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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

SEE ALSO

FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm

COPYRIGHT

Copyright (C) 2019 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.

 

 

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