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1 package Fingerprints::Fingerprints;
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2 #
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3 # $RCSfile: Fingerprints.pm,v $
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4 # $Date: 2015/02/28 20:48:54 $
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5 # $Revision: 1.33 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Exporter;
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32 use Scalar::Util ();
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33 use ObjectProperty;
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34 use MathUtil ();
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35 use TextUtil ();
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36 use Fingerprints::FingerprintsBitVector;
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37 use Fingerprints::FingerprintsVector;
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38
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39 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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40
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41 @ISA = qw(ObjectProperty Exporter);
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42 @EXPORT = qw();
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43 @EXPORT_OK = qw();
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44
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45 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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46
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47 # Setup class variables...
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48 my($ClassName);
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49 _InitializeClass();
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50
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51 # Class constructor...
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52 sub new {
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53 my($Class, %NamesAndValues) = @_;
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54
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55 # Initialize object...
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56 my $This = {};
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57 bless $This, ref($Class) || $Class;
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58 $This->_InitializeFingerprints();
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59
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60 $This->_InitializeFingerprintsProperties(%NamesAndValues);
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61
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62 return $This;
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63 }
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64
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65 # Initialize object data...
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66 #
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67 sub _InitializeFingerprints {
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68 my($This) = @_;
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69
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70 # Molecule object...
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71 $This->{Molecule} = '';
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72
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73 # Type of fingerprints...
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74 $This->{Type} = '';
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75
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76 # Type of fingerprints vector: FingerprintsBitVector or FingerprintsVector...
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77 $This->{VectorType} = '';
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78
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79 # Marks successful generation of fingerprints...
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80 $This->{FingerprintsGenerated} = 0;
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81
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82 # Initialize values for FingerprintsBitVector...
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83 _InitializeClassValuesForFingerprintsBitVector();
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84
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85 # Initialize values for FingerprintsVector...
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86 _InitializeClassValuesForFingerprintsVector();
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87 }
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88
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89 # Initialize class ...
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90 sub _InitializeClass {
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91 #Class name...
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92 $ClassName = __PACKAGE__;
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93 }
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94
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95 # Initialize class values specific to FingerprintsBitVector...
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96 #
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97 sub _InitializeClassValuesForFingerprintsBitVector {
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98 my($This) = @_;
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99
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100 # Size of FingerprintsBitVector...
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101 $This->{Size} = '';
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102
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103 # Min/Max sizes used for folding FingerprintsBitVector...
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104 $This->{MinSize} = '';
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105 $This->{MaxSize} = '';
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106
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107 # FingerprintsBitVector...
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108 $This->{FingerprintsBitVector} = '';
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109 }
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110
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111 # Initialize class values specific to FingerprintsVector...
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112 #
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113 sub _InitializeClassValuesForFingerprintsVector {
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114 my($This) = @_;
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115
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116 # Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.
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117 $This->{FingerprintsVectorType} = '';
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118
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119 # Fingerprints vector...
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120 $This->{FingerprintsVector} = '';
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121 }
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122
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123 # Initialize object properties....
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124 sub _InitializeFingerprintsProperties {
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125 my($This, %NamesAndValues) = @_;
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126
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127 my($Name, $Value, $MethodName);
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128 while (($Name, $Value) = each %NamesAndValues) {
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129 $MethodName = "Set${Name}";
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130 $This->$MethodName($Value);
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131 }
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132
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133 return $This;
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134 }
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135
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136 # Set molecule object and make sure it's not already set...
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137 #
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138 sub SetMolecule {
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139 my($This, $Molecule) = @_;
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140
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141 if ($This->{Molecule}) {
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142 croak "Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set...";
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143 }
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144 $This->{Molecule} = $Molecule;
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145
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146 # Weaken the reference to disable increment of reference count...
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147 Scalar::Util::weaken($This->{Molecule});
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148
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149 return $This;
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150 }
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151
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152 # Set type and make sure it's not already set...
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153 #
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154 sub SetType {
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155 my($This, $Type) = @_;
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156
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157 if ($This->{Type}) {
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158 croak "Error: ${ClassName}->SetType: Can't change fingerprint type: It's already set...";
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159 }
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160 $This->{Type} = $Type;
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161
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162 return $This;
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163 }
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164
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165 # Is fingerprints generation successful?
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166 #
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167 # Notes:
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168 # . The specific fingerprints generation class sets the value of FingerprinsGenerated
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169 # to 1 after the successful generation of fingerprints; otherwise, it's set to 0.
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170 #
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171 sub IsFingerprintsGenerationSuccessful {
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172 my($This) = @_;
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173
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174 return $This->{FingerprintsGenerated} ? 1 : 0;
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175 }
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176
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177 # Set vector type and make sure it's not already set...
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178 #
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179 sub SetVectorType {
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180 my($This, $VectorType) = @_;
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181
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182 if ($This->{VectorType}) {
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183 croak "Error: ${ClassName}->SetVectorType: Can't change fingerprint vector type: It's already set...";
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184 }
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185 if ($VectorType !~ /^(FingerprintsBitVector|FingerprintsVector)$/i) {
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186 croak "Error: ${ClassName}->SetVectorType: Specified value, $VectorType, for Type is not vaild. Supported types in current release of MayaChemTools: FingerprintsBitVector and FingerprintsVector...";
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187 }
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188 $This->{VectorType} = $VectorType;
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189
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190 return $This;
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191 }
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192
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193 #
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194 # Methods/functions for FingerprintsBitVector...
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195 #
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196
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197 # Initialize fingerprint bit vector...
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198 sub _InitializeFingerprintsBitVector {
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199 my($This) = @_;
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200
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201 if ($This->{VectorType} !~ /^FingerprintsBitVector$/i) {
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202 croak "Error: ${ClassName}->_InitializeFingerprintsBitVector: Can't initialize fingerprints bit vector: VectorType must be FingerprintsBitVector...";
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203 }
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204
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205 if ($This->{Size}) {
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206 $This->{FingerprintsBitVector} = new Fingerprints::FingerprintsBitVector($This->{Size});
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207 }
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208 return $This;
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209 }
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210
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211 # Set size...
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212 #
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213 sub SetSize {
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214 my($This, $Size) = @_;
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215
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216 if ($This->{MinSize} && $Size < $This->{MinSize}) {
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217 croak "Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid : It must be >= $This->{MinSize}...";
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218 }
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219 if ($This->{MaxSize} && $Size > $This->{MaxSize}) {
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220 croak "Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid: It must be <= $This->{MaxSize}...";
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221 }
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222
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223 $This->{Size} = $Size;
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224
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225 return $This;
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226 }
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227
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228 # Set FingerprintsBitVector object and make sure it's not already set...
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229 #
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230 sub SetFingerprintsBitVector {
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231 my($This, $FingerprintsBitVector) = @_;
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232
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233 if ($This->{FingerprintsBitVector}) {
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234 croak "Error: ${ClassName}->SetFingerprintsBitVector: Can't change FingerprintsBitVector object: It's already set...";
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235 }
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236 $This->{FingerprintsBitVector} = $FingerprintsBitVector;
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237
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238 return $This;
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239 }
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240
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241 # Fold fingerprints by recursively reducing its size by half untill bit density is greater than or equal to
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242 # specified bit density...
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243 #
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244 sub FoldFingerprintsByBitDensity {
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245 my($This, $BitDensity) = @_;
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246
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247 if (!($BitDensity >= 0 && $BitDensity <= 1)) {
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248 croak "Error: ${ClassName}->FoldFingerprintsByBitDensity: Specified bit density, $BitDensity, is not valid: It must be > 0 && <= 1 ...";
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249 }
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250
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251 return $This->_FoldFingerprintsBitVector('ByDensity', $BitDensity);
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252 }
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253
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254 # Fold fingerprints by recursively reducing its size by half untill size is less than or equal to
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255 # specified size...
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256 #
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257 sub FoldFingerprintsBySize {
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258 my($This, $Size, $CheckSizeValue) = @_;
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259
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260 if (!defined $CheckSizeValue) {
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261 $CheckSizeValue = 1;
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262 }
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263
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264 if ($CheckSizeValue) {
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265 if (!TextUtil::IsPositiveInteger($Size)) {
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266 croak "Error: ${ClassName}->FoldFingerprintsBySize: Specified size, $Size, is not valid: It must be a positive integer";
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267 }
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268 if (!($Size >= $This->{MinSize} && $Size < $This->{Size})) {
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269 croak "Error: ${ClassName}->FoldFingerprintsBySize: Specified size, $Size, is not valid: It must be greater than or equal to minimum size of $This->{MinSize} and less than current size of $This->{Size}...";
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270 }
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271 if (!TextUtil::IsNumberPowerOfNumber($Size, 2)) {
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272 croak "Error: ${ClassName}->FoldFingerprintsBySize: Specified size value, $Size, must be power of 2...";
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273 }
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274 }
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275
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276 return $This->_FoldFingerprintsBitVector('BySize', $Size);
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277 }
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278
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279 # Fold fingerprints bit vector using specified size of bit density...
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280 #
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281 sub _FoldFingerprintsBitVector {
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282 my($This, $Mode, $Value) = @_;
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283
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284 if (!$This->{FingerprintsBitVector}) {
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285 return $This;
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286 }
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287 my($FingerprintsBitVector, $FoldedFingerprintsBitVector);
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288
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289 $FoldedFingerprintsBitVector = '';
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290 $FingerprintsBitVector = $This->{FingerprintsBitVector};
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291 MODE: {
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292 if ($Mode =~ /^BySize$/i) { $FoldedFingerprintsBitVector = $FingerprintsBitVector->FoldFingerprintsBitVectorBySize($Value); last MODE; }
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293 if ($Mode =~ /^ByDensity$/i) { $FoldedFingerprintsBitVector = $FingerprintsBitVector->FoldFingerprintsBitVectorByDensity($Value); last MODE; }
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294 $FoldedFingerprintsBitVector = '';
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295 }
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296 if ($FoldedFingerprintsBitVector) {
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297 $This->{FingerprintsBitVector} = $FoldedFingerprintsBitVector;
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298 $This->{Size} = $FoldedFingerprintsBitVector->GetSize();
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299 }
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300 return $This;
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301 }
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302
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303 # Get fingerprints as a binary ascii string containing 0s and 1s...
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304 #
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305 sub GetFingerprintBitsAsBinaryString {
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306 my($This, $BitOrder) = @_;
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307
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308 return $This->_GetFingerprintBitsAsString('Binary', $BitOrder);
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309 }
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310
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311 # Get fingerprints as a hexadecimal string...
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312 #
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313 sub GetFingerprintBitsAsHexadecimalString {
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314 my($This, $BitOrder) = @_;
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315
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316 return $This->_GetFingerprintBitsAsString('Hexadecimal', $BitOrder);
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317 }
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318
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319 # Get fingerprints as a raw binary string containing packed bit values for each
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320 # byte...
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321 #
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322 sub GetFingerprintBitsAsRawBinaryString {
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323 my($This, $BitOrder) = @_;
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324
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325 return $This->_GetFingerprintBitsAsString('RawBinary', $BitOrder);
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326 }
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327
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328 # Get fingerprint bits as a string...
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329 #
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330 sub _GetFingerprintBitsAsString {
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331 my($This, $Format) = @_;
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332
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333 if (!$This->{FingerprintsBitVector}) {
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334 return undef;
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335 }
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336 FORMAT : {
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337 if ($Format =~ /^(Binary|Bin|BinaryString)$/i) { return $This->{FingerprintsBitVector}->GetBitsAsBinaryString(); last FORMAT; }
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338 if ($Format =~ /^(Hexadecimal|Hex|HexadecimalString)$/i) { return $This->{FingerprintsBitVector}->GetBitsAsHexadecimalString(); last FORMAT; }
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339 if ($Format =~ /^(RawBinary|RawBin|RawBinaryString)$/i) { return $This->{FingerprintsBitVector}->GetBitsAsRawBinaryString(); last FORMAT; }
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340 croak "Error: ${ClassName}->_GetFingerprintBitsAsString: Specified bit vector string format, $Format, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString, RawBinary, RawBin, RawBinaryString...";
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341 }
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342 return undef;
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343 }
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344
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345 #
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346 # Methods/functions for FingerprintsVector...
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347 #
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348
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349 # Initialize fingerprint vector...
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350 sub _InitializeFingerprintsVector {
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351 my($This) = @_;
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352
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353 if ($This->{VectorType} !~ /^FingerprintsVector$/i) {
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354 croak "Error: ${ClassName}->_InitializeFingerprintsVector: Can't initialize fingerprints vector: VectorType must be FingerprintsVector...";
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355 }
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356
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357 if ($This->{FingerprintsVectorType}) {
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358 $This->{FingerprintsVector} = new Fingerprints::FingerprintsVector('Type' => $This->{FingerprintsVectorType});
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359 }
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360 return $This;
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361 }
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362
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363 # Set FingerprintsVector object and make sure it's not already set...
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364 #
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365 sub SetFingerprintsVector {
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366 my($This, $FingerprintsVector) = @_;
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367
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368 if ($This->{FingerprintsVector}) {
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369 croak "Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVector object: It's already set...";
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370 }
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371 $This->{FingerprintsVector} = $FingerprintsVector;
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372
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373 return $This;
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374 }
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375
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376 # Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.
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377 #
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378 sub SetFingerprintsVectorType {
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379 my($This, $FingerprintsVectorType) = @_;
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380
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381 if ($This->{FingerprintsVectorType}) {
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382 croak "Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVectorType: It's already set...";
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383 }
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384 if ($FingerprintsVectorType !~ /^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i) {
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385 croak "Error: ${ClassName}->SetFingerprintsVectorType: Specified value, $FingerprintsVectorType, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues";
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386 }
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387 $This->{FingerprintsVectorType} = $FingerprintsVectorType;
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388
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389 return $This;
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390 }
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391
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392 # Get fingerprints vector values as an array or reference to an array...
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393 #
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394 sub GetFingerprintsVectorValues {
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395 my($This) = @_;
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396
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397 if (!$This->{FingerprintsVector}) {
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398 return undef;
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399 }
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400 return $This->{FingerprintsVector}->GetValues();
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401 }
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402
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403 # Get fingerprints vector value IDs as an array or reference to an array...
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404 #
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405 sub GetFingerprintsVectorValueIDs {
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406 my($This) = @_;
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407
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408 if (!$This->{FingerprintsVector}) {
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409 return undef;
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410 }
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411 return $This->{FingerprintsVector}->GetValueIDs();
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412 }
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413
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414 1;
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415
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416 __END__
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417
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418 =head1 NAME
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419
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420 Fingerprints - Fingerprints class
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421
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422 =head1 SYNOPSIS
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423
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424 use Fingerprints::Fingerprints;
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425
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426 use Fingerprints::Fingerprints qw(:all);
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427
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428 =head1 DESCRIPTION
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429
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430 B<Fingerprints> class provides the following methods:
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431
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432 new, FoldFingerprintsByBitDensity, FoldFingerprintsBySize,
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433 GetFingerprintBitsAsBinaryString, GetFingerprintBitsAsHexadecimalString,
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434 GetFingerprintBitsAsRawBinaryString, GetFingerprintsVectorValueIDs,
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435 GetFingerprintsVectorValues, IsFingerprintsGenerationSuccessful,
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436 SetFingerprintsBitVector, SetFingerprintsVector, SetFingerprintsVectorType,
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437 SetMolecule, SetSize, SetType, SetVectorType
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438
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439 B<Fingerprints> class is used as a base class for various specific fingerprint classes such as
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440 B<AtomNeighborhoodsFingerprints>, B<AtomTypesFingerprints>, B<EStateIndiciesFingerprints>,
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441 B<PathLengthFingerprints>, B<ExtendedConnectivityFingerprints>, B<MACCSKeys> and so on.
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442 It implements functionality common to fingerprint classes.
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443
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444 B<Fingerprints> class is derived from B<ObjectProperty> base class which provides methods not
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445 explicitly defined in B<Fingerprints> or B<ObjectProperty> classes using Perl's AUTOLOAD functionality.
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446 These methods are generated on-the-fly for a specified object property:
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447
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448 Set<PropertyName>(<PropertyValue>);
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449 $PropertyValue = Get<PropertyName>();
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450 Delete<PropertyName>();
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451
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452 B<Fingerprints> class uses B<FingerprintsBitVector> class to provide bits manipulation functionality.
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453
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454 =head2 METHODS
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455
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456 =over 4
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457
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458 =item B<new>
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459
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460 $NewFingerprints = new Fingerprints(%NamesAndValues);
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461
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462 Using specified I<Fingerprints> property names and values hash, B<new> method creates a new object
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463 and returns a reference to newly created B<Fingerprints> object. By default, following properties are
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464 initialized:
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465
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466 Molecule = '';
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467 Type = '';
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468 VectorType = '';
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469 Size = '';
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470 MinSize = '';
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471 MaxSize = '';
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472 FingerprintsBitVector = '';
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473 FingerprintsVectorType = '';
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474 FingerprintsVector = '';
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475
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476 =item B<FoldFingerprintsByBitDensity>
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477
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478 $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);
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479
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480 Folds fingerprints by recursively reducing its size by half until bit density is greater than or equal to
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481 specified I<BitDensity> and returns I<Fingerprints>.
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482
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483 =item B<FoldFingerprintsBySize>
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484
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485 $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);
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486
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487 Fold fingerprints by recursively reducing its size by half until size is less than or equal to specified
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488 I<Size> and returns I<Fingerprints>. By default, value I<Size> is checked to make sure it's:
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489
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490 >= MinSize and < Size and IsPowerOfTwo
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491
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492 =item B<GetFingerprintBitsAsBinaryString>
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493
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494 $BinaryASCIIString =
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495 $Fingerprints->GetFingerprintBitsAsBinaryString();
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496
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497 Returns fingerprints as a binary ASCII string containing 0s and 1s.
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498
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499 =item B<GetFingerprintBitsAsHexadecimalString>
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500
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501 $HexadecimalString =
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502 $Fingerprints->GetFingerprintBitsAsHexadecimalString();
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503
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504 Returns fingerprints as a hexadecimal string
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505
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506 =item B<GetFingerprintBitsAsRawBinaryString>
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507
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508 $RawBinaryString =
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509 $Fingerprints->GetFingerprintBitsAsRawBinaryString();
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510
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511 Returns fingerprints as a raw binary string containing packed bit values for each byte.
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512
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513 =item B<GetFingerprintsVectorValueIDs>
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514
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515 $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs();
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516 @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();
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517
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518 Returns fingerprints vector value IDs as an array or reference to an array.
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519
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520 =item B<GetFingerprintsVectorValues>
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521
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522 $ValuesRef = $Fingerprints->GetFingerprintsVectorValues();
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|
523 @Values = $Fingerprints->GetFingerprintsVectorValues();
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524
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525 Returns fingerprints vector values as an array or reference to an array.
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|
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526
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527 =item B<IsFingerprintsGenerationSuccessful>
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528
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|
529 $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();
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|
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530
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531 Returns 1 or 0 based on whether fingerprints were successfully generated.
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|
|
532
|
|
|
533 =item B<SetFingerprintsBitVector>
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|
|
534
|
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|
535 $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);
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|
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536
|
|
|
537 Sets I<FingerprintsBitVector> object for I<Fingerprints> and returns I<Fingerprints>.
|
|
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538
|
|
|
539 =item B<SetFingerprintsVector>
|
|
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540
|
|
|
541 $Fingerprints->SetFingerprintsVector();
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|
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542
|
|
|
543 Sets I<FingerprintsVector> object for I<Fingerprints> and returns I<Fingerprints>.
|
|
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544
|
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|
545 =item B<SetFingerprintsVectorType>
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|
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546
|
|
|
547 $Fingerprints->SetFingerprintsVectorType($VectorType);
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|
|
548
|
|
|
549 Sets I<FingerprintsVector> type for I<Fingerprints> and returns I<Fingerprints>. Possible
|
|
|
550 I<VectorType> values: I<OrderedNumericalValues, NumericalValues or AlphaNumericalValues>.
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|
|
551
|
|
|
552 =item B<SetMolecule>
|
|
|
553
|
|
|
554 $Fingerprints->SetMolecule($Molecule);
|
|
|
555
|
|
|
556 Sets I<Molecule> object for I<Fingerprints> and returns I<Fingerprints>.
|
|
|
557
|
|
|
558 =item B<SetSize>
|
|
|
559
|
|
|
560 $Fingerprints->SetSize($Size);
|
|
|
561
|
|
|
562 Sets I<Size> of fingerprints and returns I<Fingerprints>.
|
|
|
563
|
|
|
564 =item B<SetType>
|
|
|
565
|
|
|
566 $Fingerprints->SetType($Type);
|
|
|
567
|
|
|
568 Sets I<Type> of fingerprints and returns I<Fingerprints>.
|
|
|
569
|
|
|
570 =item B<SetVectorType>
|
|
|
571
|
|
|
572 $Fingerprints->SetVectorType($Type);
|
|
|
573
|
|
|
574 Sets I<Type> of fingerprints vector and returns I<Fingerprints>. Possible I<Type> values:
|
|
|
575 I<FingerprintsBitVector or FingerprintsVector>.
|
|
|
576
|
|
|
577 =back
|
|
|
578
|
|
|
579 =head1 AUTHOR
|
|
|
580
|
|
|
581 Manish Sud <msud@san.rr.com>
|
|
|
582
|
|
|
583 =head1 SEE ALSO
|
|
|
584
|
|
|
585 FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
|
|
|
586 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, MACCSKeys.pm,
|
|
|
587 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
|
|
|
588 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
589 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
590
|
|
|
591 =head1 COPYRIGHT
|
|
|
592
|
|
|
593 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
594
|
|
|
595 This file is part of MayaChemTools.
|
|
|
596
|
|
|
597 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
598 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
599 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
600 any later version.
|
|
|
601
|
|
|
602 =cut
|
