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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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<html> <head> <title>MayaChemTools:Documentation:InfoFingerprintsFiles.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="./InfoAminoAcids.html" title="InfoAminoAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>InfoFingerprintsFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoFingerprintsFiles.html" title="View source code">Code</a> | <a href="./../pdf/InfoFingerprintsFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoFingerprintsFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoFingerprintsFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoFingerprintsFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>InfoFingerprintsFiles.pl - List information about fingerprints data in SD, FP and CSV/TSV text file(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>InfoFingerprintsFiles.pl SDFile(s) FPFile(s) TextFile(s)...</p> <p>InfoFingerprintsFiles.pl [<strong>-a, --all</strong>] [<strong>--AverageBitDensity</strong>] [<strong>--BitDensity</strong>] [<strong>-c, --count</strong>] [<strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--DataCheck</strong>] [<strong>-d, --detail</strong> <em>InfoLevel</em>] [<strong>-e, --empty</strong>] [<strong>--FingerprintsCol</strong> <em>col number | col name</em>] [<strong>--FingerprintsField</strong> <em>FieldLabel</em>] [<strong>--FingerprintsType</strong>] [<strong>--FingerprintsDescription</strong>] [<strong>--FingerprintsSize</strong>] [<strong>--FingerprintsBitStringFormat</strong>] [<strong>--FingerprintsBitOrder</strong>] [<strong>--FingerprintsVectorValuesType</strong>] [<strong>--FingerprintsVectorValuesFormat</strong>] [<strong>-h, --help</strong>] [<strong>--InDelim</strong> <em>comma | semicolon</em>] [<strong>--NumOfOnBits</strong>] [<strong>--NumOfNonZeroValues</strong>] [<strong>-w, --WorkingDir</strong> dirname] SDFile(s) FPFile(s) TextFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>List information about fingerprints data in <em>SD, FP and CSV/TSV</em> text file(s): number of rows containing fingerprints data, type of fingerprints vector, description and size of fingerprints, bit density and average bit density for bit-vector fingerprints strings, and so on.</p> <p>The scripts InfoFingerprintsSDFiles.pl and InfoFingerprintsTextFiles.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>Format of fingerprint strings data in <em>SDFile(s), FPFile(s) and TextFile(s)</em> is automatically detected.</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>-a, --all</strong></strong></dt> <dd> <p>List all the available information.</p> </dd> <dt><strong><strong>--AverageBitDensity</strong></strong></dt> <dd> <p>List average bit density of fingerprint bit-vector strings.</p> </dd> <dt><strong><strong>--BitDensity</strong></strong></dt> <dd> <p>List bit density of fingerprints bit-vector strings data in each row.</p> </dd> <dt><strong><strong>--count</strong></strong></dt> <dd> <p>List number of data entries containing fingerprints bit-vector or vector strings data. This is <strong>default behavior</strong>.</p> </dd> <dt><strong><strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em></strong></dt> <dd> <p>Specify how columns are identified in CSV/TSV <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>-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>--DataCheck</strong></strong></dt> <dd> <p>Validate fingerprints data specified using <strong>--FingerprintsCol</strong> and list information about missing and invalid data.</p> </dd> <dt><strong><strong>-e, --empty</strong></strong></dt> <dd> <p>List number of rows containing no fingerprints data.</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 corresponds to column in CSV/TSV <em>TextFile(s)</em> containing fingerprints data. 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 listing of fingerprints information 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>--FingerprintsType</strong></strong></dt> <dd> <p>List types of fingerprint strings: FingerprintsBitVector or FingerprintsVector.</p> </dd> <dt><strong><strong>--FingerprintsDescription</strong></strong></dt> <dd> <p>List types of fingerprints: PathLengthBits, PathLengthCount, MACCSKeyCount, ExtendedConnectivity and so on.</p> </dd> <dt><strong><strong>--FingerprintsSize</strong></strong></dt> <dd> <p>List size of fingerprints.</p> </dd> <dt><strong><strong>--FingerprintsBitStringFormat</strong></strong></dt> <dd> <p>List format of fingerprint bit-vector strings: BinaryString or HexadecimalString.</p> </dd> <dt><strong><strong>--FingerprintsBitOrder</strong></strong></dt> <dd> <p>List order of bits data in fingerprint bit-vector bit strings: Ascending or Descending.</p> </dd> <dt><strong><strong>--FingerprintsVectorValuesType</strong></strong></dt> <dd> <p>List type of values in fingerprint vector strings: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</p> </dd> <dt><strong><strong>--FingerprintsVectorValuesFormat</strong></strong></dt> <dd> <p>List format of values in fingerprint vector strings: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString.</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>--NumOfOnBits</strong></strong></dt> <dd> <p>List number of on bits in fingerprints bit-vector strings data in each row.</p> </dd> <dt><strong><strong>--NumOfNonZeroValues</strong></strong></dt> <dd> <p>List number of non-zero values in fingerprints vector strings data in each row.</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 count number of lines containing fingerprints bit-vector or vector strings data present in FP file, in a column name containing Fingerprint substring in text file, and in a data field with Fingerprint substring in its label, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl SampleFPBin.csv</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl SampleFPBin.sdf SampleFPBin.fpf SampleFPBin.csv</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl SampleFPHex.sdf SampleFPHex.fpf SampleFPHex.csv</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl SampleFPcount.sdf SampleFPcount.fpf SampleFPcount.csv</div> <p>To list all available information about fingerprints bit-vector or vector strings data present in FP file, in a column name containing Fingerprint substring in text file, and in a data field with Fingerprint substring in its label, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a SampleFPHex.sdf SampleFPHex.fpf SampleFPHex.csv</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a SampleFPcount.sdf SampleFPcount.fpf SampleFPcount.csv</div> <p>To list all available information about fingerprints bit-vector or vector strings data present in a column named Fingerprints in text file, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol Fingerprints SampleFPHex.sdf</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol Fingerprints SampleFPcount.csv</div> <p>To list all available information about fingerprints bit-vector or vector strings data present in a data field names Fingerprints in SD file, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints SampleFPHex.sdf</div> <div class="ExampleBox"> % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints SampleFPcount.sdf</div> <p>To list bit density, average bit density, and number of on bits for fingerprints bit-vector strings data present in FP file, in a column name containing Fingerprint substring in text file, and in a data field with Fingerprint substring in its label, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl --BitDensity --AverageBitDensity --NumOfOnBits SampleFPBin.csv SampleFPBin.sdf SampleFPBin.fpf</div> <p>To list vector values type, format and number of non-zero values for fingerprints vector strings data present in FP file, in a column name containing Fingerprint substring in text file, and in a data field with Fingerprint substring in its label along with fingerprints type and description, type:</p> <div class="ExampleBox"> % InfoFingerprintsFiles.pl --FingerprintsType --FingerprintsDescription --FingerprintsVectorValuesType --FingerprintsVectorValuesFormat --NumOfNonZeroValues SampleFPcount.csv SampleFPcount.sdf SampleFPcount.fpf</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="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./SimilaritySearchingFingerprints.html">SimilaritySearchingFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.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="./InfoAminoAcids.html" title="InfoAminoAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoFingerprintsFiles.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>