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3 <title>MayaChemTools:Documentation:EStateIndiciesFingerprints.pl</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>EStateIndiciesFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/EStateIndiciesFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateIndiciesFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints for SD files</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>EStateIndiciesFingerprints.pl SDFile(s)...</p>
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26 <p>EStateIndiciesFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>]
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28 [<strong>--CompoundIDLabel</strong> <em>text</em>] [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
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29 [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>] [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>]
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30 [<strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize or FixedSize</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
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31 [<strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>]
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32 [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
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33 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
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34 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>] [<strong>--ValuesPrecision</strong> <em>number</em>]
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35 [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
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36 [<strong>-w, --WorkingDir</strong> <em>DirName</em>]</p>
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37 <p>
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38 </p>
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39 <h2>DESCRIPTION</h2>
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40 <p>Generate E-state indicies fingerprints [ Ref 75-78 ] for <em>SDFile(s)</em> and create appropriate SD,
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41 FP, or CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to
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42 molecular fingerprints.</p>
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43 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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44 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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45 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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46 <p>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module
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47 AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module
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48 AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values,
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49 <strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types
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50 is generated.</p>
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51 <p>Two types of E-state atom types set size are allowed:</p>
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52 <div class="OptionsBox">
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53 ArbitrarySize - Corresponds to only E-state atom types detected
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54 in molecule
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55 <br/> FixedSize - Corresponds to fixed number of E-state atom types previously
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56 defined</div>
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57 <p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to
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58 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
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59 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a
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60 fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in
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61 Ref 77 ] are used for fingerprints.</p>
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62 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
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63 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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64 MayaChemTools.</p>
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65 <p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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66 E-state indicies fingerprints:</p>
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67 <div class="OptionsBox">
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68 Type EStateAtomTypesSetToUse</div>
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69 <div class="OptionsBox">
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70 EStateIndicies ArbitrarySize [ default fingerprints ]
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71 <br/> EStateIndicies FixedSize</div>
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72 <p>Example of <em>SD</em> file containing E-state indicies fingerprints string data:</p>
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73 <div class="OptionsBox">
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74 ... ...
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75 <br/> ... ...
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76 <br/> $$$$
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77 <br/> ... ...
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78 <br/> ... ...
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79 <br/> ... ...
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80 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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81 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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82 <br/> ... ...
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83 <br/> 2 3 1 0 0 0 0
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84 <br/> ... ...
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85 <br/> M END
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86 <br/> > <CmpdID>
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87 <br/> Cmpd1</div>
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88 <div class="OptionsBox">
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89 > <EStateIndiciesFingerprints>
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90 <br/> FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
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91 <br/> ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
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92 <br/> SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3.02
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93 <br/> 4 -2.270</div>
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94 <div class="OptionsBox">
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95 $$$$
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96 <br/> ... ...
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97 <br/> ... ...</div>
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98 <p>Example of <em>FP</em> file containing E-state indicies fingerprints string data:</p>
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99 <div class="OptionsBox">
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100 #
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101 <br/> # Package = MayaChemTools 7.4
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102 <br/> # Release Date = Oct 21, 2010
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103 <br/> #
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104 <br/> # TimeStamp = Fri Mar 11 14:35:11 2011
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105 <br/> #
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106 <br/> # FingerprintsStringType = FingerprintsVector
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107 <br/> #
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108 <br/> # Description = EStateIndicies:ArbitrarySize
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109 <br/> # VectorStringFormat = IDsAndValuesString
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110 <br/> # VectorValuesType = NumericalValues
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111 <br/> #
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112 <br/> Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 -1...
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113 <br/> Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 -1.583 5.387 5.400...
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114 <br/> ... ...
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115 <br/> ... ..</div>
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116 <p>Example of CSV <em>Text</em> file containing E-state indicies fingerprints string data:</p>
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117 <div class="OptionsBox">
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118 "CompoundID","EStateIndiciesFingerprints"
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119 <br/> "Cmpd1","FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa
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120 <br/> lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC
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121 <br/> H2 SssNH SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0
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122 <br/> .073 3.024 -2.270"
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123 <br/> "Cmpd2","FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal
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124 <br/> ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss
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125 <br/> sCH;7.418 22.984 -1.583 5.387 5.400 19.852 1.737 5.624 -3.319"
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126 <br/> ... ...
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127 <br/> ... ...</div>
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128 <p>The current release of MayaChemTools generates the following types of E-state
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129 fingerprints vector strings:</p>
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130 <div class="OptionsBox">
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131 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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132 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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133 <br/> 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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134 <br/> .024 -2.270</div>
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135 <div class="OptionsBox">
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136 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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137 <br/> 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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138 <br/> 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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139 <br/> 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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140 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
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141 <div class="OptionsBox">
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142 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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143 <br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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144 <br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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145 <br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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146 <br/> 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
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147 <br/> 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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148 <br/> 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...</div>
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149 <p>
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150 </p>
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151 <h2>OPTIONS</h2>
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152 <dl>
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153 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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154 <dd>
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155 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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156 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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157 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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158 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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159 <p>The supported aromaticity model names along with model specific control parameters
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160 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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161 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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162 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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163 for detecting aromaticity corresponding to a specific model.</p>
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164 </dd>
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165 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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166 <dd>
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167 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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168 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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169 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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170 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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171 look like Cmpd<Number>.</p>
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172 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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173 <div class="OptionsBox">
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174 MolID
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175 <br/> ExtReg</div>
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176 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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177 <div class="OptionsBox">
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178 Compound</div>
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179 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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180 instead of default value of Cmpd<Number>.</p>
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181 </dd>
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182 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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183 <dd>
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184 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
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185 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
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186 </dd>
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187 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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188 <dd>
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189 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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190 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
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191 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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192 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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193 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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194 Default: <em>LabelPrefix</em>.</p>
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195 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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196 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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197 values are replaced with sequential compound IDs.</p>
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198 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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199 </dd>
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200 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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201 <dd>
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202 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
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203 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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204 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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205 <p>Examples:</p>
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206 <div class="OptionsBox">
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207 Extreg
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208 <br/> MolID,CompoundName</div>
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209 </dd>
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210 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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211 <dd>
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212 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
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213 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
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214 data field; transfer SD data files common to all compounds; extract specified data fields;
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215 generate a compound ID using molname line, a compound prefix, or a combination of both.
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216 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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217 </dd>
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218 <dt><strong><strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
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219 <dd>
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220 <p>E-state atom types set size to use during generation of E-state indicies fingerprints.
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221 Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
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222 <p><em>ArbitrarySize</em> corrresponds to only E-state atom types detected in molecule; <em>FixedSize</em>
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223 corresponds to fixed number of previously defined E-state atom types.</p>
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224 <p>For <em>EStateIndicies</em>, a fingerprint vector string is generated. The vector string corresponding to
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225 <em>EStateIndicies</em> contains sum of E-state values for E-state atom types.</p>
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226 <p>Module <strong>AtomTypes::EStateAtomTypes.pm</strong> is used to assign E-state atom types to
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227 non-hydrogen atoms in the molecule which is able to assign atom types to any valid
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228 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>,
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229 only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix
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230 III in Ref 77 ] are used for fingerprints.</p>
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231 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
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232 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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233 MayaChemTools.</p>
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234 </dd>
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235 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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236 <dd>
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237 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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238 Default value: <em>Yes</em>.</p>
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239 <p>By default, compound data is checked before calculating fingerprints and compounds containing
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240 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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241 </dd>
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242 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
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243 <dd>
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244 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
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245 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append E-state
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246 atom type value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
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247 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
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248 <em>FingerprintsLabelOnly</em>.</p>
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249 <p>This option is only used for <em>FixedSize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong> option during
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250 generation of <em>EStateIndicies</em> E-state fingerprints.</p>
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251 <p>E-state atom type IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
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252 values of <strong>--FingerprintsLabelMode</strong> correspond to fixed number of previously defined E-state
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253 atom types.</p>
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254 </dd>
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255 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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256 <dd>
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257 <p>SD data label or text file column label to use for fingerprints string in output SD or
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258 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>EStateIndiciesFingerprints</em>.</p>
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259 </dd>
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260 <dt><strong><strong>-h, --help</strong></strong></dt>
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261 <dd>
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262 <p>Print this help message.</p>
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263 </dd>
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264 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
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265 <dd>
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266 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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267 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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268 <p>For molecules containing multiple connected components, fingerprints can be generated
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269 in two different ways: use all connected components or just the largest connected
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270 component. By default, all atoms except for the largest connected component are
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271 deleted before generation of fingerprints.</p>
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272 </dd>
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273 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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274 <dd>
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275 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
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276 Default value: <em>comma</em>.</p>
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277 </dd>
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278 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
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279 <dd>
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280 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
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281 </dd>
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282 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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283 <dd>
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284 <p>Overwrite existing files.</p>
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285 </dd>
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286 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
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287 <dd>
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288 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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289 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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290 </dd>
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291 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
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292 <dd>
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293 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file
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294 names: <SDFileName><EStateIndiciesFP>.<Ext>. The file type determines <Ext> value.
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295 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
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296 delimited text files, respectively.This option is ignored for multiple input files.</p>
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297 </dd>
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298 <dt><strong><strong>--ValuesPrecision</strong> <em>number</em></strong></dt>
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299 <dd>
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300 <p>Precision of values for E-state indicies option. Default value: up to <em>3</em> decimal places.
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301 Valid values: positive integers.</p>
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302 </dd>
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303 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
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304 <dd>
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305 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
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306 <strong>--output</strong> used for <em>EStateIndicies</em>. Possible values: <em>ValuesString, IDsAndValuesString,
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307 IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p>
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308 <p>Default value during <em>ArbitrarySize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong>
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309 option: <em>IDsAndValuesString</em>. Default value during <em>FixedSize</em> value of
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310 <strong>-e, --EStateAtomTypesSetToUse</strong> option: <em>ValuesString</em>.</p>
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311 <p>Examples:</p>
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312 <div class="OptionsBox">
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313 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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314 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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315 <br/> 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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316 <br/> .024 -2.270</div>
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317 </dd>
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318 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
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319 <dd>
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320 <p>Location of working directory. Default: current directory.</p>
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321 </dd>
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322 </dl>
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323 <p>
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324 </p>
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325 <h2>EXAMPLES</h2>
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326 <p>To generate E-state fingerprints of arbitrary size in vector string format and create a
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327 SampleESFP.csv file containing sequential compound IDs along with fingerprints
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328 vector strings data, type:</p>
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329 <div class="ExampleBox">
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330 % EStateIndiciesFingerprints.pl -r SampleESFP -o Sample.sdf</div>
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331 <p>To generate E-state fingerprints of fixed size in vector string format and create a
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332 SampleESFP.csv file containing sequential compound IDs along with fingerprints
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333 vector strings data, type:</p>
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334 <div class="ExampleBox">
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335 % EStateIndiciesFingerprints.pl -e FixedSize -r SampleESFP
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336 -o Sample.sdf</div>
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337 <p>To generate E-state fingerprints of fixed size in vector string with IDsAndValues
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338 format and create a SampleESFP.csv file containing sequential compound IDs
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339 along with fingerprints vector strings data, type:</p>
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340 <div class="ExampleBox">
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341 % EStateIndiciesFingerprints.pl -e FixedSize -v IDsAndValuesString
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342 -r SampleESFP -o Sample.sdf</div>
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343 <p>To generate E-state fingerprints of fixed size in vector string format
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344 and create a SampleESFP.csv file containing compound ID from molecule
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345 name line along with fingerprints vector strings data, type</p>
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346 <div class="ExampleBox">
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347 % EStateIndiciesFingerprints.pl -e FixedSize
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348 --DataFieldsMode CompoundID --CompoundIDMode MolName
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349 -r SampleESFP -o Sample.sdf</div>
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350 <p>To generate E-state fingerprints of fixed size in vector string format
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351 and create a SampleESFP.csv file containing compound IDs using specified
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352 data field along with fingerprints vector strings data, type:</p>
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353 <div class="ExampleBox">
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354 % EStateIndiciesFingerprints.pl -e FixedSize
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355 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
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356 Mol_ID -r SampleESFP -o Sample.sdf</div>
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357 <p>To generate E-state fingerprints of fixed size in vector string format
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358 and create a SampleESFP.csv file containing compound ID using combination
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359 of molecule name line and an explicit compound prefix along with fingerprints vector
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360 strings data, type:</p>
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361 <div class="ExampleBox">
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362 % EStateIndiciesFingerprints.pl -e FixedSize
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363 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
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364 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleESFP -o Sample.sdf</div>
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365 <p>To generate E-state fingerprints of fixed size in vector string format
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366 and create a SampleESFP.csv file containing specific data fields columns along
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367 with fingerprints vector strings data, type:</p>
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368 <div class="ExampleBox">
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369 % EStateIndiciesFingerprints.pl -e FixedSize
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370 --DataFieldsMode Specify --DataFields Mol_ID -r SampleESFP
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371 -o Sample.sdf</div>
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372 <p>To generate E-state fingerprints of fixed size in vector string format
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373 and create a SampleESFP.csv file containing common data fields columns along
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374 with fingerprints vector strings data, type:</p>
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375 <div class="ExampleBox">
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376 % EStateIndiciesFingerprints.pl -e FixedSize
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377 --DataFieldsMode Common -r SampleESFP -o Sample.sdf</div>
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378 <p>To generate E-state fingerprints of fixed size in vector string format and create
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379 SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files containing all data
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380 fields columns in CSV file along with fingerprints vector strings data, type:</p>
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381 <div class="ExampleBox">
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382 % EStateIndiciesFingerprints.pl -e FixedSize
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383 --DataFieldsMode All --output all -r SampleESFP -o Sample.sdf</div>
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384 <p>
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385 </p>
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386 <h2>AUTHOR</h2>
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387 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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388 <p>
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389 </p>
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390 <h2>SEE ALSO</h2>
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391 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>, 
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392 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingeprints.html">MACCSKeysFingeprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, 
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393 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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394 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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395 </p>
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396 <p>
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397 </p>
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398 <h2>COPYRIGHT</h2>
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399 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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400 <p>This file is part of MayaChemTools.</p>
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401 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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402 the terms of the GNU Lesser General Public License as published by the Free
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403 Software Foundation; either version 3 of the License, or (at your option)
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404 any later version.</p>
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405 <p> </p><p> </p><div class="DocNav">
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406 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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407 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>EStateIndiciesFingerprints.pl</strong></td></tr>
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408 </table>
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409 </div>
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410 <br />
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411 <center>
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412 <img src="../../images/h2o2.png">
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413 </center>
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414 </body>
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415 </html>
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