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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/SimilarityMatricesFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1086 @@ +<html> +<head> +<title>MayaChemTools:Documentation:SimilarityMatricesFingerprints.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>SimilarityMatricesFingerprints.pl - Calculate similarity matrices using fingerprints strings data in SD, FP and CSV/TSV text file(s)</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)...</p> +<p>SimilarityMatricesFingerprints.pl [<strong>--alpha</strong> <em>number</em>] [<strong>--beta</strong> <em>number</em>] +[<strong>-b, --BitVectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[ TverskySimilarity, ... ]"</em>] +[<strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--CompoundIDCol</strong> <em>col number | col name</em>] +[<strong>--CompoundIDPrefix</strong> <em>text</em>] [<strong>--CompoundIDField</strong> <em>DataFieldName</em>] +[<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>] +[<strong>-d, --detail</strong> <em>InfoLevel</em>] [<strong>-f, --fast</strong>] [<strong>--FingerprintsCol</strong> <em>col number | col name</em>] +[<strong>--FingerprintsField</strong> <em>FieldLabel</em>] [<strong>-h, --help</strong>] [<strong>--InDelim</strong> <em>comma | semicolon</em>] +[<strong>--InputDataMode</strong> <em>LoadInMemory | ScanFile</em>] +[<strong>-m, --mode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em>] +[<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--OutMatrixFormat</strong> <em>RowsAndColumns | IDPairsAndValue</em>] +[<strong>--OutMatrixType</strong> <em>FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix</em>] +[<strong>-o, --overwrite</strong>] [<strong>-p, --precision</strong> <em>number</em>] +[<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] +[<strong>-v, --VectorComparisonMode</strong> <em>All | "TanimotoSimilairy, [ ManhattanDistance, ...]"</em>] +[<strong>--VectorComparisonFormulism</strong> <em>All | "AlgebraicForm, [BinaryForm, SetTheoreticForm]"</em>] +[<strong>-w, --WorkingDir</strong> dirname] SDFile(s) FPFile(s) TextFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Calculate similarity matrices using fingerprint bit-vector or vector strings data in <em>SD, FP +and CSV/TSV</em> text file(s) and generate CSV/TSV text file(s) containing values for specified +similarity and distance coefficients.</p> +<p>The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the +current release of MayaChemTools and their functionality merged with this script.</p> +<p>The valid <em>SDFile</em> extensions are <em>.sdf</em> and <em>.sd</em>. All SD files in a current directory +can be specified either by <em>*.sdf</em> or the current directory name.</p> +<p>The valid <em>FPFile</em> extensions are <em>.fpf</em> and <em>.fp</em>. All FP files in a current directory +can be specified either by <em>*.fpf</em> or the current directory name.</p> +<p>The valid <em>TextFile</em> extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab +delimited text files respectively. All other file names are ignored. All text files in a +current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory +name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file +which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p> +<p>Example of <em>FP</em> file containing fingerprints bit-vector string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # ReleaseDate = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Mon Mar 7 15:14:01 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsBitVector +<br/> # +<br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... +<br/> # Size = 1024 +<br/> # BitStringFormat = HexadecimalString +<br/> # BitsOrder = Ascending +<br/> # +<br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... +<br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120... +<br/> ... ... +<br/> ... ..</div> +<p>Example of <em>FP</em> file containing fingerprints vector string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # ReleaseDate = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Mon Mar 7 15:14:01 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<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: +<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...; +<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 +<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 ... +<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 +<br/> O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...; +<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 +<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 ... +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>SD</em> file containing fingerprints bit-vector string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <PathLengthFingerprints> +<br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt +<br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 +<br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 +<br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 +<br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a +<br/> aa0660a11014a011d46</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of CSV <em>Text</em> file containing fingerprints bit-vector string data:</p> +<div class="OptionsBox"> + "CompoundID","PathLengthFingerprints" +<br/> "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes +<br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 +<br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 +<br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools supports the following types of fingerprint +bit-vector and vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi +<br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT +<br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X +<br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A +<br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 +<br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS +<br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 +<br/> .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 +<br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div> +<div class="OptionsBox"> + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume +<br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F +<br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div> +<div class="OptionsBox"> + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN +<br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C +<br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N +<br/> 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs +<br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN +<br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 +<br/> .024 -2.270</div> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; +<br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 +<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 +<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 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi +<br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 +<br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 +<br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 +<br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 +<br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes +<br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 +<br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 +<br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; +<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 +<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> +<div class="OptionsBox"> + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +<br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 +<br/> 0000000001010000000110000011000000000000100000000000000000000000100001 +<br/> 1000000110000000000000000000000000010011000000000000000000000000010000 +<br/> 0000000000000000000000000010000000000000000001000000000000000000000000 +<br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu +<br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 +<br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 +<br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 +<br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 +<br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp +<br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 +<br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 +<br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 +<br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 +<br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 +<br/> 0000000000000000000000000000000001001000010010000000010010000000011100 +<br/> 0100101010111100011011000100110110000011011110100110111111111111011111 +<br/> 11111111111110111000</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 +<br/> 1110011111100101111111000111101100110000000000000011100010000000000000 +<br/> 0000000000000000000000000000000000000000000000101000000000000000000000 +<br/> 0000000000000000000000000000000000000000000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000011000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000000</div> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri +<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 +<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 +<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 +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri +<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 +<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 +<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 +<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 +<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> +<div class="OptionsBox"> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng +<br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 +<br/> 0100010101011000101001011100110001000010001001101000001001001001001000 +<br/> 0010110100000111001001000001001010100100100000000011000000101001011100 +<br/> 0010000001000101010100000100111100110111011011011000000010110111001101 +<br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength +<br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 +<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 +<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 +<br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO +<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> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt +<br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 +<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 +<br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 +<br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR +<br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +<br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 +<br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. +<br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi +<br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar +<br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H +<br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 +<br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- +<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 +<br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica +<br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC +<br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- +<br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 +<br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 +<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 +<br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 +<br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C +<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- +<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 +<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. +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +<br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H +<br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- +<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 +<br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +<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 +<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 +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +<br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- +<br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 +<br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- +<br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; +<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 +<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 +<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> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +<br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 +<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 +<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 +<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 +<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> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>--alpha</strong> <em>number</em></strong></dt> +<dd> +<p>Value of alpha parameter for calculating <em>Tversky</em> similarity coefficient specified for +<strong>-b, --BitVectorComparisonMode</strong> option. It corresponds to weights assigned for bits set +to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible +values: <em>0 to 1</em>. Default value: <0.5>.</p> +</dd> +<dt><strong><strong>--beta</strong> <em>number</em></strong></dt> +<dd> +<p>Value of beta parameter for calculating <em>WeightedTanimoto</em> and <em>WeightedTversky</em> +similarity coefficients specified for <strong>-b, --BitVectorComparisonMode</strong> option. It is used to +weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible +values: <em>0 to 1</em>. Default value of <1> makes <em>WeightedTanimoto</em> and <em>WeightedTversky</em> +equivalent to <em>Tanimoto</em> and <em>Tversky</em>.</p> +</dd> +<dt><strong><strong>-b, --BitVectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[TverskySimilarity,...]"</em></strong></dt> +<dd> +<p>Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector +strings data values in <em>TextFile(s)</em>: calculate similarity matrices for all supported similarity +coefficients or specify a comma delimited list of similarity coefficients. Possible values: +<em>All | "TanimotoSimilarity,[TverskySimilarity,...]</em>. Default: <em>TanimotoSimilarity</em></p> +<p><em>All</em> uses complete list of supported similarity coefficients: <em>BaroniUrbaniSimilarity, BuserSimilarity, +CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity, +Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity, +PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity, +SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity, +WeightedTanimotoSimilarity, WeightedTverskySimilarity</em>. These similarity coefficients are described below.</p> +<p>For two fingerprint bit-vectors A and B of same size, let:</p> +<div class="OptionsBox"> + Na = Number of bits set to "1" in A +<br/> Nb = Number of bits set to "1" in B +<br/> Nc = Number of bits set to "1" in both A and B +<br/> Nd = Number of bits set to "0" in both A and B</div> +<div class="OptionsBox"> + Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) +<br/> Nt = Na + Nb - Nc + Nd</div> +<div class="OptionsBox"> + Na - Nc = Number of bits set to "1" in A but not in B +<br/> Nb - Nc = Number of bits set to "1" in B but not in A</div> +<p>Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are +defined as follows:</p> +<p><em>BaroniUrbaniSimilarity</em>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</p> +<p><em>BuserSimilarity</em>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</p> +<p><em>CosineSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Ochiai)</p> +<p><em>DiceSimilarity</em>: (2 * Nc) / ( Na + Nb )</p> +<p><em>DennisSimilarity</em>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</p> +<p><em>ForbesSimilarity</em>: ( Nt * Nc ) / ( Na * Nb )</p> +<p><em>FossumSimilarity</em>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</p> +<p><em>HamannSimilarity</em>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</p> +<p><em>JaccardSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</p> +<p><em>Kulczynski1Similarity</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</p> +<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> +<p><em>MatchingSimilarity</em>: ( Nc + Nd ) / Nt</p> +<p><em>McConnaugheySimilarity</em>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</p> +<p><em>OchiaiSimilarity</em>: Nc / SQRT ( Na * Nb ) (same as Cosine)</p> +<p><em>PearsonSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</p> +<p><em>RogersTanimotoSimilarity</em>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</p> +<p><em>RussellRaoSimilarity</em>: Nc / Nt</p> +<p><em>SimpsonSimilarity</em>: Nc / MIN ( Na, Nb)</p> +<p><em>SkoalSneath1Similarity</em>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</p> +<p><em>SkoalSneath2Similarity</em>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</p> +<p><em>SkoalSneath3Similarity</em>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</p> +<p><em>TanimotoSimilarity</em>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</p> +<p><em>TverskySimilarity</em>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</p> +<p><em>YuleSimilarity</em>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</p> +<p>Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which +are set to "1" in both A and B. In order to take into account all bit positions, modified versions +of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</p> +<p>Let:</p> +<div class="OptionsBox"> + Na' = Number of bits set to "0" in A +<br/> Nb' = Number of bits set to "0" in B +<br/> Nc' = Number of bits set to "0" in both A and B</div> +<p>Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</p> +<p>Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</p> +<p>Then:</p> +<p><em>WeightedTanimotoSimilarity</em> = beta * Tanimoto + (1 - beta) * Tanimoto'</p> +<p><em>WeightedTverskySimilarity</em> = beta * Tversky + (1 - beta) * Tversky'</p> +</dd> +<dt><strong><strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em></strong></dt> +<dd> +<p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column +label. Possible values: <em>ColNum or ColLabel</em>. Default value: <em>ColNum</em>.</p> +</dd> +<dt><strong><strong>--CompoundIDCol</strong> <em>col number | col name</em></strong></dt> +<dd> +<p>This value is <strong>-c, --ColMode</strong> mode specific. It specifies input <em>TextFile(s)</em> column to use for +generating compound ID for similarity matrices in output <em>TextFile(s)</em>. Possible values: <em>col number +or col label</em>. Default value: <em>first column containing the word compoundID in its column label or sequentially +generated IDs</em>.</p> +</dd> +<dt><strong><strong>--CompoundIDPrefix</strong> <em>text</em></strong></dt> +<dd> +<p>Specify compound ID prefix to use during sequential generation of compound IDs for input <em>SDFile(s)</em> +and <em>TextFile(s)</em>. Default value: <em>Cmpd</em>. The default value generates compound IDs which look +like Cmpd<Number>.</p> +<p>For input <em>SDFile(s)</em>, this value is only used during <em>LabelPrefix | MolNameOrLabelPrefix</em> values +of <strong>--CompoundIDMode</strong> option; otherwise, it's ignored.</p> +<p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p> +<div class="OptionsBox"> + Compound</div> +<p>The values specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>.</p> +</dd> +<dt><strong><strong>--CompoundIDField</strong> <em>DataFieldName</em></strong></dt> +<dd> +<p>Specify input <em>SDFile(s)</em> datafield label for generating compound IDs. This value is only used +during <em>DataField</em> value of <strong>--CompoundIDMode</strong> option.</p> +<p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p> +<div class="OptionsBox"> + MolID +<br/> ExtReg</div> +</dd> +<dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt> +<dd> +<p>Specify how to generate compound IDs from input <em>SDFile(s)</em> for similarity matrix CSV/TSV text +file(s): use a <em>SDFile(s)</em> datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID +with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values +for empty molname lines.</p> +<p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>. +Default: <em>LabelPrefix</em>.</p> +<p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes +precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname +values are replaced with sequential compound IDs.</p> +</dd> +<dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt> +<dd> +<p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values: +<em>1, 2 or 3</em>.</p> +</dd> +<dt><strong><strong>-f, --fast</strong></strong></dt> +<dd> +<p>In this mode, fingerprints columns specified using <strong>--FingerprintsCol</strong> for <em>TextFile(s)</em> and +<strong>--FingerprintsField</strong> for <em>SDFile(s)</em> are assumed to contain valid fingerprints data and no +checking is performed before calculating similarity matrices. By default, fingerprints data is +validated before computing pairwise similarity and distance coefficients.</p> +</dd> +<dt><strong><strong>--FingerprintsCol</strong> <em>col number | col name</em></strong></dt> +<dd> +<p>This value is <strong>-c, --colmode</strong> specific. It specifies fingerprints column to use during +calculation similarity matrices for <em>TextFile(s)</em>. Possible values: <em>col number or col label</em>. +Default value: <em>first column containing the word Fingerprints in its column label</em>.</p> +</dd> +<dt><strong><strong>--FingerprintsField</strong> <em>FieldLabel</em></strong></dt> +<dd> +<p>Fingerprints field label to use during calculation similarity matrices for <em>SDFile(s)</em>. +Default value: <em>first data field label containing the word Fingerprints in its label</em></p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--InDelim</strong> <em>comma | semicolon</em></strong></dt> +<dd> +<p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>. +Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a +delimiter.</p> +</dd> +<dt><strong><strong>--InputDataMode</strong> <em>LoadInMemory | ScanFile</em></strong></dt> +<dd> +<p>Specify how fingerprints bit-vector or vector strings data from <em>SD, FP and CSV/TSV</em> +fingerprint file(s) is processed: Retrieve, process and load all available fingerprints +data in memory; Retrieve and process data for fingerprints one at a time. Possible values +: <em>LoadInMemory | ScanFile</em>. Default: <em>LoadInMemory</em>.</p> +<p>During <em>LoadInMemory</em> value of <strong>--InputDataMode</strong>, fingerprints bit-vector or vector +strings data from input file is retrieved, processed, and loaded into memory all at once +as fingerprints objects for generation for similarity matrices.</p> +<p>During <em>ScanFile</em> value of <strong>--InputDataMode</strong>, multiple passes over the input fingerprints +file are performed to retrieve and process fingerprints bit-vector or vector strings data one at +a time to generate fingerprints objects used during generation of similarity matrices. A temporary +copy of the input fingerprints file is made at the start and deleted after generating the matrices.</p> +<p><em>ScanFile</em> value of <strong>--InputDataMode</strong> allows processing of arbitrary large fingerprints files +without any additional memory requirement.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em></strong></dt> +<dd> +<p>Format of fingerprint strings data in <em>TextFile(s)</em>: automatically detect format of fingerprints +string created by MayaChemTools fingerprints generation scripts or explicitly specify its format. +Possible values: <em>AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString</em>. Default +value: <em>AutoDetect</em>.</p> +</dd> +<dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>--OutMatrixFormat</strong> <em>RowsAndColumns | IDPairsAndValue</em></strong></dt> +<dd> +<p>Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings +are written to the output CSV/TSV text file(s): Generate text files containing rows and columns +with their labels corresponding to compound IDs and each matrix element value corresponding to +similarity or distance between corresponding compounds; Generate text files containing rows containing +compoundIDs for two compounds followed by similarity or distance value between these compounds.</p> +<p>Possible values: <em>RowsAndColumns, or IDPairsAndValue</em>. Default value: <em>RowsAndColumns</em>.</p> +<p>The value of <strong>--OutMatrixFormat</strong> in conjunction with <strong>--OutMatrixType</strong> determines type +of data written to output files and allows generation of up to 6 different output data formats:</p> +<div class="OptionsBox"> + OutMatrixFormat OutMatrixType</div> +<div class="OptionsBox"> + RowsAndColumns FullMatrix [ DEFAULT ] +<br/> RowsAndColumns UpperTriangularMatrix +<br/> RowsAndColumns LowerTriangularMatrix</div> +<div class="OptionsBox"> + IDPairsAndValue FullMatrix +<br/> IDPairsAndValue UpperTriangularMatrix +<br/> IDPairsAndValue LowerTriangularMatrix</div> +<p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for +<em>FullMatrix</em> valueof <strong>--OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... +<br/> "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... +<br/> "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ... +<br/> "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ... +<br/> "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ... +<br/> "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ... +<br/> "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ... +<br/> ... ... .. +<br/> ... ... .. +<br/> ... ... ..</div> +<p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for +<em>UpperTriangularMatrix</em> value of <strong>--OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... +<br/> "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... +<br/> "Cmpd2","1","0.06","0.05","0.19","0.07",... ... +<br/> "Cmpd3","1","0.12","0.22","0.25",... ... +<br/> "Cmpd4","1","0.11","0.13",... ... +<br/> "Cmpd5","1","0.17",... ... +<br/> "Cmpd6","1",... ... +<br/> ... ... .. +<br/> ... ... .. +<br/> ... ... ..</div> +<p>Example of data in output file for <em>RowsAndColumns</em> <strong>--OutMatrixFormat</strong> value for +<em>LowerTriangularMatrix</em> value of <strong>--OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... +<br/> "Cmpd1","1" +<br/> "Cmpd2","0.04","1" +<br/> "Cmpd3","0.25","0.06","1" +<br/> "Cmpd4","0.13","0.05","0.12","1" +<br/> "Cmpd5","0.11","0.19","0.22","0.11","1" +<br/> "Cmpd6","0.2","0.07","0.25","0.13","0.17","1" +<br/> ... ... .. +<br/> ... ... .. +<br/> ... ... ..</div> +<p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for +<FullMatrix> value of <strong>OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "CmpdID1","CmpdID2","Coefficient Value" +<br/> "Cmpd1","Cmpd1","1" +<br/> "Cmpd1","Cmpd2","0.04" +<br/> "Cmpd1","Cmpd3","0.25" +<br/> "Cmpd1","Cmpd4","0.13" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ... +<br/> "Cmpd2","Cmpd1","0.04" +<br/> "Cmpd2","Cmpd2","1" +<br/> "Cmpd2","Cmpd3","0.06" +<br/> "Cmpd2","Cmpd4","0.05" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ... +<br/> "Cmpd3","Cmpd1","0.25" +<br/> "Cmpd3","Cmpd2","0.06" +<br/> "Cmpd3","Cmpd3","1" +<br/> "Cmpd3","Cmpd4","0.12" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ...</div> +<p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for +<UpperTriangularMatrix> value of <strong>--OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "CmpdID1","CmpdID2","Coefficient Value" +<br/> "Cmpd1","Cmpd1","1" +<br/> "Cmpd1","Cmpd2","0.04" +<br/> "Cmpd1","Cmpd3","0.25" +<br/> "Cmpd1","Cmpd4","0.13" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ... +<br/> "Cmpd2","Cmpd2","1" +<br/> "Cmpd2","Cmpd3","0.06" +<br/> "Cmpd2","Cmpd4","0.05" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ... +<br/> "Cmpd3","Cmpd3","1" +<br/> "Cmpd3","Cmpd4","0.12" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ...</div> +<p>Example of data in output file for <em>IDPairsAndValue</em> <strong>--OutMatrixFormat</strong> value for +<LowerTriangularMatrix> value of <strong>--OutMatrixType</strong>:</p> +<div class="OptionsBox"> + "CmpdID1","CmpdID2","Coefficient Value" +<br/> "Cmpd1","Cmpd1","1" +<br/> "Cmpd2","Cmpd1","0.04" +<br/> "Cmpd2","Cmpd2","1" +<br/> "Cmpd3","Cmpd1","0.25" +<br/> "Cmpd3","Cmpd2","0.06" +<br/> "Cmpd3","Cmpd3","1" +<br/> "Cmpd4","Cmpd1","0.13" +<br/> "Cmpd4","Cmpd2","0.05" +<br/> "Cmpd4","Cmpd3","0.12" +<br/> "Cmpd4","Cmpd4","1" +<br/> ... ... ... +<br/> ... ... ... +<br/> ... ... ...</div> +</dd> +<dt><strong><strong>--OutMatrixType</strong> <em>FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix</em></strong></dt> +<dd> +<p>Type of similarity or distance matrix to calculate for fingerprints vector and bit-vector strings: +Calculate full matrix; Calculate lower triangular matrix including diagonal; Calculate upper triangular +matrix including diagonal.</p> +<p>Possible values: <em>FullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix</em>. Default value: +<em>FullMatrix</em>.</p> +<p>The value of <strong>--OutMatrixType</strong> in conjunction with <strong>--OutMatrixFormat</strong> determines type +of data written to output files.</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files</p> +</dd> +<dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Put quote around column values in output CSV/TSV text file(s). Possible values: +<em>Yes or No</em>. Default value: <em>Yes</em>.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt> +<dd> +<p>New file name is generated using the root: <Root><BitVectorComparisonMode>.<Ext> or +<Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>. +The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files +respectively. This option is ignored for multiple input files.</p> +</dd> +<dt><strong><strong>-v, --VectorComparisonMode</strong> <em>All | "TanimotoSimilarity,[ManhattanDistance,...]"</em></strong></dt> +<dd> +<p>Specify what similarity or distance coefficients to use for calculating similarity matrices for +fingerprint vector strings data values in <em>TextFile(s)</em>: calculate similarity matrices for all +supported similarity and distance coefficients or specify a comma delimited list of similarity +and distance coefficients. Possible values: <em>All | "TanimotoSimilairy,[ManhattanDistance,..]"</em>. +Default: <em>TanimotoSimilarity</em>.</p> +<p>The value of <strong>-v, --VectorComparisonMode</strong>, in conjunction with <strong>--VectorComparisonFormulism</strong>, +decides which type of similarity and distance coefficient formulism gets used.</p> +<p><em>All</em> uses complete list of supported similarity and distance coefficients: <em>CosineSimilarity, +CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity, +CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance</em>. These +similarity and distance coefficients are described below.</p> +<p><strong>FingerprintsVector.pm</strong> module, used to calculate similarity and distance coefficients, +provides support to perform comparison between vectors containing three different types of +values:</p> +<p>Type I: OrderedNumericalValues</p> +<div class="OptionsBox"> + . Size of two vectors are same +<br/> . Vectors contain real values in a specific order. For example: MACCS keys + count, Topological pharmnacophore atom pairs and so on.</div> +<p>Type II: UnorderedNumericalValues</p> +<div class="OptionsBox"> + . Size of two vectors might not be same +<br/> . Vectors contain unordered real value identified by value IDs. For example: + Toplogical atom pairs, Topological atom torsions and so on</div> +<p>Type III: AlphaNumericalValues</p> +<div class="OptionsBox"> + . Size of two vectors might not be same +<br/> . Vectors contain unordered alphanumerical values. For example: Extended + connectivity fingerprints, atom neighborhood fingerprints.</div> +<p>Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues +or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues +using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.</p> +<p>Three forms of similarity and distance calculation between two vectors, specified using <strong>--VectorComparisonFormulism</strong> +option, are supported: <em>AlgebraicForm, BinaryForm or SetTheoreticForm</em>.</p> +<p>For <em>BinaryForm</em>, the ordered list of processed final vector values containing the value or +count of each unique value type is simply converted into a binary vector containing 1s and 0s +corresponding to presence or absence of values before calculating similarity or distance between +two vectors.</p> +<p>For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:</p> +<div class="OptionsBox"> + N = Number values in A or B</div> +<div class="OptionsBox"> + Xa = Values of vector A +<br/> Xb = Values of vector B</div> +<div class="OptionsBox"> + Xai = Value of ith element in A +<br/> Xbi = Value of ith element in B</div> +<div class="OptionsBox"> + SUM = Sum of i over N values</div> +<p>For SetTheoreticForm of calculation between two vectors, let:</p> +<div class="OptionsBox"> + SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) +<br/> SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )</div> +<p>For BinaryForm of calculation between two vectors, let:</p> +<div class="OptionsBox"> + Na = Number of bits set to "1" in A = SUM ( Xai ) +<br/> Nb = Number of bits set to "1" in B = SUM ( Xbi ) +<br/> Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi ) +<br/> Nd = Number of bits set to "0" in both A and B + = SUM ( 1 - Xai - Xbi + Xai * Xbi)</div> +<div class="OptionsBox"> + N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</div> +<p>Additionally, for BinaryForm various values also correspond to:</p> +<div class="OptionsBox"> + Na = | Xa | +<br/> Nb = | Xb | +<br/> Nc = | SetIntersectionXaXb | +<br/> Nd = N - | SetDifferenceXaXb |</div> +<div class="OptionsBox"> + | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc + = | Xa | + | Xb | - | SetIntersectionXaXb |</div> +<p>Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B +in <em>AlgebraicForm, BinaryForm and SetTheoreticForm</em> are defined as follows:</p> +<p><strong>CityBlockDistance</strong>: ( same as HammingDistance and ManhattanDistance)</p> +<p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p> +<p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p> +<p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p> +<p><strong>CosineSimilarity</strong>: ( same as OchiaiSimilarityCoefficient)</p> +<p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p> +<p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p> +<p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p> +<p><strong>CzekanowskiSimilarity</strong>: ( same as DiceSimilarity and SorensonSimilarity)</p> +<p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p> +<p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p> +<p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p> +<p><strong>DiceSimilarity</strong>: ( same as CzekanowskiSimilarity and SorensonSimilarity)</p> +<p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p> +<p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p> +<p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p> +<p><strong>EuclideanDistance</strong>:</p> +<p><em>AlgebraicForm</em>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )</p> +<p><em>BinaryForm</em>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )</p> +<p><em>SetTheoreticForm</em>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )</p> +<p><strong>HammingDistance</strong>: ( same as CityBlockDistance and ManhattanDistance)</p> +<p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p> +<p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p> +<p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p> +<p><strong>JaccardSimilarity</strong>: ( same as TanimotoSimilarity)</p> +<p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p> +<p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p> +<p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p> +<p><strong>ManhattanDistance</strong>: ( same as CityBlockDistance and HammingDistance)</p> +<p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) )</p> +<p><em>BinaryForm</em>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</p> +<p><em>SetTheoreticForm</em>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</p> +<p><strong>OchiaiSimilarity</strong>: ( same as CosineSimilarity)</p> +<p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</p> +<p><em>BinaryForm</em>: Nc / SQRT ( Na * Nb)</p> +<p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</p> +<p><strong>SorensonSimilarity</strong>: ( same as CzekanowskiSimilarity and DiceSimilarity)</p> +<p><em>AlgebraicForm</em>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</p> +<p><em>BinaryForm</em>: 2 * Nc / ( Na + Nb )</p> +<p><em>SetTheoreticForm</em>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</p> +<p><strong>SoergelDistance</strong>:</p> +<p><em>AlgebraicForm</em>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )</p> +<p><em>BinaryForm</em>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )</p> +<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> +<p><strong>TanimotoSimilarity</strong>: ( same as JaccardSimilarity)</p> +<p><em>AlgebraicForm</em>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</p> +<p><em>BinaryForm</em>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</p> +<p><em>SetTheoreticForm</em>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</p> +</dd> +<dt><strong><strong>--VectorComparisonFormulism</strong> <em>All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]"</em></strong></dt> +<dd> +<p>Specify fingerprints vector comparison formulism to use for calculation similarity and distance +coefficients during <strong>-v, --VectorComparisonMode</strong>: use all supported comparison formulisms +or specify a comma delimited. Possible values: <em>All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]"</em>. +Default value: <em>AlgebraicForm</em>.</p> +<p><em>All</em> uses all three forms of supported vector comparison formulism for values of <strong>-v, --VectorComparisonMode</strong> +option.</p> +<p>For fingerprint vector strings containing <strong>AlphaNumericalValues</strong> data values - <strong>ExtendedConnectivityFingerprints</strong>, +<strong>AtomNeighborhoodsFingerprints</strong> and so on - all three formulism result in same value during similarity and distance +calculations.</p> +</dd> +<dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column +name containing Fingerprint substring by loading all fingerprints data into memory and create a +SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name +containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD File present in a data field +with Fingerprint substring in its label by loading all fingerprints data into memory and create a +SampleFPHexTanimotoSimilarity.csv file containing sequentially generated compound IDs with +Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in FP file by loading all fingerprints +data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs +retrieved from FP file, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf</div> +<p>To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by loading all fingerprints data into memory and create +a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name +containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv</div> +<p>To generate a upper triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by loading all fingerprints data into memory and create +a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing compound IDs retrieved +from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix + SampleFPHex.csv</div> +<p>To generate a full similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column +name containing Fingerprint substring by scanning file without loading all fingerprints data into memory +and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from +column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix + SampleFPHex.csv</div> +<p>To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by scanning file without loading all fingerprints data into +memory and create a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing +compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +for fingerprints vector strings data corresponding to supported fingerprints in text file present in a column name +containing Fingerprint substring and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file +containing compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +for fingerprints vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file +containing sequentially generated compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +vector strings data corresponding to supported fingerprints in FP file and create a +SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from FP file, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column name +containing Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv file in +IDPairsAndValue format containing compound IDs retrieved from column name containing +CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file in +IDPairsAndValue format containing sequentially generated compound IDs with Cmpd prefix, +type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in FP file and create a +SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved +from FP file, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.fpf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from mol name line, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o + SampleFPHex.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from data field name Mol_ID, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField + --CompoundIDField Mol_ID -o SampleFPBin.sdf</div> +<p>To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient +for fingerprints bit-vector strings data corresponding to supported fingerprints present in a column +name containing Fingerprint substring and create SampleFPBin[CoefficientName]Similarity.csv files +containing compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.csv</div> +<p>To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient +for fingerprints bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create SampleFPBin[CoefficientName]Similarity.csv files +containing sequentially generated compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.sdf</div> +<p>To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using +algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]AlgebraicForm.csv +files containing compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.csv</div> +<p>To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using +algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]AlgebraicForm.csv +files containing sequentially generated compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.sdf</div> +<p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]Binary.csv +files containing compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.csv</div> +<p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]Binary.csv +files containing sequentially generated compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.sdf</div> +<p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +all supported comparison formulisms for fingerprints vector strings data corresponding to supported +fingerprints present in a column name containing Fingerprint substring and create +SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs retrieved from column +name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv</div> +<p>To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +all supported comparison formulisms for fingerprints vector strings data corresponding to supported +fingerprints present in a data field with Fingerprint substring in its label and create +SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated +compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity" + --VectorComparisonFormulism All -o SampleFPCount.sdf</div> +<p>To generate similarity matrices corresponding to all available similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column name +containing Fingerprint substring and create SampleFPHex[CoefficientName].csv files +containing compound IDs retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv</div> +<p>To generate similarity matrices corresponding to all available similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with Fingerprint +substring in its label and create SampleFPHex[CoefficientName].csv files containing sequentially +generated compound IDs with Cmpd prefix, type</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf</div> +<p>To generate similarity matrices corresponding to all available similarity and distance coefficients using +all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints +present in a column name containing Fingerprint substring and create +SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs +retrieved from column name containing CompoundID substring, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.csv</div> +<p>To generate similarity matrices corresponding to all available similarity and distance coefficients using +all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints +present in a data field with Fingerprint substring in its label and create +SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated +compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column number 2 +and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved column +number 1, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1 + --FingerprintsCol 2 -o SampleFPHex.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field name +Fingerprints and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs +present in data field name Mol_ID, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints + --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf</div> +<p>To generate a similarity matrix corresponding to Tversky similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column named Fingerprints +and create a SampleFPHexTverskySimilarity.tsv file containing compound IDs retrieved column named +CompoundID, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode + TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol + CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No + -o SampleFPHex.csv</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field +with Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from molname line or sequentially generated compound IDs +with Mol prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix + --CompoundIDPrefix Mol -o SampleFPHex.sdf</div> +<p>To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.tsv file +containing sequentially generated compound IDs with Cmpd prefix, type:</p> +<div class="ExampleBox"> + % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilaritySearchingFingerprints.html">SimilaritySearchingFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,  +<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,  +<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,  +<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>