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3 <title>MayaChemTools:Documentation:SimilarityMatricesFingerprints.pl</title>
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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13 <div class="DocNav">
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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="./SDToMolFiles.html" title="SDToMolFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SimilaritySearchingFingerprints.html" title="SimilaritySearchingFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>SimilarityMatricesFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/SimilarityMatricesFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/SimilarityMatricesFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SimilarityMatricesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SimilarityMatricesFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SimilarityMatricesFingerprints.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>SimilarityMatricesFingerprints.pl - Calculate similarity matrices 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>SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)...</p>
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26 <p>SimilarityMatricesFingerprints.pl [<strong>--alpha</strong> <em>number</em>] [<strong>--beta</strong> <em>number</em>]
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27 [<strong>-b, --BitVectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[ TverskySimilarity, ... ]"</em>]
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28 [<strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--CompoundIDCol</strong> <em>col number | col name</em>]
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29 [<strong>--CompoundIDPrefix</strong> <em>text</em>] [<strong>--CompoundIDField</strong> <em>DataFieldName</em>]
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30 [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
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31 [<strong>-d, --detail</strong> <em>InfoLevel</em>] [<strong>-f, --fast</strong>] [<strong>--FingerprintsCol</strong> <em>col number | col name</em>]
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32 [<strong>--FingerprintsField</strong> <em>FieldLabel</em>] [<strong>-h, --help</strong>] [<strong>--InDelim</strong> <em>comma | semicolon</em>]
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33 [<strong>--InputDataMode</strong> <em>LoadInMemory | ScanFile</em>]
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34 [<strong>-m, --mode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em>]
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35 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--OutMatrixFormat</strong> <em>RowsAndColumns | IDPairsAndValue</em>]
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36 [<strong>--OutMatrixType</strong> <em>FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix</em>]
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37 [<strong>-o, --overwrite</strong>] [<strong>-p, --precision</strong> <em>number</em>]
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38 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>]
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39 [<strong>-v, --VectorComparisonMode</strong> <em>All | "TanimotoSimilairy, [ ManhattanDistance, ...]"</em>]
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40 [<strong>--VectorComparisonFormulism</strong> <em>All | "AlgebraicForm, [BinaryForm, SetTheoreticForm]"</em>]
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41 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s) FPFile(s) TextFile(s)...</p>
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42 <p>
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43 </p>
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44 <h2>DESCRIPTION</h2>
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45 <p>Calculate similarity matrices using fingerprint bit-vector or vector strings data in <em>SD, FP
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46 and CSV/TSV</em> text file(s) and generate CSV/TSV text file(s) containing values for specified
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47 similarity and distance coefficients.</p>
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48 <p>The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the
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49 current release of MayaChemTools and their functionality merged with this script.</p>
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50 <p>The valid <em>SDFile</em> extensions are <em>.sdf</em> and <em>.sd</em>. All SD files in a current directory
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51 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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52 <p>The valid <em>FPFile</em> extensions are <em>.fpf</em> and <em>.fp</em>. All FP files in a current directory
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53 can be specified either by <em>*.fpf</em> or the current directory name.</p>
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54 <p>The valid <em>TextFile</em> extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab
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55 delimited text files respectively. All other file names are ignored. All text files in a
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56 current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory
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57 name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file
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58 which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p>
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59 <p>Example of <em>FP</em> file containing fingerprints bit-vector string data:</p>
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60 <div class="OptionsBox">
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61 #
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62 <br/> # Package = MayaChemTools 7.4
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63 <br/> # ReleaseDate = Oct 21, 2010
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64 <br/> #
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65 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
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66 <br/> #
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67 <br/> # FingerprintsStringType = FingerprintsBitVector
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68 <br/> #
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69 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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70 <br/> # Size = 1024
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71 <br/> # BitStringFormat = HexadecimalString
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72 <br/> # BitsOrder = Ascending
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73 <br/> #
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74 <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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75 <br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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76 <br/> ... ...
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77 <br/> ... ..</div>
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78 <p>Example of <em>FP</em> file containing fingerprints vector string data:</p>
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79 <div class="OptionsBox">
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80 #
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81 <br/> # Package = MayaChemTools 7.4
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82 <br/> # ReleaseDate = Oct 21, 2010
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83 <br/> #
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84 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
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85 <br/> #
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86 <br/> # FingerprintsStringType = FingerprintsVector
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87 <br/> #
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88 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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89 <br/> # VectorStringFormat = IDsAndValuesString
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90 <br/> # VectorValuesType = NumericalValues
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91 <br/> #
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92 <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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93 <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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94 <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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95 <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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96 <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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97 <br/> O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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98 <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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99 <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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100 <br/> ... ...
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101 <br/> ... ...</div>
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102 <p>Example of <em>SD</em> file containing fingerprints bit-vector string data:</p>
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103 <div class="OptionsBox">
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104 ... ...
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105 <br/> ... ...
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106 <br/> $$$$
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107 <br/> ... ...
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108 <br/> ... ...
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109 <br/> ... ...
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110 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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111 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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112 <br/> ... ...
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113 <br/> 2 3 1 0 0 0 0
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114 <br/> ... ...
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115 <br/> M END
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116 <br/> > <CmpdID>
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117 <br/> Cmpd1</div>
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118 <div class="OptionsBox">
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119 > <PathLengthFingerprints>
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120 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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121 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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122 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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123 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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124 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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125 <br/> aa0660a11014a011d46</div>
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126 <div class="OptionsBox">
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127 $$$$
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128 <br/> ... ...
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129 <br/> ... ...</div>
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130 <p>Example of CSV <em>Text</em> file containing fingerprints bit-vector string data:</p>
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131 <div class="OptionsBox">
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132 "CompoundID","PathLengthFingerprints"
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133 <br/> "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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134 <br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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135 <br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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136 <br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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137 <br/> ... ...
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138 <br/> ... ...</div>
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139 <p>The current release of MayaChemTools supports the following types of fingerprint
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140 bit-vector and vector strings:</p>
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141 <div class="OptionsBox">
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142 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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143 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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144 <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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145 <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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146 <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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147 <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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148 <div class="OptionsBox">
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149 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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150 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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151 <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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152 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
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153 <div class="OptionsBox">
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154 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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155 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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156 <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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157 <div class="OptionsBox">
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158 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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159 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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160 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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161 <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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162 <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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163 <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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164 <div class="OptionsBox">
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165 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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166 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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167 <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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168 <br/> .024 -2.270</div>
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169 <div class="OptionsBox">
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170 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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171 <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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172 <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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173 <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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174 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
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175 <div class="OptionsBox">
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176 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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177 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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178 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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179 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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180 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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181 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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182 <div class="OptionsBox">
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183 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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184 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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185 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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186 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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187 <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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188 <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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189 <div class="OptionsBox">
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190 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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191 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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192 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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193 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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194 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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195 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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196 <div class="OptionsBox">
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197 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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198 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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199 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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200 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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201 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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202 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
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203 <div class="OptionsBox">
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204 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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205 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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206 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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207 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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208 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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209 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
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210 <div class="OptionsBox">
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211 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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212 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
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213 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
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214 <br/> 11111111111110111000</div>
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215 <div class="OptionsBox">
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216 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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217 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
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218 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
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219 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
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220 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
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221 <br/> 0000000000000000000000000000000000000000</div>
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222 <div class="OptionsBox">
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223 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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224 <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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225 <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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226 <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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227 <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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228 <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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229 <div class="OptionsBox">
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230 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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231 <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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232 <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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233 <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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234 <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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235 <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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236 <div class="OptionsBox">
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237 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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238 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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239 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
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240 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
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241 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
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242 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
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243 <div class="OptionsBox">
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244 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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245 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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246 <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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247 <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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248 <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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249 <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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250 <div class="OptionsBox">
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251 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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252 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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253 <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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254 <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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255 <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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256 <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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257 <div class="OptionsBox">
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258 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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259 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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260 <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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261 <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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262 <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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263 <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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264 <div class="OptionsBox">
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265 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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266 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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267 <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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268 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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269 <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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270 <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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271 <div class="OptionsBox">
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272 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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273 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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274 <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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275 <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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276 <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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277 <div class="OptionsBox">
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278 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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279 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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280 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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281 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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282 <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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283 <div class="OptionsBox">
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284 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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285 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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286 <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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287 <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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288 <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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289 <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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290 <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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291 <div class="OptionsBox">
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292 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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293 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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294 <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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295 <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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296 <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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297 <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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298 <div class="OptionsBox">
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299 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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300 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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301 <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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302 <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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303 <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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304 <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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305 <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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306 <div class="OptionsBox">
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307 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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308 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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309 <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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310 <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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311 <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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312 <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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313 <div class="OptionsBox">
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314 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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315 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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316 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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317 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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318 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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319 <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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320 <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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321 <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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322 <div class="OptionsBox">
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323 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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324 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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325 <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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326 <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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327 <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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328 <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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329 <p>
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330 </p>
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331 <h2>OPTIONS</h2>
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332 <dl>
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333 <dt><strong><strong>--alpha</strong> <em>number</em></strong></dt>
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334 <dd>
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335 <p>Value of alpha parameter for calculating <em>Tversky</em> similarity coefficient specified for
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336 <strong>-b, --BitVectorComparisonMode</strong> option. It corresponds to weights assigned for bits set
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337 to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
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338 values: <em>0 to 1</em>. Default value: <0.5>.</p>
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339 </dd>
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340 <dt><strong><strong>--beta</strong> <em>number</em></strong></dt>
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341 <dd>
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342 <p>Value of beta parameter for calculating <em>WeightedTanimoto</em> and <em>WeightedTversky</em>
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343 similarity coefficients specified for <strong>-b, --BitVectorComparisonMode</strong> option. It is used to
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344 weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible
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345 values: <em>0 to 1</em>. Default value of <1> makes <em>WeightedTanimoto</em> and <em>WeightedTversky</em>
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346 equivalent to <em>Tanimoto</em> and <em>Tversky</em>.</p>
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347 </dd>
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348 <dt><strong><strong>-b, --BitVectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[TverskySimilarity,...]"</em></strong></dt>
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349 <dd>
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350 <p>Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector
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351 strings data values in <em>TextFile(s)</em>: calculate similarity matrices for all supported similarity
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352 coefficients or specify a comma delimited list of similarity coefficients. Possible values:
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353 <em>All | "TanimotoSimilarity,[TverskySimilarity,...]</em>. Default: <em>TanimotoSimilarity</em></p>
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354 <p><em>All</em> uses complete list of supported similarity coefficients: <em>BaroniUrbaniSimilarity, BuserSimilarity,
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355 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
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356 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
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357 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
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358 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
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359 WeightedTanimotoSimilarity, WeightedTverskySimilarity</em>. These similarity coefficients are described below.</p>
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360 <p>For two fingerprint bit-vectors A and B of same size, let:</p>
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361 <div class="OptionsBox">
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362 Na = Number of bits set to "1" in A
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363 <br/> Nb = Number of bits set to "1" in B
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364 <br/> Nc = Number of bits set to "1" in both A and B
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365 <br/> Nd = Number of bits set to "0" in both A and B</div>
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366 <div class="OptionsBox">
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367 Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
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368 <br/> Nt = Na + Nb - Nc + Nd</div>
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369 <div class="OptionsBox">
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370 Na - Nc = Number of bits set to "1" in A but not in B
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371 <br/> Nb - Nc = Number of bits set to "1" in B but not in A</div>
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372 <p>Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are
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373 defined as follows:</p>
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374 <p><em>BaroniUrbaniSimilarity</em>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</p>
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375 <p><em>BuserSimilarity</em>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</p>
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376 <p><em>CosineSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Ochiai)</p>
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377 <p><em>DiceSimilarity</em>: (2 * Nc) / ( Na + Nb )</p>
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378 <p><em>DennisSimilarity</em>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</p>
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379 <p><em>ForbesSimilarity</em>: ( Nt * Nc ) / ( Na * Nb )</p>
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380 <p><em>FossumSimilarity</em>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</p>
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381 <p><em>HamannSimilarity</em>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</p>
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382 <p><em>JaccardSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</p>
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383 <p><em>Kulczynski1Similarity</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</p>
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384 <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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385 <p><em>MatchingSimilarity</em>: ( Nc + Nd ) / Nt</p>
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386 <p><em>McConnaugheySimilarity</em>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</p>
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387 <p><em>OchiaiSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Cosine)</p>
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388 <p><em>PearsonSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</p>
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389 <p><em>RogersTanimotoSimilarity</em>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</p>
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390 <p><em>RussellRaoSimilarity</em>: Nc / Nt</p>
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391 <p><em>SimpsonSimilarity</em>: Nc / MIN ( Na, Nb)</p>
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392 <p><em>SkoalSneath1Similarity</em>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</p>
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393 <p><em>SkoalSneath2Similarity</em>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</p>
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394 <p><em>SkoalSneath3Similarity</em>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</p>
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395 <p><em>TanimotoSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</p>
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396 <p><em>TverskySimilarity</em>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</p>
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397 <p><em>YuleSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</p>
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398 <p>Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
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399 are set to "1" in both A and B. In order to take into account all bit positions, modified versions
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400 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</p>
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401 <p>Let:</p>
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402 <div class="OptionsBox">
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403 Na' = Number of bits set to "0" in A
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404 <br/> Nb' = Number of bits set to "0" in B
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405 <br/> Nc' = Number of bits set to "0" in both A and B</div>
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406 <p>Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</p>
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407 <p>Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</p>
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408 <p>Then:</p>
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409 <p><em>WeightedTanimotoSimilarity</em> = beta * Tanimoto + (1 - beta) * Tanimoto'</p>
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410 <p><em>WeightedTverskySimilarity</em> = beta * Tversky + (1 - beta) * Tversky'</p>
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411 </dd>
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412 <dt><strong><strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em></strong></dt>
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413 <dd>
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414 <p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column
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415 label. Possible values: <em>ColNum or ColLabel</em>. Default value: <em>ColNum</em>.</p>
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416 </dd>
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417 <dt><strong><strong>--CompoundIDCol</strong> <em>col number | col name</em></strong></dt>
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418 <dd>
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419 <p>This value is <strong>-c, --ColMode</strong> mode specific. It specifies input <em>TextFile(s)</em> column to use for
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420 generating compound ID for similarity matrices in output <em>TextFile(s)</em>. Possible values: <em>col number
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421 or col label</em>. Default value: <em>first column containing the word compoundID in its column label or sequentially
|
|
|
422 generated IDs</em>.</p>
|
|
|
423 </dd>
|
|
|
424 <dt><strong><strong>--CompoundIDPrefix</strong> <em>text</em></strong></dt>
|
|
|
425 <dd>
|
|
|
426 <p>Specify compound ID prefix to use during sequential generation of compound IDs for input <em>SDFile(s)</em>
|
|
|
427 and <em>TextFile(s)</em>. Default value: <em>Cmpd</em>. The default value generates compound IDs which look
|
|
|
428 like Cmpd<Number>.</p>
|
|
|
429 <p>For input <em>SDFile(s)</em>, this value is only used during <em>LabelPrefix | MolNameOrLabelPrefix</em> values
|
|
|
430 of <strong>--CompoundIDMode</strong> option; otherwise, it's ignored.</p>
|
|
|
431 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
|
|
|
432 <div class="OptionsBox">
|
|
|
433 Compound</div>
|
|
|
434 <p>The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
435 instead of default value of Cmpd<Number>.</p>
|
|
|
436 </dd>
|
|
|
437 <dt><strong><strong>--CompoundIDField</strong> <em>DataFieldName</em></strong></dt>
|
|
|
438 <dd>
|
|
|
439 <p>Specify input <em>SDFile(s)</em> datafield label for generating compound IDs. This value is only used
|
|
|
440 during <em>DataField</em> value of <strong>--CompoundIDMode</strong> option.</p>
|
|
|
441 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
|
|
|
442 <div class="OptionsBox">
|
|
|
443 MolID
|
|
|
444 <br/> ExtReg</div>
|
|
|
445 </dd>
|
|
|
446 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
|
|
|
447 <dd>
|
|
|
448 <p>Specify how to generate compound IDs from input <em>SDFile(s)</em> for similarity matrix CSV/TSV text
|
|
|
449 file(s): use a <em>SDFile(s)</em> datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID
|
|
|
450 with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values
|
|
|
451 for empty molname lines.</p>
|
|
|
452 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
|
|
|
453 Default: <em>LabelPrefix</em>.</p>
|
|
|
454 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
|
|
|
455 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
|
|
|
456 values are replaced with sequential compound IDs.</p>
|
|
|
457 </dd>
|
|
|
458 <dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt>
|
|
|
459 <dd>
|
|
|
460 <p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values:
|
|
|
461 <em>1, 2 or 3</em>.</p>
|
|
|
462 </dd>
|
|
|
463 <dt><strong><strong>-f, --fast</strong></strong></dt>
|
|
|
464 <dd>
|
|
|
465 <p>In this mode, fingerprints columns specified using <strong>--FingerprintsCol</strong> for <em>TextFile(s)</em> and
|
|
|
466 <strong>--FingerprintsField</strong> for <em>SDFile(s)</em> are assumed to contain valid fingerprints data and no
|
|
|
467 checking is performed before calculating similarity matrices. By default, fingerprints data is
|
|
|
468 validated before computing pairwise similarity and distance coefficients.</p>
|
|
|
469 </dd>
|
|
|
470 <dt><strong><strong>--FingerprintsCol</strong> <em>col number | col name</em></strong></dt>
|
|
|
471 <dd>
|
|
|
472 <p>This value is <strong>-c, --colmode</strong> specific. It specifies fingerprints column to use during
|
|
|
473 calculation similarity matrices for <em>TextFile(s)</em>. Possible values: <em>col number or col label</em>.
|
|
|
474 Default value: <em>first column containing the word Fingerprints in its column label</em>.</p>
|
|
|
475 </dd>
|
|
|
476 <dt><strong><strong>--FingerprintsField</strong> <em>FieldLabel</em></strong></dt>
|
|
|
477 <dd>
|
|
|
478 <p>Fingerprints field label to use during calculation similarity matrices for <em>SDFile(s)</em>.
|
|
|
479 Default value: <em>first data field label containing the word Fingerprints in its label</em></p>
|
|
|
480 </dd>
|
|
|
481 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
482 <dd>
|
|
|
483 <p>Print this help message.</p>
|
|
|
484 </dd>
|
|
|
485 <dt><strong><strong>--InDelim</strong> <em>comma | semicolon</em></strong></dt>
|
|
|
486 <dd>
|
|
|
487 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
|
|
|
488 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
|
|
|
489 delimiter.</p>
|
|
|
490 </dd>
|
|
|
491 <dt><strong><strong>--InputDataMode</strong> <em>LoadInMemory | ScanFile</em></strong></dt>
|
|
|
492 <dd>
|
|
|
493 <p>Specify how fingerprints bit-vector or vector strings data from <em>SD, FP and CSV/TSV</em>
|
|
|
494 fingerprint file(s) is processed: Retrieve, process and load all available fingerprints
|
|
|
495 data in memory; Retrieve and process data for fingerprints one at a time. Possible values
|
|
|
496 : <em>LoadInMemory | ScanFile</em>. Default: <em>LoadInMemory</em>.</p>
|
|
|
497 <p>During <em>LoadInMemory</em> value of <strong>--InputDataMode</strong>, fingerprints bit-vector or vector
|
|
|
498 strings data from input file is retrieved, processed, and loaded into memory all at once
|
|
|
499 as fingerprints objects for generation for similarity matrices.</p>
|
|
|
500 <p>During <em>ScanFile</em> value of <strong>--InputDataMode</strong>, multiple passes over the input fingerprints
|
|
|
501 file are performed to retrieve and process fingerprints bit-vector or vector strings data one at
|
|
|
502 a time to generate fingerprints objects used during generation of similarity matrices. A temporary
|
|
|
503 copy of the input fingerprints file is made at the start and deleted after generating the matrices.</p>
|
|
|
504 <p><em>ScanFile</em> value of <strong>--InputDataMode</strong> allows processing of arbitrary large fingerprints files
|
|
|
505 without any additional memory requirement.</p>
|
|
|
506 </dd>
|
|
|
507 <dt><strong><strong>-m, --mode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em></strong></dt>
|
|
|
508 <dd>
|
|
|
509 <p>Format of fingerprint strings data in <em>TextFile(s)</em>: automatically detect format of fingerprints
|
|
|
510 string created by MayaChemTools fingerprints generation scripts or explicitly specify its format.
|
|
|
511 Possible values: <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em>. Default
|
|
|
512 value: <em>AutoDetect</em>.</p>
|
|
|
513 </dd>
|
|
|
514 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
515 <dd>
|
|
|
516 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
|
517 Default value: <em>comma</em>.</p>
|
|
|
518 </dd>
|
|
|
519 <dt><strong><strong>--OutMatrixFormat</strong> <em>RowsAndColumns | IDPairsAndValue</em></strong></dt>
|
|
|
520 <dd>
|
|
|
521 <p>Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings
|
|
|
522 are written to the output CSV/TSV text file(s): Generate text files containing rows and columns
|
|
|
523 with their labels corresponding to compound IDs and each matrix element value corresponding to
|
|
|
524 similarity or distance between corresponding compounds; Generate text files containing rows containing
|
|
|
525 compoundIDs for two compounds followed by similarity or distance value between these compounds.</p>
|
|
|
526 <p>Possible values: <em>RowsAndColumns, or IDPairsAndValue</em>. Default value: <em>RowsAndColumns</em>.</p>
|
|
|
527 <p>The value of <strong>--OutMatrixFormat</strong> in conjunction with <strong>--OutMatrixType</strong> determines type
|
|
|
528 of data written to output files and allows generation of up to 6 different output data formats:</p>
|
|
|
529 <div class="OptionsBox">
|
|
|
530 OutMatrixFormat OutMatrixType</div>
|
|
|
531 <div class="OptionsBox">
|
|
|
532 RowsAndColumns FullMatrix [ DEFAULT ]
|
|
|
533 <br/> RowsAndColumns UpperTriangularMatrix
|
|
|
534 <br/> RowsAndColumns LowerTriangularMatrix</div>
|
|
|
535 <div class="OptionsBox">
|
|
|
536 IDPairsAndValue FullMatrix
|
|
|
537 <br/> IDPairsAndValue UpperTriangularMatrix
|
|
|
538 <br/> IDPairsAndValue LowerTriangularMatrix</div>
|
|
|
539 <p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
540 <em>FullMatrix</em> valueof <strong>--OutMatrixType</strong>:</p>
|
|
|
541 <div class="OptionsBox">
|
|
|
542 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
543 <br/> "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
544 <br/> "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ...
|
|
|
545 <br/> "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ...
|
|
|
546 <br/> "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ...
|
|
|
547 <br/> "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ...
|
|
|
548 <br/> "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ...
|
|
|
549 <br/> ... ... ..
|
|
|
550 <br/> ... ... ..
|
|
|
551 <br/> ... ... ..</div>
|
|
|
552 <p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
553 <em>UpperTriangularMatrix</em> value of <strong>--OutMatrixType</strong>:</p>
|
|
|
554 <div class="OptionsBox">
|
|
|
555 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
556 <br/> "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
557 <br/> "Cmpd2","1","0.06","0.05","0.19","0.07",... ...
|
|
|
558 <br/> "Cmpd3","1","0.12","0.22","0.25",... ...
|
|
|
559 <br/> "Cmpd4","1","0.11","0.13",... ...
|
|
|
560 <br/> "Cmpd5","1","0.17",... ...
|
|
|
561 <br/> "Cmpd6","1",... ...
|
|
|
562 <br/> ... ... ..
|
|
|
563 <br/> ... ... ..
|
|
|
564 <br/> ... ... ..</div>
|
|
|
565 <p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
566 <em>LowerTriangularMatrix</em> value of <strong>--OutMatrixType</strong>:</p>
|
|
|
567 <div class="OptionsBox">
|
|
|
568 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
569 <br/> "Cmpd1","1"
|
|
|
570 <br/> "Cmpd2","0.04","1"
|
|
|
571 <br/> "Cmpd3","0.25","0.06","1"
|
|
|
572 <br/> "Cmpd4","0.13","0.05","0.12","1"
|
|
|
573 <br/> "Cmpd5","0.11","0.19","0.22","0.11","1"
|
|
|
574 <br/> "Cmpd6","0.2","0.07","0.25","0.13","0.17","1"
|
|
|
575 <br/> ... ... ..
|
|
|
576 <br/> ... ... ..
|
|
|
577 <br/> ... ... ..</div>
|
|
|
578 <p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
579 <FullMatrix> value of <strong>OutMatrixType</strong>:</p>
|
|
|
580 <div class="OptionsBox">
|
|
|
581 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
582 <br/> "Cmpd1","Cmpd1","1"
|
|
|
583 <br/> "Cmpd1","Cmpd2","0.04"
|
|
|
584 <br/> "Cmpd1","Cmpd3","0.25"
|
|
|
585 <br/> "Cmpd1","Cmpd4","0.13"
|
|
|
586 <br/> ... ... ...
|
|
|
587 <br/> ... ... ...
|
|
|
588 <br/> ... ... ...
|
|
|
589 <br/> "Cmpd2","Cmpd1","0.04"
|
|
|
590 <br/> "Cmpd2","Cmpd2","1"
|
|
|
591 <br/> "Cmpd2","Cmpd3","0.06"
|
|
|
592 <br/> "Cmpd2","Cmpd4","0.05"
|
|
|
593 <br/> ... ... ...
|
|
|
594 <br/> ... ... ...
|
|
|
595 <br/> ... ... ...
|
|
|
596 <br/> "Cmpd3","Cmpd1","0.25"
|
|
|
597 <br/> "Cmpd3","Cmpd2","0.06"
|
|
|
598 <br/> "Cmpd3","Cmpd3","1"
|
|
|
599 <br/> "Cmpd3","Cmpd4","0.12"
|
|
|
600 <br/> ... ... ...
|
|
|
601 <br/> ... ... ...
|
|
|
602 <br/> ... ... ...</div>
|
|
|
603 <p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
604 <UpperTriangularMatrix> value of <strong>--OutMatrixType</strong>:</p>
|
|
|
605 <div class="OptionsBox">
|
|
|
606 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
607 <br/> "Cmpd1","Cmpd1","1"
|
|
|
608 <br/> "Cmpd1","Cmpd2","0.04"
|
|
|
609 <br/> "Cmpd1","Cmpd3","0.25"
|
|
|
610 <br/> "Cmpd1","Cmpd4","0.13"
|
|
|
611 <br/> ... ... ...
|
|
|
612 <br/> ... ... ...
|
|
|
613 <br/> ... ... ...
|
|
|
614 <br/> "Cmpd2","Cmpd2","1"
|
|
|
615 <br/> "Cmpd2","Cmpd3","0.06"
|
|
|
616 <br/> "Cmpd2","Cmpd4","0.05"
|
|
|
617 <br/> ... ... ...
|
|
|
618 <br/> ... ... ...
|
|
|
619 <br/> ... ... ...
|
|
|
620 <br/> "Cmpd3","Cmpd3","1"
|
|
|
621 <br/> "Cmpd3","Cmpd4","0.12"
|
|
|
622 <br/> ... ... ...
|
|
|
623 <br/> ... ... ...
|
|
|
624 <br/> ... ... ...</div>
|
|
|
625 <p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for
|
|
|
626 <LowerTriangularMatrix> value of <strong>--OutMatrixType</strong>:</p>
|
|
|
627 <div class="OptionsBox">
|
|
|
628 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
629 <br/> "Cmpd1","Cmpd1","1"
|
|
|
630 <br/> "Cmpd2","Cmpd1","0.04"
|
|
|
631 <br/> "Cmpd2","Cmpd2","1"
|
|
|
632 <br/> "Cmpd3","Cmpd1","0.25"
|
|
|
633 <br/> "Cmpd3","Cmpd2","0.06"
|
|
|
634 <br/> "Cmpd3","Cmpd3","1"
|
|
|
635 <br/> "Cmpd4","Cmpd1","0.13"
|
|
|
636 <br/> "Cmpd4","Cmpd2","0.05"
|
|
|
637 <br/> "Cmpd4","Cmpd3","0.12"
|
|
|
638 <br/> "Cmpd4","Cmpd4","1"
|
|
|
639 <br/> ... ... ...
|
|
|
640 <br/> ... ... ...
|
|
|
641 <br/> ... ... ...</div>
|
|
|
642 </dd>
|
|
|
643 <dt><strong><strong>--OutMatrixType</strong> <em>FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix</em></strong></dt>
|
|
|
644 <dd>
|
|
|
645 <p>Type of similarity or distance matrix to calculate for fingerprints vector and bit-vector strings:
|
|
|
646 Calculate full matrix; Calculate lower triangular matrix including diagonal; Calculate upper triangular
|
|
|
647 matrix including diagonal.</p>
|
|
|
648 <p>Possible values: <em>FullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix</em>. Default value:
|
|
|
649 <em>FullMatrix</em>.</p>
|
|
|
650 <p>The value of <strong>--OutMatrixType</strong> in conjunction with <strong>--OutMatrixFormat</strong> determines type
|
|
|
651 of data written to output files.</p>
|
|
|
652 </dd>
|
|
|
653 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
654 <dd>
|
|
|
655 <p>Overwrite existing files</p>
|
|
|
656 </dd>
|
|
|
657 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt>
|
|
|
658 <dd>
|
|
|
659 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places.
|
|
|
660 Valid values: positive integers.</p>
|
|
|
661 </dd>
|
|
|
662 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
663 <dd>
|
|
|
664 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
665 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
666 </dd>
|
|
|
667 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
668 <dd>
|
|
|
669 <p>New file name is generated using the root: <Root><BitVectorComparisonMode>.<Ext> or
|
|
|
670 <Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>.
|
|
|
671 The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files
|
|
|
672 respectively. This option is ignored for multiple input files.</p>
|
|
|
673 </dd>
|
|
|
674 <dt><strong><strong>-v, --VectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[ManhattanDistance,...]"</em></strong></dt>
|
|
|
675 <dd>
|
|
|
676 <p>Specify what similarity or distance coefficients to use for calculating similarity matrices for
|
|
|
677 fingerprint vector strings data values in <em>TextFile(s)</em>: calculate similarity matrices for all
|
|
|
678 supported similarity and distance coefficients or specify a comma delimited list of similarity
|
|
|
679 and distance coefficients. Possible values: <em>All | "TanimotoSimilairy,[ManhattanDistance,..]"</em>.
|
|
|
680 Default: <em>TanimotoSimilarity</em>.</p>
|
|
|
681 <p>The value of <strong>-v, --VectorComparisonMode</strong>, in conjunction with <strong>--VectorComparisonFormulism</strong>,
|
|
|
682 decides which type of similarity and distance coefficient formulism gets used.</p>
|
|
|
683 <p><em>All</em> uses complete list of supported similarity and distance coefficients: <em>CosineSimilarity,
|
|
|
684 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity,
|
|
|
685 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance</em>. These
|
|
|
686 similarity and distance coefficients are described below.</p>
|
|
|
687 <p><strong>FingerprintsVector.pm</strong> module, used to calculate similarity and distance coefficients,
|
|
|
688 provides support to perform comparison between vectors containing three different types of
|
|
|
689 values:</p>
|
|
|
690 <p>Type I: OrderedNumericalValues</p>
|
|
|
691 <div class="OptionsBox">
|
|
|
692 . Size of two vectors are same
|
|
|
693 <br/> . Vectors contain real values in a specific order. For example: MACCS keys
|
|
|
694 count, Topological pharmnacophore atom pairs and so on.</div>
|
|
|
695 <p>Type II: UnorderedNumericalValues</p>
|
|
|
696 <div class="OptionsBox">
|
|
|
697 . Size of two vectors might not be same
|
|
|
698 <br/> . Vectors contain unordered real value identified by value IDs. For example:
|
|
|
699 Toplogical atom pairs, Topological atom torsions and so on</div>
|
|
|
700 <p>Type III: AlphaNumericalValues</p>
|
|
|
701 <div class="OptionsBox">
|
|
|
702 . Size of two vectors might not be same
|
|
|
703 <br/> . Vectors contain unordered alphanumerical values. For example: Extended
|
|
|
704 connectivity fingerprints, atom neighborhood fingerprints.</div>
|
|
|
705 <p>Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
|
|
|
706 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
|
|
|
707 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.</p>
|
|
|
708 <p>Three forms of similarity and distance calculation between two vectors, specified using <strong>--VectorComparisonFormulism</strong>
|
|
|
709 option, are supported: <em>AlgebraicForm, BinaryForm or SetTheoreticForm</em>.</p>
|
|
|
710 <p>For <em>BinaryForm</em>, the ordered list of processed final vector values containing the value or
|
|
|
711 count of each unique value type is simply converted into a binary vector containing 1s and 0s
|
|
|
712 corresponding to presence or absence of values before calculating similarity or distance between
|
|
|
713 two vectors.</p>
|
|
|
714 <p>For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:</p>
|
|
|
715 <div class="OptionsBox">
|
|
|
716 N = Number values in A or B</div>
|
|
|
717 <div class="OptionsBox">
|
|
|
718 Xa = Values of vector A
|
|
|
719 <br/> Xb = Values of vector B</div>
|
|
|
720 <div class="OptionsBox">
|
|
|
721 Xai = Value of ith element in A
|
|
|
722 <br/> Xbi = Value of ith element in B</div>
|
|
|
723 <div class="OptionsBox">
|
|
|
724 SUM = Sum of i over N values</div>
|
|
|
725 <p>For SetTheoreticForm of calculation between two vectors, let:</p>
|
|
|
726 <div class="OptionsBox">
|
|
|
727 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
|
|
|
728 <br/> SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )</div>
|
|
|
729 <p>For BinaryForm of calculation between two vectors, let:</p>
|
|
|
730 <div class="OptionsBox">
|
|
|
731 Na = Number of bits set to "1" in A = SUM ( Xai )
|
|
|
732 <br/> Nb = Number of bits set to "1" in B = SUM ( Xbi )
|
|
|
733 <br/> Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
|
|
|
734 <br/> Nd = Number of bits set to "0" in both A and B
|
|
|
735 = SUM ( 1 - Xai - Xbi + Xai * Xbi)</div>
|
|
|
736 <div class="OptionsBox">
|
|
|
737 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</div>
|
|
|
738 <p>Additionally, for BinaryForm various values also correspond to:</p>
|
|
|
739 <div class="OptionsBox">
|
|
|
740 Na = | Xa |
|
|
|
741 <br/> Nb = | Xb |
|
|
|
742 <br/> Nc = | SetIntersectionXaXb |
|
|
|
743 <br/> Nd = N - | SetDifferenceXaXb |</div>
|
|
|
744 <div class="OptionsBox">
|
|
|
745 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
|
|
|
746 = | Xa | + | Xb | - | SetIntersectionXaXb |</div>
|
|
|
747 <p>Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
|
|
|
748 in <em>AlgebraicForm, BinaryForm and SetTheoreticForm</em> are defined as follows:</p>
|
|
|
749 <p><strong>CityBlockDistance</strong>: ( same as HammingDistance and ManhattanDistance)</p>
|
|
|
750 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
751 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
752 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
753 <p><strong>CosineSimilarity</strong>: ( same as OchiaiSimilarityCoefficient)</p>
|
|
|
754 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p>
|
|
|
755 <p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p>
|
|
|
756 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p>
|
|
|
757 <p><strong>CzekanowskiSimilarity</strong>: ( same as DiceSimilarity and SorensonSimilarity)</p>
|
|
|
758 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
759 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
760 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
761 <p><strong>DiceSimilarity</strong>: ( same as CzekanowskiSimilarity and SorensonSimilarity)</p>
|
|
|
762 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
763 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
764 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
765 <p><strong>EuclideanDistance</strong>:</p>
|
|
|
766 <p><em>AlgebraicForm</em>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )</p>
|
|
|
767 <p><em>BinaryForm</em>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )</p>
|
|
|
768 <p><em>SetTheoreticForm</em>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )</p>
|
|
|
769 <p><strong>HammingDistance</strong>: ( same as CityBlockDistance and ManhattanDistance)</p>
|
|
|
770 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
771 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
772 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
773 <p><strong>JaccardSimilarity</strong>: ( same as TanimotoSimilarity)</p>
|
|
|
774 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p>
|
|
|
775 <p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p>
|
|
|
776 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
777 <p><strong>ManhattanDistance</strong>: ( same as CityBlockDistance and HammingDistance)</p>
|
|
|
778 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p>
|
|
|
779 <p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p>
|
|
|
780 <p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
781 <p><strong>OchiaiSimilarity</strong>: ( same as CosineSimilarity)</p>
|
|
|
782 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p>
|
|
|
783 <p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p>
|
|
|
784 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p>
|
|
|
785 <p><strong>SorensonSimilarity</strong>: ( same as CzekanowskiSimilarity and DiceSimilarity)</p>
|
|
|
786 <p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p>
|
|
|
787 <p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p>
|
|
|
788 <p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p>
|
|
|
789 <p><strong>SoergelDistance</strong>:</p>
|
|
|
790 <p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )</p>
|
|
|
791 <p><em>BinaryForm</em>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )</p>
|
|
|
792 <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>
|
|
|
793 <p><strong>TanimotoSimilarity</strong>: ( same as JaccardSimilarity)</p>
|
|
|
794 <p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p>
|
|
|
795 <p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p>
|
|
|
796 <p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p>
|
|
|
797 </dd>
|
|
|
798 <dt><strong><strong>--VectorComparisonFormulism</strong> <em>All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]"</em></strong></dt>
|
|
|
799 <dd>
|
|
|
800 <p>Specify fingerprints vector comparison formulism to use for calculation similarity and distance
|
|
|
801 coefficients during <strong>-v, --VectorComparisonMode</strong>: use all supported comparison formulisms
|
|
|
802 or specify a comma delimited. Possible values: <em>All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]"</em>.
|
|
|
803 Default value: <em>AlgebraicForm</em>.</p>
|
|
|
804 <p><em>All</em> uses all three forms of supported vector comparison formulism for values of <strong>-v, --VectorComparisonMode</strong>
|
|
|
805 option.</p>
|
|
|
806 <p>For fingerprint vector strings containing <strong>AlphaNumericalValues</strong> data values - <strong>ExtendedConnectivityFingerprints</strong>,
|
|
|
807 <strong>AtomNeighborhoodsFingerprints</strong> and so on - all three formulism result in same value during similarity and distance
|
|
|
808 calculations.</p>
|
|
|
809 </dd>
|
|
|
810 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
811 <dd>
|
|
|
812 <p>Location of working directory. Default: current directory.</p>
|
|
|
813 </dd>
|
|
|
814 </dl>
|
|
|
815 <p>
|
|
|
816 </p>
|
|
|
817 <h2>EXAMPLES</h2>
|
|
|
818 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
819 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
820 name containing Fingerprint substring by loading all fingerprints data into memory and create a
|
|
|
821 SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
822 containing CompoundID substring, type:</p>
|
|
|
823 <div class="ExampleBox">
|
|
|
824 % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv</div>
|
|
|
825 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
826 bit-vector strings data corresponding to supported fingerprints in SD File present in a data field
|
|
|
827 with Fingerprint substring in its label by loading all fingerprints data into memory and create a
|
|
|
828 SampleFPHexTanimotoSimilarity.csv file containing sequentially generated compound IDs with
|
|
|
829 Cmpd prefix, type:</p>
|
|
|
830 <div class="ExampleBox">
|
|
|
831 % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf</div>
|
|
|
832 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
833 bit-vector strings data corresponding to supported fingerprints in FP file by loading all fingerprints
|
|
|
834 data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs
|
|
|
835 retrieved from FP file, type:</p>
|
|
|
836 <div class="ExampleBox">
|
|
|
837 % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf</div>
|
|
|
838 <p>To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
839 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
840 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
841 a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
842 containing CompoundID substring, type:</p>
|
|
|
843 <div class="ExampleBox">
|
|
|
844 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory
|
|
|
845 --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix
|
|
|
846 SampleFPHex.csv</div>
|
|
|
847 <p>To generate a upper triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
848 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
849 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
850 a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing compound IDs retrieved
|
|
|
851 from column name containing CompoundID substring, type:</p>
|
|
|
852 <div class="ExampleBox">
|
|
|
853 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory
|
|
|
854 --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix
|
|
|
855 SampleFPHex.csv</div>
|
|
|
856 <p>To generate a full similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
857 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
858 name containing Fingerprint substring by scanning file without loading all fingerprints data into memory
|
|
|
859 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from
|
|
|
860 column name containing CompoundID substring, type:</p>
|
|
|
861 <div class="ExampleBox">
|
|
|
862 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile
|
|
|
863 --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix
|
|
|
864 SampleFPHex.csv</div>
|
|
|
865 <p>To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
866 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
867 column name containing Fingerprint substring by scanning file without loading all fingerprints data into
|
|
|
868 memory and create a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing
|
|
|
869 compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
870 <div class="ExampleBox">
|
|
|
871 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile
|
|
|
872 --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix
|
|
|
873 SampleFPHex.csv</div>
|
|
|
874 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
875 for fingerprints vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
876 containing Fingerprint substring and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
877 containing compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
878 <div class="ExampleBox">
|
|
|
879 % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv</div>
|
|
|
880 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
881 for fingerprints vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
882 Fingerprint substring in its label and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
883 containing sequentially generated compound IDs with Cmpd prefix, type:</p>
|
|
|
884 <div class="ExampleBox">
|
|
|
885 % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf</div>
|
|
|
886 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
887 vector strings data corresponding to supported fingerprints in FP file and create a
|
|
|
888 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from FP file, type:</p>
|
|
|
889 <div class="ExampleBox">
|
|
|
890 % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf</div>
|
|
|
891 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
892 bit-vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
893 containing Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
894 IDPairsAndValue format containing compound IDs retrieved from column name containing
|
|
|
895 CompoundID substring, type:</p>
|
|
|
896 <div class="ExampleBox">
|
|
|
897 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
898 SampleFPHex.csv</div>
|
|
|
899 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
900 bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
901 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
902 IDPairsAndValue format containing sequentially generated compound IDs with Cmpd prefix,
|
|
|
903 type:</p>
|
|
|
904 <div class="ExampleBox">
|
|
|
905 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
906 SampleFPHex.sdf</div>
|
|
|
907 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
908 bit-vector strings data corresponding to supported fingerprints in FP file and create a
|
|
|
909 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved
|
|
|
910 from FP file, type:</p>
|
|
|
911 <div class="ExampleBox">
|
|
|
912 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
913 SampleFPHex.fpf</div>
|
|
|
914 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
915 bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
916 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
917 containing compound IDs from mol name line, type:</p>
|
|
|
918 <div class="ExampleBox">
|
|
|
919 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o
|
|
|
920 SampleFPHex.sdf</div>
|
|
|
921 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
922 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
923 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
924 containing compound IDs from data field name Mol_ID, type:</p>
|
|
|
925 <div class="ExampleBox">
|
|
|
926 % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField
|
|
|
927 --CompoundIDField Mol_ID -o SampleFPBin.sdf</div>
|
|
|
928 <p>To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
929 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a column
|
|
|
930 name containing Fingerprint substring and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
931 containing compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
932 <div class="ExampleBox">
|
|
|
933 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity,
|
|
|
934 TanimotoSimilarity" -o SampleFPBin.csv</div>
|
|
|
935 <p>To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
936 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
937 Fingerprint substring in its label and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
938 containing sequentially generated compound IDs with Cmpd prefix, type:</p>
|
|
|
939 <div class="ExampleBox">
|
|
|
940 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity,
|
|
|
941 TanimotoSimilarity" -o SampleFPBin.sdf</div>
|
|
|
942 <p>To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
943 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
944 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
945 files containing compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
946 <div class="ExampleBox">
|
|
|
947 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
948 TanimotoSimilarity" -o SampleFPCount.csv</div>
|
|
|
949 <p>To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
950 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
951 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
952 files containing sequentially generated compound IDs with Cmpd prefix, type:</p>
|
|
|
953 <div class="ExampleBox">
|
|
|
954 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
955 TanimotoSimilarity" -o SampleFPCount.sdf</div>
|
|
|
956 <p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
957 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
958 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
959 files containing compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
960 <div class="ExampleBox">
|
|
|
961 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
962 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o
|
|
|
963 SampleFPCount.csv</div>
|
|
|
964 <p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
965 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
966 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
967 files containing sequentially generated compound IDs with Cmpd prefix, type:</p>
|
|
|
968 <div class="ExampleBox">
|
|
|
969 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
970 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o
|
|
|
971 SampleFPCount.sdf</div>
|
|
|
972 <p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
973 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
974 fingerprints present in a column name containing Fingerprint substring and create
|
|
|
975 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs retrieved from column
|
|
|
976 name containing CompoundID substring, type:</p>
|
|
|
977 <div class="ExampleBox">
|
|
|
978 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
979 TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv</div>
|
|
|
980 <p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
981 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
982 fingerprints present in a data field with Fingerprint substring in its label and create
|
|
|
983 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
984 compound IDs with Cmpd prefix, type:</p>
|
|
|
985 <div class="ExampleBox">
|
|
|
986 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity"
|
|
|
987 --VectorComparisonFormulism All -o SampleFPCount.sdf</div>
|
|
|
988 <p>To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
989 bit-vector strings data corresponding to supported fingerprints present in a column name
|
|
|
990 containing Fingerprint substring and create SampleFPHex[CoefficientName].csv files
|
|
|
991 containing compound IDs retrieved from column name containing CompoundID substring, type:</p>
|
|
|
992 <div class="ExampleBox">
|
|
|
993 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode
|
|
|
994 All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv</div>
|
|
|
995 <p>To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
996 bit-vector strings data corresponding to supported fingerprints present in a data field with Fingerprint
|
|
|
997 substring in its label and create SampleFPHex[CoefficientName].csv files containing sequentially
|
|
|
998 generated compound IDs with Cmpd prefix, type</p>
|
|
|
999 <div class="ExampleBox">
|
|
|
1000 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode
|
|
|
1001 All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf</div>
|
|
|
1002 <p>To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
1003 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
1004 present in a column name containing Fingerprint substring and create
|
|
|
1005 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs
|
|
|
1006 retrieved from column name containing CompoundID substring, type:</p>
|
|
|
1007 <div class="ExampleBox">
|
|
|
1008 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode
|
|
|
1009 All --VectorComparisonFormulism All -o SampleFPCount.csv</div>
|
|
|
1010 <p>To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
1011 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
1012 present in a data field with Fingerprint substring in its label and create
|
|
|
1013 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
1014 compound IDs with Cmpd prefix, type:</p>
|
|
|
1015 <div class="ExampleBox">
|
|
|
1016 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode
|
|
|
1017 All --VectorComparisonFormulism All -o SampleFPCount.sdf</div>
|
|
|
1018 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1019 bit-vector strings data corresponding to supported fingerprints present in a column number 2
|
|
|
1020 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved column
|
|
|
1021 number 1, type:</p>
|
|
|
1022 <div class="ExampleBox">
|
|
|
1023 % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1
|
|
|
1024 --FingerprintsCol 2 -o SampleFPHex.csv</div>
|
|
|
1025 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1026 bit-vector strings data corresponding to supported fingerprints present in a data field name
|
|
|
1027 Fingerprints and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs
|
|
|
1028 present in data field name Mol_ID, type:</p>
|
|
|
1029 <div class="ExampleBox">
|
|
|
1030 % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints
|
|
|
1031 --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf</div>
|
|
|
1032 <p>To generate a similarity matrix corresponding to Tversky similarity coefficient for fingerprints
|
|
|
1033 bit-vector strings data corresponding to supported fingerprints present in a column named Fingerprints
|
|
|
1034 and create a SampleFPHexTverskySimilarity.tsv file containing compound IDs retrieved column named
|
|
|
1035 CompoundID, type:</p>
|
|
|
1036 <div class="ExampleBox">
|
|
|
1037 % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode
|
|
|
1038 TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol
|
|
|
1039 CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No
|
|
|
1040 -o SampleFPHex.csv</div>
|
|
|
1041 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1042 bit-vector strings data corresponding to supported fingerprints present in a data field
|
|
|
1043 with Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
1044 containing compound IDs from molname line or sequentially generated compound IDs
|
|
|
1045 with Mol prefix, type:</p>
|
|
|
1046 <div class="ExampleBox">
|
|
|
1047 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix
|
|
|
1048 --CompoundIDPrefix Mol -o SampleFPHex.sdf</div>
|
|
|
1049 <p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1050 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
1051 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.tsv file
|
|
|
1052 containing sequentially generated compound IDs with Cmpd prefix, type:</p>
|
|
|
1053 <div class="ExampleBox">
|
|
|
1054 % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf</div>
|
|
|
1055 <p>
|
|
|
1056 </p>
|
|
|
1057 <h2>AUTHOR</h2>
|
|
|
1058 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
1059 <p>
|
|
|
1060 </p>
|
|
|
1061 <h2>SEE ALSO</h2>
|
|
|
1062 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilaritySearchingFingerprints.html">SimilaritySearchingFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>, 
|
|
|
1063 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, 
|
|
|
1064 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
|
|
|
1065 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
|
|
|
1066 </p>
|
|
|
1067 <p>
|
|
|
1068 </p>
|
|
|
1069 <h2>COPYRIGHT</h2>
|
|
|
1070 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
1071 <p>This file is part of MayaChemTools.</p>
|
|
|
1072 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1073 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1074 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1075 any later version.</p>
|
|
|
1076 <p> </p><p> </p><div class="DocNav">
|
|
|
1077 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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1078 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDToMolFiles.html" title="SDToMolFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SimilaritySearchingFingerprints.html" title="SimilaritySearchingFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SimilarityMatricesFingerprints.pl</strong></td></tr>
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1079 </table>
|
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|
1080 </div>
|
|
|
1081 <br />
|
|
|
1082 <center>
|
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1083 <img src="../../images/h2o2.png">
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1084 </center>
|
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1085 </body>
|
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1086 </html>
|
