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diff mayachemtools/docs/scripts/man1/AtomNeighborhoodsFingerprints.1 @ 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/scripts/man1/AtomNeighborhoodsFingerprints.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,763 @@ +.\" 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" +AtomNeighborhoodsFingerprints.pl \- Generate atom neighborhoods fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +AtomNeighborhoodsFingerprints.pl SDFile(s)... +.PP +AtomNeighborhoodsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | +DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR] +[\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR] +[\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\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\-\-MinNeighborhoodRadius\fR \fInumber\fR] [\fB\-\-MaxNeighborhoodRadius\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\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate atom neighborhoods fingerprints [ Ref 53\-56, Ref 73 ] 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 atom neighborhoods fingerprints +corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR, +initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods +around each non-hydrogen central atom corresponding to radii between specified values +\&\fB\-\-MinNeighborhoodRadius\fR and \fB\-\-MaxNeighborhoodRadius\fR, unique atom types at +each radii level are counted and an atom neighborhood identifier is generated. +.PP +The format of an atom neighborhood identifier around a central non-hydrogen atom at a +specific radius is: +.PP +.Vb 1 +\& NR<n>\-<AtomType>\-ATC<n> +\& +\& NR: Neighborhood radius +\& AtomType: Assigned atom type +\& ATC: Atom type count +.Ve +.PP +The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii +is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter: +.PP +.Vb 1 +\& NR<n>\-<AtomType>\-ATC<n>:NR<n>\-<AtomType>\-ATC<n>:... +.Ve +.PP +The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are +concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule. +.PP +Example of \fI\s-1SD\s0\fR file containing atom neighborhood fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <AtomNeighborhoodsFingerprints> +\& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu +\& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-ATC1 +\& :NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X1.B +\& O1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 +\& NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C... +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing atom neighborhood fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 14:15:27 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu... +\& # VectorStringFormat = ValuesString +\& # VectorValuesType = AlphaNumericalValues +\& # +\& Cmpd1 41;NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-A... +\& Cmpd2 23;NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR2\-C.X3.BO3.H1\-A... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing atom neighborhood fingerprints string data: +.PP +.Vb 8 +\& "CompoundID","AtomNeighborhoodsFingerprints" +\& "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes +\& :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.B +\& O1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 +\& NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3 +\& .BO4\-ATC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1..." +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of atom neighborhoods +fingerprints 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;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR +\& adius2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1: +\& NR1\-O_2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N +\& _3\-ATC1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-AT +\& C1:NR2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR +\& 1\-N_R\-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-... +\& +\& FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad +\& ius2;41;AlphaNumericalValues;ValuesString;NR0\-aaCH\-ATC1:NR1\-aaCH\-ATC1: +\& NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-aaCH\-ATC1:NR +\& 1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\- +\& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 NR0\- +\& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 N... +\& +\& FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu +\& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-Ar\-ATC1:NR1\-Ar\- +\& ATC1:NR1\-Ar.HBA\-ATC1:NR1\-None\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC4 NR0\-Ar\-AT +\& C1:NR1\-Ar\-ATC2:NR1\-Ar.HBA\-ATC1:NR2\-Ar\-ATC5:NR2\-None\-ATC1 NR0\-Ar\-ATC1:N +\& R1\-Ar\-ATC2:NR1\-HBD\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC1 NR0\-Ar\-ATC1:NR1\-Ar\-A +\& TC2:NR1\-Hal\-ATC1:NR2\-Ar\-ATC2 NR0\-Ar\-ATC1:NR1\-Ar\-ATC2:NR1\-None\-ATC1:... +\& +\& FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad +\& ius2;41;AlphaNumericalValues;ValuesString;NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR +\& 1\-CB\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C5B\-ATC1:NR2\-CB\-ATC3:NR2\-CR\-ATC +\& 1 NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR1\-CR\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C +\& 5B\-ATC1:NR2\-C=ON\-ATC1:NR2\-CR\-ATC3 NR0\-C5B\-ATC1:NR1\-C5A\-ATC1:NR1\-C5B\-AT +\& C1:NR1\-C=ON\-ATC1:NR2\-C5A\-ATC1:NR2\-CB\-ATC1:NR2\-CR\-ATC1:NR2\-N5\-ATC1:N... +\& +\& FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi +\& us2;41;AlphaNumericalValues;ValuesString;NR0\-C1\-ATC1:NR1\-C10\-ATC1:NR1\- +\& CS\-ATC1:NR2\-C1\-ATC1:NR2\-N11\-ATC1:NR2\-O2\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1: +\& NR2\-C1\-ATC1:NR2\-C21\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:NR2\-C1\-ATC1:NR2\-C21\- +\& ATC1 NR0\-C1\-ATC1:NR1\-C5\-ATC1:NR1\-CS\-ATC1:NR2\-C1\-ATC1:NR2\-O2\-ATC2:NR2\-O +\& 9\-ATC1 NR0\-C1\-ATC1:NR1\-CS\-ATC2:NR2\-C1\-ATC2:NR2\-O2\-ATC2 NR0\-C10\-ATC1... +\& +\& FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi +\& us2;41;AlphaNumericalValues;ValuesString;NR0\-C.2\-ATC1:NR1\-C.3\-ATC1:NR1 +\& \-O.co2\-ATC2:NR2\-C.3\-ATC1 NR0\-C.2\-ATC1:NR1\-C.ar\-ATC1:NR1\-N.am\-ATC1:NR1\- +\& O.2\-ATC1:NR2\-C.ar\-ATC3 NR0\-C.3\-ATC1:NR1\-C.2\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\- +\& ATC1:NR2\-O.3\-ATC1:NR2\-O.co2\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR1\-N.ar\-AT +\& C1:NR2\-C.3\-ATC1:NR2\-C.ar\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-ATC... +\& +\& FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu +\& s2;41;AlphaNumericalValues;ValuesString;NR0\-N21\-ATC1:NR1\-None\-ATC3:NR2 +\& \-None\-ATC5 NR0\-N7\-ATC1:NR1\-None\-ATC2:NR2\-None\-ATC3:NR2\-O3\-ATC1 NR0\-Non +\& e\-ATC1:NR1\-N21\-ATC1:NR1\-None\-ATC1:NR2\-None\-ATC3 NR0\-None\-ATC1:NR1\-N21\- +\& ATC1:NR1\-None\-ATC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N21\-ATC1:NR1\-None\-A +\& TC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N7\-ATC1:NR1\-None\-ATC1:NR1\-O3\-AT... +\& +\& FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius +\& 2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:NR1\-O +\& _2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N_3\-AT +\& C1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-ATC1:NR +\& 2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR1\-N_R +\& \-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-C_3\-A... +.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 | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4 +.IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes" +Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of atom neighborhoods fingerprints. Possible values in the current +release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, 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 invariants 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: \fI\s-1AS\s0,X,BO,H,FC\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. +.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: \fIAtomNeighborhoodsFingerprints\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\-\-MinNeighborhoodRadius\fR \fInumber\fR" 4 +.IX Item "--MinNeighborhoodRadius number" +Minimum atom neighborhood radius for generating atom neighborhoods. Default value: \fI0\fR. +Valid values: positive integers and less than \fB\-\-MaxNeighborhoodRadius\fR. Neighborhood +radius of zero corresponds to list of non-hydrogen atoms. +.IP "\fB\-\-MaxNeighborhoodRadius\fR \fInumber\fR" 4 +.IX Item "--MaxNeighborhoodRadius number" +Maximum atom neighborhood radius for generating atom neighborhoods. Default value: \fI2\fR. +Valid values: positive integers and greater than \fB\-\-MineighborhoodRadius\fR. +.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><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext> +value. The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. +.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 atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 1 +\& % AtomNeighborhoodsFingerprints.pl \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1DREIDING\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a DREIDINGAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a EStateAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a SYBYLAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a FunctionalClassAtomTypes +\& \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1MMFF94\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a MMFF94AtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using SLogP atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a SLogPAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a SYBYLAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1TPSA\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a TPSAAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using \s-1UFF\s0 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a UFFAtomTypes \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create SampleANFP.sdf, +SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along +with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-\-output all \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to +3 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-MinNeighborhoodRadius 1 \-\-MaxNeighborhoodRadius 3 \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using only \s-1AS\s0,X atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-AtomicInvariantsToUse "AS,X" \-\-MinNeighborhoodRadius 0 +\& \-\-MaxNeighborhoodRadius 3 \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolName +\& \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode DataField \-\-CompoundID +\& Mol_ID \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +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 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleANFP +\& \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Common \-r SampleANFP \-o Sample.sdf +.Ve +.PP +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create SampleANFP.sdf, + SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in \s-1CSV\s0 file along with +fingerprints data, type: +.PP +.Vb 3 +\& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode All \-\-output all \-r SampleANFP +\& \-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, SimilaritySearchingFingerprints.pl, +ExtendedConnectivityFingerprints.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.