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.IX Title "TOPOLOGICALPHARMACOPHOREATOMTRIPLETSFINGERPRINTS 1"
.TH TOPOLOGICALPHARMACOPHOREATOMTRIPLETSFINGERPRINTS 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"
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 <[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,
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.