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diff mayachemtools/docs/modules/man3/FingerprintsFPFileIO.3 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/FingerprintsFPFileIO.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,794 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +FingerprintsFPFileIO +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use FileIO::FingerprintsFPFileIO; +.PP +use FileIO::FingerprintsFPFileIO qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBFingerprintsFPFileIO\fR class provides the following methods: +.PP +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 +.PP +The following methods can also be used as functions: +.PP +IsFingerprintsFPFile +.PP +\&\fBFingerprintsFPFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support +generic file related functionality. +.PP +The MayaChemTools fingerprints file (\s-1FP\s0) format with \fB.fpf\fR or \fB.fp\fR file extensions supports +two types of fingerprints data: fingerprints bit-vectors and fingerprints vectors. +.PP +Example of \s-1FP\s0 file format containing fingerprints bit-vector string data: +.PP +.Vb 10 +\& # +\& # 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... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1FP\s0 file format containing fingerprints vector string data: +.PP +.Vb 10 +\& # +\& # 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 ... +\& ... ... +\& ... ... +.Ve +.PP +\&\fB\s-1FP\s0\fR 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. +.PP +The key = value data specification in the header section and its processing follows these +rules: +.PP +.Vb 3 +\& 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 +.Ve +.PP +The default optional header data section key = value pairs are: +.PP +.Vb 2 +\& # Package = MayaChemTools 7.4 +\& # ReleaseDate = Oct 21, 2010 +.Ve +.PP +The \fBFingerprintsStringType\fR key is required data header key for both fingerprints bit-vector +and vector strings. Possible key values: \fIFingerprintsBitVector or FingerprintsVector\fR. +For example: +.PP +.Vb 1 +\& # FingerprintsStringType = FingerprintsBitVector +.Ve +.PP +The required data header keys for fingerprints bit-vector string are: \fBDescription, Size, +BitStringFormat, and BitsOrder\fR. Possible values for \fBBitStringFormat\fR: \fIHexadecimalString +or BinaryString\fR. Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR. The \fBDescription\fR +key contains information about various parameters used to generate fingerprints bit-vector +string. The \fBSize\fR 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: +.PP +.Vb 4 +\& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... +\& # Size = 1024 +\& # BitStringFormat = HexadecimalString +\& # BitsOrder = Ascending +.Ve +.PP +The required data header keys for fingerprints vector string are: \fBDescription, VectorStringFormat, +and VectorValuesType\fR. Possible values for \fBVectorStringFormat\fR: \fIDsAndValuesString, +IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString\fR. +Possible values for \fBVectorValuesType\fR: \fINumericalValues, OrderedNumericalValues or +AlphaNumericalValues\fR. The \fBDescription\fR keys contains information various parameters used +to generate fingerprints vector string. For example: +.PP +.Vb 3 +\& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... +\& # VectorStringFormat = IDsAndValuesString +\& # VectorValuesType = NumericalValues +.Ve +.PP +The fingerprints data section for fingerprints bit-vector string contains data in the following +format: +.PP +.Vb 3 +\& ... ... +\& CmpdID FingerprintsPartialBitVectorString +\& ... ... +.Ve +.PP +For example: +.PP +.Vb 3 +\& ... ... +\& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... +\& ... ... +.Ve +.PP +The fingerprints data section for fingerprints vector string contains data in the following +format: +.PP +.Vb 3 +\& ... ... +\& CmpdID Size;FingerprintsPartialVectorString +\& ... ... +.Ve +.PP +For example: +.PP +.Vb 6 +\& ... ... +\& 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 ... +\& ... ... +.Ve +.PP +Unlike fingerprints bit-vector string, \fISize\fR is specified for each partial fingerprints vector string: +It may change from molecule to molecule for same type of fingerprints. +.PP +Values IDs are optional for fingerprints vector string containing \fIOrderedNumericalValues or +AlphaNumericalValues\fR; however, they must be present for for \fINumericalValues\fR. Due to +various possible values for \fBVectorStringFormat\fR, the fingerprints data section for fingerprints +vector string supports following type of data formats: +.PP +.Vb 5 +\& 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 ... +.Ve +.PP +However, all the fingerprints vector string data present in \s-1FP\s0 file must correspond to only +one of the formats shown above; multiple data formats in the same file are not allowed. +.PP +The current release of MayaChemTools supports the following types of fingerprint +bit-vector and vector strings: +.PP +.Vb 6 +\& 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 ... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 1 +\& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters); +.Ve +.Sp +Using specified \fIIOParameters\fR names and values hash, \fBnew\fR method creates a new +object and returns a reference to a newly created \fBFingerprintsFPFileIO\fR object. By default, +the following properties are initialized during \fIRead\fR mode: +.Sp +.Vb 6 +\& Name = \*(Aq\*(Aq; +\& Mode = \*(AqRead\*(Aq; +\& Status = 0; +\& FingerprintsStringMode = \*(AqAutoDetect\*(Aq; +\& ValidateData = 1; +\& DetailLevel = 1; +.Ve +.Sp +During \fIWrite\fR mode, the following properties get initialize by default: +.Sp +.Vb 1 +\& FingerprintsStringMode = undef; +\& +\& BitStringFormat = HexadecimalString; +\& BitsOrder = Ascending; +\& +\& VectorStringFormat = NumericalValuesString or ValuesString; +.Ve +.Sp +Examples: +.Sp +.Vb 5 +\& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( +\& \*(AqName\*(Aq => \*(AqSample.fpf\*(Aq, +\& \*(AqMode\*(Aq => \*(AqRead\*(Aq, +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqAutoDetect\*(Aq); +\& +\& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( +\& \*(AqName\*(Aq => \*(AqSample.fpf\*(Aq, +\& \*(AqMode\*(Aq => \*(AqWrite\*(Aq, +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqFingerprintsBitVectorString\*(Aq, +\& \*(AqOverwrite\*(Aq => 1, +\& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq, +\& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq); +\& +\& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO( +\& \*(AqName\*(Aq => \*(AqSample.fp\*(Aq, +\& \*(AqMode\*(Aq => \*(AqWrite\*(Aq, +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqFingerprintsVectorString\*(Aq, +\& \*(AqOverwrite\*(Aq => 1, +\& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq); +.Ve +.IP "\fBGetFingerprints\fR" 4 +.IX Item "GetFingerprints" +.Vb 1 +\& $FingerprintsObject = $FingerprintsFPFileIO\->GetFingerprints(); +.Ve +.Sp +Returns \fBFingerprintsObject\fR 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. +.IP "\fBGetFingerprintsString\fR" 4 +.IX Item "GetFingerprintsString" +.Vb 1 +\& $FingerprintsString = $FingerprintsFPFileIO\->GetFingerprintsString(); +.Ve +.Sp +Returns \fBFingerprintsString\fR for current data line. +.IP "\fBGetHeaderDataKeyValue\fR" 4 +.IX Item "GetHeaderDataKeyValue" +.Vb 1 +\& $KeyValue = $FingerprintsFPFileIO\->GetHeaderDataKeyValue($Key); +.Ve +.Sp +Returns \fBKeyValue\fR of a data header \fIKey\fR. +.IP "\fBGetHeaderDataKeys\fR" 4 +.IX Item "GetHeaderDataKeys" +.Vb 2 +\& @Keys = $FingerprintsFPFileIO\->GetHeaderDataKeys(); +\& $NumOfKeys = $FingerprintsFPFileIO\->GetHeaderDataKeys(); +.Ve +.Sp +Returns an array of data header \fBKeys\fR retrieved from data header section of fingerprints +file. In scalar context, it returns number of keys. +.IP "\fBGetHeaderDataKeysAndValues\fR" 4 +.IX Item "GetHeaderDataKeysAndValues" +.Vb 1 +\& %KeysAndValues = $FingerprintsFPFileIO\->GetHeaderDataKeysAndValues(); +.Ve +.Sp +Returns a hash of data header keys and values retrieved from data header section of fingerprints +file. +.IP "\fBGetPartialFingerprintsString\fR" 4 +.IX Item "GetPartialFingerprintsString" +.Vb 1 +\& $FingerprintsString = $FingerprintsFPFileIO\->GetPartialFingerprintsString(); +.Ve +.Sp +Returns partial \fBFingerprintsString\fR for current data line. It corresponds to fingerprints string +specified present in a line. +.IP "\fBGetRequiredHeaderDataKeys\fR" 4 +.IX Item "GetRequiredHeaderDataKeys" +.Vb 2 +\& @Keys = $FingerprintsFPFileIO\->GetRequiredHeaderDataKeys(); +\& $NumOfKeys = $FingerprintsFPFileIO\->GetRequiredHeaderDataKeys(); +.Ve +.Sp +Returns an array of required data header \fBKeys\fR for a fingerprints file containing bit-vector or +vector strings data. In scalar context, it returns number of keys. +.IP "\fBGetRequiredHeaderDataKeysAndValues\fR" 4 +.IX Item "GetRequiredHeaderDataKeysAndValues" +.Vb 2 +\& %KeysAndValues = $FingerprintsFPFileIO\-> +\& GetRequiredHeaderDataKeysAndValues(); +.Ve +.Sp +Returns a hash of required data header keys and values for a fingerprints file containing bit-vector or +vector strings data +.IP "\fBIsFingerprintsDataValid\fR" 4 +.IX Item "IsFingerprintsDataValid" +.Vb 1 +\& $Status = $FingerprintsFPFileIO\->IsFingerprintsDataValid(); +.Ve +.Sp +Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid. +.IP "\fBIsFingerprintsFPFile\fR" 4 +.IX Item "IsFingerprintsFPFile" +.Vb 2 +\& $Status = $FingerprintsFPFileIO\->IsFingerprintsFPFile($FileName); +\& $Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName); +.Ve +.Sp +Returns 1 or 0 based on whether \fIFileName\fR is a \s-1FP\s0 file. +.IP "\fBIsFingerprintsFileDataValid\fR" 4 +.IX Item "IsFingerprintsFileDataValid" +.Vb 1 +\& $Status = $FingerprintsFPFileIO\->IsFingerprintsFileDataValid(); +.Ve +.Sp +Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data. +.IP "\fBIsHeaderDataKeyPresent\fR" 4 +.IX Item "IsHeaderDataKeyPresent" +.Vb 1 +\& $Status = $FingerprintsFPFileIO\->IsHeaderDataKeyPresent($Key); +.Ve +.Sp +Returns 1 or 0 based on whether data header \fIKey\fR is present in data header +section of a \s-1FP\s0 file. +.IP "\fBNext or Read\fR" 4 +.IX Item "Next or Read" +.Vb 2 +\& $FingerprintsFPFileIO = $FingerprintsFPFileIO\->Next(); +\& $FingerprintsFPFileIO = $FingerprintsFPFileIO\->Read(); +.Ve +.Sp +Reads next available fingerprints line in \s-1FP\s0 file, processes the data, generates appropriate fingerprints +object, and returns \fBFingerprintsFPFileIO\fR. The generated fingerprints object is available using +method \fBGetFingerprints\fR. +.IP "\fBSetBitStringFormat\fR" 4 +.IX Item "SetBitStringFormat" +.Vb 1 +\& $FingerprintsFPFileIO\->SetBitStringFormat($Format); +.Ve +.Sp +Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. +Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR. +.IP "\fBSetBitsOrder\fR" 4 +.IX Item "SetBitsOrder" +.Vb 1 +\& $FingerprintsFPFileIO\->SetBitsOrder($BitsOrder); +.Ve +.Sp +Sets \fIBitsOrder\fR for fingerprints bit-vector string data in a \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. +Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR. +.IP "\fBSetCompoundID\fR" 4 +.IX Item "SetCompoundID" +.Vb 1 +\& $FingerprintsFPFileIO\->SetCompoundID($ID); +.Ve +.Sp +Sets compound \s-1ID\s0 for current data line and returns \fBFingerprintsFPFileIO\fR. Spaces are not allowed +in compound IDs. +.IP "\fBSetDetailLevel\fR" 4 +.IX Item "SetDetailLevel" +.Vb 1 +\& $FingerprintsFPFileIO\->SetDetailLevel($Level); +.Ve +.Sp +Sets details \fILevel\fR for generating diagnostics messages during \s-1FP\s0 file processing and returns +\&\fBFingerprintsFPFileIO\fR. Possible values: \fIPositive integers\fR. +.IP "\fBSetFingerprints\fR" 4 +.IX Item "SetFingerprints" +.Vb 1 +\& $FingerprintsFPFileIO\->SetFingerprints($FingerprintsObject); +.Ve +.Sp +Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsFPFileIO\fR. +.IP "\fBSetFingerprintsString\fR" 4 +.IX Item "SetFingerprintsString" +.Vb 1 +\& $FingerprintsFPFileIO\->SetFingerprintsString($FingerprintsString); +.Ve +.Sp +Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsFPFileIO\fR. +.IP "\fBSetFingerprintsStringMode\fR" 4 +.IX Item "SetFingerprintsStringMode" +.Vb 1 +\& $FingerprintsFPFileIO\->SetFingerprintsStringMode($Mode); +.Ve +.Sp +Sets \fIFingerprintsStringMode\fR for \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. +Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR +.IP "\fBSetPartialFingerprintsString\fR" 4 +.IX Item "SetPartialFingerprintsString" +.Vb 1 +\& $FingerprintsFPFileIO\->SetPartialFingerprintsString($PartialString); +.Ve +.Sp +Sets \fIPartialFingerprintsString\fR for current data line and returns \fBFingerprintsFPFileIO\fR. +.IP "\fBSetVectorStringFormat\fR" 4 +.IX Item "SetVectorStringFormat" +.Vb 1 +\& $FingerprintsFPFileIO\->SetVectorStringFormat($Format); +.Ve +.Sp +Sets \fIVectorStringFormat\fR for \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. Possible values: +\&\fIIDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR. +.IP "\fBWriteFingerprints\fR" 4 +.IX Item "WriteFingerprints" +.Vb 2 +\& $FingerprintsFPFileIO\->WriteFingerprints($FingerprintsObject, +\& $CompoundID); +.Ve +.Sp +Writes fingerprints string generated from \fIFingerprintsObject\fR object and other data including +\&\fICompoundID\fR to \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. +.IP "\fBWriteFingerprintsString\fR" 4 +.IX Item "WriteFingerprintsString" +.Vb 2 +\& $FingerprintsFPFileIO\->WriteFingerprints($FingerprintsString, +\& $CompoundID); +.Ve +.Sp +Writes \fIFingerprintsString\fR and other data including \fICompoundID\fR to \s-1FP\s0 file and returns +\&\fBFingerprintsFPFileIO\fR. +.Sp +Caveats: +.Sp +.Vb 5 +\& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat +\& values are ignored during writing of fingerprints and it\*(Aqs written to +\& the file as it is. +\& o FingerprintsString is a regular fingerprints string as oppose to a +\& partial fingerprints string. +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.