Mercurial > repos > deepakjadmin > mayatool3_test2

diff docs/modules/txt/FingerprintsFPFileIO.txt @ 0:4816e4a8ae95 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/modules/txt/FingerprintsFPFileIO.txt	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,607 @@
+NAME
+    FingerprintsFPFileIO
+
+SYNOPSIS
+    use FileIO::FingerprintsFPFileIO;
+
+    use FileIO::FingerprintsFPFileIO qw(:all);
+
+DESCRIPTION
+    FingerprintsFPFileIO class provides the following methods:
+
+    new, GetFingerprints, GetFingerprintsString, GetHeaderDataKeyValue,
+    GetHeaderDataKeys, GetHeaderDataKeysAndValues,
+    GetPartialFingerprintsString, GetRequiredHeaderDataKeys,
+    GetRequiredHeaderDataKeysAndValues, IsFingerprintsDataValid,
+    IsFingerprintsFPFile, IsFingerprintsFileDataValid,
+    IsHeaderDataKeyPresent, Next, Read, SetBitStringFormat, SetBitsOrder,
+    SetCompoundID, SetDetailLevel, SetFingerprints, SetFingerprintsString,
+    SetFingerprintsStringMode, SetPartialFingerprintsString,
+    SetVectorStringFormat, WriteFingerprints, WriteFingerprintsString
+
+    The following methods can also be used as functions:
+
+    IsFingerprintsFPFile
+
+    FingerprintsFPFileIO class is derived from *FileIO* class and uses its
+    methods to support generic file related functionality.
+
+    The MayaChemTools fingerprints file (FP) format with .fpf or .fp file
+    extensions supports two types of fingerprints data: fingerprints
+    bit-vectors and fingerprints vectors.
+
+    Example of 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 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 ...
+        ... ...
+        ... ...
+
+    FP 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.
+
+    The key = value data specification in the header section and its
+    processing follows these rules:
+
+        o Leading and trailing spaces for key = value pairs are ignored
+        o Key and value strings may contain spaces
+        o Multiple key = value pairs on a single are delimited by semicolon
+
+    The default optional header data section key = value pairs are:
+
+        # Package = MayaChemTools 7.4
+        # ReleaseDate = Oct 21, 2010
+
+    The FingerprintsStringType key is required data header key for both
+    fingerprints bit-vector and vector strings. Possible key values:
+    *FingerprintsBitVector or FingerprintsVector*. For example:
+
+        # FingerprintsStringType = FingerprintsBitVector
+
+    The required data header keys for fingerprints bit-vector string are:
+    Description, Size, BitStringFormat, and BitsOrder. Possible values for
+    BitStringFormat: *HexadecimalString or BinaryString*. Possible values
+    for BitsOrder: *Ascending or Descending*. The Description key contains
+    information about various parameters used to generate fingerprints
+    bit-vector string. The Size 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:
+
+        # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
+        # Size = 1024
+        # BitStringFormat = HexadecimalString
+        # BitsOrder = Ascending
+
+    The required data header keys for fingerprints vector string are:
+    Description, VectorStringFormat, and VectorValuesType. Possible values
+    for VectorStringFormat: *DsAndValuesString, IDsAndValuesPairsString,
+    ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString*. Possible
+    values for VectorValuesType: *NumericalValues, OrderedNumericalValues or
+    AlphaNumericalValues*. The Description keys contains information various
+    parameters used to generate fingerprints vector string. For example:
+
+        # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
+        # VectorStringFormat = IDsAndValuesString
+        # VectorValuesType = NumericalValues
+
+    The fingerprints data section for fingerprints bit-vector string
+    contains data in the following format:
+
+        ... ...
+        CmpdID FingerprintsPartialBitVectorString
+        ... ...
+
+    For example:
+
+        ... ...
+        Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
+        ... ...
+
+    The fingerprints data section for fingerprints vector string contains
+    data in the following format:
+
+        ... ...
+        CmpdID Size;FingerprintsPartialVectorString
+        ... ...
+
+    For example:
+
+        ... ...
+        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 ...
+        ... ...
+
+    Unlike fingerprints bit-vector string, *Size* is specified for each
+    partial fingerprints vector string: It may change from molecule to
+    molecule for same type of fingerprints.
+
+    Values IDs are optional for fingerprints vector string containing
+    *OrderedNumericalValues or AlphaNumericalValues*; however, they must be
+    present for for *NumericalValues*. Due to various possible values for
+    VectorStringFormat, the fingerprints data section for fingerprints
+    vector string supports following type of data formats:
+
+        CmpdID Size;ID1 ID2 ID3...;Value1 Value2 Value3...
+        CmpdID Size;ID1 Value1 ID2 Value2 ID3 Value3... ...
+        CmpdID Size;ValuesAndIDsString: Value1 Value2 Value3...;ID1 ID2 ID3...
+        CmpdID Size;ValuesAndIDsPairsString: Value1 ID1 Value2 ID2 Value3 ID3... ...
+        CmpdID Size;Value1 Value2 Value3 ...
+
+    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.
+
+    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 ...
+
+  METHODS
+    new
+            $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters);
+
+        Using specified *IOParameters* names and values hash, new method
+        creates a new object and returns a reference to a newly created
+        FingerprintsFPFileIO object. By default, the following properties
+        are initialized during *Read* mode:
+
+            Name = '';
+            Mode = 'Read';
+            Status = 0;
+            FingerprintsStringMode = 'AutoDetect';
+            ValidateData = 1;
+            DetailLevel = 1;
+
+        During *Write* mode, the following properties get initialize by
+        default:
+
+            FingerprintsStringMode = undef;
+
+            BitStringFormat = HexadecimalString;
+            BitsOrder = Ascending;
+
+            VectorStringFormat = NumericalValuesString or ValuesString;
+
+        Examples:
+
+            $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
+                                       'Name' => 'Sample.fpf',
+                                       'Mode' => 'Read',
+                                       'FingerprintsStringMode' =>
+                                               'AutoDetect');
+
+            $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
+                                       'Name' => 'Sample.fpf',
+                                       'Mode' => 'Write',
+                                       'FingerprintsStringMode' =>
+                                               'FingerprintsBitVectorString',
+                                       'Overwrite' => 1,
+                                       'BitStringFormat' => 'HexadecimalString',
+                                       'BitsOrder' => 'Ascending');
+
+            $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
+                                       'Name' => 'Sample.fp',
+                                       'Mode' => 'Write',
+                                       'FingerprintsStringMode' =>
+                                               'FingerprintsVectorString',
+                                       'Overwrite' => 1,
+                                       'VectorStringFormat' => 'IDsAndValuesString');
+
+    GetFingerprints
+            $FingerprintsObject = $FingerprintsFPFileIO->GetFingerprints();
+
+        Returns FingerprintsObject 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.
+
+    GetFingerprintsString
+            $FingerprintsString = $FingerprintsFPFileIO->GetFingerprintsString();
+
+        Returns FingerprintsString for current data line.
+
+    GetHeaderDataKeyValue
+            $KeyValue = $FingerprintsFPFileIO->GetHeaderDataKeyValue($Key);
+
+        Returns KeyValue of a data header *Key*.
+
+    GetHeaderDataKeys
+            @Keys = $FingerprintsFPFileIO->GetHeaderDataKeys();
+            $NumOfKeys = $FingerprintsFPFileIO->GetHeaderDataKeys();
+
+        Returns an array of data header Keys retrieved from data header
+        section of fingerprints file. In scalar context, it returns number
+        of keys.
+
+    GetHeaderDataKeysAndValues
+            %KeysAndValues = $FingerprintsFPFileIO->GetHeaderDataKeysAndValues();
+
+        Returns a hash of data header keys and values retrieved from data
+        header section of fingerprints file.
+
+    GetPartialFingerprintsString
+            $FingerprintsString = $FingerprintsFPFileIO->GetPartialFingerprintsString();
+
+        Returns partial FingerprintsString for current data line. It
+        corresponds to fingerprints string specified present in a line.
+
+    GetRequiredHeaderDataKeys
+            @Keys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();
+            $NumOfKeys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();
+
+        Returns an array of required data header Keys for a fingerprints
+        file containing bit-vector or vector strings data. In scalar
+        context, it returns number of keys.
+
+    GetRequiredHeaderDataKeysAndValues
+            %KeysAndValues = $FingerprintsFPFileIO->
+                             GetRequiredHeaderDataKeysAndValues();
+
+        Returns a hash of required data header keys and values for a
+        fingerprints file containing bit-vector or vector strings data
+
+    IsFingerprintsDataValid
+            $Status = $FingerprintsFPFileIO->IsFingerprintsDataValid();
+
+        Returns 1 or 0 based on whether FingerprintsObject is valid.
+
+    IsFingerprintsFPFile
+            $Status = $FingerprintsFPFileIO->IsFingerprintsFPFile($FileName);
+            $Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName);
+
+        Returns 1 or 0 based on whether *FileName* is a FP file.
+
+    IsFingerprintsFileDataValid
+            $Status = $FingerprintsFPFileIO->IsFingerprintsFileDataValid();
+
+        Returns 1 or 0 based on whether fingerprints file contains valid
+        fingerprints data.
+
+    IsHeaderDataKeyPresent
+            $Status = $FingerprintsFPFileIO->IsHeaderDataKeyPresent($Key);
+
+        Returns 1 or 0 based on whether data header *Key* is present in data
+        header section of a FP file.
+
+    Next or Read
+            $FingerprintsFPFileIO = $FingerprintsFPFileIO->Next();
+            $FingerprintsFPFileIO = $FingerprintsFPFileIO->Read();
+
+        Reads next available fingerprints line in FP file, processes the
+        data, generates appropriate fingerprints object, and returns
+        FingerprintsFPFileIO. The generated fingerprints object is available
+        using method GetFingerprints.
+
+    SetBitStringFormat
+            $FingerprintsFPFileIO->SetBitStringFormat($Format);
+
+        Sets bit string *Format* for fingerprints bit-vector string data in
+        a FP file and returns FingerprintsFPFileIO. Possible values for
+        BitStringFormat: *BinaryString or HexadecimalString*.
+
+    SetBitsOrder
+            $FingerprintsFPFileIO->SetBitsOrder($BitsOrder);
+
+        Sets *BitsOrder* for fingerprints bit-vector string data in a FP
+        file and returns FingerprintsFPFileIO. Possible values for
+        BitsOrder: *Ascending or Descending*.
+
+    SetCompoundID
+            $FingerprintsFPFileIO->SetCompoundID($ID);
+
+        Sets compound ID for current data line and returns
+        FingerprintsFPFileIO. Spaces are not allowed in compound IDs.
+
+    SetDetailLevel
+            $FingerprintsFPFileIO->SetDetailLevel($Level);
+
+        Sets details *Level* for generating diagnostics messages during FP
+        file processing and returns FingerprintsFPFileIO. Possible values:
+        *Positive integers*.
+
+    SetFingerprints
+            $FingerprintsFPFileIO->SetFingerprints($FingerprintsObject);
+
+        Sets *FingerprintsObject* for current data line and returns
+        FingerprintsFPFileIO.
+
+    SetFingerprintsString
+            $FingerprintsFPFileIO->SetFingerprintsString($FingerprintsString);
+
+        Sets *FingerprintsString* for current data line and returns
+        FingerprintsFPFileIO.
+
+    SetFingerprintsStringMode
+            $FingerprintsFPFileIO->SetFingerprintsStringMode($Mode);
+
+        Sets *FingerprintsStringMode* for FP file and returns
+        FingerprintsFPFileIO. Possible values: *AutoDetect,
+        FingerprintsBitVectorString, or FingerprintsVectorString*
+
+    SetPartialFingerprintsString
+            $FingerprintsFPFileIO->SetPartialFingerprintsString($PartialString);
+
+        Sets *PartialFingerprintsString* for current data line and returns
+        FingerprintsFPFileIO.
+
+    SetVectorStringFormat
+            $FingerprintsFPFileIO->SetVectorStringFormat($Format);
+
+        Sets *VectorStringFormat* for FP file and returns
+        FingerprintsFPFileIO. Possible values: *IDsAndValuesString,
+        IDsAndValuesPairsString, ValuesAndIDsString,
+        ValuesAndIDsPairsString*.
+
+    WriteFingerprints
+            $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
+                                                    $CompoundID);
+
+        Writes fingerprints string generated from *FingerprintsObject*
+        object and other data including *CompoundID* to FP file and returns
+        FingerprintsFPFileIO.
+
+    WriteFingerprintsString
+            $FingerprintsFPFileIO->WriteFingerprints($FingerprintsString,
+                                                    $CompoundID);
+
+        Writes *FingerprintsString* and other data including *CompoundID* to
+        FP file and returns FingerprintsFPFileIO.
+
+        Caveats:
+
+            o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
+              values are ignored during writing of fingerprints and it's written to
+              the file as it is.
+            o FingerprintsString is a regular fingerprints string as oppose to a
+              partial fingerprints string.
+
+AUTHOR
+    Manish Sud <msud@san.rr.com>
+
+SEE ALSO
+    FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
+
+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.
+