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<html> <head> <title>MayaChemTools:Documentation:FileIO::FingerprintsFPFileIO.pm</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="./FileIO.html" title="FileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsSDFileIO.html" title="FingerprintsSDFileIO.html">Next</a></td><td width="34%" align="middle"><strong>FileIO::FingerprintsFPFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsFPFileIO.html" title="View source code">Code</a> | <a href="./../pdf/FingerprintsFPFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/FingerprintsFPFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/FingerprintsFPFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/FingerprintsFPFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>FingerprintsFPFileIO</p> <p> </p> <h2>SYNOPSIS</h2> <p>use FileIO::FingerprintsFPFileIO;</p> <p>use FileIO::FingerprintsFPFileIO qw(:all);</p> <p> </p> <h2>DESCRIPTION</h2> <p><strong>FingerprintsFPFileIO</strong> class provides the following methods:</p> <p> <a href="#new">new</a>, <a href="#getfingerprints">GetFingerprints</a>, <a href="#getfingerprintsstring">GetFingerprintsString</a>, <a href="#getheaderdatakeyvalue">GetHeaderDataKeyValue</a> , <a href="#getheaderdatakeys">GetHeaderDataKeys</a>, <a href="#getheaderdatakeysandvalues">GetHeaderDataKeysAndValues</a>, <a href="#getpartialfingerprintsstring">GetPartialFingerprintsString</a> , <a href="#getrequiredheaderdatakeys">GetRequiredHeaderDataKeys</a>, <a href="#getrequiredheaderdatakeysandvalues">GetRequiredHeaderDataKeysAndValues</a> , <a href="#isfingerprintsdatavalid">IsFingerprintsDataValid</a>, <a href="#isfingerprintsfpfile">IsFingerprintsFPFile</a>, <a href="#isfingerprintsfiledatavalid">IsFingerprintsFileDataValid</a> , <a href="#isheaderdatakeypresent">IsHeaderDataKeyPresent</a>, <a href="#next">Next</a>, <a href="#read">Read</a>, <a href="#setbitstringformat">SetBitStringFormat</a>, <a href="#setbitsorder">SetBitsOrder</a> , <a href="#setcompoundid">SetCompoundID</a>, <a href="#setdetaillevel">SetDetailLevel</a>, <a href="#setfingerprints">SetFingerprints</a>, <a href="#setfingerprintsstring">SetFingerprintsString</a> , <a href="#setfingerprintsstringmode">SetFingerprintsStringMode</a>, <a href="#setpartialfingerprintsstring">SetPartialFingerprintsString</a>, <a href="#setvectorstringformat">SetVectorStringFormat</a> , <a href="#writefingerprints">WriteFingerprints</a>, <a href="#writefingerprintsstring">WriteFingerprintsString</a> </p><p>The following methods can also be used as functions:</p> <p>IsFingerprintsFPFile</p> <p><strong>FingerprintsFPFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support generic file related functionality.</p> <p>The MayaChemTools fingerprints file (FP) format with <strong>.fpf</strong> or <strong>.fp</strong> file extensions supports two types of fingerprints data: fingerprints bit-vectors and fingerprints vectors.</p> <p>Example of FP file format 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 FP file format 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><strong>FP</strong> file data format consists of two main sections: header section and fingerprints string data section. The header section lines start with # and the first line not starting with # represents the start of fingerprints string data section. The header section contains both the required and optional information which is specified as key = value pairs. The required information describes fingerprints bit-vector and vector strings and used to generate fingerprints objects; the optional information is ignored during generation of fingerpints objects.</p> <p>The key = value data specification in the header section and its processing follows these rules:</p> <div class="OptionsBox"> o Leading and trailing spaces for key = value pairs are ignored <br/> o Key and value strings may contain spaces <br/> o Multiple key = value pairs on a single are delimited by semicolon</div> <p>The default optional header data section key = value pairs are:</p> <div class="OptionsBox"> # Package = MayaChemTools 7.4 <br/> # ReleaseDate = Oct 21, 2010</div> <p>The <strong>FingerprintsStringType</strong> key is required data header key for both fingerprints bit-vector and vector strings. Possible key values: <em>FingerprintsBitVector or FingerprintsVector</em>. For example:</p> <div class="OptionsBox"> # FingerprintsStringType = FingerprintsBitVector</div> <p>The required data header keys for fingerprints bit-vector string are: <strong>Description, Size, BitStringFormat, and BitsOrder</strong>. Possible values for <strong>BitStringFormat</strong>: <em>HexadecimalString or BinaryString</em>. Possible values for <strong>BitsOrder</strong>: <em>Ascending or Descending</em>. The <strong>Description</strong> key contains information about various parameters used to generate fingerprints bit-vector string. The <strong>Size</strong> corresponds to number of fingerprints bits and is always less than or equal to number of bits in bit-vetor string which might contain extra bits at the end to round off the size to make it multiple of 8. For example:</p> <div class="OptionsBox"> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... <br/> # Size = 1024 <br/> # BitStringFormat = HexadecimalString <br/> # BitsOrder = Ascending</div> <p>The required data header keys for fingerprints vector string are: <strong>Description, VectorStringFormat, and VectorValuesType</strong>. Possible values for <strong>VectorStringFormat</strong>: <em>DsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString</em>. Possible values for <strong>VectorValuesType</strong>: <em>NumericalValues, OrderedNumericalValues or AlphaNumericalValues</em>. The <strong>Description</strong> keys contains information various parameters used to generate fingerprints vector string. For example:</p> <div class="OptionsBox"> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... <br/> # VectorStringFormat = IDsAndValuesString <br/> # VectorValuesType = NumericalValues</div> <p>The fingerprints data section for fingerprints bit-vector string contains data in the following format:</p> <div class="OptionsBox"> ... ... <br/> CmpdID FingerprintsPartialBitVectorString <br/> ... ...</div> <p>For example:</p> <div class="OptionsBox"> ... ... <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... <br/> ... ...</div> <p>The fingerprints data section for fingerprints vector string contains data in the following format:</p> <div class="OptionsBox"> ... ... <br/> CmpdID Size;FingerprintsPartialVectorString <br/> ... ...</div> <p>For example:</p> <div class="OptionsBox"> ... ... <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/> ... ...</div> <p>Unlike fingerprints bit-vector string, <em>Size</em> is specified for each partial fingerprints vector string: It may change from molecule to molecule for same type of fingerprints.</p> <p>Values IDs are optional for fingerprints vector string containing <em>OrderedNumericalValues or AlphaNumericalValues</em>; however, they must be present for for <em>NumericalValues</em>. Due to various possible values for <strong>VectorStringFormat</strong>, the fingerprints data section for fingerprints vector string supports following type of data formats:</p> <div class="OptionsBox"> CmpdID Size;ID1 ID2 ID3...;Value1 Value2 Value3... <br/> CmpdID Size;ID1 Value1 ID2 Value2 ID3 Value3... ... <br/> CmpdID Size;ValuesAndIDsString: Value1 Value2 Value3...;ID1 ID2 ID3... <br/> CmpdID Size;ValuesAndIDsPairsString: Value1 ID1 Value2 ID2 Value3 ID3... ... <br/> CmpdID Size;Value1 Value2 Value3 ...</div> <p>However, all the fingerprints vector string data present in FP file must correspond to only one of the formats shown above; multiple data formats in the same file are not allowed.</p> <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>METHODS</h2> <dl> <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters);</div> <p>Using specified <em>IOParameters</em> names and values hash, <strong>new</strong> method creates a new object and returns a reference to a newly created <strong>FingerprintsFPFileIO</strong> object. By default, the following properties are initialized during <em>Read</em> mode:</p> <div class="OptionsBox"> Name = ''; <br/> Mode = 'Read'; <br/> Status = 0; <br/> FingerprintsStringMode = 'AutoDetect'; <br/> ValidateData = 1; <br/> DetailLevel = 1;</div> <p>During <em>Write</em> mode, the following properties get initialize by default:</p> <div class="OptionsBox"> FingerprintsStringMode = undef;</div> <div class="OptionsBox"> BitStringFormat = HexadecimalString; <br/> BitsOrder = Ascending;</div> <div class="OptionsBox"> VectorStringFormat = NumericalValuesString or ValuesString;</div> <p>Examples:</p> <div class="OptionsBox"> $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fpf', 'Mode' => 'Read', 'FingerprintsStringMode' => 'AutoDetect');</div> <div class="OptionsBox"> $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fpf', 'Mode' => 'Write', 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'Overwrite' => 1, 'BitStringFormat' => 'HexadecimalString', 'BitsOrder' => 'Ascending');</div> <div class="OptionsBox"> $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( 'Name' => 'Sample.fp', 'Mode' => 'Write', 'FingerprintsStringMode' => 'FingerprintsVectorString', 'Overwrite' => 1, 'VectorStringFormat' => 'IDsAndValuesString');</div> </dd> <dt><strong><a name="getfingerprints" class="item"><strong>GetFingerprints</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsObject = $FingerprintsFPFileIO->GetFingerprints();</div> <p>Returns <strong>FingerprintsObject</strong> generated for current data line using fingerprints bit-vector or vector string data. The fingerprints object corresponds to any of the supported fingerprints such as PathLengthFingerprints, ExtendedConnectivity, and so on.</p> </dd> <dt><strong><a name="getfingerprintsstring" class="item"><strong>GetFingerprintsString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsString = $FingerprintsFPFileIO->GetFingerprintsString();</div> <p>Returns <strong>FingerprintsString</strong> for current data line.</p> </dd> <dt><strong><a name="getheaderdatakeyvalue" class="item"><strong>GetHeaderDataKeyValue</strong></a></strong></dt> <dd> <div class="OptionsBox"> $KeyValue = $FingerprintsFPFileIO->GetHeaderDataKeyValue($Key);</div> <p>Returns <strong>KeyValue</strong> of a data header <em>Key</em>.</p> </dd> <dt><strong><a name="getheaderdatakeys" class="item"><strong>GetHeaderDataKeys</strong></a></strong></dt> <dd> <div class="OptionsBox"> @Keys = $FingerprintsFPFileIO->GetHeaderDataKeys(); <br/> $NumOfKeys = $FingerprintsFPFileIO->GetHeaderDataKeys();</div> <p>Returns an array of data header <strong>Keys</strong> retrieved from data header section of fingerprints file. In scalar context, it returns number of keys.</p> </dd> <dt><strong><a name="getheaderdatakeysandvalues" class="item"><strong>GetHeaderDataKeysAndValues</strong></a></strong></dt> <dd> <div class="OptionsBox"> %KeysAndValues = $FingerprintsFPFileIO->GetHeaderDataKeysAndValues();</div> <p>Returns a hash of data header keys and values retrieved from data header section of fingerprints file.</p> </dd> <dt><strong><a name="getpartialfingerprintsstring" class="item"><strong>GetPartialFingerprintsString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsString = $FingerprintsFPFileIO->GetPartialFingerprintsString();</div> <p>Returns partial <strong>FingerprintsString</strong> for current data line. It corresponds to fingerprints string specified present in a line.</p> </dd> <dt><strong><a name="getrequiredheaderdatakeys" class="item"><strong>GetRequiredHeaderDataKeys</strong></a></strong></dt> <dd> <div class="OptionsBox"> @Keys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys(); <br/> $NumOfKeys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();</div> <p>Returns an array of required data header <strong>Keys</strong> for a fingerprints file containing bit-vector or vector strings data. In scalar context, it returns number of keys.</p> </dd> <dt><strong><a name="getrequiredheaderdatakeysandvalues" class="item"><strong>GetRequiredHeaderDataKeysAndValues</strong></a></strong></dt> <dd> <div class="OptionsBox"> %KeysAndValues = $FingerprintsFPFileIO-> GetRequiredHeaderDataKeysAndValues();</div> <p>Returns a hash of required data header keys and values for a fingerprints file containing bit-vector or vector strings data</p> </dd> <dt><strong><a name="isfingerprintsdatavalid" class="item"><strong>IsFingerprintsDataValid</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $FingerprintsFPFileIO->IsFingerprintsDataValid();</div> <p>Returns 1 or 0 based on whether <strong>FingerprintsObject</strong> is valid.</p> </dd> <dt><strong><a name="isfingerprintsfpfile" class="item"><strong>IsFingerprintsFPFile</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $FingerprintsFPFileIO->IsFingerprintsFPFile($FileName); <br/> $Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName);</div> <p>Returns 1 or 0 based on whether <em>FileName</em> is a FP file.</p> </dd> <dt><strong><a name="isfingerprintsfiledatavalid" class="item"><strong>IsFingerprintsFileDataValid</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $FingerprintsFPFileIO->IsFingerprintsFileDataValid();</div> <p>Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.</p> </dd> <dt><strong><a name="isheaderdatakeypresent" class="item"><strong>IsHeaderDataKeyPresent</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $FingerprintsFPFileIO->IsHeaderDataKeyPresent($Key);</div> <p>Returns 1 or 0 based on whether data header <em>Key</em> is present in data header section of a FP file.</p> </dd> <dt><strong><a name="next_or_read" class="item"><strong>Next or Read</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO = $FingerprintsFPFileIO->Next(); <br/> $FingerprintsFPFileIO = $FingerprintsFPFileIO->Read();</div> <p>Reads next available fingerprints line in FP file, processes the data, generates appropriate fingerprints object, and returns <strong>FingerprintsFPFileIO</strong>. The generated fingerprints object is available using method <strong>GetFingerprints</strong>.</p> </dd> <dt><strong><a name="setbitstringformat" class="item"><strong>SetBitStringFormat</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetBitStringFormat($Format);</div> <p>Sets bit string <em>Format</em> for fingerprints bit-vector string data in a FP file and returns <strong>FingerprintsFPFileIO</strong>. Possible values for <strong>BitStringFormat</strong>: <em>BinaryString or HexadecimalString</em>.</p> </dd> <dt><strong><a name="setbitsorder" class="item"><strong>SetBitsOrder</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetBitsOrder($BitsOrder);</div> <p>Sets <em>BitsOrder</em> for fingerprints bit-vector string data in a FP file and returns <strong>FingerprintsFPFileIO</strong>. Possible values for <strong>BitsOrder</strong>: <em>Ascending or Descending</em>.</p> </dd> <dt><strong><a name="setcompoundid" class="item"><strong>SetCompoundID</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetCompoundID($ID);</div> <p>Sets compound ID for current data line and returns <strong>FingerprintsFPFileIO</strong>. Spaces are not allowed in compound IDs.</p> </dd> <dt><strong><a name="setdetaillevel" class="item"><strong>SetDetailLevel</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetDetailLevel($Level);</div> <p>Sets details <em>Level</em> for generating diagnostics messages during FP file processing and returns <strong>FingerprintsFPFileIO</strong>. Possible values: <em>Positive integers</em>.</p> </dd> <dt><strong><a name="setfingerprints" class="item"><strong>SetFingerprints</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetFingerprints($FingerprintsObject);</div> <p>Sets <em>FingerprintsObject</em> for current data line and returns <strong>FingerprintsFPFileIO</strong>.</p> </dd> <dt><strong><a name="setfingerprintsstring" class="item"><strong>SetFingerprintsString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetFingerprintsString($FingerprintsString);</div> <p>Sets <em>FingerprintsString</em> for current data line and returns <strong>FingerprintsFPFileIO</strong>.</p> </dd> <dt><strong><a name="setfingerprintsstringmode" class="item"><strong>SetFingerprintsStringMode</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetFingerprintsStringMode($Mode);</div> <p>Sets <em>FingerprintsStringMode</em> for FP file and returns <strong>FingerprintsFPFileIO</strong>. Possible values: <em>AutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString</em></p> </dd> <dt><strong><a name="setpartialfingerprintsstring" class="item"><strong>SetPartialFingerprintsString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetPartialFingerprintsString($PartialString);</div> <p>Sets <em>PartialFingerprintsString</em> for current data line and returns <strong>FingerprintsFPFileIO</strong>.</p> </dd> <dt><strong><a name="setvectorstringformat" class="item"><strong>SetVectorStringFormat</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->SetVectorStringFormat($Format);</div> <p>Sets <em>VectorStringFormat</em> for FP file and returns <strong>FingerprintsFPFileIO</strong>. Possible values: <em>IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p> </dd> <dt><strong><a name="writefingerprints" class="item"><strong>WriteFingerprints</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject, $CompoundID);</div> <p>Writes fingerprints string generated from <em>FingerprintsObject</em> object and other data including <em>CompoundID</em> to FP file and returns <strong>FingerprintsFPFileIO</strong>.</p> </dd> <dt><strong><a name="writefingerprintsstring" class="item"><strong>WriteFingerprintsString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsFPFileIO->WriteFingerprints($FingerprintsString, $CompoundID);</div> <p>Writes <em>FingerprintsString</em> and other data including <em>CompoundID</em> to FP file and returns <strong>FingerprintsFPFileIO</strong>.</p> <p>Caveats:</p> <div class="OptionsBox"> o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat values are ignored during writing of fingerprints and it's written to the file as it is. <br/> o FingerprintsString is a regular fingerprints string as oppose to a partial fingerprints string.</div> </dd> </dl> <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="./FingerprintsSDFileIO.html">FingerprintsSDFileIO.pm</a>, <a href="./FingerprintsTextFileIO.html">FingerprintsTextFileIO.pm</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="./FileIO.html" title="FileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsSDFileIO.html" title="FingerprintsSDFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>FileIO::FingerprintsFPFileIO.pm</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>