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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/TopologicalPharmacophoreAtomPairsFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,811 @@ +.\" 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" +TopologicalPharmacophoreAtomPairsFingerprints.pl \- Generate topological pharmacophore atom pairs fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)... +.PP +TopologicalPharmacophoreAtomPairsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-\-AtomPairsSetSizeToUse\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\-f, \-\-Filter\fR \fIYes | No\fR] +[\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR] +[\fB\-\-FuzzifyAtomPairsCount\fR \fIYes | No\fR] [\fB\-\-FuzzificationMode\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR] +[\fB\-\-FuzzificationMethodology\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR] [\fB\-\-FuzzFactor\fR \fInumber\fR] +[\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] [\fB\-\-MinDistance\fR \fInumber\fR] +[\fB\-\-MaxDistance\fR \fInumber\fR] [\fB\-n, \-\-NormalizationMethodology\fR \fINone | ByHeavyAtomsCount | ByAtomTypesCount\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\-\-ValuesPrecision\fR \fInumber\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 pairs fingerprints [ Ref 60\-62, Ref 65, Ref 68 ] 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. +A pharmacophore atom pairs basis set is initialized for all unique possible pairs within +\&\fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR range. +.PP +.Vb 1 +\& Let: +\& +\& P = Valid pharmacophore atom type +\& +\& Px = Pharmacophore atom type x +\& Py = Pharmacophore atom type y +\& +\& 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 atoms +\& +\& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at +\& distance Dn +\& +\& P = Number of pharmacophore atom types to consider +\& PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn +\& +\& PPT = Total number of possible pharmacophore atom pairs at all distances +\& between Dmin and Dmax +\& +\& Then: +\& +\& PPD = (P * (P \- 1))/2 + P +\& +\& PPT = ((Dmax \- Dmin) + 1) * ((P * (P \- 1))/2 + P) +\& = ((Dmax \- Dmin) + 1) * PPD +\& +\& So for default values of Dmin = 1, Dmax = 10 and P = 5, +\& +\& PPD = (5 * (5 \- 1))/2 + 5 = 15 +\& PPT = ((10 \- 1) + 1) * 15 = 150 +\& +\& The pharmacophore atom pairs bais set includes 150 values. +\& +\& The atom pair IDs correspond to: +\& +\& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at +\& distance Dn +\& +\& For example: H\-D1\-H, H\-D2\-HBA, PI\-D5\-PI and so on +.Ve +.PP +Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom +pairs is counted. The contribution of each atom type to atom pair interaction is optionally +weighted by specified \fB\-\-AtomTypesWeight\fR before assigning its count to appropriate distance +bin. Based on \fB\-\-NormalizationMethodology\fR option, pharmacophore atom pairs count is optionally +normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after +the normalization controlled by values of \fB\-\-FuzzifyAtomPairsCount\fR, \fB\-\-FuzzificationMode\fR, +\&\fB\-\-FuzzificationMethodology\fR and \fB\-\-FuzzFactor\fR options. +.PP +The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen +atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs +fingerprints of the molecule. +.PP +For \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector correspond to +only those topological pharmacophore atom pairs which are present and have non-zero count. However, +for \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector contains all possible +valid topological pharmacophore atom pairs with both zero and non-zero count values. +.PP +Example of \fI\s-1SD\s0\fR file containing topological pharmacophore atom pairs fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <TopologicalPharmacophoreAtomPairsFingerprints> +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +\& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H +\& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\- +\& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D...; +\& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 +\& 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing topological pharmacophore atom pairs fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 15:32:48 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10 +\& # VectorStringFormat = IDsAndValuesString +\& # VectorValuesType = NumericalValues +\& # +\& Cmpd1 54;H\-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA...;18 1 2... +\& Cmpd2 61;H\-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA...;5 1 2 ... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing topological pharmacophore atom pairs fingerprints string data: +.PP +.Vb 9 +\& "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints" +\& "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary +\& Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H +\& \-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA H +\& BA\-D2\-HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4...; +\& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 +\& 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1" +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of topological pharmacophore +atom pairs fingerprints vector strings: +.PP +.Vb 7 +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +\& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H +\& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\- +\& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H +\& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...; +\& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 +\& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +\& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +\& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 +\& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 +\& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 +\& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +\& ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1 +\& \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H +\& BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D +\& 2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...; +\& 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 +\& 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 +\& 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 +.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\-\-AtomPairsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR" 4 +.IX Item "--AtomPairsSetSizeToUse ArbitrarySize | FixedSize" +Atom pairs set size to use during generation of topological pharmacophore atom pairs +fingerprints. +.Sp +Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR. +.Sp +For \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector +correspond to only those topological pharmacophore atom pairs which are present and +have non-zero count. However, for \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR +option, the fingerprint vector contains all possible valid topological pharmacophore atom +pairs 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 pairs. 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 60\-62 ] : \fI\s-1HBD\s0,HBA,PI,NI,H\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 +.ie n .IP "\fB\-\-AtomTypesWeight\fR \fI""AtomType1,Weight1,AtomType2,Weight2...""\fR" 4 +.el .IP "\fB\-\-AtomTypesWeight\fR \fI``AtomType1,Weight1,AtomType2,Weight2...''\fR" 4 +.IX Item "--AtomTypesWeight AtomType1,Weight1,AtomType2,Weight2..." +Weights of specified pharmacophore atom types to use during calculation of their contribution +to atom pair count. Default value: \fINone\fR. Valid values: real numbers greater than 0. In general +it's comma delimited list of valid atom type and its weight. +.Sp +The weight values allow to increase the importance of specific pharmacophore atom type +in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to +atom pair count where as weight value of 2 doubles its contribution. +.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\-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\-\-AtomPairsSetSizeToUse\fR option and topological atom pairs 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: \fITopologicalPharmacophoreAtomPairsFingerprints\fR. +.IP "\fB\-\-FuzzifyAtomPairsCount\fR \fIYes | No\fR" 4 +.IX Item "--FuzzifyAtomPairsCount Yes | No" +To fuzzify or not to fuzzify atom pairs count. Possible values: \fIYes or No\fR. Default value: +\&\fINo\fR. +.IP "\fB\-\-FuzzificationMode\fR \fIBeforeNormalization | AfterNormalization\fR" 4 +.IX Item "--FuzzificationMode BeforeNormalization | AfterNormalization" +When to fuzzify atom pairs count. Possible values: \fIBeforeNormalization | AfterNormalizationYes\fR. +Default value: \fIAfterNormalization\fR. +.IP "\fB\-\-FuzzificationMethodology\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR" 4 +.IX Item "--FuzzificationMethodology FuzzyBinning | FuzzyBinSmoothing" +How to fuzzify atom pairs count. Possible values: \fIFuzzyBinning | FuzzyBinSmoothing\fR. +Default value: \fIFuzzyBinning\fR. +.Sp +In conjunction with values for options \fB\-\-FuzzifyAtomPairsCount\fR, \fB\-\-FuzzificationMode\fR and +\&\fB\-\-FuzzFactor\fR, \fB\-\-FuzzificationMethodology\fR option is used to fuzzify pharmacophore atom +pairs count. +.Sp +Let: +.Sp +.Vb 3 +\& Px = Pharmacophore atom type x +\& Py = Pharmacophore atom type y +\& PPxy = Pharmacophore atom pair between atom type Px and Py +\& +\& PPxyDn = Pharmacophore atom pairs count between atom type Px and Py +\& at distance Dn +\& PPxyDn\-1 = Pharmacophore atom pairs count between atom type Px and Py +\& at distance Dn \- 1 +\& PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py +\& at distance Dn + 1 +\& +\& FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing +.Ve +.Sp +Then: +.Sp +For \fIFuzzyBinning\fR: +.Sp +.Vb 1 +\& PPxyDn = PPxyDn (Unchanged) +\& +\& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF +\& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF +.Ve +.Sp +For \fIFuzzyBinSmoothing\fR: +.Sp +.Vb 2 +\& PPxyDn = PPxyDn \- PPxyDn * 2FF for Dmin < Dn < Dmax +\& PPxyDn = PPxyDn \- PPxyDn * FF for Dn = Dmin or Dmax +\& +\& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF +\& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF +.Ve +.Sp +In both fuzzification schemes, a value of 0 for \s-1FF\s0 implies no fuzzification of occurrence counts. +A value of 1 during \fIFuzzyBinning\fR corresponds to maximum fuzzification of occurrence counts; +however, a value of 1 during \fIFuzzyBinSmoothing\fR ends up completely distributing the value over +the previous and next distance bins. +.Sp +So for default value of \fB\-\-FuzzFactor\fR (\s-1FF\s0) 0.15, the occurrence count of pharmacohore atom pairs +at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn \-1 and Dn + 1 +are incremented by PPxyDn * 0.15. +.Sp +And during \fIFuzzyBinSmoothing\fR the occurrence counts at Distance Dn is scaled back using multiplicative +factor of (1 \- 2*0.15) and the occurrence counts at distances Dn \-1 and Dn + 1 are incremented by +PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the +previous and next distance value. +.IP "\fB\-\-FuzzFactor\fR \fInumber\fR" 4 +.IX Item "--FuzzFactor number" +Specify by how much to fuzzify atom pairs count. Default value: \fI0.15\fR. Valid values: For +\&\fIFuzzyBinning\fR value of \fB\-\-FuzzificationMethodology\fR option: \fIbetween 0 and 1.0\fR; For +\&\fIFuzzyBinSmoothing\fR value of \fB\-\-FuzzificationMethodology\fR option: \fIbetween 0 and 0.5\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 for generating topological pharmacophore atom +pairs. Default value: \fI1\fR. Valid values: positive integers including 0 and less than \fB\-\-MaxDistance\fR. +.IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4 +.IX Item "--MaxDistance number" +Maximum bond distance between atom pairs for generating topological pharmacophore atom + pairs. Default value: \fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR. +.IP "\fB\-n, \-\-NormalizationMethodology\fR \fINone | ByHeavyAtomsCount | ByAtomTypesCount\fR" 4 +.IX Item "-n, --NormalizationMethodology None | ByHeavyAtomsCount | ByAtomTypesCount" +Normalization methodology to use for scaling the occurrence count of pharmacophore atom +pairs within specified distance range. Possible values: \fINone, ByHeavyAtomsCount or +ByAtomTypesCount\fR. Default value: \fINone\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><TopologicalPharmacophoreAtomPairsFP>.<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\-\-ValuesPrecision\fR \fInumber\fR" 4 +.IX Item "--ValuesPrecision number" +Precision of atom pairs count real values which might be generated after normalization +or fuzzification. Default value: up to \fI2\fR decimal places. Valid values: positive integers. +.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. +.Sp +Default value during \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option: \fIValuesString\fR. Default +value during \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option: \fIIDsAndValuesString\fR. +.Sp +\&\fIValuesString\fR option value is not allowed for \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR +option. +.Sp +Examples: +.Sp +.Vb 7 +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +\& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H +\& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\- +\& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H +\& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...; +\& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 +\& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +\& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +\& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 +\& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 +\& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 +\& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +\& ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1 +\& \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H +\& BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D +\& 2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...; +\& 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 +\& 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 +\& 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 +.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 pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-r SampleTPAPFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl +\& \-\-AtomPairsSetSizeToUse FixedSize \-r SampleTPAPFP\-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing +sequential compound IDs in \s-1CSV\s0 file along with fingerprints vector strings data in ValuesString +format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-output all +\& \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in IDsAndValuesPairsString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-VectorStringFormat +\& IDsAndValuesPairsString \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 6 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1 +\& \-MaxDistance 6 \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using \*(L"\s-1HBD\s0,HBA,PI,NI\*(R" atom types with double the weighting for \*(L"\s-1HBD\s0,HBA\*(R" and +normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a +SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings +data in ValuesString format, type: +.PP +.Vb 4 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1 +\& \-MaxDistance 10 \-\-AtomTypesToUse "HBD,HBA,PI, NI" \-\-AtomTypesWeight +\& "HBD,2,HBA,2,PI,1,NI,1" \-\-NormalizationMethodology ByHeavyAtomsCount +\& \-\-FuzzifyAtomPairsCount No \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to +distances from 1 through 10 using \*(L"\s-1HBD\s0,HBA,PI,NI,H\*(R" atom types with no weighting of atom types and +normalization but with fuzzification of atom pairs count using FuzzyBinning methodology +with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type: +.PP +.Vb 5 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1 +\& \-\-MaxDistance 10 \-\-AtomTypesToUse "HBD,HBA,PI, NI,H" \-\-AtomTypesWeight +\& "HBD,1,HBA,1,PI,1,NI,1,H,1" \-\-NormalizationMethodology None +\& \-\-FuzzifyAtomPairsCount Yes \-\-FuzzificationMethodology FuzzyBinning +\& \-\-FuzzFactor 0.5 \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode MolName \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID +\& \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.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 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& CompoundID \-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& Specify \-\-DataFields Mol_ID \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& Common \-r SampleTPAPFP \-o Sample.sdf +.Ve +.PP +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, +and SampleTPAPFP.csv files containing all data fields columns in \s-1CSV\s0 file along with fingerprints +data, type: +.PP +.Vb 2 +\& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode +\& All \-\-output all \-r SampleTPAPFP \-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, +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.