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153 | * \param *Walker first BondedParticle
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154 | * \param *OtherWalker second BondedParticle
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155 | * \param &MinDistance lower bond bound on return
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156 | * \param &MaxDistance upper bond bound on return
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157 | * \param IsAngstroem whether units are in angstroem or bohr radii
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158 | */
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159 | void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
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160 | {
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161 | if (BondLengthMatrix == NULL) {// safety measure if no matrix has been parsed yet
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162 | DoeLog(2) && (eLog()<< Verbose(2) << "BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl);
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163 | CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
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164 | } else {
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165 | MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
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166 | MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
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167 | MaxDistance = MinDistance + BONDTHRESHOLD;
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168 | MinDistance -= BONDTHRESHOLD;
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169 | }
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170 | };
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