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diff lib/Fingerprints/FingerprintsFileUtil.pm @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/Fingerprints/FingerprintsFileUtil.pm Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,536 @@ +package Fingerprints::FingerprintsFileUtil; +# +# $RCSfile: FingerprintsFileUtil.pm,v $ +# $Date: 2015/02/28 20:48:54 $ +# $Revision: 1.14 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# Copyright (C) 2015 Manish Sud. All rights reserved. +# +# This file is part of MayaChemTools. +# +# 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. +# +# MayaChemTools is distributed in the hope that it will be useful, but without +# any warranty; without even the implied warranty of merchantability of fitness +# for a particular purpose. See the GNU Lesser General Public License for more +# details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or +# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, +# Boston, MA, 02111-1307, USA. +# + +use strict; +use Exporter; +use Carp; +use TextUtil (); +use FileUtil (); +use FileIO::FingerprintsSDFileIO; +use FileIO::FingerprintsTextFileIO; +use FileIO::FingerprintsFPFileIO; + +use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); + +@ISA = qw(Exporter); +@EXPORT = qw(); +@EXPORT_OK = qw(GetFingerprintsFileType ReadAndProcessFingerpritsData NewFingerprintsFileIO); + +%EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); + +# Generate new FingerprintsFileIO object for a SD, FP or Text fingerprints file specified using file name +# along other appropriate parameters... +# +sub NewFingerprintsFileIO { + my(%FingerprintsFileIOParams) = @_; + my($FingerprintsFileIO, $FileType); + + if (!(exists($FingerprintsFileIOParams{Name}) && TextUtil::IsNotEmpty($FingerprintsFileIOParams{Name}))) { + carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File name is not specified...\n"; + return undef; + } + + if (!(exists($FingerprintsFileIOParams{Mode}) && TextUtil::IsNotEmpty($FingerprintsFileIOParams{Mode}))) { + carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File mode is not specified...\n"; + return undef; + } + + $FileType = GetFingerprintsFileType($FingerprintsFileIOParams{Name}); + if (TextUtil::IsEmpty($FileType)) { + carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File type is not specified...\n"; + return undef; + } + + # Generate fingerprints IO object... + FILETYPE: { + if ($FileType =~ /^SD$/i) { + $FingerprintsFileIO = new FileIO::FingerprintsSDFileIO(%FingerprintsFileIOParams); + last FILETYPE; + } + if ($FileType =~ /^FP$/i) { + $FingerprintsFileIO = new FileIO::FingerprintsFPFileIO(%FingerprintsFileIOParams); + last FILETYPE; + } + if ($FileType =~ /^Text$/i) { + $FingerprintsFileIO = new FileIO::FingerprintsTextFileIO(%FingerprintsFileIOParams); + last FILETYPE; + } + $FingerprintsFileIO = undef; + carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"; + } + + return $FingerprintsFileIO; +} + +# Get fingerpritns file type from fingerprints file name... +# +sub GetFingerprintsFileType { + my($FileName) = @_; + my($FileType); + + $FileType = ''; + FILETYPE: { + if (FileUtil::CheckFileType($FileName, "sdf sd")) { + $FileType = 'SD'; + last FILETYPE; + } + if (FileUtil::CheckFileType($FileName, "fpf fp")) { + $FileType = 'FP'; + last FILETYPE; + } + if (FileUtil::CheckFileType($FileName, "csv tsv")) { + $FileType = 'Text'; + last FILETYPE; + } + $FileType = ''; + carp "Warning: Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType: Can't determine fingerprints file type for $FileName: It's not a fingerprints file...\n"; + } + + return $FileType; +} + + +# Process fingerprints bit-vector and vector string data in a file using FingerprintsFileIO +# object and return a references to arrays of CompoundIDs and FingerprintsObjects... +# +# Note: +# . The file open and close is automatically performed during processing. +# +sub ReadAndProcessFingerpritsData { + my($FingerprintsFileIO, $CheckCompoundIDs) = @_; + my($CompoundID, $FingerprintsCount, $IgnoredFingerprintsCount, @CompundIDs, @FingerprintsObjects, %UniqueCompoundIDs); + + if (!$FingerprintsFileIO) { + return (undef, undef); + } + $CheckCompoundIDs = defined $CheckCompoundIDs ? $CheckCompoundIDs : 0; + + print "\nReading and processing fingerprints data...\n"; + + ($FingerprintsCount, $IgnoredFingerprintsCount) = (0) x 3; + + @CompundIDs = (); + @FingerprintsObjects = (); + + %UniqueCompoundIDs = (); + + # Check and open file for reading... + if (!$FingerprintsFileIO->GetStatus()) { + $FingerprintsFileIO->Open(); + } + + FINGERPRINTS: while ($FingerprintsFileIO->Read()) { + $FingerprintsCount++; + + if (!$FingerprintsFileIO->IsFingerprintsDataValid()) { + $IgnoredFingerprintsCount++; + next FINGERPRINTS; + } + + if ($CheckCompoundIDs) { + $CompoundID = $FingerprintsFileIO->GetCompoundID(); + if (exists $UniqueCompoundIDs{$CompoundID}) { + warn "Warning: Ignoring fingerprints data for compound ID $CompoundID: Multiple entries for compound ID in fingerprints file.\n"; + $IgnoredFingerprintsCount++; + next FINGERPRINTS; + } + $UniqueCompoundIDs{$CompoundID} = $CompoundID; + } + + push @FingerprintsObjects, $FingerprintsFileIO->GetFingerprints(); + push @CompundIDs, $FingerprintsFileIO->GetCompoundID(); + } + $FingerprintsFileIO->Close(); + + print "Number of fingerprints data entries: $FingerprintsCount\n"; + print "Number of fingerprints date entries processed successfully: ", ($FingerprintsCount - $IgnoredFingerprintsCount) , "\n"; + print "Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"; + + return (\@CompundIDs, \@FingerprintsObjects); +} + + +1; + +__END__ + +=head1 NAME + +FingerprintsFileUtil + +=head1 SYNOPSIS + +use Fingerprints::FingerprintsFileUtil; + +use Fingerprints::FingerprintsFileUtil qw(:all); + +=head1 DESCRIPTION + +B<FingerprintsFileUtil> module provides the following functions: + +GetFingerprintsFileType, NewFingerprintsFileIO, ReadAndProcessFingerpritsData + +B<FingerprintsFileUtil> module provides function to handle fingerprints data strings +in FP, SD and CSV/TSV text files present in one of the following two types: fingerprints +bit-vectors and fingerprints vector strings + +Example of B<FP> file format containing fingerprints bit-vector string data: + + # + # Package = MayaChemTools 7.4 + # ReleaseDate = Oct 21, 2010 + # + # TimeStamp = Mon Mar 7 15:14:01 2011 + # + # FingerprintsStringType = FingerprintsBitVector + # + # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... + # Size = 1024 + # BitStringFormat = HexadecimalString + # BitsOrder = Ascending + # + Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... + Cmpd2 000000249400840040100042011001001980410c000000001010088001120... + ... ... + ... .. + +Example of B<FP> file format containing fingerprints vector string data: + + # + # Package = MayaChemTools 7.4 + # ReleaseDate = Oct 21, 2010 + # + # TimeStamp = Mon Mar 7 15:14:01 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + 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: + 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...; + 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 + 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 ... + 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 + O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...; + 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 + 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 ... + ... ... + ... ... + +Example of B<SD> file format containing fingerprints vector string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Test + + > <PathLengthFingerprints> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt + h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 + 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 + 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 + 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a + aa0660a11014a011d46 + + $$$$ + ... ... + ... ... + +Example of CSV B<text> file format containing fingerprints bit-vector string data: + + "CompoundID","PathLengthFingerprints" + "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes + :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 + 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 + 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." + ... ... + ... ... + +The current release of MayaChemTools supports the following types of fingerprint +bit-vector and vector strings: + + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi + us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT + C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X + 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A + TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 + -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B... + + FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS + ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 + .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 + O.X1.BO2;2 4 14 3 10 1 1 1 3 2 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume + ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F + N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN + umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C + 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N + 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 + 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 + 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... + + FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs + AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN + H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 + .024 -2.270 + + FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; + ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 + 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 + 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 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi + us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 + 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 + 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 + 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 + 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303... + + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes + :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 + 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 + 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; + 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 + 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 + + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp + es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 + 0000000001010000000110000011000000000000100000000000000000000000100001 + 1000000110000000000000000000000000010011000000000000000000000000010000 + 0000000000000000000000000010000000000000000001000000000000000000000000 + 0000000000010000100001000000000000101000000000000000100000000000000... + + FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu + s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 + 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 + 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 + 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 + 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404... + + FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp + haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 + 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 + 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 + 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 + 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566... + + FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 + 0000000000000000000000000000000001001000010010000000010010000000011100 + 0100101010111100011011000100110110000011011110100110111111111111011111 + 11111111111110111000 + + FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 + 1110011111100101111111000111101100110000000000000011100010000000000000 + 0000000000000000000000000000000000000000000000101000000000000000000000 + 0000000000000000000000000000000000000000000000000000000000000000000000 + 0000000000000000000000000000000000000011000000000000000000000000000000 + 0000000000000000000000000000000000000000 + + FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri + 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 + 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 + 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 + 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 + 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 + + FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri + 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 + 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 + 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 + 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 + 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 ... + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 + 0100010101011000101001011100110001000010001001101000001001001001001000 + 0010110100000111001001000001001010100100100000000011000000101001011100 + 0010000001000101010100000100111100110111011011011000000010110111001101 + 0101100011000000010001000011000010100011101100001000001000100000000... + + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength + 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 + 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 + 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 + 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO + 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... + + FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt + h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 + 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 + 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 + CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR + OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... + + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD + istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 + .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. + H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; + 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 + 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... + + FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi + stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar + Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H + BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; + 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 + 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 ... + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- + C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO + 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; + 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 + + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica + lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC + H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- + ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; + 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 + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 + .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 + 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 + -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; + 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 + 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... + + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 + :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C + .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- + 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 + -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. + 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... + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + 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 + BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; + 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 + 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 + 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 + 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 + 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 + 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... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 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 + 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 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 + 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 + 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 + 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 + 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 ... + +=head1 FUNCTIONS + +=over 4 + +=item B<GetFingerprintsFileType> + + $FileType = GetFingerprintsFileType($FileName); + +Returns fingerprints B<FileType> of I<FileName> determined using extension of file name. +Possible B<FileType> values: I<FP, SD, Text>. Supported file name extensions for various +file types are: B<FP> - I<fpf, fp>; B<SD> - I<sdf, sd>; B<Text> - I<csv, tsv>. + +=item B<NewFingerprintsFileIO> + + $FingerprintsFileIO = NewFingerprintsFileIO(%IOParameters); + +Using specified I<IOParameters> property names and values hash, B<NewFingerprintsFileIO> +method creates a new object using appropriate fingerprints file IO class - B<FingerprintsFPFileIO, +FingerprintsSDFileIO, or FingerprintsTextFileIO> - and returns a reference to a newly created +B<FingerprintsFileIO> object. + +The I<IOParameters> hash must contain I<Name> and I<Mode> as key/value pairs to create +a new B<FingerprintsFileIO> object. + +Based on type of file - B<FP, SD or Text> - B<NewFingerprintsFileIO> use B<new> method +from appropriate class - B<FingerprintsFPFileIO> - along with I<IOParameters> to create +B<FingerprintsFileIO> object. + +=item B<ReadAndProcessFingerpritsData> + + ($CompoundIDsRef, $FingerprintsObjectRef) = + ReadAndProcessFingerpritsData($FingerprintsFileIO); + +Processes fingerprints bit-vector and vector string data in a file using I<FingerprintsFileIO> +object and returns a references to arrays of B<CompoundIDs> and I<FingerprintsObjects>. + +The file open and close is automatically performed during processing. + +=back + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +FingerprintsFPFileIO.pm, FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +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. + +=cut