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NAME

AtomTypesFingerprints

SYNOPSIS

use AtomTypesFingerprints;

use AtomTypesFingerprints qw(:all);

DESCRIPTION

AtomTypesFingerprints class provides the following methods:

new, GenerateFingerprints, SetAtomIdentifierType, SetAtomTypesSetToUse , SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetType , StringifyAtomTypesFingerprints

AtomTypesFingerprints is derived from Fingerprints class which in turn is derived from ObjectProperty base class that provides methods not explicitly defined in AtomNeighborhoodsFingerprints, 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 AtomTypesFingerpritns corresponding to following AtomIdentifierTypes:

Based on the values specified for AtomIdentifierType along with other specified parameters such as AtomicInvariantsToUse and FunctionalClassesToUse, initial atom types are assigned to all non-hydrogen atoms or all atoms in a molecule.

Using the assigned atom types and specified Type, one of the following types of fingerprints are generated:

For AtomTypesCount fingerprints, two types of atom types set size is allowed:

For AtomTypesBits fingerprints, only FixedSize atom type set is allowed.

ArbitrarySize corresponds to atom types detected in a molecule where as FixedSize implies a fix number of all possible atom types previously defined for a specific AtomIdentifierType.

Fix number of all possible atom types for supported AtomIdentifierTypes in current release of MayaChemTools are:

Combination of Type and AtomTypesSetToUse along with AtomtomIdentifierType allows generation of following different atom types fingerprints:

The current release of MayaChemTools generates the following types of atom types fingerprints bit-vector and vector strings:

METHODS

new

$NewAtomTypesFingerprints = new AtomTypesFingerprints(%NamesAndValues);

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

Molecule = '';
Type = ''
AtomIdentifierType = ''
AtomTypesSetToUse = ''
IgnoreHydrogens = 1
AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']

Examples:

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes');

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => 'AtomicInvariantsAtomTypes', 'AtomicInvariantsToUse' => ['AS', 'X', 'BO', 'H', 'FC'] );

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => 'DREIDINGAtomTypes');

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => 'EStateAtomTypes', 'AtomTypesSetToUse' => 'ArbitrarySize');

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => 'SLogPAtomTypes', 'AtomTypesSetToUse' => 'FixedSize');

$AtomTypesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'Type' => 'AtomTypesBits', 'AtomIdentifierType' => 'MMFF94AtomTypes', 'AtomTypesSetToUse' => 'FixedSize');

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

GenerateFingerprints

$AtomTypesFingerprints->GenerateFingerprints();

Generates atom types fingerprints and returns AtomTypesFingerprints.

SetAtomIdentifierType

$AtomTypesFingerprints->SetAtomIdentifierType($IdentifierType);

Sets atom IdentifierType to use during atom types fingerprints generation and returns AtomTypesFingerprints.

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

SetAtomTypesSetToUse

$AtomTypesFingerprints->SetAtomTypesSetToUse($Value);

Sets Value of AtomTypesSetToUse and returns AtomTypesFingerprints. Possible values: ArbitrarySize or FixedSize. Default for AtomTypesCount value of AtomTypesSetToUse: ArbitrarySize.

SetAtomicInvariantsToUse

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

Sets atomic invariants to use during AtomicInvariantsAtomTypes value of AtomIdentifierType for atom neighborhood fingerprints generation and returns AtomTypesFingerprints.

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.

SetFunctionalClassesToUse

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

Sets functional classes invariants to use during FunctionalClassAtomTypes value of AtomIdentifierType for atom types fingerprints generation and returns AtomTypesFingerprints.

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

SetType

$AtomTypesFingerprints->SetType($Type);

Sets type of AtomTypes fingerpritns and returns AtomTypesFingerprints. Possible values: AtomTypesFingerprintsBits or AtomTypesFingerprintsCount.

StringifyAtomTypesFingerprints

$String = $AtomTypesFingerprints->StringifyAtomTypesFingerprints();

Returns a string containing information about AtomTypesFingerprints object.

AUTHOR

Manish Sud

SEE ALSO

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

COPYRIGHT

Copyright (C) 2004-2010 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.