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NAME

ExtendedConnectivityFingerprints

SYNOPSIS

use Fingerprints::ExtendedConnectivityFingerprints;

use Fingerprints::ExtendedConnectivityFingerprints qw(:all);

DESCRIPTION

ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods:

new, GenerateFingerprints, GetDescription, SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetNeighborhoodRadius, StringifyExtendedConnectivityFingerprints

ExtendedConnectivityFingerprints is derived from Fingerprints class which in turn is derived from ObjectProperty base class that provides methods not explicitly defined in ExtendedConnectivityFingerprints, Fingerprints 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 generation of ExtendedConnectivityFingerprints corresponding to following AtomtomIdentifierTypes:

Based on the values specified for AtomIdentifierType, AtomicInvariantsToUse and FunctionalClassesToUse, initial atom types are assigned to all non-hydrogen atoms in a molecule and these atom types strings are converted into initial atom identifier integers using TextUtil::HashCode function. The duplicate atom identifiers are removed.

For NeighborhoodRadius value of 0, the initial set of unique atom identifiers comprises the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen atom up-to specified NeighborhoodRadius value. For each non-hydrogen central atom at a specific radius, its neighbors at next radius level along with their bond orders and previously calculated atom identifiers are collected which in turn are used to generate a new integer atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order followed by atom identifiers to make these values graph invariant.

After integer atom identifiers have been generated for all non-hydrogen atoms at all specified neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code value generated using TextUtil::HashCode are tracked by keeping the atom identifiers at lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified radius are also tracked by identifying equivalent atom and bonds corresponding to substructures used for generating atom identifier and keeping integer atom identifier with lowest value.

For ExtendedConnnectivity value of fingerprints Type, the duplicate identifiers are removed from the list and the unique atom identifiers constitute the extended connectivity fingerprints of a molecule.

For ExtendedConnnectivityCount value of fingerprints Type, the occurrence of each unique atom identifiers appears is counted and the unique atom identifiers along with their count constitute the extended connectivity fingerprints of a molecule.

For ExtendedConnectivityBits value of fingerprints -m, --mode, the unique atom identifiers are used as a random number seed to generate a random integer value between 0 and --Size which in turn is used to set corresponding bits in the fingerprint bit-vector string.

The current release of MayaChemTools generates the following types of extended connectivity fingerprints vector strings:

METHODS

new

$NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( %NamesAndValues);

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

Molecule = ''
Type = 'ExtendedConnectivity'
NeighborhoodRadius = 2
AtomIdentifierType = ''
AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']

Examples:

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Molecule' => $Molecule, 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivityCount', 'Molecule' => $Molecule, 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivityBits', 'Molecule' => $Molecule, 'Size' => 1024, 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivity', 'Molecule' => $Molecule, 'NeighborhoodRadius' => 2, 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes', 'AtomicInvariantsToUse' => ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivity', 'Molecule' => $Molecule, 'NeighborhoodRadius' => 2, 'AtomIdentifierType' => 'FunctionalClassAtomTypes', 'FunctionalClassesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivity', 'Molecule' => $Molecule,; 'AtomIdentifierType' => 'MMFF94AtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivityCount', 'Molecule' => $Molecule,; 'AtomIdentifierType' => 'MMFF94AtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivityCount', 'Molecule' => $Molecule,; 'AtomIdentifierType' => 'SLogPAtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivity', 'Molecule' => $Molecule,; 'AtomIdentifierType' => 'SLogPAtomTypes');

$ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( 'Type' => 'ExtendedConnectivity', 'Molecule' => $Molecule,; 'AtomIdentifierType' => 'SYBYLAtomTypes');

$ExtendedConnectivityFingerprints->GenerateFingerprints();
print "$ExtendedConnectivityFingerprints\n";

GenerateFingerprints

$ExtendedConnectivityFingerprints->GenerateFingerprints();

Generates extended connectivity fingerprints and returns ExtendedConnectivityFingerprints.

GetDescription

$Description = $ExtendedConnectivityFingerprints->GetDescription();

Returns a string containing description of extended connectivity fingerprints fingerprints.

SetAtomIdentifierType

$ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);

Sets atom IdentifierType to use during extended connectivity fingerprints generation and returns ExtendedConnectivityFingerprints.

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

SetAtomicInvariantsToUse

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

Sets atomic invariants to use during AtomicInvariantsAtomTypes value of AtomIdentifierType for extended connectivity fingerprints generation and returns ExtendedConnectivityFingerprints.

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.

SetFunctionalClassesToUse

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

Sets functional classes invariants to use during FunctionalClassAtomTypes value of AtomIdentifierType for extended connectivity fingerprints generation and returns ExtendedConnectivityFingerprints.

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

SetNeighborhoodRadius

$ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);

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

StringifyExtendedConnectivityFingerprints

$String = $Fingerprints->StringifyExtendedConnectivityFingerprints();

Returns a string containing information about ExtendedConnectivityFingerprints object.

AUTHOR

Manish Sud

SEE ALSO

Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm, TopologicalPharmacophoreAtomTripletsFingerprints.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.