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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ExtendedConnectivityFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,967 @@ +.\" 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. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ExtendedConnectivityFingerprints.pl \- Generate extended connectivity fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ExtendedConnectivityFingerprints.pl SDFile(s)... +.PP +ExtendedConnectivityFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR] +[\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR] +[\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR] +[\fB\-\-BitsOrder\fR \fIAscending | Descending\fR] [\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR] +[\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR] +[\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR] +[\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR] +[\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] +[\fB\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits\fR] +[\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR] [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] +[\fB\-o, \-\-overwrite\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-size\fR \fInumber\fR] +[\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR] +[\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for \fISDFile(s)\fR and create appropriate +\&\s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to molecular fingerprints. +.PP +Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR +and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory +can be specified either by \fI*.sdf\fR or the current directory name. +.PP +The current release of MayaChemTools supports generation of extended connectivity fingerprints +corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on values specified for \fB\-a, \-\-AtomIdentifierType\fR, \fB\-\-AtomicInvariantsToUse\fR +and \fB\-\-FunctionalClassesToUse\fR, initial atom types are assigned to all non-hydrogen atoms in +a molecule and these atom types strings are converted into initial atom identifier integers using +\&\fBTextUtil::HashCode\fR function. The duplicate atom identifiers are removed. +.PP +For \fB\-n, \-\-NeighborhoodRadius\fR value of \fI0\fR, the initial set of unique atom identifiers comprises +the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen +atom up to specified \fB\-n, \-\-NeighborhoodRadius\fR value. For each non-hydrogen central atom +at a specific radius, its neighbors at next radius level along with their bond orders and previously +calculated atom identifiers are collected which in turn are used to generate a new integer +atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order +followed by atom identifiers to make these values graph invariant. +.PP +After integer atom identifiers have been generated for all non-hydrogen atoms at all specified +neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code +value generated using \fBTextUtil::HashCode\fR are tracked by keeping the atom identifiers at +lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified +radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures +used for generating atom identifier and keeping integer atom identifier with lowest value. +.PP +For \fIExtendedConnnectivity\fR value of fingerprints \fB\-m, \-\-mode\fR, the duplicate identifiers are +removed from the list and the unique atom identifiers constitute the extended connectivity +fingerprints of a molecule. +.PP +For \fIExtendedConnnectivityCount\fR value of fingerprints \fB\-m, \-\-mode\fR, the occurrence of each +unique atom identifiers appears is counted and the unique atom identifiers along with their +count constitute the extended connectivity fingerprints of a molecule. +.PP +For \fIExtendedConnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, the unique atom identifiers +are used as a random number seed to generate a random integer value between 0 and \fB\-\-Size\fR which +in turn is used to set corresponding bits in the fingerprint bit-vector string. +.PP +Example of \fI\s-1SD\s0\fR file containing extended connectivity fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <ExtendedConnectivityFingerprints> +\& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu +\& s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66 +\& 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087 +\& 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90 +\& 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853... +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing extended connectivity fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 14:43:57 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2 +\& # VectorStringFormat = ValuesString +\& # VectorValuesType = AlphaNumericalValues +\& # +\& Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432... +\& Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing extended connectivity fingerprints string data: +.PP +.Vb 8 +\& "CompoundID","ExtendedConnectivityFingerprints" +\& "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy +\& pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352 +\& 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 +\& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551 +\& 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..." +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of extended connectivity +fingerprints vector strings: +.PP +.Vb 6 +\& 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... +\& +\& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +\& es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803 +\& 0300000091000004000000020000100000000124008200020000000040020000000000 +\& 2080000000820040010020000000008040000000000080001000000000400000000000 +\& 4040000090000061010000000800200000000000001400000000020080000000000020 +\& 00008020200000408000 +\& +\& 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;ExtendedConnectivityCount:FunctionalClassAtomTypes: +\& Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039 +\& 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32 +\& 9205671 571109041 639579325 683993318 723853089 810600886 885767127...; +\& 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2 +\& 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1 +\& +\& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType +\& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 +\& 0000000001000100000000001000000000000000000000000000000000101000000010 +\& 0000001000000000010000000000000000000000000000000000000000000000000100 +\& 0000000000001000000000000001000000000001001000000000000000000000000000 +\& 0000000000000000100000000000001000000000000000000000000000000000000... +\& +\& FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A +\& lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822 +\& 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094 +\& 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076 +\& 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070 +\& 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ... +\& +\& 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... +\& +\& FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp +\& haNumericalValues;ValuesString;224051550 746527773 998750766 103704190 +\& 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20 +\& 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344 +\& 041929 581773587 638555787 692022098 811840536 929651561 936421792 988 +\& 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271... +\& +\& FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph +\& aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1 +\& 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654 +\& 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981 +\& 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6 +\& 41915747 679881756 721736571 794256218 908276640 992898760 10987549... +\& +\& FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph +\& aNumericalValues;ValuesString;199957044 313356892 455463968 465982819 +\& 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153 +\& 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906 +\& 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138 +\& 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ... +\& +\& FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha +\& NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1 +\& 700688206 265614156 363161397 681332588 810600886 885767127 950172500 +\& 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189 +\& 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327 +\& 654 256360355 279492740 291251259 317592700 333763396 972105960 101... +\& +\& FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN +\& umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1 +\& 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813 +\& 335715751 534801009 684609658 829361048 972945982 999881534 1007655741 +\& 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162 +\& 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344... +.Ve +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4 +.IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel" +Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR. +.Sp +The supported aromaticity model names along with model specific control parameters +are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release +and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from +this file during class instantiation and makes it available to method \fBDetectAromaticity\fR +for detecting aromaticity corresponding to a specific model. +.IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4 +.IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes" +Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values +in the current release are: \fIAtomicInvariantsAtomTypes, FunctionalClassAtomTypes, +DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR. +.ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4 +.el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4 +.IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..." +This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid atomic invariant atom types. +.Sp +Possible values for atomic invarians are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, +H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\fR. +.Sp +The atomic invariants abbreviations correspond to: +.Sp +.Vb 1 +\& AS = Atom symbol corresponding to element symbol +\& +\& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms +\& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms +\& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms +\& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms +\& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms +\& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms +\& H<n> = Number of implicit and explicit hydrogens for atom +\& Ar = Aromatic annotation indicating whether atom is aromatic +\& RA = Ring atom annotation indicating whether atom is a ring +\& FC<+n/\-n> = Formal charge assigned to atom +\& MN<n> = Mass number indicating isotope other than most abundant isotope +\& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or +\& 3 (triplet) +.Ve +.Sp +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: +.Sp +.Vb 1 +\& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n> +.Ve +.Sp +Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values. +.Sp +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: +.Sp +.Vb 12 +\& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors +\& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms +\& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms +\& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms +\& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms +\& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms +\& H : NumOfImplicitAndExplicitHydrogens +\& Ar : Aromatic +\& RA : RingAtom +\& FC : FormalCharge +\& MN : MassNumber +\& SM : SpinMultiplicity +.Ve +.Sp +\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant +atom types. +.IP "\fB\-\-BitsOrder\fR \fIAscending | Descending\fR" 4 +.IX Item "--BitsOrder Ascending | Descending" +Bits order to use during generation of fingerprints bit-vector string for \fIExtendedConnectivityBits\fR +value of \fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR. +.Sp +\&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as +opposed to the highest bit. +.Sp +Internally, bits are stored in \fIAscending\fR order using Perl vec function. Regardless +of machine order, big-endian or little-endian, vec function always considers first +string byte as the lowest byte and first bit within each byte as the lowest bit. +.IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4 +.IX Item "-b, --BitStringFormat BinaryString | HexadecimalString" +Format of fingerprints bit-vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by +\&\fB\-\-output\fR used during \fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR option. Possible +values: \fIBinaryString, HexadecimalString\fR. Default value: \fIBinaryString\fR. +.Sp +\&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR +contains bit values in \s-1ASCII\s0 hexadecimal format. +.Sp +Examples: +.Sp +.Vb 6 +\& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +\& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 +\& 0000000001010000000110000011000000000000100000000000000000000000100001 +\& 1000000110000000000000000000000000010011000000000000000000000000010000 +\& 0000000000000000000000000010000000000000000001000000000000000000000000 +\& 0000000000010000100001000000000000101000000000000000100000000000000... +\& +\& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType +\& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 +\& 0000000001000100000000001000000000000000000000000000000000101000000010 +\& 0000001000000000010000000000000000000000000000000000000000000000000100 +\& 0000000000001000000000000001000000000001001000000000000000000000000000 +\& 0000000000000000100000000000001000000000000000000000000000000000000... +.Ve +.ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4 +.el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4 +.IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..." +This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid functional classes. +.Sp +Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR. +Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR. +.Sp +The functional class abbreviations correspond to: +.Sp +.Vb 9 +\& HBD: HydrogenBondDonor +\& HBA: HydrogenBondAcceptor +\& PI : PositivelyIonizable +\& NI : NegativelyIonizable +\& Ar : Aromatic +\& Hal : Halogen +\& H : Hydrophobic +\& RA : RingAtom +\& CA : ChainAtom +\& +\& Functional class atom type specification for an atom corresponds to: +\& +\& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom +types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]: +.Sp +.Vb 4 +\& HydrogenBondDonor: NH, NH2, OH +\& HydrogenBondAcceptor: N[!H], O +\& PositivelyIonizable: +, NH2 +\& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH +.Ve +.IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4 +.IX Item "--CompoundID DataFieldName or LabelPrefixString" +This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated. +.Sp +For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name +whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which +look like Cmpd<Number>. +.Sp +Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 2 +\& MolID +\& ExtReg +.Ve +.Sp +Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 1 +\& Compound +.Ve +.Sp +The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. +.IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4 +.IX Item "--CompoundIDLabel text" +Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value +of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR. +.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 +.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" +Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated +fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value; +use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. +.Sp +Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. +Default: \fILabelPrefix\fR. +.Sp +For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes +precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname +values are replaced with sequential compound IDs. +.Sp +This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option. +.ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4 +.el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4 +.IX Item "--DataFields FieldLabel1,FieldLabel2,..." +Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option. +.Sp +This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option. +.Sp +Examples: +.Sp +.Vb 2 +\& Extreg +\& MolID,CompoundName +.Ve +.IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4 +.IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID" +Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0 +data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields; +generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both. +Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR. +.IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4 +.IX Item "-f, --Filter Yes | No" +Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR. +Default value: \fIYes\fR. +.Sp +By default, compound data is checked before calculating fingerprints and compounds containing +atom data corresponding to non-element symbols or no atom data are ignored. +.IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4 +.IX Item "--FingerprintsLabel text" +\&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or +\&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIExtendedConnectivityFingerprints\fR. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4 +.IX Item "-k, --KeepLargestComponent Yes | No" +Generate fingerprints for only the largest component in molecule. Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.Sp +For molecules containing multiple connected components, fingerprints can be generated +in two different ways: use all connected components or just the largest connected +component. By default, all atoms except for the largest connected component are +deleted before generation of fingerprints. +.IP "\fB\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits\fR" 4 +.IX Item "-m, --mode ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits" +Specify type of extended connectivity fingerprints to generate for molecules in \fISDFile(s)\fR. +Possible values: \fIExtendedConnectivity, ExtendedConnecticityCount or +ExtendedConnectivityBits\fR. Default value: \fIExtendedConnectivity\fR. +.Sp +For \fIExtendedConnnectivity\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector +containing unique atom identifiers constitute the extended connectivity fingerprints +of a molecule. +.Sp +For \fIExtendedConnnectivityCount\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector +containing unique atom identifiers along with their count constitute the extended connectivity +fingerprints of a molecule. +.Sp +For \fIExtendedConnnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint bit vector +indicating presence/absence of structurally unique atom identifiers constitute the extended +connectivity fingerprints of a molecule. +.IP "\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR" 4 +.IX Item "-n, --NeighborhoodRadius number" +Atomic neighborhood radius for generating extended connectivity neighborhoods. Default +value: \fI2\fR. Valid values: >= 0. Neighborhood radius of zero correspond to just the list +of non-hydrogen atoms. +.Sp +Default value of \fI2\fR for atomic neighborhood radius generates extended connectivity +fingerprints corresponding to path length or diameter value of \fI4\fR [ Ref 52b ]. +.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--OutDelim comma | tab | semicolon" +Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR. +.IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4 +.IX Item "--output SD | FP | text | all" +Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4 +.IX Item "-q, --quote Yes | No" +Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4 +.IX Item "-r, --root RootName" +New file name is generated using the root: <Root>.<Ext>. Default for new file names: +<SDFileName><ExtendedConnectivityFP>.<Ext>. The file type determines <Ext> +value. The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. +.IP "\fB\-s, \-\-size\fR \fInumber\fR" 4 +.IX Item "-s, --size number" +Size of bit-vector to use during generation of fingerprints bit-vector string for +\&\fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR. Default value: \fI1024\fR. +Valid values correspond to any positive integer which satisfies the following criteria: +power of 2, >= 32 and <= 2 ** 32. +.Sp +Examples: +.Sp +.Vb 3 +\& 512 +\& 1024 +\& 2048 +.Ve +.IP "\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR" 4 +.IX Item "--UsePerlCoreRandom Yes | No" +Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function +during random number generation for setting bits in fingerprints bit-vector strings. Possible +values: \fIYes or No\fR. Default value: \fIYes\fR. +.Sp +\&\fINo\fR value option for \fB\-\-UsePerlCoreRandom\fR allows the generation of fingerprints +bit-vector strings which are same across different platforms. +.Sp +The random number generator implemented in MayaChemTools is a variant of +linear congruential generator (\s-1LCG\s0) as described by Miller et al. [ Ref 120 ]. +It is also referred to as Lehmer random number generator or Park-Miller +random number generator. +.Sp +Unlike Perl's core random number generator function rand, the random number +generator implemented in MayaChemTools, MathUtil::random, generates consistent +random values across different platforms for a specific random seed and leads +to generation of portable fingerprints bit-vector strings. +.IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4 +.IX Item "-v, --VectorStringFormat ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString" +Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by +\&\fB\-\-output\fR used during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option. Possible +values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString\fR. +.Sp +Default value during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option: +\&\fIIDsAndValuesString\fR. +.Sp +Default value during <ExtendedConnectivity> value of \fB\-m, \-\-mode\fR option: \fIValuesString\fR. +.Sp +Examples: +.Sp +.Vb 6 +\& 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 +.Ve +.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 +.IX Item "-w, --WorkingDir DirName" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 1 +\& % ExtendedConnectivityFingerprints.pl \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity count fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount +\& \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to +neighborhood radius up to 2 using atomic invariants atom types in vector string format and +create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits +\& \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity bits fingerprints as binary bit-string corresponding to +neighborhood radius up to 2 using atomic invariants atom types in vector string format and +create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits +\& \-\-BitStringFormat BinaryString \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf +and SampleECAIFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints +vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-\-output all \-r SampleECAIFP +\& \-o Sample.sdf +.Ve +.PP +To generate extended connectivity count fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf +and SampleECAIFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints +vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount +\& \-\-output all \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes +\& \-r SampleECFCFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using \s-1DREIDING\s0 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a DREIDINGAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using E\-state atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a EStateAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using \s-1MMFF94\s0 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a MMFF94AtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using SLogP atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a SLogPAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a SYBYLAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using \s-1TPSA\s0 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a TPSAAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using \s-1UFF\s0 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a UFFAtomTypes +\& \-r SampleECFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes \-n 3 +\& \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +3 using functional class atom types in vector string format and create a SampleECFCFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes \-n 3 +\& \-r SampleECFCFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using only \s-1AS\s0,X atomic invariants atom types in vector string format and create a +SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector +strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-AtomicInvariantsToUse "AS,X" \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using only \s-1HBD\s0,HBA functional class atom types in vector string format and create a +SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector +strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes +\& \-\-FunctionalClassesToUse "HBD,HBA" \-r SampleECFCFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName +\& \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID +\& \-r SampleECFCFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv +file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound +prefix along with fingerprints vector strings data, type: +.PP +.Vb 3 +\& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes +\& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleECFCFP +\& \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv +file containing common data fields columns along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Common \-r SampleECAIFP \-o Sample.sdf +.Ve +.PP +To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf +and SampleECFCFP.csv files containing all data fields columns in \s-1CSV\s0 file along with fingerprints +vector strings data, type: +.PP +.Vb 3 +\& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes +\& \-\-DataFieldsMode All \-\-output all \-r SampleECFCFP +\& \-o Sample.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl +.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.