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1 package Fingerprints::FingerprintsStringUtil;
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2 #
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3 # $RCSfile: FingerprintsStringUtil.pm,v $
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4 # $Date: 2015/02/28 20:48:54 $
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5 # $Revision: 1.24 $
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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 Exporter;
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31 use Carp;
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32 use TextUtil ();
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33 use Fingerprints::FingerprintsBitVector;
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34 use Fingerprints::FingerprintsVector;
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35
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36 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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37
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38 @ISA = qw(Exporter);
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39 @EXPORT = qw();
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40 @EXPORT_OK = qw(AreFingerprintsStringValuesValid GenerateFingerprintsString GenerateFingerprintsBitVectorString GenerateFingerprintsVectorString GetFingerprintsStringTypeAndDescription GetDefaultBitsOrder GetDefaultBitStringFormat GetDefaultVectorStringFormat GetFingeprintsStringDelimiter GetFingerprintsStringValues ParseFingerprintsString ParseFingerprintsBitVectorString ParseFingerprintsVectorString);
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41
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42 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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43
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44 # Fingerprint string values delimiter...
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45 my($FPStringDelim) = ';';
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46
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47 # Generate fingerprints string...
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48 #
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49 sub GenerateFingerprintsString {
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50 my($FingerprintsObject) = @_;
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51 my($VectorType);
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52
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53 $VectorType = $FingerprintsObject->GetVectorType();
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54
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55 VECTORTYPE : {
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56 if ($VectorType =~ /^FingerprintsBitVector$/i) { return GenerateFingerprintsBitVectorString(@_); last VECTORTYPE; }
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57 if ($VectorType =~ /^FingerprintsVector$/i) { return GenerateFingerprintsVectorString(@_); last VECTORTYPE; }
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58 croak "Error: FingerprintsStringUtil::GenerateFingerprintsString: Fingerprints object vector type, $VectorType, is not supported. Valid values: FingerprintsBitVector or FingerprintsVector...";
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59 }
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60 return '';
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61 }
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62
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63 # Generate fingerprints bit vector string...
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64 #
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65 sub GenerateFingerprintsBitVectorString {
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66 my($FingerprintsObject, $BitStringFormat, $BitsOrder) = @_;
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67 my($FingerprintsString, $FingerprintsBitVector, @FingerprintsStringValues);
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68
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69 if (!$BitStringFormat) { $BitStringFormat = GetDefaultBitStringFormat(); }
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70 if (!$BitsOrder) {$BitsOrder = GetDefaultBitsOrder(); }
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71
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72 $FingerprintsString = '';
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73 $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::IsFingerprintsBitVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsBitVector();
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74
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75 # Use specified size instead of size: it corresponds to actual size of the fingerprints bit vector;
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76 # size reflects actual internal size including any padding.
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77 #
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78
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79 @FingerprintsStringValues = ();
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80 push @FingerprintsStringValues, ($FingerprintsObject->GetVectorType(), _GetFingerprintsDescription($FingerprintsObject), $FingerprintsBitVector->GetSpecifiedSize(), $BitStringFormat, $BitsOrder);
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81
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82 $FingerprintsString = join("${FPStringDelim}", @FingerprintsStringValues) . "${FPStringDelim}" . _GetFingerprintBitVectorString($FingerprintsBitVector, $BitStringFormat, $BitsOrder);
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83
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84 return $FingerprintsString;
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85 }
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86
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87 # Get fingerprint bit vector string...
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88 #
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89 sub _GetFingerprintBitVectorString {
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90 my($FingerprintsBitVector, $BitStringFormat, $BitsOrder) = @_;
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91 my($FingerprintBitString);
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92
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93 if (!$BitStringFormat) { $BitStringFormat = GetDefaultBitStringFormat(); }
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94 if (!$BitsOrder) {$BitsOrder = GetDefaultBitsOrder(); }
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95
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96 $FingerprintBitString = '';
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97 if (!$FingerprintsBitVector) {return $FingerprintBitString;}
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98
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99 BITSTRINGFORMAT : {
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100 if ($BitStringFormat =~ /^(BinaryString|Binary|Bin)$/i) { return $FingerprintsBitVector->GetBitsAsBinaryString($BitsOrder); last BITSTRINGFORMAT; }
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101 if ($BitStringFormat =~ /^(HexadecimalString|Hexadecimal|Hex)$/i) { return $FingerprintsBitVector->GetBitsAsHexadecimalString($BitsOrder); last BITSTRINGFORMAT; }
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102 croak "Error: FingerprintsStringUtil::_GetFingerprintBitsAsString: Specified bit vector string format, $BitStringFormat, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString...";
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103 }
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104 return $FingerprintBitString;
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105 }
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106
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107 # Generate fingerprints vector string...
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108 #
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109 sub GenerateFingerprintsVectorString {
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110 my($FingerprintsObject, $VectorStringFormat) = @_;
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111 my($FingerprintsString, $FingerprintsVector, @FingerprintsStringValues);
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112
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113 $FingerprintsString = '';
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114 $FingerprintsVector = Fingerprints::FingerprintsVector::IsFingerprintsVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsVector();
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115
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116 if (!$VectorStringFormat) { $VectorStringFormat = _GetDefaultVectorStringFormat($FingerprintsVector); }
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117
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118 @FingerprintsStringValues = ();
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119 push @FingerprintsStringValues, ($FingerprintsObject->GetVectorType(), _GetFingerprintsDescription($FingerprintsObject), $FingerprintsVector->GetNumOfValues(), $FingerprintsVector->GetType(), $VectorStringFormat);
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120
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121 $FingerprintsString = join("${FPStringDelim}", @FingerprintsStringValues) . "${FPStringDelim}" . _GetFingerprintVectorString($FingerprintsVector, $VectorStringFormat);
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122
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123 return $FingerprintsString;
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124 }
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125
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126 # Get fingerprint vector string...
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127 #
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128 sub _GetFingerprintVectorString {
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129 my($FingerprintsVector, $VectorStringFormat) = @_;
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130 my($FingerprintString);
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131
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132 if (!$VectorStringFormat) { $VectorStringFormat = _GetDefaultVectorStringFormat($FingerprintsVector);}
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133
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134 $FingerprintString = '';
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135 if (!$FingerprintsVector) {return $FingerprintString;}
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136
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137 VECTORSTRINGFORMAT : {
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138 if ($VectorStringFormat =~ /^(IDsAndValuesString|IDsAndValues)$/i) { return $FingerprintsVector->GetIDsAndValuesString(); last VECTORSTRINGFORMAT; }
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139 if ($VectorStringFormat =~ /^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i) { return $FingerprintsVector->GetIDsAndValuesPairsString(); last VECTORSTRINGFORMAT; }
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140 if ($VectorStringFormat =~ /^(ValuesAndIDsString|ValuesAndIDs)$/i) { return $FingerprintsVector->GetValuesAndIDsString(); last VECTORSTRINGFORMAT; }
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141 if ($VectorStringFormat =~ /^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i) { return $FingerprintsVector->GetValuesAndIDsPairsString(); last VECTORSTRINGFORMAT; }
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142 if ($VectorStringFormat =~ /^(ValuesString|Values)$/i) { return $FingerprintsVector->GetValuesString(); last VECTORSTRINGFORMAT; }
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143 croak "Error: FingerprintsStringUtil::_GetFingerprintVectorString: Specified vector string format, $VectorStringFormat, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values...";
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144 }
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145 return $FingerprintString;
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146 }
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147
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148 # Get fingerprints string type and description...
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149 sub GetFingerprintsStringTypeAndDescription {
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150 my($FingerprintsString) = @_;
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151 my($Type, $Description);
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152
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153 ($Type, $Description) = _ParseFingerprintsStringValues($FingerprintsString);
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154
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155 return ($Type, $Description);
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156 }
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157
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158 # Get all fingerprints string values...
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159 sub GetFingerprintsStringValues {
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160 my($FingerprintsString) = @_;
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161
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162 return _ParseFingerprintsStringValues($FingerprintsString);
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163 }
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164
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165 # Parse fingerprints string and return FingerprintsBitVector or FingerprintsVector object...
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166 #
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167 sub ParseFingerprintsString {
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168 my($FingerprintsString) = @_;
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169
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170 VECTORTYPE : {
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171 if ($FingerprintsString =~ /^FingerprintsBitVector/i) { return ParseFingerprintsBitVectorString(@_); last VECTORTYPE; }
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172 if ($FingerprintsString =~ /^FingerprintsVector/i) { return ParseFingerprintsVectorString(@_); last VECTORTYPE; }
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173 croak "Error: FingerprintsStringUtil::ParseFingerprintsString: Fingerprints string vector type is not supported. Valid values: FingerprintsBitVector or FingerprintsVector...";
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174 }
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175 return undef;
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176 }
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177
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178 # Parse fingerprints bit vector string and retrun bit vector...
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179 #
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180 sub ParseFingerprintsBitVectorString {
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181 my($FingerprintsString, $ValidateValues) = @_;
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182 my($ErrorMsgPrefix, $VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);
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183
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184 $ErrorMsgPrefix = "Error: ParsePathLengthFingerprintsBitVectorString";
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185 ($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString) = _ParseFingerprintsStringValues($FingerprintsString);
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186 if ($ValidateValues) {
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187 _ValidateFingerprintsStringValues($ErrorMsgPrefix, $VectorType, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);
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188 }
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189
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190 return _GenerateFingerprintBitVector($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString);
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191 }
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192
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193 # Generate fingerints bit vector...
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194 #
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195 sub _GenerateFingerprintBitVector {
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196 my($VectorType, $Description, $Size, $BitStringFormat, $BitsOrder, $BitVectorString) = @_;
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197 my($FingerprintsBitVector);
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198
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199 $FingerprintsBitVector = undef;
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200
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201 BITSTRINGFORMAT : {
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202 if ($BitStringFormat =~ /^(BinaryString|Binary|Bin)$/i) {
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203 $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString($BitVectorString, $BitsOrder);
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204 last BITSTRINGFORMAT;
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205 }
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206 if ($BitStringFormat =~ /^(HexadecimalString|Hexadecimal|Hex)$/i) {
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207 $FingerprintsBitVector = Fingerprints::FingerprintsBitVector::NewFromHexadecimalString($BitVectorString, $BitsOrder);
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208 last BITSTRINGFORMAT;
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209 }
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210 croak "Error: FingerprintsStringUtil::_GenerateFingerprintBitVector: Specified bit vector string format, $BitStringFormat, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString...";
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211 }
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212
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213 if (defined $FingerprintsBitVector) {
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214 # Set fingerints vector type and description...
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215 $FingerprintsBitVector->SetVectorType($VectorType);
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216 $FingerprintsBitVector->SetDescription($Description);
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217
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218 # Set specified size which might be different from the bit string size due to padding
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219 # used by Perl vec function to handle bit vectors in BitVectot class...
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220 #
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221 $FingerprintsBitVector->SetSpecifiedSize($Size);
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222 }
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223
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224 return $FingerprintsBitVector;
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225 }
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226
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227 # Parse fingerprints vector string and retrun vector...
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228 #
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229 sub ParseFingerprintsVectorString {
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230 my($FingerprintsString, $ValidateValues) = @_;
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231 my($ErrorMsgPrefix, $VectorType, $Description, $NumOfValues, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2);
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232
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233 $ErrorMsgPrefix = "Error: ParseFingerprintsVectorString";
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234 ($VectorType, $Description, $NumOfValues, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2) = _ParseFingerprintsStringValues($FingerprintsString);
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235
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236 # No need to check $VectorString1 and $VectorString2 values as they would be
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237 # checked later during the creation of FingerprintsVector...
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238 #
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239 if ($ValidateValues) {
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240 _ValidateFingerprintsStringValues($ErrorMsgPrefix, $VectorType, $NumOfValues, $VectorValuesType, $VectorStringFormat);
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241 }
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242
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243 return _GenerateFingerprintVector($VectorType, $Description, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2);
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244 }
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245
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246 # Generate fingerints vector...
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247 #
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248 sub _GenerateFingerprintVector {
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249 my($VectorType, $Description, $VectorValuesType, $VectorStringFormat, $VectorString1, $VectorString2) = @_;
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250 my($FingerprintsVector, $VectorString);
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251
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252 $VectorString = TextUtil::IsEmpty($VectorString2) ? $VectorString1 : "${VectorString1};${VectorString2}";
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253 $FingerprintsVector = undef;
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254
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255 VECTORSTRINGFORMAT : {
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256 if ($VectorStringFormat =~ /^(ValuesString|Values)$/i) {
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257 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString($VectorValuesType, $VectorString);
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258 last VECTORSTRINGFORMAT;
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259 }
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260 if ($VectorStringFormat =~ /^(IDsAndValuesString|IDsAndValues)$/i) {
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261 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString($VectorValuesType, $VectorString);
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262 last VECTORSTRINGFORMAT;
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263 }
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264 if ($VectorStringFormat =~ /^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i) {
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265 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString($VectorValuesType, $VectorString);
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266 last VECTORSTRINGFORMAT;
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267 }
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268 if ($VectorStringFormat =~ /^(ValuesAndIDsString|ValuesAndIDs)$/i) {
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269 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString($VectorValuesType, $VectorString);
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270 last VECTORSTRINGFORMAT;
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271 }
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272 if ($VectorStringFormat =~ /^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i) {
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273 $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString($VectorValuesType, $VectorString);
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274 last VECTORSTRINGFORMAT;
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275 }
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276 croak "Error: FingerprintsStringUtil::_GenerateFingerprintVector: Specified vector string format, $VectorStringFormat, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values...";
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277 }
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278
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279 if (defined $FingerprintsVector) {
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280 # Set fingerints vector type and description...
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281 $FingerprintsVector->SetVectorType($VectorType);
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282 $FingerprintsVector->SetDescription($Description);
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283 }
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284
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285 return $FingerprintsVector;
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286 }
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287
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288 # Validate fingerint string values...
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289 #
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290 sub AreFingerprintsStringValuesValid {
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291 my($FingerprintsString) = @_;
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292 my($Value);
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293
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294 for $Value (_ParseFingerprintsStringValues($FingerprintsString)) {
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295 if (TextUtil::IsEmpty($Value)) {
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296 return 0;
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297 }
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298 }
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299 return 1;
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300 }
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301
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302 # Get fingerprints description...
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303 #
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304 sub _GetFingerprintsDescription {
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305 my($FingerprintsObject) = @_;
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306 my($Description);
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307
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308 $Description = $FingerprintsObject->GetDescription();
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309
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310 return TextUtil::IsEmpty($Description) ? 'No description available for fingerprints' : $Description;
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311 }
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312
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313 # Parse fingerprints string values...
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314 #
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315 sub _ParseFingerprintsStringValues {
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316 my($FingerprintsString) = @_;
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317
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318 return split "${FPStringDelim}", $FingerprintsString;
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319 }
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320
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321 # Check to make sure already parsed fingerprints string values are valid....
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322 #
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323 sub _ValidateFingerprintsStringValues {
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324 my($ErrorMsgPrefix, @Values) = @_;
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325 my($Value);
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326
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327 for $Value (@Values) {
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328 if (TextUtil::IsEmpty($Value)) {
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329 croak("${ErrorMsgPrefix}: _ValidateFingerprintsStringValues: Fingerprints string format is not valid: An empty value found...");
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330 }
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331 }
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332 }
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333
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334 # Default bit string format...
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335 #
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336 sub GetDefaultBitStringFormat {
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337 return 'HexadecimalString';
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338 }
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339
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340 # Default bit order...
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341 #
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342 sub GetDefaultBitsOrder {
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343 return 'Ascending';
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344 }
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345
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346 # Default vector string format using fingerprints or fingerprints vector object...
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347 #
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348 sub GetDefaultVectorStringFormat {
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349 my($FingerprintsObject) = @_;
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350 my($FingerprintsVector);
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351
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352 $FingerprintsVector = Fingerprints::FingerprintsVector::IsFingerprintsVector($FingerprintsObject) ? $FingerprintsObject : $FingerprintsObject->GetFingerprintsVector();
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353
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354 return _GetDefaultVectorStringFormat($FingerprintsVector);
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355 }
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356
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357 # Default vector string format using fingerprits vector object...
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358 #
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359 sub _GetDefaultVectorStringFormat {
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360 my($FingerprintsVector) = @_;
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361 my($Type);
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362
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363 $Type = $FingerprintsVector->GetType();
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364
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365 return ($Type =~ /^NumericalValues$/i) ? 'IDsAndValuesString' : 'ValuesString';
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366 }
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367
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368 # Fingerprints string delimiter...
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369 #
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370 sub GetFingeprintsStringDelimiter {
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371 return $FPStringDelim;
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372 }
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373
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374 1;
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375
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376 __END__
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377
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378 =head1 NAME
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379
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380 FingerprintsStringUtil
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381
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382 =head1 SYNOPSIS
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383
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384 use Fingerprints::FingerprintsStringUtil;
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385
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386 use Fingerprints::FingerprintsStringUtil qw(:all);
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387
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388 =head1 DESCRIPTION
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389
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390 B<FingerprintsStringUtil> module provides the following functions:
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391
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392 AreFingerprintsStringValuesValid, GenerateFingerprintsBitVectorString,
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393 GenerateFingerprintsString, GenerateFingerprintsVectorString,
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394 GetDefaultBitStringFormat, GetDefaultBitsOrder, GetDefaultVectorStringFormat,
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395 GetFingeprintsStringDelimiter, GetFingerprintsStringTypeAndDescription,
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396 GetFingerprintsStringValues, ParseFingerprintsBitVectorString,
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397 ParseFingerprintsString, ParseFingerprintsVectorString
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398
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399 The current release of MayaChemTools supports the following types of fingerprint
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400 bit-vector and vector strings:
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401
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402 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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403 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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404 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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405 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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406 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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407 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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408
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409 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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410 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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411 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
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412 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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413
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414 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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415 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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416 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
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417
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418 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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419 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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420 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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421 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
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422 O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
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423 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...
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424
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425 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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426 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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427 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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428 .024 -2.270
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429
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430 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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431 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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432 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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433 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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434 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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435
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436 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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437 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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438 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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439 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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440 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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441 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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442
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443 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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444 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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445 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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446 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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447 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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448 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
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449
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450 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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451 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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452 0000000001010000000110000011000000000000100000000000000000000000100001
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453 1000000110000000000000000000000000010011000000000000000000000000010000
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454 0000000000000000000000000010000000000000000001000000000000000000000000
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455 0000000000010000100001000000000000101000000000000000100000000000000...
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456
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457 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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458 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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|
459 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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460 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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461 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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462 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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463
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464 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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465 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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466 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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467 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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468 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
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|
469 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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470
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471 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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472 0000000000000000000000000000000001001000010010000000010010000000011100
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473 0100101010111100011011000100110110000011011110100110111111111111011111
|
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|
474 11111111111110111000
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475
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|
476 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
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477 1110011111100101111111000111101100110000000000000011100010000000000000
|
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478 0000000000000000000000000000000000000000000000101000000000000000000000
|
|
|
479 0000000000000000000000000000000000000000000000000000000000000000000000
|
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480 0000000000000000000000000000000000000011000000000000000000000000000000
|
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481 0000000000000000000000000000000000000000
|
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482
|
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483 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
484 ng;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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|
485 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
|
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486 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
|
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|
487 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
|
|
|
488 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
|
|
|
489
|
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|
490 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
491 ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
|
|
|
492 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
|
|
|
493 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 0
|
|
|
494 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
|
|
|
495 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 ...
|
|
|
496
|
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497 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
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|
498 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
499 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
500 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
501 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
502 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
503
|
|
|
504 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
505 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
506 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
|
|
|
507 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
508 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
509 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
510
|
|
|
511 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
512 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
513 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
|
|
|
514 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
515 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
516 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
517
|
|
|
518 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
519 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
520 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
521 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
522 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
523 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
524
|
|
|
525 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
526 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
527 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
528 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
529 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
|
|
|
530 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
|
|
|
531
|
|
|
532 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
533 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
534 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
535 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
536 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
|
|
|
537
|
|
|
538 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
539 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
|
|
|
540 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
|
|
|
541 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
|
|
|
542 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
|
|
|
543
|
|
|
544 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
545 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
546 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
|
|
|
547 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
|
|
|
548 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
549 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
|
|
|
550 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
|
|
|
551
|
|
|
552 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
553 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
|
|
|
554 .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
|
|
|
555 D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
|
|
|
556 -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
|
|
|
557 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...
|
|
|
558
|
|
|
559 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
560 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
561 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
562 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
|
|
|
563 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
564 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
565 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
566
|
|
|
567 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
568 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
569 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
570 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
571 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
572 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
573
|
|
|
574 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
575 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
|
|
|
576 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
|
|
|
577 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
578 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
|
|
|
579 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
|
|
|
580 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
|
|
|
581 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
582
|
|
|
583 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
584 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
585 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
|
|
|
586 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
587 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
|
|
|
588 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
|
|
|
589
|
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590 =head1 FUNCTIONS
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591
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592 =over 4
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593
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594 =item B<AreFingerprintsStringValuesValid>
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595
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596 $Status = AreFingerprintsStringValuesValid($FPString);
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597
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598 Returns 0 or 1 based on whether I<FingerprintsString> contains valid values.
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599
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600 =item B<GetDefaultBitStringFormat>
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601
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602 $BitStringFormat = GetDefaultBitStringFormat();
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603
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604 Returns default B<BitStringFormat> for fingerprints bit-vector strings.
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605
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606 =item B<GetDefaultBitsOrder>
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607
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608 $BitsOrder = GetDefaultBitsOrder();
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609
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610 Returns default B<BitsOrder> for fingerprints bit-vector fingerprints.
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611
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612 =item B<GetDefaultVectorStringFormat>
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613
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614 $StringFormat = GetDefaultVectorStringFormat();
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615
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616 Returns default B<VectorStringFormat> for fingerprints vector strings.
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617
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618 =item B<GetFingeprintsStringDelimiter>
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619
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620 $Delimiter = GetFingeprintsStringDelimiter();
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621
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622 Returns string B<Delimiter> used to generate fingerprints bit-vector and vector strings.
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623
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624 =item B<GenerateFingerprintsBitVectorString>
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625
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626 $FPString = GenerateFingerprintsBitVectorString($FPBitVectorObject,
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627 [$BitStringFormat, $BitsOrder]);
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628
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629 Returns a B<FingerprintsString> generated using I<FingerprintsBitVectorObject> and
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630 optionally specified I<BitStringFormat> and I<BitsOrder> values.
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631
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632 Possible I<BitStringFormat> values: I<BinaryString, Binary, Bin, HexadecimalString,
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633 Hexadecimal, or Hex>. Default I<BitStringFormat> value: I<BinaryString>.
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634
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635 Possible I<BitsOrder> values: I<Ascending or Descending>. Default I<BitsOrder> value:
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636 I<Ascending>.
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637
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638 =item B<GenerateFingerprintsVectorString>
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639
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640 $FPString = GenerateFingerprintsVectorString($FPVectorObject,
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641 [$VectorStringFormat]);
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642
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643 Returns a B<FingerprintsString> generated using I<FingerprintsVectorObject> and optionally
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644 specified I<VectorStringFormat>.
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645
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646 Possible I<VectorStringFormat> values: I<IDsAndValuesString, IDsAndValues,
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647 IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs,
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648 ValuesAndIDsPairsString, ValuesAndIDsPairs, ValuesString, Values>.
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649
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650 Default I<VectorStringFormat> value: for I<NumericalValues> I<FPVectorType> -
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651 I<IDsAndValuesString>; for all other I<FPVectorType>s - I<ValuesString>.
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652
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653 =item B<GenerateFingerprintsString>
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654
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655 $FPString = GenerateFingerprintsBitVectorString($FPBitVectorObject,
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656 [$BitStringFormat, $BitsOrder]);
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657
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658 $FPString = GenerateFingerprintsVectorString($FPVectorObject,
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659 [$VectorStringFormat]);
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660
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661 Returns a B<FingerprintsString> generated using I<FingerprintsBitVectorObject> or
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662 I<FingerprintsVectorObject> and optionally specified parameters.
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663
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664 =item B<GetFingerprintsStringTypeAndDescription>
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665
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666 ($FPType, $FPDescription) = GetFingerprintsStringTypeAndDescription(
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667 $FPString);
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668
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669 Returns B<FingerprintsStringType> and I<FingerprintsStringDescription> strings for
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670 B<FingerprintsString> corresponding to B<FingerprintsBitVectorObject> or
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671 B<FingerprintsVectorObject>.
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672
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673 =item B<GetFingerprintsStringValues>
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674
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675 @FPStringValues = GetFingerprintsStringValues($FPString);
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676
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677 Parses B<FingerprintsString> corresponding to B<FingerprintsBitVectorObject> or
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678 B<FingerprintsVectorObject> and returns its individual component values as an
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679 array.
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680
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681 =item B<ParseFingerprintsBitVectorString>
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682
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683 $FPBitVectorObject = ParseFingerprintsBitVectorString($FPBitVectorString,
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684 [$ValidateValues]);
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685
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686 Returns B<FingerprintsBitVectorObject> generated by parsing I<FingerprintsBitVectorString>
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687 with optional validation of its component values.
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688
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689 =item B<ParseFingerprintsString>
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690
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691 $FPBitVectorObject = ParseFingerprintsBitVectorString($FPBitVectorString,
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692 [$ValidateValues]);
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693
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694 $FPVectorObject = ParseFingerprintsVectorString($FPVectorString,
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695 [$ValidateValues]);
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696
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697 Returns B<FingerprintsBitVectorObject> or I<B<FingerprintsVectorObject>> generated
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698 by parsing I<FingerprintsBitVectorString> or I<FingerprintsVectorString> with
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699 optional validation of its component values.
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700
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701 =item B<ParseFingerprintsVectorString>
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702
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703 $FPVectorObject = ParseFingerprintsVectorString($FPVectorString,
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704 [$ValidateValues]);
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705
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706 Returns B<FingerprintsVectorObject> generated by parsing I<FingerprintsVectorString>
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707 with optional validation of its component values.
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708
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709 =back
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710
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711 =head1 AUTHOR
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712
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713 Manish Sud <msud@san.rr.com>
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714
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715 =head1 SEE ALSO
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716
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717 BitVector.pm, FingerprintsBitVector.pm, FingerprintsVector.pm, Vector.pm
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718
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719 =head1 COPYRIGHT
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720
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721 Copyright (C) 2015 Manish Sud. All rights reserved.
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722
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723 This file is part of MayaChemTools.
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724
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725 MayaChemTools is free software; you can redistribute it and/or modify it under
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726 the terms of the GNU Lesser General Public License as published by the Free
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727 Software Foundation; either version 3 of the License, or (at your option)
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728 any later version.
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729
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730 =cut
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