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+NAME
+    CalculatePhysicochemicalProperties.pl - Calculate physicochemical
+    properties for SD files
+
+SYNOPSIS
+    CalculatePhysicochemicalProperties.pl SDFile(s)...
+
+    PhysicochemicalProperties.pl [--AromaticityModel *AromaticityModelType*]
+    [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel
+    text] [--CompoundIDMode] [--DataFields "FieldLabel1, FieldLabel2,..."]
+    [-d, --DataFieldsMode All | Common | Specify | CompoundID] [-f, --Filter
+    Yes | No] [-h, --help] [--HydrogenBonds HBondsType1 | HBondsType2] [-k,
+    --KeepLargestComponent Yes | No] [-m, --mode All | RuleOf5 | RuleOf3 |
+    "name1, [name2,...]"] [--MolecularComplexity *Name,Value,
+    [Name,Value,...]*] [--OutDelim comma | tab | semicolon] [--output SD |
+    text | both] [-o, --overwrite] [--Precision
+    Name,Number,[Name,Number,..]] [--RotatableBonds Name,Value,
+    [Name,Value,...]] [--RuleOf3Violations Yes | No] [--RuleOf5Violations
+    Yes | No] [-q, --quote Yes | No] [-r, --root RootName] [-w, --WorkingDir
+    dirname] SDFile(s)...
+
+DESCRIPTION
+    Calculate physicochemical properties for *SDFile(s)* and create
+    appropriate SD or CSV/TSV text file(s) containing calculated properties.
+
+    The current release of MayaChemTools supports the calculation of these
+    physicochemical properties:
+
+        MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
+        van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
+        HydrogenBondDonors, HydrogenBondAcceptors, LogP and
+        Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
+        Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
+        and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ],
+        MolecularComplexity [ Ref 117-119 ]
+
+    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 calculation of molecular complexity using *MolecularComplexityType*
+    parameter corresponds to the number of bits-set or unique keys [ Ref
+    117-119 ] in molecular fingerprints. Default value for
+    *MolecularComplexityType*: *MACCSKeys* of size 166. The calculation of
+    MACCSKeys is relatively expensive and can take rather substantial amount
+    of time.
+
+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.
+
+    --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 CSV/TSV text
+        file(s) along with calculated physicochemical properties for *text |
+        both* 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 calculated physicochemical
+        properties for *text | both* 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 calculated physicochemical
+        properties for *text | both* 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
+        physiochemical properties and compounds containing atom data
+        corresponding to non-element symbols or no atom data are ignored.
+
+    -h, --help
+        Print this help message.
+
+    --HydrogenBonds *HBondsType1 | HBondsType2*
+        Parameters to control calculation of hydrogen bond donors and
+        acceptors. Possible values: *HBondsType1, HydrogenBondsType1,
+        HBondsType2, HydrogenBondsType2*. Default value: *HBondsType2* which
+        corresponds to RuleOf5 definition for number of hydrogen bond donors
+        and acceptors.
+
+        The current release of MayaChemTools supports identification of two
+        types of hydrogen bond donor and acceptor atoms with these names:
+
+            HBondsType1 or HydrogenBondsType1
+            HBondsType2 or HydrogenBondsType2
+
+        The names of these hydrogen bond types are rather arbitrary.
+        However, their definitions have specific meaning and are as follows:
+
+            HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
+
+                Donor: NH, NH2, OH - Any N and O with available H
+                Acceptor: N[!H], O - Any N without available H and any O
+
+            HydrogenBondsType2 [ Ref 91 ]:
+
+                Donor: NH, NH2, OH - N and O with available H
+                Acceptor: N, O - And N and O
+
+    -k, --KeepLargestComponent *Yes | No*
+        Calculate physicochemical properties for only the largest component
+        in molecule. Possible values: *Yes or No*. Default value: *Yes*.
+
+        For molecules containing multiple connected components,
+        physicochemical properties can be calculated 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 calculation of physicochemical
+        properties.
+
+    -m, --mode *All | RuleOf5 | RuleOf3 | "name1, [name2,...]"*
+        Specify physicochemical properties to calculate for SDFile(s):
+        calculate all available physical chemical properties; calculate
+        properties corresponding to Rule of 5; or use a comma delimited list
+        of supported physicochemical properties. Possible values: *All |
+        RuleOf5 | RuleOf3 | "name1, [name2,...]"*.
+
+        Default value: *MolecularWeight, HeavyAtoms, MolecularVolume,
+        RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
+        TPSA*. These properties are calculated by default.
+
+        *RuleOf5* [ Ref 91 ] includes these properties: *MolecularWeight,
+        HydrogenBondDonors, HydrogenBondAcceptors, SLogP*. *RuleOf5* states:
+        MolecularWeight <= 500, HydrogenBondDonors <= 5,
+        HydrogenBondAcceptors <= 10, and logP <= 5.
+
+        *RuleOf3* [ Ref 92 ] includes these properties: *MolecularWeight,
+        RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
+        TPSA*. *RuleOf3* states: MolecularWeight <= 300, RotatableBonds <=
+        3, HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3,
+        and TPSA <= 60.
+
+        *All* calculates all supported physicochemical properties:
+        *MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
+        MolecularVolume, RotatableBonds, HydrogenBondDonors,
+        HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons,
+        MolecularComplexity*.
+
+    --MolecularComplexity *Name,Value, [Name,Value,...]*
+        Parameters to control calculation of molecular complexity: it's a
+        comma delimited list of parameter name and value pairs.
+
+        Possible parameter names: *MolecularComplexityType,
+        AtomIdentifierType, AtomicInvariantsToUse, FunctionalClassesToUse,
+        MACCSKeysSize, NeighborhoodRadius, MinPathLength, MaxPathLength,
+        UseBondSymbols, MinDistance, MaxDistance, UseTriangleInequality,
+        DistanceBinSize, NormalizationMethodology*.
+
+        The valid paramater valuse for each parameter name are described in
+        the following sections.
+
+        The current release of MayaChemTools supports calculation of
+        molecular complexity using *MolecularComplexityType* parameter
+        corresponding to the number of bits-set or unique keys [ Ref 117-119
+        ] in molecular fingerprints. The valid values for
+        *MolecularComplexityType* are:
+
+            AtomTypesFingerprints
+            ExtendedConnectivityFingerprints
+            MACCSKeys
+            PathLengthFingerprints
+            TopologicalAtomPairsFingerprints
+            TopologicalAtomTripletsFingerprints
+            TopologicalAtomTorsionsFingerprints
+            TopologicalPharmacophoreAtomPairsFingerprints
+            TopologicalPharmacophoreAtomTripletsFingerprints
+
+        Default value for *MolecularComplexityType*: *MACCSKeys*.
+
+        *AtomIdentifierType* parameter name correspods to atom types used
+        during generation of fingerprints. The valid values for
+        *AtomIdentifierType* are: *AtomicInvariantsAtomTypes,
+        DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,
+        MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes,
+        UFFAtomTypes*. *AtomicInvariantsAtomTypes* is not supported for
+        during the following values of *MolecularComplexityType*:
+        *MACCSKeys, TopologicalPharmacophoreAtomPairsFingerprints,
+        TopologicalPharmacophoreAtomTripletsFingerprints*.
+        *FunctionalClassAtomTypes* is the only valid value for
+        *AtomIdentifierType* for topological pharmacophore fingerprints.
+
+        Default value for *AtomIdentifierType*: *AtomicInvariantsAtomTypes*
+        for all except topological pharmacophore fingerprints where it is
+        *FunctionalClassAtomTypes*.
+
+        *AtomicInvariantsToUse* parameter name and values are used during
+        *AtomicInvariantsAtomTypes* value of parameter *AtomIdentifierType*.
+        It's a list of space 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 for
+        *AtomicInvariantsToUse* parameter are set differently for different
+        fingerprints using *MolecularComplexityType* parameter as shown
+        below:
+
+            MolecularComplexityType              AtomicInvariantsToUse
+
+            AtomTypesFingerprints                AS X BO H FC
+            TopologicalAtomPairsFingerprints     AS X BO H FC
+            TopologicalAtomTripletsFingerprints  AS X BO H FC
+            TopologicalAtomTorsionsFingerprints  AS X BO H FC
+
+            ExtendedConnectivityFingerprints     AS X  BO H FC MN
+            PathLengthFingerprints               AS
+
+        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* parameter name and values are used during
+        *FunctionalClassAtomTypes* value of parameter *AtomIdentifierType*.
+        It's a list of space separated valid atomic invariant atom types.
+
+        Possible values for atom functional classes are: *Ar, CA, H, HBA,
+        HBD, Hal, NI, PI, RA*.
+
+        Default value for *FunctionalClassesToUse* parameter is set to:
+
+            HBD HBA PI NI Ar Hal
+
+        for all fingerprints except for the following two
+        *MolecularComplexityType* fingerints:
+
+            MolecularComplexityType                           FunctionalClassesToUse
+
+            TopologicalPharmacophoreAtomPairsFingerprints     HBD HBA P, NI H
+            TopologicalPharmacophoreAtomTripletsFingerprints  HBD HBA PI NI H Ar
+
+        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
+
+        *MACCSKeysSize* parameter name is only used during *MACCSKeys* value
+        of *MolecularComplexityType* and corresponds to the size of MACCS
+        key set. Possible values: *166 or 322*. Default value: *166*.
+
+        *NeighborhoodRadius* parameter name is only used during
+        *ExtendedConnectivityFingerprints* value of
+        *MolecularComplexityType* and corresponds to atomic neighborhoods
+        radius for generating extended connectivity fingerprints. Possible
+        values: positive integer. Default value: *2*.
+
+        *MinPathLength* and *MaxPathLength* parameters are only used during
+        *PathLengthFingerprints* value of *MolecularComplexityType* and
+        correspond to minimum and maximum path lengths to use for generating
+        path length fingerprints. Possible values: positive integers.
+        Default value: *MinPathLength - 1*; *MaxPathLength - 8*.
+
+        *UseBondSymbols* parameter is only used during
+        *PathLengthFingerprints* value of *MolecularComplexityType* and
+        indicates whether bond symbols are included in atom path strings
+        used to generate path length fingerprints. Possible value: *Yes or
+        No*. Default value: *Yes*.
+
+        *MinDistance* and *MaxDistance* parameters are only used during
+        *TopologicalAtomPairsFingerprints* and
+        *TopologicalAtomTripletsFingerprints* values of
+        *MolecularComplexityType* and correspond to minimum and maximum bond
+        distance between atom pairs during topological pharmacophore
+        fingerprints. Possible values: positive integers. Default value:
+        *MinDistance - 1*; *MaxDistance - 10*.
+
+        *UseTriangleInequality* parameter is used during these values for
+        *MolecularComplexityType*: *TopologicalAtomTripletsFingerprints* and
+        *TopologicalPharmacophoreAtomTripletsFingerprints*. Possible values:
+        *Yes or No*. It determines wheter to apply triangle inequality to
+        distance triplets. Default value:
+        *TopologicalAtomTripletsFingerprints - No*;
+        *TopologicalPharmacophoreAtomTripletsFingerprints - Yes*.
+
+        *DistanceBinSize* parameter is used during
+        *TopologicalPharmacophoreAtomTripletsFingerprints* value of
+        *MolecularComplexityType* and correspons to distance bin size used
+        for binning distances during generation of topological pharmacophore
+        atom triplets fingerprints. Possible value: positive integer.
+        Default value: *2*.
+
+        *NormalizationMethodology* is only used for these values for
+        *MolecularComplexityType*: *ExtendedConnectivityFingerprints*,
+        *TopologicalPharmacophoreAtomPairsFingerprints* and
+        *TopologicalPharmacophoreAtomTripletsFingerprints*. It corresponds
+        to normalization methodology to use for scaling the number of
+        bits-set or unique keys during generation of fingerprints. Possible
+        values during *ExtendedConnectivityFingerprints*: *None or
+        ByHeavyAtomsCount*; Default value: *None*. Possible values during
+        topological pharmacophore atom pairs and tripletes fingerprints:
+        *None or ByPossibleKeysCount*; Default value: *None*.
+        *ByPossibleKeysCount* corresponds to total number of possible
+        topological pharmacophore atom pairs or triplets in a molecule.
+
+        Examples of *MolecularComplexity* name and value parameters:
+
+            MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
+            AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC
+
+            MolecularComplexityType,ExtendedConnectivityFingerprints,
+            AtomIdentifierType,AtomicInvariantsAtomTypes,
+            AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
+            NormalizationMethodology,None
+
+            MolecularComplexityType,MACCSKeys,MACCSKeysSize,166
+
+            MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
+            AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
+            1,MaxPathLength,8,UseBondSymbols,Yes
+
+            MolecularComplexityType,TopologicalAtomPairsFingerprints,
+            AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
+            AS X BO H FC,MinDistance,1,MaxDistance,10
+
+            MolecularComplexityType,TopologicalAtomTripletsFingerprints,
+            AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
+            AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No
+
+            MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
+            AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
+            AS X BO H FC
+
+            MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
+            AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
+            HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
+            None
+
+            MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
+            AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
+            HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
+            None,UseTriangleInequality,Yes,NormalizationMethodology,None,
+            DistanceBinSize,2
+
+    --OutDelim *comma | tab | semicolon*
+        Delimiter for output CSV/TSV text file(s). Possible values: *comma,
+        tab, or semicolon* Default value: *comma*.
+
+    --output *SD | text | both*
+        Type of output files to generate. Possible values: *SD, text, or
+        both*. Default value: *text*.
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    --Precision *Name,Number,[Name,Number,..]*
+        Precision of calculated property values in the output file: it's a
+        comma delimited list of property name and precision value pairs.
+        Possible property names: *MolecularWeight, ExactMass*. Possible
+        values: positive intergers. Default value: *MolecularWeight,2,
+        ExactMass,4*.
+
+        Examples:
+
+            ExactMass,3
+            MolecularWeight,1,ExactMass,2
+
+    -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><PhysicochemicalProperties>.<Ext>. The
+        file type determines <Ext> value. The sdf, csv, and tsv <Ext> values
+        are used for SD, comma/semicolon, and tab delimited text files,
+        respectively.This option is ignored for multiple input files.
+
+    --RotatableBonds *Name,Value, [Name,Value,...]*
+        Parameters to control calculation of rotatable bonds [ Ref 92 ]:
+        it's a comma delimited list of parameter name and value pairs.
+        Possible parameter names: *IgnoreTerminalBonds,
+        IgnoreBondsToTripleBonds, IgnoreAmideBonds, IgnoreThioamideBonds,
+        IgnoreSulfonamideBonds*. Possible parameter values: *Yes or No*. By
+        default, value of all parameters is set to *Yes*.
+
+    --RuleOf3Violations *Yes | No*
+        Specify whether to calculate RuleOf3Violations for SDFile(s).
+        Possible values: *Yes or No*. Default value: *No*.
+
+        For *Yes* value of RuleOf3Violations, in addition to calculating
+        total number of RuleOf3 violations, individual violations for
+        compounds are also written to output files.
+
+        RuleOf3 [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <=
+        3, HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3,
+        and TPSA <= 60.
+
+    --RuleOf5Violations *Yes | No*
+        Specify whether to calculate RuleOf5Violations for SDFile(s).
+        Possible values: *Yes or No*. Default value: *No*.
+
+        For *Yes* value of RuleOf5Violations, in addition to calculating
+        total number of RuleOf5 violations, individual violations for
+        compounds are also written to output files.
+
+        RuleOf5 [ Ref 91 ] states: MolecularWeight <= 500,
+        HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
+
+    --TPSA *Name,Value, [Name,Value,...]*
+        Parameters to control calculation of TPSA: it's a comma delimited
+        list of parameter name and value pairs. Possible parameter names:
+        *IgnorePhosphorus, IgnoreSulfur*. Possible parameter values: *Yes or
+        No*. By default, value of all parameters is set to *Yes*.
+
+        By default, TPSA atom contributions from Phosphorus and Sulfur atoms
+        are not included during TPSA calculations. [ Ref 91 ]
+
+    -w, --WorkingDir *DirName*
+        Location of working directory. Default value: current directory.
+
+EXAMPLES
+    To calculate default set of physicochemical properties -
+    MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds,
+    HydrogenBondDonor, HydrogenBondAcceptors, SLogP, TPSA - and generate a
+    SamplePhysicochemicalProperties.csv file containing sequential compound
+    IDs along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate both
+    SampleAllProperties.csv and SampleAllProperties.sdf files containing
+    sequential compound IDs in CSV file along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All --output both
+          -r SampleAllProperties -o Sample.sdf
+
+    To calculate RuleOf5 physicochemical properties and generate a
+    SampleRuleOf5Properties.csv file containing sequential compound IDs
+    along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m RuleOf5
+          -r SampleRuleOf5Properties -o Sample.sdf
+
+    To calculate RuleOf5 physicochemical properties along with counting
+    RuleOf5 violations and generate a SampleRuleOf5Properties.csv file
+    containing sequential compound IDs along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
+          -r SampleRuleOf5Properties -o Sample.sdf
+
+    To calculate RuleOf3 physicochemical properties and generate a
+    SampleRuleOf3Properties.csv file containing sequential compound IDs
+    along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m RuleOf3
+          -r SampleRuleOf3Properties -o Sample.sdf
+
+    To calculate RuleOf3 physicochemical properties along with counting
+    RuleOf3 violations and generate a SampleRuleOf3Properties.csv file
+    containing sequential compound IDs along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes
+          -r SampleRuleOf3Properties -o Sample.sdf
+
+    To calculate a specific set of physicochemical properties and generate a
+    SampleProperties.csv file containing sequential compound IDs along with
+    properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings"
+          -r SampleProperties -o Sample.sdf
+
+    To calculate HydrogenBondDonors and HydrogenBondAcceptors using
+    HydrogenBondsType1 definition and generate a SampleProperties.csv file
+    containing sequential compound IDs along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors"
+          --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf
+
+    To calculate TPSA using sulfur and phosphorus atoms along with nitrogen
+    and oxygen atoms and generate a SampleProperties.csv file containing
+    sequential compound IDs along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No,
+          IgnoreSulfur,No" -r SampleProperties -o Sample.sdf
+
+    To calculate MolecularComplexity using extendend connectivity
+    fingerprints corresponding to atom neighborhood radius of 2 with atomic
+    invariant atom types without any scaling and generate a
+    SampleProperties.csv file containing sequential compound IDs along with
+    properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity
+          "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2,
+          AtomIdentifierType, AtomicInvariantsAtomTypes,
+          AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None"
+          -r SampleProperties -o Sample.sdf
+
+    To calculate RuleOf5 physicochemical properties along with counting
+    RuleOf5 violations and generate a SampleRuleOf5Properties.csv file
+    containing compound IDs from molecule name line along with properties
+    data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
+          --DataFieldsMode CompoundID --CompoundIDMode MolName
+          -r SampleRuleOf5Properties -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate a
+    SampleAllProperties.csv file containing compound ID using specified data
+    field along with along with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All
+          --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID
+          -r SampleAllProperties -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate a
+    SampleAllProperties.csv file containing compound ID using combination of
+    molecule name line and an explicit compound prefix along with properties
+    data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All
+          --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
+          --CompoundID Cmpd --CompoundIDLabel MolID  -r SampleAllProperties
+          -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate a
+    SampleAllProperties.csv file containing specific data fields columns
+    along with with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All
+          --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties
+          -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate a
+    SampleAllProperties.csv file containing common data fields columns along
+    with with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All
+          --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf
+
+    To calculate all available physicochemical properties and generate both
+    SampleAllProperties.csv and CSV files containing all data fields columns
+    in CSV files along with with properties data, type:
+
+        % CalculatePhysicochemicalProperties.pl -m All
+          --DataFieldsMode All  --output both -r SampleAllProperties
+          -o Sample.sdf
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    ExtractFromSDtFiles.pl, ExtractFromTextFiles.pl, InfoSDFiles.pl,
+    InfoTextFiles.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.
+