diff docs/scripts/txt/TopologicalAtomTorsionsFingerprints.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/scripts/txt/TopologicalAtomTorsionsFingerprints.txt	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,616 @@
+NAME
+    TopologicalAtomTorsionsFingerprints.pl - Generate topological atom
+    torsions fingerprints for SD files
+
+SYNOPSIS
+    TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
+
+    TopologicalAtomTorsionsFingerprints.pl [--AromaticityModel
+    *AromaticityModelType*] [-a, --AtomIdentifierType
+    *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse
+    *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
+    *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName
+    or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode]
+    [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
+    *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
+    [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
+    *Yes | No*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP |
+    text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root
+    *RootName*] [-v, --VectorStringFormat] [-w, --WorkingDir dirname]
+    SDFile(s)...
+
+DESCRIPTION
+    Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for
+    *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
+    containing fingerprints vector strings corresponding to molecular
+    fingerprints.
+
+    Multiple SDFile names are separated by spaces. The valid file extensions
+    are *.sdf* and *.sd*. All other file names are ignored. All the SD files
+    in a current directory can be specified either by **.sdf* or the current
+    directory name.
+
+    The current release of MayaChemTools supports generation of topological
+    atom torsions fingerprints corresponding to following -a,
+    --AtomIdentifierTypes:
+
+        AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
+        FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
+        SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
+
+    Based on the values specified for -a, --AtomIdentifierType and
+    --AtomicInvariantsToUse, initial atom types are assigned to all
+    non-hydrogen atoms in a molecule. All unique atom torsions are
+    identified and an atom torsion identifier is generated; the format of
+    atom torsion identifier is:
+
+        <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>
+
+        AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
+
+        where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
+
+    The atom torsion identifiers for all unique atom torsions corresponding
+    to non-hydrogen atoms constitute topological atom torsions fingerprints
+    of the molecule.
+
+    Example of *SD* file containing topological atom torsions fingerprints
+    string data:
+
+        ... ...
+        ... ...
+        $$$$
+        ... ...
+        ... ...
+        ... ...
+        41 44  0  0  0  0  0  0  0  0999 V2000
+         -3.3652    1.4499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        ... ...
+        2  3  1  0  0  0  0
+        ... ...
+        M  END
+        >  <CmpdID>
+        Cmpd1
+
+        >  <TopologicalAtomTorsionsFingerprints>
+        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
+        ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
+        X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
+        2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
+        2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
+
+        $$$$
+        ... ...
+        ... ...
+
+    Example of *FP* file containing topological atom torsions fingerprints
+    string data:
+
+        #
+        # Package = MayaChemTools 7.4
+        # Release Date = Oct 21, 2010
+        #
+        # TimeStamp = Fri Mar 11 15:17:20 2011
+        #
+        # FingerprintsStringType = FingerprintsVector
+        #
+        # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
+        # VectorStringFormat = IDsAndValuesString
+        # VectorValuesType = NumericalValues
+        #
+        Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
+        Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
+        ... ...
+        ... ..
+
+    Example of CSV *Text* file containing topological atom torsions
+    fingerprints string data:
+
+        "CompoundID","TopologicalAtomTorsionsFingerprints"
+        "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
+        mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
+        X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
+        .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
+        2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
+        ... ...
+        ... ...
+
+    The current release of MayaChemTools generates the following types of
+    topological atom torsions fingerprints vector strings:
+
+        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
+        3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
+        C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
+        2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
+        ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
+
+        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
+        3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
+        .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
+        2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
+        O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
+        O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
+
+        FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
+        calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
+        _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
+        C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
+        1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
+
+        FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
+        lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
+        H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
+        ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
+        4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
+
+        FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
+        ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
+        Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
+        -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
+        32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
+
+        FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
+        lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
+        B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
+        A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
+        1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
+        1 1 2 1 1 3 1 3
+
+        FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
+        Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
+        1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
+        2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
+        C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
+        2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...
+
+        FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
+        Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
+        -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
+        ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
+        -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
+        ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...
+
+        FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
+        lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
+        None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
+        None-None 44 None-None-None-O3 3 None-None-None-O4 5
+
+        FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
+        lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
+        _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
+        -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
+        _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
+         C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...
+
+OPTIONS
+    --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
+    MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
+    ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
+    MayaChemToolsAromaticityModel*
+        Specify aromaticity model to use during detection of aromaticity.
+        Possible values in the current release are: *MDLAromaticityModel,
+        TriposAromaticityModel, MMFFAromaticityModel,
+        ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
+        DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
+        value: *MayaChemToolsAromaticityModel*.
+
+        The supported aromaticity model names along with model specific
+        control parameters are defined in AromaticityModelsData.csv, which
+        is distributed with the current release and is available under
+        lib/data directory. Molecule.pm module retrieves data from this file
+        during class instantiation and makes it available to method
+        DetectAromaticity for detecting aromaticity corresponding to a
+        specific model.
+
+    -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
+    | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
+    SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
+        Specify atom identifier type to use for assignment of initial atom
+        identifier to non-hydrogen atoms during calculation of topological
+        atom torsions fingerprints. Possible values in the current release
+        are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
+        FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
+        SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
+        *AtomicInvariantsAtomTypes*.
+
+    --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
+        This value is used during *AtomicInvariantsAtomTypes* value of a,
+        --AtomIdentifierType option. It's a list of comma separated valid
+        atomic invariant atom types.
+
+        Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
+        TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
+
+        The atomic invariants abbreviations correspond to:
+
+            AS = Atom symbol corresponding to element symbol
+
+            X<n>   = Number of non-hydrogen atom neighbors or heavy atoms
+            BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
+            LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
+            SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
+            DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
+            TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
+            H<n>   = Number of implicit and explicit hydrogens for atom
+            Ar     = Aromatic annotation indicating whether atom is aromatic
+            RA     = Ring atom annotation indicating whether atom is a ring
+            FC<+n/-n> = Formal charge assigned to atom
+            MN<n> = Mass number indicating isotope other than most abundant isotope
+            SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
+                    3 (triplet)
+
+        Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
+        corresponds to:
+
+            AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
+
+        Except for AS which is a required atomic invariant in atom types,
+        all other atomic invariants are optional. Atom type specification
+        doesn't include atomic invariants with zero or undefined values.
+
+        In addition to usage of abbreviations for specifying atomic
+        invariants, the following descriptive words are also allowed:
+
+            X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
+            BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
+            LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
+            SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
+            DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
+            TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
+            H :  NumOfImplicitAndExplicitHydrogens
+            Ar : Aromatic
+            RA : RingAtom
+            FC : FormalCharge
+            MN : MassNumber
+            SM : SpinMultiplicity
+
+        *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
+        atomic invariant atom types.
+
+    --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
+        This value is used during *FunctionalClassAtomTypes* value of a,
+        --AtomIdentifierType option. It's a list of comma separated valid
+        functional classes.
+
+        Possible values for atom functional classes are: *Ar, CA, H, HBA,
+        HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
+        *HBD,HBA,PI,NI,Ar,Hal*.
+
+        The functional class abbreviations correspond to:
+
+            HBD: HydrogenBondDonor
+            HBA: HydrogenBondAcceptor
+            PI :  PositivelyIonizable
+            NI : NegativelyIonizable
+            Ar : Aromatic
+            Hal : Halogen
+            H : Hydrophobic
+            RA : RingAtom
+            CA : ChainAtom
+
+         Functional class atom type specification for an atom corresponds to:
+
+            Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
+
+        *AtomTypes::FunctionalClassAtomTypes* module is used to assign
+        functional class atom types. It uses following definitions [ Ref
+        60-61, Ref 65-66 ]:
+
+            HydrogenBondDonor: NH, NH2, OH
+            HydrogenBondAcceptor: N[!H], O
+            PositivelyIonizable: +, NH2
+            NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
+
+    --CompoundID *DataFieldName or LabelPrefixString*
+        This value is --CompoundIDMode specific and indicates how compound
+        ID is generated.
+
+        For *DataField* value of --CompoundIDMode option, it corresponds to
+        datafield label name whose value is used as compound ID; otherwise,
+        it's a prefix string used for generating compound IDs like
+        LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
+        IDs which look like Cmpd<Number>.
+
+        Examples for *DataField* value of --CompoundIDMode:
+
+            MolID
+            ExtReg
+
+        Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
+        --CompoundIDMode:
+
+            Compound
+
+        The value specified above generates compound IDs which correspond to
+        Compound<Number> instead of default value of Cmpd<Number>.
+
+    --CompoundIDLabel *text*
+        Specify compound ID column label for CSV/TSV text file(s) used
+        during *CompoundID* value of --DataFieldsMode option. Default value:
+        *CompoundID*.
+
+    --CompoundIDMode *DataField | MolName | LabelPrefix |
+    MolNameOrLabelPrefix*
+        Specify how to generate compound IDs and write to FP or CSV/TSV text
+        file(s) along with generated fingerprints for *FP | text | all*
+        values of --output option: use a *SDFile(s)* datafield value; use
+        molname line from *SDFile(s)*; generate a sequential ID with
+        specific prefix; use combination of both MolName and LabelPrefix
+        with usage of LabelPrefix values for empty molname lines.
+
+        Possible values: *DataField | MolName | LabelPrefix |
+        MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
+
+        For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
+        in *SDFile(s)* takes precedence over sequential compound IDs
+        generated using *LabelPrefix* and only empty molname values are
+        replaced with sequential compound IDs.
+
+        This is only used for *CompoundID* value of --DataFieldsMode option.
+
+    --DataFields *"FieldLabel1,FieldLabel2,..."*
+        Comma delimited list of *SDFiles(s)* data fields to extract and
+        write to CSV/TSV text file(s) along with generated fingerprints for
+        *text | all* values of --output option.
+
+        This is only used for *Specify* value of --DataFieldsMode option.
+
+        Examples:
+
+            Extreg
+            MolID,CompoundName
+
+    -d, --DataFieldsMode *All | Common | Specify | CompoundID*
+        Specify how data fields in *SDFile(s)* are transferred to output
+        CSV/TSV text file(s) along with generated fingerprints for *text |
+        all* values of --output option: transfer all SD data field; transfer
+        SD data files common to all compounds; extract specified data
+        fields; generate a compound ID using molname line, a compound
+        prefix, or a combination of both. Possible values: *All | Common |
+        specify | CompoundID*. Default value: *CompoundID*.
+
+    -f, --Filter *Yes | No*
+        Specify whether to check and filter compound data in SDFile(s).
+        Possible values: *Yes or No*. Default value: *Yes*.
+
+        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.
+
+    --FingerprintsLabel *text*
+        SD data label or text file column label to use for fingerprints
+        string in output SD or CSV/TSV text file(s) specified by --output.
+        Default value: *TopologicalAtomTorsionsFingerprints*.
+
+    -h, --help
+        Print this help message.
+
+    -k, --KeepLargestComponent *Yes | No*
+        Generate fingerprints for only the largest component in molecule.
+        Possible values: *Yes or No*. Default value: *Yes*.
+
+        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.
+
+    --OutDelim *comma | tab | semicolon*
+        Delimiter for output CSV/TSV text file(s). Possible values: *comma,
+        tab, or semicolon* Default value: *comma*.
+
+    --output *SD | FP | text | all*
+        Type of output files to generate. Possible values: *SD, FP, text, or
+        all*. Default value: *text*.
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    -q, --quote *Yes | No*
+        Put quote around column values in output CSV/TSV text file(s).
+        Possible values: *Yes or No*. Default value: *Yes*
+
+    -r, --root *RootName*
+        New file name is generated using the root: <Root>.<Ext>. Default for
+        new file names: <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The
+        file type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext>
+        values are used for SD, FP, comma/semicolon, and tab delimited text
+        files, respectively.This option is ignored for multiple input files.
+
+    -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
+    ValuesAndIDsString | ValuesAndIDsPairsString*
+        Format of fingerprints vector string data in output SD, FP or
+        CSV/TSV text file(s) specified by --output option. Possible values:
+        *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
+        ValuesAndIDsPairsString*. Defaultvalue: *IDsAndValuesString*.
+
+        Examples:
+
+            FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
+            3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
+            C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
+            2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
+            2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
+
+            FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
+            3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
+            .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
+            2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
+            O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
+            O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
+
+    -w, --WorkingDir *DirName*
+        Location of working directory. Default value: current directory.
+
+EXAMPLES
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing sequential compound IDs along with
+    fingerprints vector strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create
+    SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
+    sequential compound IDs in CSV file along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
+          -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesPairsString format and create a
+    SampleTATFP.csv file containing sequential compound IDs along with
+    fingerprints vector strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
+          IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using DREIDING atom
+    types in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using E-state atom
+    types in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using functional
+    class atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing sequential compound IDs along with
+    fingerprints vector strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using MMFF94 atom
+    types in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using SLogP atom
+    types in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using SYBYL atom
+    types in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using TPSA atom types
+    in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using UFF atom types
+    in IDsAndValuesString format and create a SampleTATFP.csv file
+    containing sequential compound IDs along with fingerprints vector
+    strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using only AS,X
+    atomic invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing sequential compound IDs along with
+    fingerprints vector strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+         --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing compoundID from molecule name line along
+    with fingerprints vector strings, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode CompoundID -CompoundIDMode MolName
+          -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing compound IDs using specified data field
+    along with fingerprints vector strings, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
+          Mol_ID -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing compound ID using combination of
+    molecule name line and an explicit compound prefix along with
+    fingerprints vector strings data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
+          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing specific data fields columns along with
+    fingerprints vector strings, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
+          -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create a
+    SampleTATFP.csv file containing common data fields columns along with
+    fingerprints vector strings, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode Common -r SampleTATFP -o Sample.sdf
+
+    To generate topological atom torsions fingerprints using atomic
+    invariants atom types in IDsAndValuesString format and create
+    SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
+    all data fields columns in CSV file along with fingerprints data, type:
+
+        % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
+          --DataFieldsMode All  --output all -r SampleTATFP
+          -o Sample.sdf
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
+    AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
+    MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
+    TopologicalAtomPairsFingerprints.pl,
+    TopologicalPharmacophoreAtomPairsFingerprints.pl,
+    TopologicalPharmacophoreAtomTripletsFingerprints.pl
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+