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.IX Title "TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1"
.TH TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
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 <[e-mail]>
.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.