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3 <title>MayaChemTools:Documentation:SimilaritySearchingFingerprints.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="./SimilarityMatricesFingerprints.html" title="SimilarityMatricesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SortSDFiles.html" title="SortSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>SimilaritySearchingFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/SimilaritySearchingFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/SimilaritySearchingFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SimilaritySearchingFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SimilaritySearchingFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SimilaritySearchingFingerprints.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>SimilaritySearchingFingerprints.pl - Perform similarity search using fingerprints strings data in SD, FP and CSV/TSV text file(s)</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>SimilaritySearchingFingerprints.pl ReferenceFPFile DatabaseFPFile</p>
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26 <p>SimilaritySearchingFingerprints.pl [<strong>--alpha</strong> <em>number</em>] [<strong>--beta</strong> <em>number</em>]
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27 [<strong>-b, --BitVectorComparisonMode</strong> <em>TanimotoSimilarity | TverskySimilarity | ...</em>]
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28 [<strong>--DatabaseColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--DatabaseCompoundIDCol</strong> <em>col number | col name</em>]
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29 [<strong>--DatabaseCompoundIDPrefix</strong> <em>text</em>] [<strong>--DatabaseCompoundIDField</strong> <em>DataFieldName</em>]
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30 [<strong>--DatabaseCompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
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31 [<strong>--DatabaseDataCols</strong> <em>"DataColNum1, DataColNum2,... " | DataColLabel1, DataCoLabel2,... "</em>]
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32 [<strong>--DatabaseDataColsMode</strong> <em>All | Specify | CompoundID</em>] [<strong>--DatabaseDataFields</strong> <em>"FieldLabel1, FieldLabel2,... "</em>]
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33 [<strong>--DatabaseDataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>]
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34 [<strong>--DatabaseFingerprintsCol</strong> <em>col number | col name</em>] [<strong>--DatabaseFingerprintsField</strong> <em>FieldLabel</em>]
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35 []<strong>--DistanceCutoff</strong> <em>number</em>] [<strong>-d, --detail</strong> <em>InfoLevel</em>] [<strong>-f, --fast</strong>]
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36 [<strong>--FingerprintsMode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em>]
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37 [<strong>-g, --GroupFusionRule</strong> <em>Max, Mean, Median, Min, Sum, Euclidean</em>] [<strong>--GroupFusionApplyCutoff</strong> <em>Yes | No</em>]
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38 [<strong>-h, --help</strong>] [<strong>--InDelim</strong> <em>comma | semicolon</em>] [<strong>-k, --KNN</strong> <em>all | number</em>]
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39 [<strong>-m, --mode</strong> <em>IndividualReference | MultipleReferences</em>]
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40 [<strong>-n, --NumOfSimilarMolecules</strong> <em>number</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>]
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41 [<strong>--output</strong> <em>SD | text | both</em>] [<strong>-o, --overwrite</strong>]
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42 [<strong>-p, --PercentSimilarMolecules</strong> <em>number</em>] [<strong>--precision</strong> <em>number</em>] [<strong>-q, --quote</strong> <em>Yes | No</em>]
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43 [<strong>--ReferenceColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--ReferenceCompoundIDCol</strong> <em>col number | col name</em>]
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44 [<strong>--ReferenceCompoundIDPrefix</strong> <em>text</em>] [<strong>--ReferenceCompoundIDField</strong> <em>DataFieldName</em>]
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45 [<strong>--ReferenceCompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
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46 [<strong>--ReferenceFingerprintsCol</strong> <em>col number | col name</em>] [<strong>--ReferenceFingerprintsField</strong> <em>FieldLabel</em>]
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47 [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --SearchMode</strong> <em>SimilaritySearch | DissimilaritySearch</em>]
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48 [<strong>--SimilarCountMode</strong> <em>NumOfSimilar | PercentSimilar</em>] [<strong>--SimilarityCutoff</strong> <em>number</em>]
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49 [<strong>-v, --VectorComparisonMode</strong> <em>TanimotoSimilairy | ... | ManhattanDistance | ...</em>]
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50 [<strong>--VectorComparisonFormulism</strong> <em>AlgebraicForm | BinaryForm | SetTheoreticForm</em>]
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51 [<strong>-w, --WorkingDir</strong> dirname] ReferenceFingerprintsFile DatabaseFingerprintsFile</p>
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52 <p>
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53 </p>
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54 <h2>DESCRIPTION</h2>
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55 <p>Perform molecular similarity search [ Ref 94-113 ] using fingerprint bit-vector or vector strings
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56 data in <em>SD, FP, or CSV/TSV text</em> files corresponding to <em>ReferenceFingerprintsFile</em> and
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57 <em>DatabaseFingerprintsFile</em>, and generate SD and CSV/TSV text file(s) containing database
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58 molecules which are similar to reference molecule(s). The reference molecules are also referred
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59 to as query or seed molecules and database molecules as target molecules in the literature.</p>
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60 <p>The current release of MayaChemTools supports two types of similarity search modes:
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61 <em>IndividualReference or MultipleReferences</em>. For default value of <em>MultipleReferences</em> for <strong>-m, --mode</strong>
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62 option, reference molecules are considered as a set and <strong>-g, --GroupFusionRule</strong> is used to calculate
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63 similarity of a database molecule against reference molecules set. The group fusion rule is also
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64 referred to as data fusion of consensus scoring in the literature. However, for <em>IndividualReference</em>
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65 value of <strong>-m, --mode</strong> option, reference molecules are treated as individual molecules and each reference
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66 molecule is compared against a database molecule by itself to identify similar molecules.</p>
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67 <p>The molecular dissimilarity search can also be performed using <em>DissimilaritySearch</em> value for
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68 <strong>-s, --SearchMode</strong> option. During dissimilarity search or usage of distance comparison coefficient
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69 in similarity similarity search, the meaning of fingerprints comparison value is automatically reversed
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70 as shown below:</p>
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71 <div class="OptionsBox">
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72 SeachMode ComparisonCoefficient ResultsSort ComparisonValues</div>
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73 <div class="OptionsBox">
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74 Similarity SimilarityCoefficient Descending Higher value imples
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75 high similarity
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76 <br/> Similarity DistanceCoefficient Ascending Lower value implies
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77 high similarity</div>
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78 <div class="OptionsBox">
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79 Dissimilarity SimilarityCoefficient Ascending Lower value implies
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80 high dissimilarity
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81 <br/> Dissimilarity DistanceCoefficient Descending Higher value implies
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82 high dissimilarity</div>
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83 <p>During <em>IndividualReference</em> value of <strong>-m, --Mode</strong> option for similarity search, fingerprints bit-vector
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84 or vector string of each reference molecule is compared with database molecules using specified
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85 similarity or distance coefficients to identify most similar molecules for each reference molecule.
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86 Based on value of <strong>--SimilarCountMode</strong>, up to <strong>--n, --NumOfSimilarMolecules</strong> or <strong>-p,
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87 --PercentSimilarMolecules</strong> at specified <strong>--SimilarityCutoff</strong> or <strong>--DistanceCutoff</strong> are
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88 identified for each reference molecule.</p>
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89 <p>During <em>MultipleReferences</em> value <strong>-m, --mode</strong> option for similarity search, all reference molecules
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90 are considered as a set and <strong>-g, --GroupFusionRule</strong> is used to calculate similarity of a database
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91 molecule against reference molecules set either using all reference molecules or number of k-nearest
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92 neighbors (k-NN) to a database molecule specified using <strong>-k, --kNN</strong>. The fingerprints bit-vector
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93 or vector string of each reference molecule in a set is compared with a database molecule using
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94 a similarity or distance coefficient specified via <strong>-b, --BitVectorComparisonMode</strong> or <strong>-v,
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95 --VectorComparisonMode</strong>. The reference molecules whose comparison values with a database
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96 molecule fall outside specified <strong>--SimilarityCutoff</strong> or <strong>--DistanceCutoff</strong> are ignored during <em>Yes</em>
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97 value of <strong>--GroupFusionApplyCutoff</strong>. The specified <strong>-g, --GroupFusionRule</strong> is applied to
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98 <strong>-k, --kNN</strong> reference molecules to calculate final similarity value between a database molecule
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99 and reference molecules set.</p>
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100 <p>The input fingerprints <em>SD, FP, or Text (CSV/TSV)</em> files for <em>ReferenceFingerprintsFile</em> and
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101 <em>DatabaseTextFile</em> must contain valid fingerprint bit-vector or vector strings data corresponding to
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102 same type of fingerprints.</p>
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103 <p>The valid fingerprints <em>SDFile</em> extensions are <em>.sdf</em> and <em>.sd</em>. The valid fingerprints <em>FPFile</em>
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104 extensions are <em>.fpf</em> and <em>.fp</em>. The valid fingerprints <em>TextFile (CSV/TSV)</em> extensions are
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105 <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab delimited text files respectively. The <strong>--indelim</strong>
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106 option determines the format of <em>TextFile</em>. Any file which doesn't correspond to the format indicated
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107 by <strong>--indelim</strong> option is ignored.</p>
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108 <p>Example of <em>FP</em> file containing fingerprints bit-vector string data:</p>
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109 <div class="OptionsBox">
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110 #
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111 <br/> # Package = MayaChemTools 7.4
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112 <br/> # ReleaseDate = Oct 21, 2010
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113 <br/> #
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114 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
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115 <br/> #
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116 <br/> # FingerprintsStringType = FingerprintsBitVector
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117 <br/> #
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118 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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119 <br/> # Size = 1024
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120 <br/> # BitStringFormat = HexadecimalString
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121 <br/> # BitsOrder = Ascending
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122 <br/> #
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123 <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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124 <br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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125 <br/> ... ...
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126 <br/> ... ..</div>
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127 <p>Example of <em>FP</em> file containing fingerprints vector string data:</p>
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128 <div class="OptionsBox">
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129 #
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130 <br/> # Package = MayaChemTools 7.4
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131 <br/> # ReleaseDate = Oct 21, 2010
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132 <br/> #
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133 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
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134 <br/> #
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135 <br/> # FingerprintsStringType = FingerprintsVector
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136 <br/> #
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137 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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138 <br/> # VectorStringFormat = IDsAndValuesString
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139 <br/> # VectorValuesType = NumericalValues
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140 <br/> #
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141 <br/> Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
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142 <br/> N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
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143 <br/> 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
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144 <br/> 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
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145 <br/> Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
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146 <br/> O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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147 <br/> 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
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148 <br/> 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
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149 <br/> ... ...
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150 <br/> ... ...</div>
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151 <p>Example of <em>SD</em> file containing fingerprints bit-vector string data:</p>
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152 <div class="OptionsBox">
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153 ... ...
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154 <br/> ... ...
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155 <br/> $$$$
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156 <br/> ... ...
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157 <br/> ... ...
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158 <br/> ... ...
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159 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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160 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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161 <br/> ... ...
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162 <br/> 2 3 1 0 0 0 0
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163 <br/> ... ...
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164 <br/> M END
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165 <br/> > <CmpdID>
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166 <br/> Cmpd1</div>
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167 <div class="OptionsBox">
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168 > <PathLengthFingerprints>
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169 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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170 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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171 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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172 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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173 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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174 <br/> aa0660a11014a011d46</div>
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175 <div class="OptionsBox">
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176 $$$$
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177 <br/> ... ...
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178 <br/> ... ...</div>
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179 <p>Example of CSV <em>TextFile</em> containing fingerprints bit-vector string data:</p>
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180 <div class="OptionsBox">
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181 "CompoundID","PathLengthFingerprints"
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182 <br/> "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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183 <br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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184 <br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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185 <br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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186 <br/> ... ...
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187 <br/> ... ...</div>
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188 <p>The current release of MayaChemTools supports the following types of fingerprint
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189 bit-vector and vector strings:</p>
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190 <div class="OptionsBox">
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191 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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192 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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193 <br/> 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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194 <br/> 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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195 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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196 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
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197 <div class="OptionsBox">
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198 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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199 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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200 <br/> .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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201 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
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202 <div class="OptionsBox">
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203 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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204 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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205 <br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div>
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206 <div class="OptionsBox">
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207 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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208 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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209 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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210 <br/> 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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211 <br/> 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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212 <br/> 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...</div>
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213 <div class="OptionsBox">
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214 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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215 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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216 <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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217 <br/> .024 -2.270</div>
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218 <div class="OptionsBox">
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219 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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220 <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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221 <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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222 <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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223 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
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224 <div class="OptionsBox">
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225 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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226 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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227 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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228 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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229 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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230 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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231 <div class="OptionsBox">
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232 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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233 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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234 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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235 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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236 <br/> 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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237 <br/> 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</div>
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238 <div class="OptionsBox">
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239 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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240 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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241 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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242 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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243 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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244 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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245 <div class="OptionsBox">
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246 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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247 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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248 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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249 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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250 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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251 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
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252 <div class="OptionsBox">
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253 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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254 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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255 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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256 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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257 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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258 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
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259 <div class="OptionsBox">
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260 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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261 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
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262 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
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263 <br/> 11111111111110111000</div>
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264 <div class="OptionsBox">
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265 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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266 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
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267 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
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268 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
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269 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
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270 <br/> 0000000000000000000000000000000000000000</div>
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271 <div class="OptionsBox">
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272 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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273 <br/> 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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274 <br/> 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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275 <br/> 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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276 <br/> 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
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277 <br/> 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</div>
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278 <div class="OptionsBox">
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279 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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280 <br/> 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
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281 <br/> 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
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282 <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 0
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283 <br/> 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
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284 <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 ...</div>
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285 <div class="OptionsBox">
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286 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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287 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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288 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
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289 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
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290 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
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291 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
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292 <div class="OptionsBox">
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293 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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294 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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295 <br/> 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
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296 <br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
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297 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
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298 <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div>
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299 <div class="OptionsBox">
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300 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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301 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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302 <br/> 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
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303 <br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
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304 <br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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305 <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div>
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306 <div class="OptionsBox">
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307 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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308 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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309 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
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310 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
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311 <br/> 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
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312 <br/> 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...</div>
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313 <div class="OptionsBox">
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314 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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315 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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316 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
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317 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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318 <br/> 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
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319 <br/> 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 ...</div>
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320 <div class="OptionsBox">
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321 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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322 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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323 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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324 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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325 <br/> 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</div>
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326 <div class="OptionsBox">
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327 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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328 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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329 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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330 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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331 <br/> 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</div>
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332 <div class="OptionsBox">
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333 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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334 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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335 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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336 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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337 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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338 <br/> 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
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339 <br/> 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...</div>
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340 <div class="OptionsBox">
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341 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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342 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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343 <br/> .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-
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344 <br/> 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
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345 <br/> -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.
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346 <br/> 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...</div>
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347 <div class="OptionsBox">
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348 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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349 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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350 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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351 <br/> 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
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352 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
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353 <br/> 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
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354 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
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355 <div class="OptionsBox">
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356 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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357 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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358 <br/> 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
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359 <br/> 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
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360 <br/> 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
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361 <br/> 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...</div>
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362 <div class="OptionsBox">
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363 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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364 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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365 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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366 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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367 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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368 <br/> 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
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369 <br/> 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
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370 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
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371 <div class="OptionsBox">
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372 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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373 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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374 <br/> 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
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375 <br/> 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
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376 <br/> 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
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377 <br/> 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 ...</div>
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378 <p>
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379 </p>
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380 <h2>OPTIONS</h2>
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381 <dl>
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382 <dt><strong><strong>--alpha</strong> <em>number</em></strong></dt>
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383 <dd>
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384 <p>Value of alpha parameter for calculating <em>Tversky</em> similarity coefficient specified for
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385 <strong>-b, --BitVectorComparisonMode</strong> option. It corresponds to weights assigned for bits set
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386 to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
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387 values: <em>0 to 1</em>. Default value: <0.5>.</p>
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388 </dd>
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389 <dt><strong><strong>--beta</strong> <em>number</em></strong></dt>
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390 <dd>
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391 <p>Value of beta parameter for calculating <em>WeightedTanimoto</em> and <em>WeightedTversky</em>
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392 similarity coefficients specified for <strong>-b, --BitVectorComparisonMode</strong> option. It is used to
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393 weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible
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394 values: <em>0 to 1</em>. Default value of <1> makes <em>WeightedTanimoto</em> and <em>WeightedTversky</em>
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395 equivalent to <em>Tanimoto</em> and <em>Tversky</em>.</p>
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396 </dd>
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397 <dt><strong><strong>-b, --BitVectorComparisonMode</strong> <em>TanimotoSimilarity | TverskySimilarity | ...</em></strong></dt>
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398 <dd>
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399 <p>Specify what similarity coefficient to use for calculating similarity between fingerprints bit-vector
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400 string data values in <em>ReferenceFingerprintsFile</em> and <em>DatabaseFingerprintsFile</em> during similarity
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401 search. Possible values: <em>TanimotoSimilarity | TverskySimilarity | ...</em>. Default: <em>TanimotoSimilarity</em></p>
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402 <p>The current release supports the following similarity coefficients: <em>BaroniUrbaniSimilarity, BuserSimilarity,
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403 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
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404 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
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405 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
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406 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
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407 WeightedTanimotoSimilarity, WeightedTverskySimilarity</em>. These similarity coefficients are described below.</p>
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408 <p>For two fingerprint bit-vectors A and B of same size, let:</p>
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409 <div class="OptionsBox">
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410 Na = Number of bits set to "1" in A
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411 <br/> Nb = Number of bits set to "1" in B
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412 <br/> Nc = Number of bits set to "1" in both A and B
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413 <br/> Nd = Number of bits set to "0" in both A and B</div>
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414 <div class="OptionsBox">
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415 Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
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416 <br/> Nt = Na + Nb - Nc + Nd</div>
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417 <div class="OptionsBox">
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418 Na - Nc = Number of bits set to "1" in A but not in B
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419 <br/> Nb - Nc = Number of bits set to "1" in B but not in A</div>
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420 <p>Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are
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421 defined as follows:</p>
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422 <p><em>BaroniUrbaniSimilarity</em>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</p>
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423 <p><em>BuserSimilarity</em>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</p>
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424 <p><em>CosineSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Ochiai)</p>
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425 <p><em>DiceSimilarity</em>: (2 * Nc) / ( Na + Nb )</p>
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426 <p><em>DennisSimilarity</em>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</p>
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427 <p><em>ForbesSimilarity</em>: ( Nt * Nc ) / ( Na * Nb )</p>
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428 <p><em>FossumSimilarity</em>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</p>
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429 <p><em>HamannSimilarity</em>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</p>
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430 <p><em>JaccardSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</p>
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431 <p><em>Kulczynski1Similarity</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</p>
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432 <p><em>Kulczynski2Similarity</em>: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )</p>
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|
433 <p><em>MatchingSimilarity</em>: ( Nc + Nd ) / Nt</p>
|
|
|
434 <p><em>McConnaugheySimilarity</em>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</p>
|
|
|
435 <p><em>OchiaiSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Cosine)</p>
|
|
|
436 <p><em>PearsonSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</p>
|
|
|
437 <p><em>RogersTanimotoSimilarity</em>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</p>
|
|
|
438 <p><em>RussellRaoSimilarity</em>: Nc / Nt</p>
|
|
|
439 <p><em>SimpsonSimilarity</em>: Nc / MIN ( Na, Nb)</p>
|
|
|
440 <p><em>SkoalSneath1Similarity</em>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</p>
|
|
|
441 <p><em>SkoalSneath2Similarity</em>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</p>
|
|
|
442 <p><em>SkoalSneath3Similarity</em>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</p>
|
|
|
443 <p><em>TanimotoSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</p>
|
|
|
444 <p><em>TverskySimilarity</em>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</p>
|
|
|
445 <p><em>YuleSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</p>
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|
|
446 <p>Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
|
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|
447 are set to "1" in both A and B. In order to take into account all bit positions, modified versions
|
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|
448 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</p>
|
|
|
449 <p>Let:</p>
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450 <div class="OptionsBox">
|
|
|
451 Na' = Number of bits set to "0" in A
|
|
|
452 <br/> Nb' = Number of bits set to "0" in B
|
|
|
453 <br/> Nc' = Number of bits set to "0" in both A and B</div>
|
|
|
454 <p>Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</p>
|
|
|
455 <p>Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</p>
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|
456 <p>Then:</p>
|
|
|
457 <p><em>WeightedTanimotoSimilarity</em> = beta * Tanimoto + (1 - beta) * Tanimoto'</p>
|
|
|
458 <p><em>WeightedTverskySimilarity</em> = beta * Tversky + (1 - beta) * Tversky'</p>
|
|
|
459 </dd>
|
|
|
460 <dt><strong><strong>--DatabaseColMode</strong> <em>ColNum | ColLabel</em></strong></dt>
|
|
|
461 <dd>
|
|
|
462 <p>Specify how columns are identified in database fingerprints <em>TextFile</em>: using column
|
|
|
463 number or column label. Possible values: <em>ColNum or ColLabel</em>. Default value: <em>ColNum</em>.</p>
|
|
|
464 </dd>
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|
|
465 <dt><strong><strong>--DatabaseCompoundIDCol</strong> <em>col number | col name</em></strong></dt>
|
|
|
466 <dd>
|
|
|
467 <p>This value is <strong>--DatabaseColMode</strong> mode specific. It specifies column to use for retrieving compound
|
|
|
468 ID from database fingerprints <em>TextFile</em> during similarity and dissimilarity search for output SD and
|
|
|
469 CSV/TSV text files. Possible values: <em>col number or col label</em>. Default value: <em>first column containing
|
|
|
470 the word compoundID in its column label or sequentially generated IDs</em>.</p>
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|
|
471 <p>This is only used for <em>CompoundID</em> value of <strong>--DatabaseDataColsMode</strong> option.</p>
|
|
|
472 </dd>
|
|
|
473 <dt><strong><strong>--DatabaseCompoundIDPrefix</strong> <em>text</em></strong></dt>
|
|
|
474 <dd>
|
|
|
475 <p>Specify compound ID prefix to use during sequential generation of compound IDs for database fingerprints
|
|
|
476 <em>SDFile</em> and <em>TextFile</em>. Default value: <em>Cmpd</em>. The default value generates compound IDs which look
|
|
|
477 like Cmpd<Number>.</p>
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|
|
478 <p>For database fingerprints <em>SDFile</em>, this value is only used during <em>LabelPrefix | MolNameOrLabelPrefix</em>
|
|
|
479 values of <strong>--DatabaseCompoundIDMode</strong> option; otherwise, it's ignored.</p>
|
|
|
480 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--DatabaseCompoundIDMode</strong>:</p>
|
|
|
481 <div class="OptionsBox">
|
|
|
482 Compound</div>
|
|
|
483 <p>The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
484 instead of default value of Cmpd<Number>.</p>
|
|
|
485 </dd>
|
|
|
486 <dt><strong><strong>--DatabaseCompoundIDField</strong> <em>DataFieldName</em></strong></dt>
|
|
|
487 <dd>
|
|
|
488 <p>Specify database fingerprints <em>SDFile</em> datafield label for generating compound IDs. This value is
|
|
|
489 only used during <em>DataField</em> value of <strong>--DatabaseCompoundIDMode</strong> option.</p>
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|
|
490 <p>Examples for <em>DataField</em> value of <strong>--DatabaseCompoundIDMode</strong>:</p>
|
|
|
491 <div class="OptionsBox">
|
|
|
492 MolID
|
|
|
493 <br/> ExtReg</div>
|
|
|
494 </dd>
|
|
|
495 <dt><strong><strong>--DatabaseCompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
|
|
|
496 <dd>
|
|
|
497 <p>Specify how to generate compound IDs from database fingerprints <em>SDFile</em> during similarity and
|
|
|
498 dissimilarity search for output SD and CSV/TSV text files: use a <em>SDFile</em> datafield value; use
|
|
|
499 molname line from <em>SDFile</em>; generate a sequential ID with specific prefix; use combination of both
|
|
|
500 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
|
|
|
501 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
|
|
|
502 Default: <em>LabelPrefix</em>.</p>
|
|
|
503 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--DatabaseCompoundIDMode</strong>, molname line in <em>SDFile</em> takes
|
|
|
504 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
|
|
|
505 values are replaced with sequential compound IDs.</p>
|
|
|
506 <p>This is only used for <em>CompoundID</em> value of <strong>--DatabaseDataFieldsMode</strong> option.</p>
|
|
|
507 </dd>
|
|
|
508 <dt><strong><strong>--DatabaseDataCols</strong> <em>"DataColNum1,DataColNum2,... " | DataColLabel1,DataCoLabel2,... "</em></strong></dt>
|
|
|
509 <dd>
|
|
|
510 <p>This value is <strong>--DatabaseColMode</strong> mode specific. It is a comma delimited list of database fingerprints
|
|
|
511 <em>TextFile</em> data column numbers or labels to extract and write to SD and CSV/TSV text files along with
|
|
|
512 other information for <em>SD | text | both</em> values of <strong>--output</strong> option.</p>
|
|
|
513 <p>This is only used for <em>Specify</em> value of <strong>--DatabaseDataColsMode</strong> option.</p>
|
|
|
514 <p>Examples:</p>
|
|
|
515 <div class="OptionsBox">
|
|
|
516 1,2,3
|
|
|
517 <br/> CompoundName,MolWt</div>
|
|
|
518 </dd>
|
|
|
519 <dt><strong><strong>--DatabaseDataColsMode</strong> <em>All | Specify | CompoundID</em></strong></dt>
|
|
|
520 <dd>
|
|
|
521 <p>Specify how data columns from database fingerprints <em>TextFile</em> are transferred to output SD and
|
|
|
522 CSV/TSV text files along with other information for <em>SD | text | both</em> values of <strong>--output</strong> option:
|
|
|
523 transfer all data columns; extract specified data columns; generate a compound ID database compound
|
|
|
524 prefix. Possible values: <em>All | Specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
|
|
|
525 </dd>
|
|
|
526 <dt><strong><strong>--DatabaseDataFields</strong> <em>"FieldLabel1,FieldLabel2,... "</em></strong></dt>
|
|
|
527 <dd>
|
|
|
528 <p>Comma delimited list of database fingerprints <em>SDFile</em> data fields to extract and write to SD
|
|
|
529 and CSV/TSV text files along with other information for <em>SD | text | both</em> values of
|
|
|
530 <strong>--output</strong> option.</p>
|
|
|
531 <p>This is only used for <em>Specify</em> value of <strong>--DatabaseDataFieldsMode</strong> option.</p>
|
|
|
532 <p>Examples:</p>
|
|
|
533 <div class="OptionsBox">
|
|
|
534 Extreg
|
|
|
535 <br/> MolID,CompoundName</div>
|
|
|
536 </dd>
|
|
|
537 <dt><strong><strong>--DatabaseDataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
|
|
|
538 <dd>
|
|
|
539 <p>Specify how data fields from database fingerprints <em>SDFile</em> are transferred to output SD and
|
|
|
540 CSV/TSV text files along with other information for <em>SD | text | both</em> values of <strong>--output</strong>
|
|
|
541 option: transfer all SD data field; transfer SD data files common to all compounds; extract
|
|
|
542 specified data fields; generate a compound ID using molname line, a compound prefix, or a
|
|
|
543 combination of both. Possible values: <em>All | Common | specify | CompoundID</em>. Default value:
|
|
|
544 <em>CompoundID</em>.</p>
|
|
|
545 </dd>
|
|
|
546 <dt><strong><strong>--DatabaseFingerprintsCol</strong> <em>col number | col name</em></strong></dt>
|
|
|
547 <dd>
|
|
|
548 <p>This value is <strong>--DatabaseColMode</strong> specific. It specifies fingerprints column to use during similarity
|
|
|
549 and dissimilarity search for database fingerprints <em>TextFile</em>. Possible values: <em>col number or col label</em>.
|
|
|
550 Default value: <em>first column containing the word Fingerprints in its column label</em>.</p>
|
|
|
551 </dd>
|
|
|
552 <dt><strong><strong>--DatabaseFingerprintsField</strong> <em>FieldLabel</em></strong></dt>
|
|
|
553 <dd>
|
|
|
554 <p>Fingerprints field label to use during similarity and dissimilarity search for database fingerprints <em>SDFile</em>.
|
|
|
555 Default value: <em>first data field label containing the word Fingerprints in its label</em></p>
|
|
|
556 </dd>
|
|
|
557 <dt><strong><strong>--DistanceCutoff</strong> <em>number</em></strong></dt>
|
|
|
558 <dd>
|
|
|
559 <p>Distance cutoff value to use during comparison of distance value between a pair of database
|
|
|
560 and reference molecule calculated by distance comparison methods for fingerprints vector
|
|
|
561 string data values. Possible values: <em>Any valid number</em>. Default value: <em>10</em>.</p>
|
|
|
562 <p>The comparison value between a pair of database and reference molecule must meet the cutoff
|
|
|
563 criterion as shown below:</p>
|
|
|
564 <div class="OptionsBox">
|
|
|
565 SeachMode CutoffCriterion ComparisonValues</div>
|
|
|
566 <div class="OptionsBox">
|
|
|
567 Similarity <= Lower value implies high similarity
|
|
|
568 <br/> Dissimilarity >= Higher value implies high dissimilarity</div>
|
|
|
569 <p>This option is only used during distance coefficients values of <strong>-v, --VectorComparisonMode</strong>
|
|
|
570 option.</p>
|
|
|
571 <p>This option is ignored during <em>No</em> value of <strong>--GroupFusionApplyCutoff</strong> for <em>MultipleReferences</em>
|
|
|
572 <strong>-m, --mode</strong>.</p>
|
|
|
573 </dd>
|
|
|
574 <dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt>
|
|
|
575 <dd>
|
|
|
576 <p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values:
|
|
|
577 <em>1, 2 or 3</em>.</p>
|
|
|
578 </dd>
|
|
|
579 <dt><strong><strong>-f, --fast</strong></strong></dt>
|
|
|
580 <dd>
|
|
|
581 <p>In this mode, fingerprints columns specified using <strong>--FingerprintsCol</strong> for reference and database
|
|
|
582 fingerprints <em>TextFile(s)</em>, and <strong>--FingerprintsField</strong> for reference and database fingerprints <em>SDFile(s)</em>
|
|
|
583 are assumed to contain valid fingerprints data and no checking is performed before performing similarity
|
|
|
584 and dissimilarity search. By default, fingerprints data is validated before computing pairwise similarity and
|
|
|
585 distance coefficients.</p>
|
|
|
586 </dd>
|
|
|
587 <dt><strong><strong>--FingerprintsMode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em></strong></dt>
|
|
|
588 <dd>
|
|
|
589 <p>Format of fingerprint strings data in reference and database fingerprints <em>SD, FP, or Text (CSV/TSV)</em>
|
|
|
590 files: automatically detect format of fingerprints string created by MayaChemTools fingerprints
|
|
|
591 generation scripts or explicitly specify its format. Possible values: <em>AutoDetect | FingerprintsBitVectorString |
|
|
|
592 FingerprintsVectorString</em>. Default value: <em>AutoDetect</em>.</p>
|
|
|
593 </dd>
|
|
|
594 <dt><strong><strong>-g, --GroupFusionRule</strong> <em>Max, Min, Mean, Median, Sum, Euclidean</em></strong></dt>
|
|
|
595 <dd>
|
|
|
596 <p>Specify what group fusion [ Ref 94-97, Ref 100, Ref 105 ] rule to use for calculating similarity of
|
|
|
597 a database molecule against a set of reference molecules during <em>MultipleReferences</em> value of
|
|
|
598 similarity search <strong>-m, --mode</strong>. Possible values: <em>Max, Min, Mean, Median, Sum, Euclidean</em>. Default
|
|
|
599 value: <em>Max</em>. <em>Mean</em> value corresponds to average or arithmetic mean. The group fusion rule is
|
|
|
600 also referred to as data fusion of consensus scoring in the literature.</p>
|
|
|
601 <p>For a reference molecules set and a database molecule, let:</p>
|
|
|
602 <div class="OptionsBox">
|
|
|
603 N = Number of reference molecules in a set</div>
|
|
|
604 <div class="OptionsBox">
|
|
|
605 i = ith reference reference molecule in a set
|
|
|
606 <br/> n = Nth reference reference molecule in a set</div>
|
|
|
607 <div class="OptionsBox">
|
|
|
608 d = dth database molecule</div>
|
|
|
609 <div class="OptionsBox">
|
|
|
610 Crd = Fingerprints comparison value between rth reference and dth database
|
|
|
611 molecule - similarity/dissimilarity comparison using similarity or
|
|
|
612 distance coefficient</div>
|
|
|
613 <p>Then, various group fusion rules to calculate fused similarity between a database molecule and
|
|
|
614 reference molecules set are defined as follows:</p>
|
|
|
615 <p><strong>Max</strong>: MAX ( C1d, C2d, ..., Cid, ..., Cnd )</p>
|
|
|
616 <p><strong>Min</strong>: MIN ( C1d, C2d, ..., Cid, ..., Cnd )</p>
|
|
|
617 <p><strong>Mean</strong>: SUM ( C1d, C2d, ..., Cid, ..., Cnd ) / N</p>
|
|
|
618 <p><strong>Median</strong>: MEDIAN ( C1d, C2d, ..., Cid, ..., Cnd )</p>
|
|
|
619 <p><strong>Sum</strong>: SUM ( C1d, C2d, ..., Cid, ..., Cnd )</p>
|
|
|
620 <p><strong>Euclidean</strong>: SQRT( SUM( C1d ** 2, C2d ** 2, ..., Cid ** 2, ..., Cnd *** 2) )</p>
|
|
|
621 <p>The fingerprints bit-vector or vector string of each reference molecule in a set is compared
|
|
|
622 with a database molecule using a similarity or distance coefficient specified via <strong>-b,
|
|
|
623 --BitVectorComparisonMode</strong> or <strong>-v, --VectorComparisonMode</strong>. The reference molecules
|
|
|
624 whose comparison values with a database molecule fall outside specified <strong>--SimilarityCutoff</strong>
|
|
|
625 or <strong>--DistanceCutoff</strong> are ignored during <em>Yes</em> value of <strong>--GroupFusionApplyCutoff</strong>. The
|
|
|
626 specified <strong>-g, --GroupFusionRule</strong> is applied to <strong>-k, --kNN</strong> reference molecules to calculate
|
|
|
627 final fused similarity value between a database molecule and reference molecules set.</p>
|
|
|
628 <p>During dissimilarity search or usage of distance comparison coefficient in similarity search,
|
|
|
629 the meaning of fingerprints comaprison value is automatically reversed as shown below:</p>
|
|
|
630 <div class="OptionsBox">
|
|
|
631 SeachMode ComparisonCoefficient ComparisonValues</div>
|
|
|
632 <div class="OptionsBox">
|
|
|
633 Similarity SimilarityCoefficient Higher value imples high similarity
|
|
|
634 <br/> Similarity DistanceCoefficient Lower value implies high similarity</div>
|
|
|
635 <div class="OptionsBox">
|
|
|
636 Dissimilarity SimilarityCoefficient Lower value implies high
|
|
|
637 dissimilarity
|
|
|
638 <br/> Dissimilarity DistanceCoefficient Higher value implies high
|
|
|
639 dissimilarity</div>
|
|
|
640 <p>Consequently, <em>Max</em> implies highest and lowest comparison value for usage of similarity and
|
|
|
641 distance coefficient respectively during similarity search. And it corresponds to lowest and highest
|
|
|
642 comparison value for usage of similarity and distance coefficient respectively during dissimilarity
|
|
|
643 search. During <em>Min</em> fusion rule, the highest and lowest comparison values are appropriately
|
|
|
644 reversed.</p>
|
|
|
645 </dd>
|
|
|
646 <dt><strong><strong>--GroupFusionApplyCutoff</strong> <em>Yes | No</em></strong></dt>
|
|
|
647 <dd>
|
|
|
648 <p>Specify whether to apply <strong>--SimilarityCutoff</strong> or <strong>--DistanceCutoff</strong> values during application
|
|
|
649 of <strong>-g, --GroupFusionRule</strong> to reference molecules set. Possible values: <em>Yes or No</em>. Default
|
|
|
650 value: <em>Yes</em>.</p>
|
|
|
651 <p>During <em>Yes</em> value of <strong>--GroupFusionApplyCutoff</strong>, the reference molecules whose comparison
|
|
|
652 values with a database molecule fall outside specified <strong>--SimilarityCutoff</strong> or <strong>--DistanceCutoff</strong>
|
|
|
653 are not used to calculate final fused similarity value between a database molecule and reference
|
|
|
654 molecules set.</p>
|
|
|
655 </dd>
|
|
|
656 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
657 <dd>
|
|
|
658 <p>Print this help message.</p>
|
|
|
659 </dd>
|
|
|
660 <dt><strong><strong>--InDelim</strong> <em>comma | semicolon</em></strong></dt>
|
|
|
661 <dd>
|
|
|
662 <p>Input delimiter for reference and database fingerprints CSV <em>TextFile(s)</em>. Possible values:
|
|
|
663 <em>comma or semicolon</em>. Default value: <em>comma</em>. For TSV files, this option is ignored
|
|
|
664 and <em>tab</em> is used as a delimiter.</p>
|
|
|
665 </dd>
|
|
|
666 <dt><strong><strong>-k, --kNN</strong> <em>all | number</em></strong></dt>
|
|
|
667 <dd>
|
|
|
668 <p>Number of k-nearest neighbors (k-NN) reference molecules to use during <strong>-g, --GroupFusionRule</strong>
|
|
|
669 for calculating similarity of a database molecule against a set of reference molecules. Possible values:
|
|
|
670 <em>all | positive integers</em>. Default: <em>all</em>.</p>
|
|
|
671 <p>After ranking similarity values between a database molecule and reference molecules during
|
|
|
672 <em>MultipleReferences</em> value of similarity search <strong>-m, --mode</strong> option, a top <strong>-k, --KNN</strong> reference
|
|
|
673 molecule are selected and used during <strong>-g, --GroupFusionRule</strong>.</p>
|
|
|
674 <p>This option is <strong>-s, --SearchMode</strong> dependent: It corresponds to dissimilar molecules during
|
|
|
675 <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option.</p>
|
|
|
676 </dd>
|
|
|
677 <dt><strong><strong>-m, --mode</strong> <em>IndividualReference | MultipleReferences</em></strong></dt>
|
|
|
678 <dd>
|
|
|
679 <p>Specify how to treat reference molecules in <em>ReferenceFingerprintsFile</em> during similarity search:
|
|
|
680 Treat each reference molecule individually during similarity search or perform similarity
|
|
|
681 search by treating multiple reference molecules as a set. Possible values: <em>IndividualReference
|
|
|
682 | MultipleReferences</em>. Default value: <em>MultipleReferences</em>.</p>
|
|
|
683 <p>During <em>IndividualReference</em> value of <strong>-m, --Mode</strong> for similarity search, fingerprints bit-vector
|
|
|
684 or vector string of each reference molecule is compared with database molecules using specified
|
|
|
685 similarity or distance coefficients to identify most similar molecules for each reference molecule.
|
|
|
686 Based on value of <strong>--SimilarCountMode</strong>, upto <strong>--n, NumOfSimilarMolecules</strong> or <strong>-p,
|
|
|
687 --PercentSimilarMolecules</strong> at specified <--SimilarityCutoff> or <strong>--DistanceCutoff</strong> are
|
|
|
688 identified for each reference molecule.</p>
|
|
|
689 <p>During <em>MultipleReferences</em> value <strong>-m, --mode</strong> for similarity search, all reference molecules
|
|
|
690 are considered as a set and <strong>-g, --GroupFusionRule</strong> is used to calculate similarity of a database
|
|
|
691 molecule against reference molecules set either using all reference molecules or number of k-nearest
|
|
|
692 neighbors (k-NN) to a database molecule specified using <strong>-k, --kNN</strong>. The fingerprints bit-vector
|
|
|
693 or vector string of each reference molecule in a set is compared with a database molecule using
|
|
|
694 a similarity or distance coefficient specified via <strong>-b, --BitVectorComparisonMode</strong> or <strong>-v,
|
|
|
695 --VectorComparisonMode</strong>. The reference molecules whose comparison values with a database
|
|
|
696 molecule fall outside specified <strong>--SimilarityCutoff</strong> or <strong>--DistanceCutoff</strong> are ignored. The
|
|
|
697 specified <strong>-g, --GroupFusionRule</strong> is applied to rest of <strong>-k, --kNN</strong> reference molecules to calculate
|
|
|
698 final similarity value between a database molecule and reference molecules set.</p>
|
|
|
699 <p>The meaning of similarity and distance is automatically reversed during <em>DissimilaritySearch</em> value
|
|
|
700 of <strong>-s, --SearchMode</strong> along with appropriate handling of <strong>--SimilarityCutoff</strong> or
|
|
|
701 <strong>--DistanceCutoff</strong> values.</p>
|
|
|
702 </dd>
|
|
|
703 <dt><strong><strong>-n, --NumOfSimilarMolecules</strong> <em>number</em></strong></dt>
|
|
|
704 <dd>
|
|
|
705 <p>Maximum number of most similar database molecules to find for each reference molecule or set of
|
|
|
706 reference molecules based on <em>IndividualReference</em> or <em>MultipleReferences</em> value of similarity
|
|
|
707 search <strong>-m, --mode</strong> option. Default: <em>10</em>. Valid values: positive integers.</p>
|
|
|
708 <p>This option is ignored during <em>PercentSimilar</em> value of <strong>--SimilarCountMode</strong> option.</p>
|
|
|
709 <p>This option is <strong>-s, --SearchMode</strong> dependent: It corresponds to dissimilar molecules during
|
|
|
710 <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option.</p>
|
|
|
711 </dd>
|
|
|
712 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
713 <dd>
|
|
|
714 <p>Delimiter for output CSV/TSV text file. Possible values: <em>comma, tab, or semicolon</em>
|
|
|
715 Default value: <em>comma</em>.</p>
|
|
|
716 </dd>
|
|
|
717 <dt><strong><strong>--output</strong> <em>SD | text | both</em></strong></dt>
|
|
|
718 <dd>
|
|
|
719 <p>Type of output files to generate. Possible values: <em>SD, text, or both</em>. Default value: <em>text</em>.</p>
|
|
|
720 </dd>
|
|
|
721 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
722 <dd>
|
|
|
723 <p>Overwrite existing files</p>
|
|
|
724 </dd>
|
|
|
725 <dt><strong><strong>-p, --PercentSimilarMolecules</strong> <em>number</em></strong></dt>
|
|
|
726 <dd>
|
|
|
727 <p>Maximum percent of mosy similar database molecules to find for each reference molecule or set of
|
|
|
728 reference molecules based on <em>IndividualReference</em> or <em>MultipleReferences</em> value of similarity
|
|
|
729 search <strong>-m, --mode</strong> option. Default: <em>1</em> percent of database molecules. Valid values: non-zero values
|
|
|
730 in between <em>0 to 100</em>.</p>
|
|
|
731 <p>This option is ignored during <em>NumOfSimilar</em> value of <strong>--SimilarCountMode</strong> option.</p>
|
|
|
732 <p>During <em>PercentSimilar</em> value of <strong>--SimilarCountMode</strong> option, the number of molecules
|
|
|
733 in <em>DatabaseFingerprintsFile</em> is counted and number of similar molecules correspond to
|
|
|
734 <strong>--PercentSimilarMolecules</strong> of the total number of database molecules.</p>
|
|
|
735 <p>This option is <strong>-s, --SearchMode</strong> dependent: It corresponds to dissimilar molecules during
|
|
|
736 <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option.</p>
|
|
|
737 </dd>
|
|
|
738 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
|
|
|
739 <dd>
|
|
|
740 <p>Precision of calculated similarity values for comparison and generating output files. Default: up to <em>2</em>
|
|
|
741 decimal places. Valid values: positive integers.</p>
|
|
|
742 </dd>
|
|
|
743 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
744 <dd>
|
|
|
745 <p>Put quote around column values in output CSV/TSV text file. Possible values:
|
|
|
746 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
747 </dd>
|
|
|
748 <dt><strong><strong>--ReferenceColMode</strong> <em>ColNum | ColLabel</em></strong></dt>
|
|
|
749 <dd>
|
|
|
750 <p>Specify how columns are identified in reference fingerprints <em>TextFile</em>: using column
|
|
|
751 number or column label. Possible values: <em>ColNum or ColLabel</em>. Default value: <em>ColNum</em>.</p>
|
|
|
752 </dd>
|
|
|
753 <dt><strong><strong>--ReferenceCompoundIDCol</strong> <em>col number | col name</em></strong></dt>
|
|
|
754 <dd>
|
|
|
755 <p>This value is <strong>--ReferenceColMode</strong> mode specific. It specifies column to use for retrieving compound
|
|
|
756 ID from reference fingerprints <em>TextFile</em> during similarity and dissimilarity search for output SD and CSV/TSV
|
|
|
757 text files. Possible values: <em>col number or col label</em>. Default value: <em>first column containing the word compoundID
|
|
|
758 in its column label or sequentially generated IDs</em>.</p>
|
|
|
759 </dd>
|
|
|
760 <dt><strong><strong>--ReferenceCompoundIDPrefix</strong> <em>text</em></strong></dt>
|
|
|
761 <dd>
|
|
|
762 <p>Specify compound ID prefix to use during sequential generation of compound IDs for reference fingerprints
|
|
|
763 <em>SDFile</em> and <em>TextFile</em>. Default value: <em>Cmpd</em>. The default value generates compound IDs which looks
|
|
|
764 like Cmpd<Number>.</p>
|
|
|
765 <p>For reference fingerprints <em>SDFile</em>, this value is only used during <em>LabelPrefix | MolNameOrLabelPrefix</em>
|
|
|
766 values of <strong>--ReferenceCompoundIDMode</strong> option; otherwise, it's ignored.</p>
|
|
|
767 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--DatabaseCompoundIDMode</strong>:</p>
|
|
|
768 <div class="OptionsBox">
|
|
|
769 Compound</div>
|
|
|
770 <p>The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
771 instead of default value of Cmpd<Number>.</p>
|
|
|
772 </dd>
|
|
|
773 <dt><strong><strong>--ReferenceCompoundIDField</strong> <em>DataFieldName</em></strong></dt>
|
|
|
774 <dd>
|
|
|
775 <p>Specify reference fingerprints <em>SDFile</em> datafield label for generating compound IDs.
|
|
|
776 This value is only used during <em>DataField</em> value of <strong>--ReferenceCompoundIDMode</strong> option.</p>
|
|
|
777 <p>Examples for <em>DataField</em> value of <strong>--ReferenceCompoundIDMode</strong>:</p>
|
|
|
778 <div class="OptionsBox">
|
|
|
779 MolID
|
|
|
780 <br/> ExtReg</div>
|
|
|
781 </dd>
|
|
|
782 <dt><strong><strong>--ReferenceCompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
|
|
|
783 <dd>
|
|
|
784 <p>Specify how to generate compound IDs from reference fingerprints <em>SDFile</em> during similarity and
|
|
|
785 dissimilarity search for output SD and CSV/TSV text files: use a <em>SDFile</em> datafield value; use
|
|
|
786 molname line from <em>SDFile</em>; generate a sequential ID with specific prefix; use combination of both
|
|
|
787 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
|
|
|
788 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
|
|
|
789 Default: <em>LabelPrefix</em>.</p>
|
|
|
790 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--ReferenceCompoundIDMode</strong>, molname line in <em>SDFiles</em>
|
|
|
791 takes precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
|
|
|
792 values are replaced with sequential compound IDs.</p>
|
|
|
793 </dd>
|
|
|
794 <dt><strong><strong>--ReferenceFingerprintsCol</strong> <em>col number | col name</em></strong></dt>
|
|
|
795 <dd>
|
|
|
796 <p>This value is <strong>--ReferenceColMode</strong> specific. It specifies fingerprints column to use during similarity
|
|
|
797 and dissimilarity search for reference fingerprints <em>TextFile</em>. Possible values: <em>col number or col label</em>.
|
|
|
798 Default value: <em>first column containing the word Fingerprints in its column label</em>.</p>
|
|
|
799 </dd>
|
|
|
800 <dt><strong><strong>--ReferenceFingerprintsField</strong> <em>FieldLabel</em></strong></dt>
|
|
|
801 <dd>
|
|
|
802 <p>Fingerprints field label to use during similarity and dissimilarity search for reference fingerprints <em>SDFile</em>.
|
|
|
803 Default value: <em>first data field label containing the word Fingerprints in its label</em></p>
|
|
|
804 </dd>
|
|
|
805 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
806 <dd>
|
|
|
807 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file name:
|
|
|
808 <ReferenceFileName>SimilaritySearching.<Ext>. The output file type determines <Ext>
|
|
|
809 value. The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab delimited
|
|
|
810 text files respectively.</p>
|
|
|
811 </dd>
|
|
|
812 <dt><strong><strong>-s, --SearchMode</strong> <em>SimilaritySearch | DissimilaritySearch</em></strong></dt>
|
|
|
813 <dd>
|
|
|
814 <p>Specify how to find molecules from database molecules for individual reference molecules or
|
|
|
815 set of reference molecules: Find similar molecules or dissimilar molecules from database molecules.
|
|
|
816 Possible values: <em>SimilaritySearch | DissimilaritySearch</em>. Default value: <em>SimilaritySearch</em>.</p>
|
|
|
817 <p>During <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option, the meaning of the following
|
|
|
818 options is switched and they correspond to dissimilar molecules instead of similar molecules:
|
|
|
819 <strong>--SimilarCountMode</strong>, <strong>-n, --NumOfSimilarMolecules</strong>, <strong>--PercentSimilarMolecules</strong>,
|
|
|
820 <strong>-k, --kNN</strong>.</p>
|
|
|
821 </dd>
|
|
|
822 <dt><strong><strong>--SimilarCountMode</strong> <em>NumOfSimilar | PercentSimilar</em></strong></dt>
|
|
|
823 <dd>
|
|
|
824 <p>Specify method used to count similar molecules found from database molecules for individual
|
|
|
825 reference molecules or set of reference molecules: Find number of similar molecules or percent
|
|
|
826 of similar molecules from database molecules. Possible values: <em>NumOfSimilar | PercentSimilar</em>.
|
|
|
827 Default value: <em>NumOfSimilar</em>.</p>
|
|
|
828 <p>The values for number of similar molecules and percent similar molecules are specified
|
|
|
829 using options <strong>-n, NumOfSimilarMolecule</strong> and <strong>--PercentSimilarMolecules</strong>.</p>
|
|
|
830 <p>This option is <strong>-s, --SearchMode</strong> dependent: It corresponds to dissimilar molecules during
|
|
|
831 <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option.</p>
|
|
|
832 </dd>
|
|
|
833 <dt><strong><strong>--SimilarityCutoff</strong> <em>number</em></strong></dt>
|
|
|
834 <dd>
|
|
|
835 <p>Similarity cutoff value to use during comparison of similarity value between a pair of database
|
|
|
836 and reference molecules calculated by similarity comparison methods for fingerprints bit-vector
|
|
|
837 vector strings data values. Possible values: <em>Any valid number</em>. Default value: <em>0.75</em>.</p>
|
|
|
838 <p>The comparison value between a pair of database and reference molecule must meet the cutoff
|
|
|
839 criterion as shown below:</p>
|
|
|
840 <div class="OptionsBox">
|
|
|
841 SeachMode CutoffCriterion ComparisonValues</div>
|
|
|
842 <div class="OptionsBox">
|
|
|
843 Similarity >= Higher value implies high similarity
|
|
|
844 <br/> Dissimilarity <= Lower value implies high dissimilarity</div>
|
|
|
845 <p>This option is ignored during <em>No</em> value of <strong>--GroupFusionApplyCutoff</strong> for <em>MultipleReferences</em>
|
|
|
846 <strong>-m, --mode</strong>.</p>
|
|
|
847 <p>This option is <strong>-s, --SearchMode</strong> dependent: It corresponds to dissimilar molecules during
|
|
|
848 <em>DissimilaritySearch</em> value of <strong>-s, --SearchMode</strong> option.</p>
|
|
|
849 </dd>
|
|
|
850 <dt><strong><strong>-v, --VectorComparisonMode</strong> <em>SupportedSimilarityName | SupportedDistanceName</em></strong></dt>
|
|
|
851 <dd>
|
|
|
852 <p>Specify what similarity or distance coefficient to use for calculating similarity between fingerprint
|
|
|
853 vector strings data values in <em>ReferenceFingerprintsFile</em> and <em>DatabaseFingerprintsFile</em> during
|
|
|
854 similarity search. Possible values: <em>TanimotoSimilairy | ... | ManhattanDistance | ...</em>. Default
|
|
|
855 value: <em>TanimotoSimilarity</em>.</p>
|
|
|
856 <p>The value of <strong>-v, --VectorComparisonMode</strong>, in conjunction with <strong>--VectorComparisonFormulism</strong>,
|
|
|
857 decides which type of similarity and distance coefficient formulism gets used.</p>
|
|
|
858 <p>The current releases supports the following similarity and distance coefficients: <em>CosineSimilarity,
|
|
|
859 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity,
|
|
|
860 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance</em>. These
|
|
|
861 similarity and distance coefficients are described below.</p>
|
|
|
862 <p><strong>FingerprintsVector.pm</strong> module, used to calculate similarity and distance coefficients,
|
|
|
863 provides support to perform comparison between vectors containing three different types of
|
|
|
864 values:</p>
|
|
|
865 <p>Type I: OrderedNumericalValues</p>
|
|
|
866 <div class="OptionsBox">
|
|
|
867 . Size of two vectors are same
|
|
|
868 <br/> . Vectors contain real values in a specific order. For example: MACCS keys
|
|
|
869 count, Topological pharmnacophore atom pairs and so on.</div>
|
|
|
870 <p>Type II: UnorderedNumericalValues</p>
|
|
|
871 <div class="OptionsBox">
|
|
|
872 . Size of two vectors might not be same
|
|
|
873 <br/> . Vectors contain unordered real value identified by value IDs. For example:
|
|
|
874 Toplogical atom pairs, Topological atom torsions and so on</div>
|
|
|
875 <p>Type III: AlphaNumericalValues</p>
|
|
|
876 <div class="OptionsBox">
|
|
|
877 . Size of two vectors might not be same
|
|
|
878 <br/> . Vectors contain unordered alphanumerical values. For example: Extended
|
|
|
879 connectivity fingerprints, atom neighborhood fingerprints.</div>
|
|
|
880 <p>Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
|
|
|
881 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
|
|
|
882 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.</p>
|
|
|
883 <p>Three forms of similarity and distance calculation between two vectors, specified using <strong>--VectorComparisonFormulism</strong>
|
|
|
884 option, are supported: <em>AlgebraicForm, BinaryForm or SetTheoreticForm</em>.</p>
|
|
|
885 <p>For <em>BinaryForm</em>, the ordered list of processed final vector values containing the value or
|
|
|
886 count of each unique value type is simply converted into a binary vector containing 1s and 0s
|
|
|
887 corresponding to presence or absence of values before calculating similarity or distance between
|
|
|
888 two vectors.</p>
|
|
|
889 <p>For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:</p>
|
|
|
890 <div class="OptionsBox">
|
|
|
891 N = Number values in A or B</div>
|
|
|
892 <div class="OptionsBox">
|
|
|
893 Xa = Values of vector A
|
|
|
894 <br/> Xb = Values of vector B</div>
|
|
|
895 <div class="OptionsBox">
|
|
|
896 Xai = Value of ith element in A
|
|
|
897 <br/> Xbi = Value of ith element in B</div>
|
|
|
898 <div class="OptionsBox">
|
|
|
899 SUM = Sum of i over N values</div>
|
|
|
900 <p>For SetTheoreticForm of calculation between two vectors, let:</p>
|
|
|
901 <div class="OptionsBox">
|
|
|
902 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
|
|
|
903 <br/> SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )</div>
|
|
|
904 <p>For BinaryForm of calculation between two vectors, let:</p>
|
|
|
905 <div class="OptionsBox">
|
|
|
906 Na = Number of bits set to "1" in A = SUM ( Xai )
|
|
|
907 <br/> Nb = Number of bits set to "1" in B = SUM ( Xbi )
|
|
|
908 <br/> Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
|
|
|
909 <br/> Nd = Number of bits set to "0" in both A and B
|
|
|
910 = SUM ( 1 - Xai - Xbi + Xai * Xbi)</div>
|
|
|
911 <div class="OptionsBox">
|
|
|
912 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</div>
|
|
|
913 <p>Additionally, for BinaryForm various values also correspond to:</p>
|
|
|
914 <div class="OptionsBox">
|
|
|
915 Na = | Xa |
|
|
|
916 <br/> Nb = | Xb |
|
|
|
917 <br/> Nc = | SetIntersectionXaXb |
|
|
|
918 <br/> Nd = N - | SetDifferenceXaXb |</div>
|
|
|
919 <div class="OptionsBox">
|
|
|
920 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
|
|
|
921 = | Xa | + | Xb | - | SetIntersectionXaXb |</div>
|
|
|
922 <p>Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
|
|
|
923 in <em>AlgebraicForm, BinaryForm and SetTheoreticForm</em> are defined as follows:</p>
|
|
|
924 <p><strong>CityBlockDistance</strong>: ( same as HammingDistance and ManhattanDistance)</p>
|
|
|
925 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
926 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
927 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
928 <p><strong>CosineSimilarity</strong>: ( same as OchiaiSimilarityCoefficient)</p>
|
|
|
929 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p>
|
|
|
930 <p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p>
|
|
|
931 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p>
|
|
|
932 <p><strong>CzekanowskiSimilarity</strong>: ( same as DiceSimilarity and SorensonSimilarity)</p>
|
|
|
933 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
934 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
935 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
936 <p><strong>DiceSimilarity</strong>: ( same as CzekanowskiSimilarity and SorensonSimilarity)</p>
|
|
|
937 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
938 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
939 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
940 <p><strong>EuclideanDistance</strong>:</p>
|
|
|
941 <p><em>AlgebraicForm</em>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )</p>
|
|
|
942 <p><em>BinaryForm</em>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )</p>
|
|
|
943 <p><em>SetTheoreticForm</em>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )</p>
|
|
|
944 <p><strong>HammingDistance</strong>: ( same as CityBlockDistance and ManhattanDistance)</p>
|
|
|
945 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
946 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
947 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
948 <p><strong>JaccardSimilarity</strong>: ( same as TanimotoSimilarity)</p>
|
|
|
949 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p>
|
|
|
950 <p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p>
|
|
|
951 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
952 <p><strong>ManhattanDistance</strong>: ( same as CityBlockDistance and HammingDistance)</p>
|
|
|
953 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
954 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
955 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
956 <p><strong>OchiaiSimilarity</strong>: ( same as CosineSimilarity)</p>
|
|
|
957 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p>
|
|
|
958 <p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p>
|
|
|
959 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p>
|
|
|
960 <p><strong>SorensonSimilarity</strong>: ( same as CzekanowskiSimilarity and DiceSimilarity)</p>
|
|
|
961 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
962 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
963 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
964 <p><strong>SoergelDistance</strong>:</p>
|
|
|
965 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )</p>
|
|
|
966 <p><em>BinaryForm</em>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )</p>
|
|
|
967 <p><em>SetTheoreticForm</em>: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
968 <p><strong>TanimotoSimilarity</strong>: ( same as JaccardSimilarity)</p>
|
|
|
969 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p>
|
|
|
970 <p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p>
|
|
|
971 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
972 </dd>
|
|
|
973 <dt><strong><strong>--VectorComparisonFormulism</strong> <em>AlgebraicForm | BinaryForm | SetTheoreticForm</em></strong></dt>
|
|
|
974 <dd>
|
|
|
975 <p>Specify fingerprints vector comparison formulism to use for calculation similarity and distance
|
|
|
976 coefficients during <strong>-v, --VectorComparisonMode</strong>. Possible values: <em>AlgebraicForm | BinaryForm |
|
|
|
977 SetTheoreticForm</em>. Default value: <em>AlgebraicForm</em>.</p>
|
|
|
978 <p>For fingerprint vector strings containing <strong>AlphaNumericalValues</strong> data values - <strong>ExtendedConnectivityFingerprints</strong>,
|
|
|
979 <strong>AtomNeighborhoodsFingerprints</strong> and so on - all three formulism result in same value during similarity and distance
|
|
|
980 calculations.</p>
|
|
|
981 </dd>
|
|
|
982 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
983 <dd>
|
|
|
984 <p>Location of working directory. Default: current directory.</p>
|
|
|
985 </dd>
|
|
|
986 </dl>
|
|
|
987 <p>
|
|
|
988 </p>
|
|
|
989 <h2>EXAMPLES</h2>
|
|
|
990 <p>To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
991 to find 10 most similar database molecules with application of Max group fusion rule and similarity
|
|
|
992 cutoff to supported fingerprints strings data in SD fingerprints files present in a data fields with
|
|
|
993 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing
|
|
|
994 sequentially generated database compound IDs with Cmpd prefix, type:</p>
|
|
|
995 <div class="ExampleBox">
|
|
|
996 % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPHex.sdf
|
|
|
997 DatabaseSampleFPHex.sdf</div>
|
|
|
998 <p>To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
999 to find 10 most similar database molecules with application of Max group fusion rule and similarity
|
|
|
1000 cutoff to supported fingerprints strings data in FP fingerprints files, and create a
|
|
|
1001 SimilaritySearchResults.csv file containing database compound IDs retireved from FP file, type:</p>
|
|
|
1002 <div class="ExampleBox">
|
|
|
1003 % SimilaritySearchingFingerprints.pl -r SimilaritySearchResults -o
|
|
|
1004 ReferenceSampleFPBin.fpf DatabaseSampleFPBin.fpf</div>
|
|
|
1005 <p>To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
1006 to find 10 most similar database database molecules with application of Max group fusion rule and
|
|
|
1007 similarity cutoff to supported fingerprints strings data in text fingerprints files present in a column
|
|
|
1008 names containing Fingerprint substring in their names, and create a ReferenceFPHexSimilaritySearching.csv
|
|
|
1009 file containing database compound IDs retireved column name containing CompoundID substring or
|
|
|
1010 sequentially generated compound IDs, type:</p>
|
|
|
1011 <div class="ExampleBox">
|
|
|
1012 % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPCount.csv
|
|
|
1013 DatabaseSampleFPCount.csv</div>
|
|
|
1014 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1015 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
1016 supported fingerprints strings data in SD fingerprints files present in a data fields with Fingerprint substring
|
|
|
1017 in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated
|
|
|
1018 reference and database compound IDs with Cmpd prefix, type:</p>
|
|
|
1019 <div class="ExampleBox">
|
|
|
1020 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
1021 ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf</div>
|
|
|
1022 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1023 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
1024 supported fingerprints strings data in FP fingerprints files, and create a ReferenceFPHexSimilaritySearching.csv
|
|
|
1025 file containing references and database compound IDs retireved from FP file, type:</p>
|
|
|
1026 <div class="ExampleBox">
|
|
|
1027 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
1028 ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf</div>
|
|
|
1029 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1030 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
1031 supported fingerprints strings data in text fingerprints files present in a column names containing Fingerprint
|
|
|
1032 substring in their names, and create a ReferenceFPHexSimilaritySearching.csv file containing reference and
|
|
|
1033 database compound IDs retrieved column name containing CompoundID substring or sequentially generated
|
|
|
1034 compound IDs, type:</p>
|
|
|
1035 <div class="ExampleBox">
|
|
|
1036 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
1037 ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv</div>
|
|
|
1038 <p>To perform dissimilarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
1039 to find 10 most dissimilar database molecules with application of Max group fusion rule and similarity
|
|
|
1040 cutoff to supported fingerprints strings data in SD fingerprints files present in a data fields with
|
|
|
1041 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing
|
|
|
1042 sequentially generated database compound IDs with Cmpd prefix, type:</p>
|
|
|
1043 <div class="ExampleBox">
|
|
|
1044 % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
|
|
|
1045 DissimilaritySearch -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf</div>
|
|
|
1046 <p>To perform similarity search using CityBlock distance by treating reference molecules as individual molecules
|
|
|
1047 to find 10 most similar database molecules for each reference molecule with application of distance cutoff
|
|
|
1048 to supported vector fingerprints strings data in SD fingerprints files present in a data fields with Fingerprint
|
|
|
1049 substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated
|
|
|
1050 reference and database compound IDs with Cmpd prefix, type:</p>
|
|
|
1051 <div class="ExampleBox">
|
|
|
1052 % SimilaritySearchingFingerprints.pl -mode IndividualReference
|
|
|
1053 --VectorComparisonMode CityBlockDistance --VectorComparisonFormulism
|
|
|
1054 AlgebraicForm --DistanceCutoff 10 -o
|
|
|
1055 ReferenceSampleFPCount.sdf DatabaseSampleFPCount.sdf</div>
|
|
|
1056 <p>To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
1057 to find 100 most similar database molecules with application of Mean group fusion rule to to top 10
|
|
|
1058 reference molecules with in similarity cutoff of 0.75 to supported fingerprints strings data in FP fingerprints
|
|
|
1059 files, and create a ReferenceFPHexSimilaritySearching.csv file containing database compound IDs retrieved
|
|
|
1060 from FP file, type:</p>
|
|
|
1061 <div class="ExampleBox">
|
|
|
1062 % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
|
|
|
1063 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
1064 --GroupFusionRule Mean --GroupFusionApplyCutoff Yes --kNN 10
|
|
|
1065 --SimilarityCutoff 0.75 --SimilarCountMode NumOfSimilar
|
|
|
1066 --NumOfSimilarMolecules 100 -o
|
|
|
1067 ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf</div>
|
|
|
1068 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1069 to find 2 percent of most similar database molecules for each reference molecule with application of similarity
|
|
|
1070 cutoff of 0.85 to supported fingerprints strings data in text fingerprints files present in specific columns and
|
|
|
1071 create a ReferenceFPHexSimilaritySearching.csv file containing reference and database compoundIDs retrieved
|
|
|
1072 from specific columns, type:</p>
|
|
|
1073 <div class="ExampleBox">
|
|
|
1074 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
1075 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
1076 --ReferenceColMode ColLabel --ReferenceFingerprintsCol Fingerprints
|
|
|
1077 --ReferenceCompoundIDCol CompoundID --DatabaseColMode Collabel
|
|
|
1078 --DatabaseCompoundIDCol CompoundID --DatabaseFingerprintsCol
|
|
|
1079 Fingerprints --SimilarityCutoff 0.85 --SimilarCountMode PercentSimilar
|
|
|
1080 --PercentSimilarMolecules 2 -o
|
|
|
1081 ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv</div>
|
|
|
1082 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1083 to find top 50 most similar database molecules for each reference molecule with application of similarity
|
|
|
1084 cutoff of 0.85 to supported fingerprints strings data in SD fingerprints files present in specific data fields and
|
|
|
1085 create both ReferenceFPHexSimilaritySearching.csv and ReferenceFPHexSimilaritySearching.sdf files containing
|
|
|
1086 reference and database compoundIDs retrieved from specific data fields, type:</p>
|
|
|
1087 <div class="ExampleBox">
|
|
|
1088 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
1089 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
1090 --ReferenceFingerprintsField Fingerprints
|
|
|
1091 --DatabaseFingerprintsField Fingerprints
|
|
|
1092 --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
|
|
|
1093 --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
|
|
|
1094 --SimilarityCutoff 0.85 --SimilarCountMode NumOfSimilar
|
|
|
1095 --NumOfSimilarMolecules 50 --output both -o
|
|
|
1096 ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf</div>
|
|
|
1097 <p>To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
1098 to find 1 percent of most similar database molecules for each reference molecule with application of similarity
|
|
|
1099 cutoff to supported fingerprints strings data in SD fingerprints files present in specific data field labels, and create
|
|
|
1100 both ReferenceFPHexSimilaritySearching.csv ReferenceFPHexSimilaritySearching.sdf files containing reference and
|
|
|
1101 database compound IDs retrieved from specific data field labels along with other specific data for database
|
|
|
1102 molecules, type:</p>
|
|
|
1103 <div class="ExampleBox">
|
|
|
1104 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
1105 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
1106 --ReferenceFingerprintsField Fingerprints
|
|
|
1107 --DatabaseFingerprintsField Fingerprints
|
|
|
1108 --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
|
|
|
1109 --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
|
|
|
1110 --DatabaseDataFieldsMode Specify --DatabaseDataFields "TPSA,SLogP"
|
|
|
1111 --SimilarityCutoff 0.75 --SimilarCountMode PercentSimilar
|
|
|
1112 --PercentSimilarMolecules 1 --output both --OutDelim comma --quote Yes
|
|
|
1113 --precision 3 -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf</div>
|
|
|
1114 <p>
|
|
|
1115 </p>
|
|
|
1116 <h2>AUTHOR</h2>
|
|
|
1117 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
1118 <p>
|
|
|
1119 </p>
|
|
|
1120 <h2>SEE ALSO</h2>
|
|
|
1121 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>, 
|
|
|
1122 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, 
|
|
|
1123 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
|
|
|
1124 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
|
|
|
1125 </p>
|
|
|
1126 <p>
|
|
|
1127 </p>
|
|
|
1128 <h2>COPYRIGHT</h2>
|
|
|
1129 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
1130 <p>This file is part of MayaChemTools.</p>
|
|
|
1131 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1132 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1133 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1134 any later version.</p>
|
|
|
1135 <p> </p><p> </p><div class="DocNav">
|
|
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1136 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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1137 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SimilarityMatricesFingerprints.html" title="SimilarityMatricesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SortSDFiles.html" title="SortSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SimilaritySearchingFingerprints.pl</strong></td></tr>
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1138 </table>
|
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1139 </div>
|
|
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1140 <br />
|
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1141 <center>
|
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1142 <img src="../../images/h2o2.png">
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1143 </center>
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1144 </body>
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1145 </html>
|
