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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:

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:

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:

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:

for all fingerprints except for the following two MolecularComplexityType fingerints:

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

SEE ALSO

MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm

COPYRIGHT

Copyright (C) 2024 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.