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1 NAME
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2 EStateIndiciesFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::EStateIndiciesFingerprints;
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6
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7 use Fingerprints::EStateIndiciesFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 EStateIndiciesFingerprints [ Ref 75-78 ] class provides the following
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11 methods:
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12
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13 new, GenerateFingerprints, GetDescription, SetEStateAtomTypesSetToUse,
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14 SetValuesPrecision, StringifyEStateIndiciesFingerprints
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15
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16 EStateIndiciesFingerprints is derived from Fingerprints class which in
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17 turn is derived from ObjectProperty base class that provides methods not
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18 explicitly defined in AtomNeighborhoodsFingerprints, Fingerprints or
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19 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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20 methods are generated on-the-fly for a specified object property:
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21
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22 Set<PropertyName>(<PropertyValue>);
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23 $PropertyValue = Get<PropertyName>();
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24 Delete<PropertyName>();
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25
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26 E-state atom types are assigned to all non-hydrogen atoms in a molecule
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27 using module AtomTypes::EStateAtomTypes.pm and E-state values are
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28 calculated using module AtomicDescriptors::EStateValues.pm. Using
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29 E-state atom types and E-state values, EStateIndiciesFingerprints
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30 constituting sum of E-state values for E-sate atom types are generated.
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31
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32 Two types of E-state atom types set size are allowed:
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33
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34 ArbitrarySize - Corresponds to only E-state atom types detected
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35 in molecule
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36 FixedSize - Corresponds to fixed number of E-state atom types previously
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37 defined
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38
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39 Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types
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40 to non-hydrogen atoms in the molecule, is able to assign atom types to
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41 any valid atom group. However, for *FixedSize* value of
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42 EStateAtomTypesSetToUse, only a fixed set of E-state atom types
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43 corresponding to specific atom groups [ Appendix III in Ref 77 ] are
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44 used for fingerprints.
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45
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46 The fixed size E-state atom type set size used during generation of
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47 fingerprints contains 87 E-state non-hydrogen atom types in
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48 EStateAtomTypes.csv data file distributed with MayaChemTools.
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49
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50 Combination of Type and EStateAtomTypesSetToUse allow generation of 2
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51 different types of E-state indicies fingerprints:
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52
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53 Type EStateAtomTypesSetToUse
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54
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55 EStateIndicies ArbitrarySize [ default fingerprints ]
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56 EStateIndicies FixedSize
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57
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58 The current release of MayaChemTools generates the following types of
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59 E-state fingerprints vector strings:
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60
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61 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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62 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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63 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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64 .024 -2.270
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65
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66 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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67 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
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68 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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69 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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70 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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71
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72 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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73 IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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74 SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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75 C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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76 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
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77 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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79
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80 METHODS
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81 new
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82 $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);
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83
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84 Using specified *EStateIndiciesFingerprints* property names and
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85 values hash, new method creates a new object and returns a reference
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86 to newly created PathLengthFingerprints object. By default, the
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87 following properties are initialized:
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88
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89 Molecule = '';
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90 Type = 'EStateIndicies'
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91 EStateAtomTypesSetToUse = 'ArbitrarySize'
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92 ValuesPrecision = 3
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93
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94 Examples:
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95
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96 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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97 'Molecule' => $Molecule,
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98 'EStateAtomTypesSetToUse' =>
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99 'ArbitrarySize');
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100
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101 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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102 'Molecule' => $Molecule,
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103 'EStateAtomTypesSetToUse' =>
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104 'FixedSize');
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105
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106 $EStateIndiciesFingerprints->GenerateFingerprints();
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107 print "$EStateIndiciesFingerprints\n";
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108
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109 GenerateFingerprints
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110 $EStateIndiciesFingerprints = $EStateIndiciesFingerprints->
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111 GenerateEStateIndiciesFingerprints();
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112
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113 Generates EState keys fingerprints and returns
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114 *EStateIndiciesFingerprints*.
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115
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116 GetDescription
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117 $Description = $EStateIndiciesFingerprints->GetDescription();
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118
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119 Returns a string containing description of EState keys fingerprints.
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120
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121 SetEStateAtomTypesSetToUse
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122 $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($Value);
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123
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124 Sets *Value* of *EStateAtomTypesSetToUse* and returns
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125 *EStateIndiciesFingerprints*. Possible values: *ArbitrarySize or
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126 FixedSize*. Default value: *ArbitrarySize*.
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127
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128 SetValuesPrecision
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129 $EStateIndiciesFingerprints->SetValuesPrecision($Precision);
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130
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131 Sets precesion of E-state values to use during generation of E-state
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132 indices fingerprints and returns *EStateIndiciesFingerprints*.
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133 Possible values: *Positive integers*. Default value: *3*.
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134
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135 StringifyEStateIndiciesFingerprints
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136 $String = $EStateIndiciesFingerprints->StringifyEStateIndiciesFingerprints();
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137
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138 Returns a string containing information about
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139 *EStateIndiciesFingerprints* object.
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140
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141 AUTHOR
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142 Manish Sud <msud@san.rr.com>
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143
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144 SEE ALSO
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145 Fingerprints.pm, FingerprintsStringUtil.pm,
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146 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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147 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm,
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148 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
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149 TopologicalAtomTripletsFingerprints.pm,
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150 TopologicalAtomTorsionsFingerprints.pm,
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151 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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152 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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153
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154 COPYRIGHT
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155 Copyright (C) 2015 Manish Sud. All rights reserved.
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156
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157 This file is part of MayaChemTools.
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158
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159 MayaChemTools is free software; you can redistribute it and/or modify it
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160 under the terms of the GNU Lesser General Public License as published by
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161 the Free Software Foundation; either version 3 of the License, or (at
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162 your option) any later version.
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163
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