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diff mayachemtools/docs/modules/man3/FingerprintsSDFileIO.3 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
|---|---|
| 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/FingerprintsSDFileIO.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,622 @@ +.\" 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++. Capital omega is used to do unbreakable dashes and +.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, +.\" nothing in troff, for use with C<>. +.tr \(*W- +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" Escape single quotes in literal strings from groff's Unicode transform. +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.ie \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.el \{\ +. de IX +.. +.\} +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.rm #[ #] #H #V #F C +.\" ======================================================================== +.\" +.IX Title "FINGERPRINTSSDFILEIO 1" +.TH FINGERPRINTSSDFILEIO 1 "2015-03-29" "perl v5.14.2" "MayaChemTools" +.\" For nroff, turn off justification. Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +FingerprintsSDFileIO +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use FileIO::FingerprintsSDFileIO; +.PP +use FileIO::FingerprintsSDFileIO qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBFingerprintsSDFileIO\fR class provides the following methods: +.PP +new, GetCompoundString, GetFingerprints, GetFingerprintsString, +IsFingerprintsDataValid, IsFingerprintsFileDataValid, IsFingerprintsSDFile, Next, +Read, SetBitStringFormat, SetBitsOrder, SetCompoundIDMode, SetCompoundString, +SetDetailLevel, SetFingerprints, SetFingerprintsString, SetFingerprintsStringMode, +SetVectorStringFormat, WriteFingerprints, WriteFingerprintsString +.PP +The following methods can also be used as functions: +.PP +IsFingerprintsSDFile +.PP +\&\fBFingerprintsSDFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support +generic file related functionality. +.PP +The fingerprints \s-1SD\s0 file format with \fB.sdf\fR or \fB.sd\fR file extensions supports two types of +fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The fingerprints +string data is treated as value of a fingerprints data field label in a \s-1SD\s0 file. +.PP +Example of \s-1SD\s0 file format containing fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Test +\& +\& > <PathLengthFingerprints> +\& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt +\& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 +\& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 +\& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 +\& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a +\& aa0660a11014a011d46 +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.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 +\& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%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 \fBFingerprintsSDFileIO\fR object. By default, +the following properties are initialized during \fIRead\fR mode: +.Sp +.Vb 10 +\& Name = \*(Aq\*(Aq; +\& Mode = \*(AqRead\*(Aq; +\& Status = 0; +\& FingerprintsStringMode = \*(AqAutoDetect\*(Aq; +\& FingerprintsFieldLabel = \*(AqAutoDetect\*(Aq; +\& CompoundIDMode = \*(AqLabelPrefix\*(Aq; +\& CompoundIDFieldLabel = undef; +\& CompoundIDPrefix = \*(AqCmpd\*(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 3 +\& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO( +\& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq, +\& \*(AqMode\*(Aq => \*(AqRead\*(Aq); +\& +\& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO( +\& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq, +\& \*(AqMode\*(Aq => \*(AqRead\*(Aq,; +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqAutoDetect\*(Aq, +\& \*(AqFingerprintsFieldLabel\*(Aq => +\& \*(AqFingerprints\*(Aq, +\& \*(AqCompoundIDMode\*(Aq => +\& \*(AqDataField\*(Aq, +\& \*(AqCompoundIDFieldLabel\*(Aq => +\& \*(AqCompoundID\*(Aq); +\& +\& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO( +\& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq, +\& \*(AqMode\*(Aq => \*(AqWrite\*(Aq, +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqFingerprintsBitVectorString\*(Aq, +\& \*(AqOverwrite\*(Aq => 1, +\& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq, +\& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq); +\& +\& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO( +\& \*(AqName\*(Aq => \*(AqSample.sd\*(Aq, +\& \*(AqMode\*(Aq => \*(AqWrite\*(Aq, +\& \*(AqFingerprintsStringMode\*(Aq => +\& \*(AqFingerprintsVectorString\*(Aq, +\& \*(AqOverwrite\*(Aq => 1, +\& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq, +\& \*(AqFingerprintsLabel\*(Aq => \*(AqFingerprints\*(Aq); +.Ve +.IP "\fBGetCompoundString\fR" 4 +.IX Item "GetCompoundString" +.Vb 1 +\& $CompoundString = $FingerprintsSDFileIO\->GetCompoundString(); +.Ve +.Sp +Returns \fBCompoundString\fR for current compound. +.IP "\fBGetFingerprints\fR" 4 +.IX Item "GetFingerprints" +.Vb 1 +\& $FingerprintsObject = $FingerprintsSDFileIO\->GetFingerprints(); +.Ve +.Sp +Returns \fBFingerprintsObject\fR generated for current compound 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 = $FingerprintsSDFileIO\->GetFingerprintsString(); +.Ve +.Sp +Returns \fBFingerprintsString\fR for current compound. +.IP "\fBIsFingerprintsDataValid\fR" 4 +.IX Item "IsFingerprintsDataValid" +.Vb 1 +\& $Status = $FingerprintsSDFileIO\->IsFingerprintsDataValid(); +.Ve +.Sp +Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid. +.IP "\fBIsFingerprintsFileDataValid\fR" 4 +.IX Item "IsFingerprintsFileDataValid" +.Vb 1 +\& $Status = $FingerprintsSDFileIO\->IsFingerprintsFileDataValid(); +.Ve +.Sp +Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data. +.IP "\fBIsFingerprintsSDFile\fR" 4 +.IX Item "IsFingerprintsSDFile" +.Vb 2 +\& $Status = $FingerprintsSDFileIO\->IsFingerprintsSDFile($FileName); +\& $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName); +.Ve +.Sp +Returns 1 or 0 based on whether \fIFileName\fR is a \s-1SD\s0 file. +.IP "\fBNext or Read\fR" 4 +.IX Item "Next or Read" +.Vb 2 +\& $FingerprintsSDFileIO = $FingerprintsSDFileIO\->Next(); +\& $FingerprintsSDFileIO = $FingerprintsSDFileIO\->Read(); +.Ve +.Sp +Reads next available compound fingerprints in \s-1SD\s0 file, processes the data, generates appropriate +fingerprints object, and returns \fBFingerprintsSDFileIO\fR. The generated fingerprints object is available +using method \fBGetFingerprints\fR. +.IP "\fBSetBitStringFormat\fR" 4 +.IX Item "SetBitStringFormat" +.Vb 1 +\& $FingerprintsSDFileIO\->SetBitStringFormat($Format); +.Ve +.Sp +Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR. +Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR. +.IP "\fBSetBitsOrder\fR" 4 +.IX Item "SetBitsOrder" +.Vb 1 +\& $FingerprintsSDFileIO\->SetBitsOrder($BitsOrder); +.Ve +.Sp +Sets \fIBitsOrder\fR for fingerprints bit-vector string data in \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR. +Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR. +.IP "\fBSetCompoundIDMode\fR" 4 +.IX Item "SetCompoundIDMode" +.Vb 1 +\& $FingerprintsSDFileIO\->SetCompoundIDMode($Mode); +.Ve +.Sp +Sets compound \s-1ID\s0 \fIMode\fR for fingerprints bit-vector string data in a \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR. +Possible values for \fBCompoundIDMode\fR: \fIDataField, MolName, LabelPrefix, or MolNameOrLabelPrefix\fR. +.IP "\fBSetCompoundString\fR" 4 +.IX Item "SetCompoundString" +.Vb 1 +\& $FingerprintsSDFileIO\->SetCompoundString($CompoundString); +.Ve +.Sp +Sets \fICompoundString\fR and returns \fBFingerprintsSDFileIO\fR. +.IP "\fBSetDetailLevel\fR" 4 +.IX Item "SetDetailLevel" +.Vb 1 +\& $FingerprintsSDFileIO\->SetDetailLevel($Level); +.Ve +.Sp +Sets details \fILevel\fR for generating diagnostics messages during \s-1SD\s0 file processing and returns +\&\fBFingerprintsSDFileIO\fR. Possible values: \fIPositive integers\fR. +.IP "\fBSetFingerprints\fR" 4 +.IX Item "SetFingerprints" +.Vb 1 +\& $FingerprintsSDFileIO\->SetFingerprints($FingerprintsObject); +.Ve +.Sp +Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsSDFileIO\fR. +.IP "\fBSetFingerprintsString\fR" 4 +.IX Item "SetFingerprintsString" +.Vb 1 +\& $FingerprintsSDFileIO\->SetFingerprintsString($FingerprintsString); +.Ve +.Sp +Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsSDFileIO\fR. +.IP "\fBSetFingerprintsStringMode\fR" 4 +.IX Item "SetFingerprintsStringMode" +.Vb 1 +\& $FingerprintsSDFileIO\->SetFingerprintsStringMode($Mode); +.Ve +.Sp +Sets \fIFingerprintsStringMode\fR for \s-1SD\s0 file and returns \fBFingerprintsFPFileIO\fR. +Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR +.IP "\fBSetVectorStringFormat\fR" 4 +.IX Item "SetVectorStringFormat" +.Vb 1 +\& $FingerprintsSDFileIO\->SetVectorStringFormat($Format); +.Ve +.Sp +Sets \fIVectorStringFormat\fR for \s-1SD\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-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR. +.IP "\fBWriteFingerprintsString\fR" 4 +.IX Item "WriteFingerprintsString" +.Vb 2 +\& $FingerprintsSDFileIO\->WriteFingerprints($FingerprintsString, +\& $CompoundID); +.Ve +.Sp +Writes \fIFingerprintsString\fR and other data including \fICompoundID\fR to \s-1SD\s0 file and returns +\&\fBFingerprintsSDFileIO\fR. +.Sp +Caveats: +.Sp +.Vb 4 +\& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat +\& values are ignored during writing of fingerprints and it\*(Aqs written to the file +\& as it is. +\& o CompoundString is not checked to remove any existing fingerprints data +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +FingerprintsTextFileIO.pm, FingerprintsFPFileIO.pm, SDFileIO.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.