NAME
    MolecularComplexityDescriptors

SYNOPSIS
    use MolecularDescriptors::MolecularComplexityDescriptors;

    use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);

DESCRIPTION
    MolecularComplexityDescriptors class provides the following methods:

    new, GenerateDescriptors, GetDescriptorNames,
    GetMolecularComplexityTypeAbbreviation, MACCSKeysSize,
    SetAtomIdentifierType, SetAtomicInvariantsToUse, SetDistanceBinSize,
    SetFunctionalClassesToUse, SetMaxDistance, SetMaxPathLength,
    SetMinDistance, SetMinPathLength, SetMolecularComplexityType,
    SetNeighborhoodRadius, SetNormalizationMethodology,
    StringifyMolecularComplexityDescriptors

    MolecularComplexityDescriptors is derived from MolecularDescriptors
    class which in turn is derived from ObjectProperty base class that
    provides methods not explicitly defined in
    MolecularComplexityDescriptors, MolecularDescriptors or ObjectProperty
    classes using Perl's AUTOLOAD functionality. These methods are generated
    on-the-fly for a specified object property:

        Set<PropertyName>(<PropertyValue>);
        $PropertyValue = Get<PropertyName>();
        Delete<PropertyName>();

    The current release of MayaChemTools supports calculation of molecular
    complexity using *MolecularComplexityType* parameter corresponding to
    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 corresponds 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 following values of
    *MolecularComplexityType*: *MACCSKeys,
    TopologicalPharmacophoreAtomPairsFingerprints,
    TopologicalPharmacophoreAtomTripletsFingerprints*.
    *FunctionalClassAtomTypes* is the only valid value of
    *AtomIdentifierType* for topological pharmacophore fingerprints.

    Default value for *AtomIdentifierType*: *AtomicInvariantsAtomTypes* for
    all fingerprints; *FunctionalClassAtomTypes* for topological
    pharmacophore fingerprints.

    *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

    *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

    *MACCSKeysSize* parameter name is only used during *MACCSKeys* value of
    *MolecularComplexityType* and corresponds to 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 corresponds 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 triplets fingerprints: *None or ByPossibleKeysCount*; Default
    value: *None*. *ByPossibleKeysCount* corresponds to total number of
    possible topological pharmacophore atom pairs or triplets in a molecule.

  METHODS
    new
            $NewMolecularComplexityDescriptors = new MolecularDescriptors::
                                                 MolecularComplexityDescriptors(
                                                     %NamesAndValues);

        Using specified *MolecularComplexityDescriptors* property names and
        values hash, new method creates a new object and returns a reference
        to newly created MolecularComplexityDescriptors object. By default,
        the following properties are initialized:

            Molecule = ''
            Type = 'MolecularComplexity'
            MolecularComplexityType = 'MACCSKeys'
            AtomIdentifierType = ''
            MACCSKeysSize = 166
            NeighborhoodRadius = 2
            MinPathLength = 1
            MaxPathLength = 8
            UseBondSymbols = 1
            MinDistance = 1
            MaxDistance = 10
            UseTriangleInequality = ''
            DistanceBinSize = 2
            NormalizationMethodology = 'None'
            @DescriptorNames = ('MolecularComplexity')
            @DescriptorValues = ('None')

        Examples:

            $MolecularComplexityDescriptors = new MolecularDescriptors::
                                              MolecularComplexityDescriptors(
                                              'Molecule' => $Molecule);

            $MolecularComplexityDescriptors = new MolecularDescriptors::
                                              MolecularComplexityDescriptors();

            $MolecularComplexityDescriptors->SetMolecule($Molecule);
            $MolecularComplexityDescriptors->GenerateDescriptors();
            print "MolecularComplexityDescriptors: $MolecularComplexityDescriptors\n";

    GenerateDescriptors
            $MolecularComplexityDescriptors->GenerateDescriptors();

        Calculates MolecularComplexity value for a molecule and returns
        *MolecularComplexityDescriptors*.

    GetDescriptorNames
            @DescriptorNames = $MolecularComplexityDescriptors->GetDescriptorNames();
            @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
                               GetDescriptorNames();

        Returns all available descriptor names as an array.

    GetMolecularComplexityTypeAbbreviation
            $Abbrev = $MolecularComplexityDescriptors->
                          GetMolecularComplexityTypeAbbreviation();
            $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
                          GetMolecularComplexityTypeAbbreviation($ComplexityType);

        Returns abbreviation for a specified molecular complexity type or
        corresponding to *MolecularComplexityDescriptors* object.

    SetMACCSKeysSize
            $MolecularComplexityDescriptors->MACCSKeysSize($Size);

        Sets MACCS keys size and returns *MolecularComplexityDescriptors*.

    SetAtomIdentifierType
            $MolecularComplexityDescriptors->SetAtomIdentifierType($IdentifierType);

        Sets atom *IdentifierType* to use during fingerprints generation
        corresponding to *MolecularComplexityType* and returns
        *MolecularComplexityDescriptors*.

        Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
        EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
        SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.

    SetAtomicInvariantsToUse
            $MolecularComplexityDescriptors->SetAtomicInvariantsToUse($ValuesRef);
            $MolecularComplexityDescriptors->SetAtomicInvariantsToUse(@Values);

        Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
        value of *AtomIdentifierType* for fingerprints generation and
        returns *MolecularComplexityDescriptors*.

        Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
        TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
        *AS,X,BO,H,FC,MN*.

        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.

    SetDistanceBinSize
            $MolecularComplexityDescriptors->SetDistanceBinSize($BinSize);

        Sets distance bin size used to bin distances between atom pairs in
        atom triplets for topological pharmacophore atom triplets
        fingerprints generation and returns
        *MolecularComplexityDescriptors*.

    SetFunctionalClassesToUse
            $MolecularComplexityDescriptors->SetFunctionalClassesToUse($ValuesRef);
            $MolecularComplexityDescriptors->SetFunctionalClassesToUse(@Values);

        Sets functional classes invariants to use during
        *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
        fingerprints generation and returns
        *MolecularComplexityDescriptors*.

        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 or None

        *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

    SetMaxDistance
            $MolecularComplexityDescriptors->SetMaxDistance($MaxDistance);

        Sets maximum distance to use during topological atom pairs and
        triplets fingerprints generation and returns
        *MolecularComplexityDescriptors*.

    SetMaxPathLength
            $MolecularComplexityDescriptors->SetMaxPathLength($Length);

        Sets maximum path length to use during path length fingerprints
        generation and returns *MolecularComplexityDescriptors*.

    SetMinDistance
            $MolecularComplexityDescriptors->SetMinDistance($MinDistance);

        Sets minimum distance to use during topological atom pairs and
        triplets fingerprints generation and returns
        *MolecularComplexityDescriptors*.

    SetMinPathLength
            $MolecularComplexityDescriptors->SetMinPathLength($MinPathLength);

        Sets minimum path length to use during path length fingerprints
        generation and returns *MolecularComplexityDescriptors*.

    SetMolecularComplexityType
            $MolecularComplexityDescriptors->SetMolecularComplexityType($ComplexityType);

        Sets molecular complexity type to use for calculating its value and
        returns *MolecularComplexityDescriptors*.

    SetNeighborhoodRadius
            $MolecularComplexityDescriptors->SetNeighborhoodRadius($Radius);

        Sets neighborhood radius to use during extended connectivity
        fingerprints generation and returns
        *MolecularComplexityDescriptors*.

    SetNormalizationMethodology
            $MolecularComplexityDescriptors->SetNormalizationMethodology($Methodology);

        Sets normalization methodology to use during calculation of
        molecular complexity corresponding to extended connectivity,
        topological pharmacophore atom pairs and tripletes fingerprints
        returns *MolecularComplexityDescriptors*.

    StringifyMolecularComplexityDescriptors
            $String = $MolecularComplexityDescriptors->
                          StringifyMolecularComplexityDescriptors();

        Returns a string containing information about
        *MolecularComplexityDescriptors* object.

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm

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.

