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1 NAME
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2 Fingerprints - Fingerprints class
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3
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4 SYNOPSIS
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5 use Fingerprints::Fingerprints;
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6
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7 use Fingerprints::Fingerprints qw(:all);
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8
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9 DESCRIPTION
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10 Fingerprints class provides the following methods:
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11
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12 new, FoldFingerprintsByBitDensity, FoldFingerprintsBySize,
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13 GetFingerprintBitsAsBinaryString, GetFingerprintBitsAsHexadecimalString,
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14 GetFingerprintBitsAsRawBinaryString, GetFingerprintsVectorValueIDs,
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15 GetFingerprintsVectorValues, IsFingerprintsGenerationSuccessful,
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16 SetFingerprintsBitVector, SetFingerprintsVector,
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17 SetFingerprintsVectorType, SetMolecule, SetSize, SetType, SetVectorType
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18
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19 Fingerprints class is used as a base class for various specific
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20 fingerprint classes such as AtomNeighborhoodsFingerprints,
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21 AtomTypesFingerprints, EStateIndiciesFingerprints,
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22 PathLengthFingerprints, ExtendedConnectivityFingerprints, MACCSKeys and
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23 so on. It implements functionality common to fingerprint classes.
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24
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25 Fingerprints class is derived from ObjectProperty base class which
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26 provides methods not explicitly defined in Fingerprints or
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27 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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28 methods are generated on-the-fly for a specified object property:
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29
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30 Set<PropertyName>(<PropertyValue>);
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31 $PropertyValue = Get<PropertyName>();
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32 Delete<PropertyName>();
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33
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34 Fingerprints class uses FingerprintsBitVector class to provide bits
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35 manipulation functionality.
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36
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37 METHODS
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38 new
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39 $NewFingerprints = new Fingerprints(%NamesAndValues);
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40
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41 Using specified *Fingerprints* property names and values hash, new
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42 method creates a new object and returns a reference to newly created
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43 Fingerprints object. By default, following properties are
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44 initialized:
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45
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46 Molecule = '';
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47 Type = '';
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48 VectorType = '';
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49 Size = '';
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50 MinSize = '';
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51 MaxSize = '';
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52 FingerprintsBitVector = '';
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53 FingerprintsVectorType = '';
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54 FingerprintsVector = '';
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55
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56 FoldFingerprintsByBitDensity
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57 $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);
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58
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59 Folds fingerprints by recursively reducing its size by half until
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60 bit density is greater than or equal to specified *BitDensity* and
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61 returns *Fingerprints*.
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62
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63 FoldFingerprintsBySize
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64 $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);
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65
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66 Fold fingerprints by recursively reducing its size by half until
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67 size is less than or equal to specified *Size* and returns
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68 *Fingerprints*. By default, value *Size* is checked to make sure
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69 it's:
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70
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71 >= MinSize and < Size and IsPowerOfTwo
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72
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73 GetFingerprintBitsAsBinaryString
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74 $BinaryASCIIString =
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75 $Fingerprints->GetFingerprintBitsAsBinaryString();
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76
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77 Returns fingerprints as a binary ASCII string containing 0s and 1s.
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78
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79 GetFingerprintBitsAsHexadecimalString
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80 $HexadecimalString =
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81 $Fingerprints->GetFingerprintBitsAsHexadecimalString();
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82
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83 Returns fingerprints as a hexadecimal string
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84
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85 GetFingerprintBitsAsRawBinaryString
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86 $RawBinaryString =
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87 $Fingerprints->GetFingerprintBitsAsRawBinaryString();
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88
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89 Returns fingerprints as a raw binary string containing packed bit
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90 values for each byte.
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91
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92 GetFingerprintsVectorValueIDs
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93 $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs();
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94 @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();
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95
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96 Returns fingerprints vector value IDs as an array or reference to an
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97 array.
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98
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99 GetFingerprintsVectorValues
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100 $ValuesRef = $Fingerprints->GetFingerprintsVectorValues();
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101 @Values = $Fingerprints->GetFingerprintsVectorValues();
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102
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103 Returns fingerprints vector values as an array or reference to an
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104 array.
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105
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106 IsFingerprintsGenerationSuccessful
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107 $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();
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108
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109 Returns 1 or 0 based on whether fingerprints were successfully
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110 generated.
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111
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112 SetFingerprintsBitVector
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113 $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);
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114
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115 Sets *FingerprintsBitVector* object for *Fingerprints* and returns
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116 *Fingerprints*.
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117
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118 SetFingerprintsVector
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119 $Fingerprints->SetFingerprintsVector();
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120
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121 Sets *FingerprintsVector* object for *Fingerprints* and returns
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122 *Fingerprints*.
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123
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124 SetFingerprintsVectorType
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125 $Fingerprints->SetFingerprintsVectorType($VectorType);
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126
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127 Sets *FingerprintsVector* type for *Fingerprints* and returns
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128 *Fingerprints*. Possible *VectorType* values:
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129 *OrderedNumericalValues, NumericalValues or AlphaNumericalValues*.
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130
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131 SetMolecule
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132 $Fingerprints->SetMolecule($Molecule);
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133
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134 Sets *Molecule* object for *Fingerprints* and returns
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135 *Fingerprints*.
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136
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137 SetSize
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138 $Fingerprints->SetSize($Size);
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139
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140 Sets *Size* of fingerprints and returns *Fingerprints*.
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141
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142 SetType
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143 $Fingerprints->SetType($Type);
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144
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145 Sets *Type* of fingerprints and returns *Fingerprints*.
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146
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147 SetVectorType
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148 $Fingerprints->SetVectorType($Type);
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149
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150 Sets *Type* of fingerprints vector and returns *Fingerprints*.
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151 Possible *Type* values: *FingerprintsBitVector or
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152 FingerprintsVector*.
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153
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154 AUTHOR
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155 Manish Sud <msud@san.rr.com>
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156
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157 SEE ALSO
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158 FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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159 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
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160 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm,
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161 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
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162 TopologicalAtomTripletsFingerprints.pm,
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163 TopologicalAtomTorsionsFingerprints.pm,
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164 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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165 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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166
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167 COPYRIGHT
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168 Copyright (C) 2015 Manish Sud. All rights reserved.
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169
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170 This file is part of MayaChemTools.
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171
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172 MayaChemTools is free software; you can redistribute it and/or modify it
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173 under the terms of the GNU Lesser General Public License as published by
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174 the Free Software Foundation; either version 3 of the License, or (at
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175 your option) any later version.
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176
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