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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/TopologicalPharmacophoreAtomTripletsFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,757 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TopologicalPharmacophoreAtomTripletsFingerprints.pl \- Generate topological pharmacophore atom triplets fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)... +.PP +TopologicalPharmacophoreAtomTripletsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-\-AtomTripletsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR] +[\fB\-a, \-\-AtomTypesToUse\fR \fI\*(L"AtomType1, AtomType2...\*(R"\fR] +[\fB\-\-AtomTypesWeight\fR \fI\*(L"AtomType1, Weight1, AtomType2, Weight2...\*(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\-\-DistanceBinSize\fR \fInumber\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR] +[\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR] +[\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] [\fB\-\-MinDistance\fR \fInumber\fR] [\fB\-\-MaxDistance\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\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR] +[\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate topological pharmacophore atom triplets fingerprints [ Ref 66, Ref 68\-71 ] 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 +Based on the values specified for \fB\-\-AtomTypesToUse\fR, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +Using \fB\-\-MinDistance\fR, \fB\-\-MaxDistance\fR, and \fB\-\-DistanceBinSize\fR values, a +binned distance matrix is generated with lower bound on the distance bin as the distance +in distance matrix; the lower bound on the distance bin is also used as the distance between +atom pairs for generation of atom triplet identifiers. +.PP +A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting +atom pairs binned distances between \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR. The value +of \fB\-\-UseTriangleInequality\fR determines whether the triangle inequality test is applied during +generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore +types, is used during generation of atom triplet IDs. +.PP +.Vb 1 +\& Let: +\& +\& P = Valid pharmacophore atom type +\& +\& Px = Pharmacophore atom x +\& Py = Pharmacophore atom y +\& Pz = Pharmacophore atom z +\& +\& Dmin = Minimum distance corresponding to number of bonds between two atoms +\& Dmax = Maximum distance corresponding to number of bonds between two atoms +\& D = Distance corresponding to number of bonds between two atom +\& +\& Bsize = Distance bin size +\& Nbins = Number of distance bins +\& +\& Dxy = Distance or lower bound of binned distance between Px and Py +\& Dxz = Distance or lower bound of binned distance between Px and Pz +\& Dyz = Distance or lower bound of binned distance between Py and Pz +\& +\& Then: +\& +\& PxDyz\-PyDxz\-PzDxy = Pharmacophore atom triplet IDs for atom types Px, +\& Py, and Pz +\& +\& For example: H1\-H1\-H1, H2\-HBA\-H2 and so on +\& +\& For default values of Dmin = 1 , Dmax = 10 and Bsize = 2: +\& +\& the number of distance bins, Nbins = 5, are: +\& +\& [1, 2] [3, 4] [5, 6] [7, 8] [9 10] +\& +\& and atom triplet basis set size is 2692. +\& +\& Atom triplet basis set size for various values of Dmin, Dmax and Bsize in +\& conjunction with usage of triangle inequality is: +\& +\& Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize +\& 1 10 2 No 4960 +\& 1 10 2 Yes 2692 [ Default ] +\& 2 12 2 No 8436 +\& 2 12 2 Yes 4494 +.Ve +.PP +Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore +atom triplets is counted. +.PP +The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen +atoms constitute pharmacophore topological atom triplets fingerprints of the molecule. +.PP +For \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector correspond to +only those topological pharmacophore atom triplets which are present and have non-zero count. However, +for \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values. +.PP +Example of \fI\s-1SD\s0\fR file containing topological pharmacophore atom triplets fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <TopologicalPharmacophoreAtomTripletsFingerprints> +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +\& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\- +\& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1 +\& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\- +\& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...; +\& 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 +\& 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 +\& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing topological pharmacophore atom triplets fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 15:38:58 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M... +\& # VectorStringFormat = IDsAndValuesString +\& # VectorValuesType = NumericalValues +\& # +\& Cmpd1 696;Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1...;;46 106... +\& Cmpd2 251;H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-H1\-NI1...;4 1 3 1 1 2 2... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing topological pharmacophore atom triplets fingerprints string data: +.PP +.Vb 11 +\& "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints" +\& "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr +\& arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri +\& ng;Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HB +\& A1 Ar1\-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA +\& 1 H1\-HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 A...; +\& 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 ... +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of topological pharmacophore +atom triplets fingerprints vector strings: +.PP +.Vb 8 +\& 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 ... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +\& istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString; +\& Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-Ar1\-NI1 Ar1\-Ar1\-P +\& I1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1\-H1\-HBD1 Ar1\-H1\-NI1 Ar1\-H1\-PI1 Ar1\-HBA1\-HB +\& A1 Ar1\-HBA1\-HBD1 Ar1\-HBA1\-NI1 Ar1\-HBA1\-PI1 Ar1\-HBD1\-HBD1 Ar1\-HBD1\-...; +\& 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 ... +.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\-\-AtomTripletsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR" 4 +.IX Item "--AtomTripletsSetSizeToUse ArbitrarySize | FixedSize" +Atom triplets set size to use during generation of topological pharmacophore atom triplets +fingerprints. +.Sp +Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR. +.Sp +For \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector +correspond to only those topological pharmacophore atom triplets which are present and +have non-zero count. However, for \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR +option, the fingerprint vector contains all possible valid topological pharmacophore atom +triplets with both zero and non-zero count values. +.ie n .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI""AtomType1,AtomType2,...""\fR" 4 +.el .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI``AtomType1,AtomType2,...''\fR" 4 +.IX Item "-a, --AtomTypesToUse AtomType1,AtomType2,..." +Pharmacophore atom types to use during generation of topological phramacophore +atom triplets. It's a list of comma separated valid pharmacophore atom types. +.Sp +Possible values for pharmacophore atom types 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 71 ] : \fI\s-1HBD\s0,HBA,PI,NI,H,Ar\fR. +.Sp +The pharmacophore atom types abbreviations correspond to: +.Sp +.Vb 9 +\& HBD: HydrogenBondDonor +\& HBA: HydrogenBondAcceptor +\& PI : PositivelyIonizable +\& NI : NegativelyIonizable +\& Ar : Aromatic +\& Hal : Halogen +\& H : Hydrophobic +\& RA : RingAtom +\& CA : ChainAtom +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore 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-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value +of \fB\-\-DataFieldsMode\fR option. Default value: \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 value: \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\-\-DistanceBinSize\fR \fInumber\fR" 4 +.IX Item "--DistanceBinSize number" +Distance bin size used to bin distances between atom pairs in atom triplets. Default value: \fI2\fR. +Valid values: positive integers. +.Sp +For default \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR values of 1 and 10 with \fB\-\-DistanceBinSize\fR +of 2 [ Ref 70 ], the following 5 distance bins are generated: +.Sp +.Vb 1 +\& [1, 2] [3, 4] [5, 6] [7, 8] [9 10] +.Ve +.Sp +The lower distance bound on the distance bin is uses to bin the distance between atom pairs in +atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance +bin, atom pairs with distances 3 and 4 fall in second distance bin and so on. +.Sp +In order to distribute distance bins of equal size, the last bin is allowed to go past \fB\-\-MaxDistance\fR +by up to distance bin size. For example, \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR values of 2 and 10 +with \fB\-\-DistanceBinSize\fR of 2 generates the following 6 distance bins: +.Sp +.Vb 1 +\& [2, 3] [4, 5] [6, 7] [8, 9] [10 11] +.Ve +.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\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR" 4 +.IX Item "--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs" +Specify how fingerprints label is generated in conjunction with \fB\-\-FingerprintsLabel\fR option value: +use fingerprints label generated only by \fB\-\-FingerprintsLabel\fR option value or append topological +atom pair count value IDs to \fB\-\-FingerprintsLabel\fR option value. +.Sp +Possible values: \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR. Default value: +\&\fIFingerprintsLabelOnly\fR. +.Sp +Topological atom pairs IDs appended to \fB\-\-FingerprintsLabel\fR value during \fIFingerprintsLabelWithIDs\fR +values of \fB\-\-FingerprintsLabelMode\fR correspond to atom pair count values in fingerprint vector string. +.Sp +\&\fIFingerprintsLabelWithIDs\fR value of \fB\-\-FingerprintsLabelMode\fR is ignored during \fIArbitrarySize\fR value +of \fB\-\-AtomTripletsSetSizeToUse\fR option and topological atom triplets IDs not appended to the label. +.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: \fITopologicalPharmacophoreAtomTripletsFingerprints\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\-\-MinDistance\fR \fInumber\fR" 4 +.IX Item "--MinDistance number" +Minimum bond distance between atom pairs corresponding to atom triplets for generating +topological pharmacophore atom triplets. Default value: \fI1\fR. Valid values: positive integers and +less than \fB\-\-MaxDistance\fR. +.IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4 +.IX Item "--MaxDistance number" +Maximum bond distance between atom pairs corresponding to atom triplets for generating +topological pharmacophore atom triplets. Default value: \fI10\fR. Valid values: positive integers and +greater than \fB\-\-MinDistance\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><TopologicalPharmacophoreAtomTripletsFP>.<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\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR" 4 +.IX Item "-u, --UseTriangleInequality Yes | No" +Specify whether to imply triangle distance inequality test to distances between atom pairs in +atom triplets during generation of atom triplets basis set generation. Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.Sp +Triangle distance inequality test implies that distance or binned distance between any two atom +pairs in an atom triplet must be less than the sum of distances or binned distances between other +two atoms pairs and greater than the difference of their distances. +.Sp +.Vb 1 +\& For atom triplet PxDyz\-PyDxz\-PzDxy to satisfy triangle inequality: +\& +\& Dyz > |Dxz \- Dxy| and Dyz < Dxz + Dxy +\& Dxz > |Dyz \- Dxy| and Dyz < Dyz + Dxy +\& Dxy > |Dyz \- Dxz| and Dxy < Dyz + Dxz +.Ve +.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 option. Possible values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | +ValuesAndIDsString | ValuesAndIDsPairsString\fR. Defaultvalue: \fIValuesString\fR. +.Sp +Default value during \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option: \fIValuesString\fR. Default +value during \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option: \fIIDsAndValuesString\fR. +.Sp +\&\fIValuesString\fR option value is not allowed for \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR +option. +.Sp +Examples: +.Sp +.Vb 8 +\& 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 ... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +\& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt +\& ring;46 Ar1\-Ar1\-Ar1 106 Ar1\-Ar1\-H1 8 Ar1\-Ar1\-HBA1 3 Ar1\-Ar1\-HBD1 0 Ar1 +\& \-Ar1\-NI1 0 Ar1\-Ar1\-PI1 83 Ar1\-H1\-H1 11 Ar1\-H1\-HBA1 4 Ar1\-H1\-HBD1 0 Ar1 +\& \-H1\-NI1 0 Ar1\-H1\-PI1 0 Ar1\-HBA1\-HBA1 1 Ar1\-HBA1\-HBD1 0 Ar1\-HBA1\-NI1 0 +\& Ar1\-HBA1\-PI1 0 Ar1\-HBD1\-HBD1 0 Ar1\-HBD1\-NI1 0 Ar1\-HBD1\-PI1 0 Ar1\-NI... +.Ve +.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 +.IX Item "-w, --WorkingDir DirName" +Location of working directory. Default value: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-r SampleTPATFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl +\& \-\-AtomTripletsSetSizeToUse FixedSize \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with \s-1CSV\s0 file containing +sequential compound IDs along with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-output all +\& \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format and atom triplets IDs in the +fingerprint data column label starting with Fingerprints, type: +.PP +.Vb 3 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl +\& \-\-FingerprintsLabelMode FingerprintsLabelWithIDs \-\-FingerprintsLabel +\& Fingerprints \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl +\& \-\-UseTriangleInequality No \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 3 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl +\& \-\-UseTriangleInequality Yes \-\-MinDistance 1 \-\-MaxDistance 12 +\& \-\-DistanceBinSIze 2 \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using \*(L"\s-1HBD\s0,HBA,PI, \s-1NI\s0, H, Ar\*(R" atoms with distances +satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 4 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl +\& \-\-AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" \-\-UseTriangleInequality Yes +\& \-\-MinDistance 1 \-\-MaxDistance 12 \-\-DistanceBinSIze 2 +\& \-\-VectorStringFormat ValuesString \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs from +molecule name line along with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode MolName \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +specified data field along with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 3 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID +\& \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +combination of molecule name line and an explicit compound prefix along with fingerprints vector +strings data, type: +.PP +.Vb 4 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleSampleTPATFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing specific data fields columns along +with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& Specify \-\-DataFields Mol_ID \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing common data fields columns along +with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& Common \-r SampleTPATFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all +data fields columns in \s-1CSV\s0 file along with fingerprints data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode +\& All \-\-output all \-r SampleTPATFP \-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, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.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.