MayaChemTools:Documentation:Fingerprints::EStateIndiciesFingerprints.pm

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Fingerprints::EStateIndiciesFingerprints.pm

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NAME

EStateIndiciesFingerprints

SYNOPSIS

use EStateIndiciesFingerprints;

use EStateIndiciesFingerprints qw(:all);

DESCRIPTION

EStateIndiciesFingerprints [ Ref 75-78 ] class provides the following methods:

new, GenerateFingerprints, SetEStateAtomTypesSetToUse , SetValuesPrecision, StringifyEStateIndiciesFingerprints

EStateIndiciesFingerprints 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:

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

E-state atom types are assigned to all non-hydrogen atoms in a molecule using module AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values, EStateIndiciesFingerprints constituting sum of E-state values for E-sate atom types are generated.

Two types of E-state atom types set size are allowed:

ArbitrarySize - Corresponds to only E-state atom types detected in molecule
FixedSize - Corresponds to fixed number of E-state atom types previously defined

Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to non-hydrogen atoms in the molecule, is able to assign atom types to any valid atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in Ref 77 ] are used for fingerprints.

The fixed size E-state atom type set size used during generation of fingerprints contains 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with MayaChemTools.

Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of E-state indicies fingerprints:

Type EStateAtomTypesSetToUse

EStateIndicies ArbitrarySize [ default fingerprints ]
EStateIndicies FixedSize

The current release of MayaChemTools generates the following types of E-state fingerprints vector strings:

EStateIndicies;9;NumericalValues;IDsAndValuesString;SdNH SdO SdssC SsCH
3 SsNH2 SsOH SssCH2 SssNH SsssCH;7.418 22.984 -1.583 5.387 5.400 19.852
1.737 5.624 -3.319

FingerprintsVector;EStateIndicies;87;OrderedNumericalValues;ValuesString
;0 0 0 0 0 0 0 5.387 0 1.737 0 0 0 -3.319 0 0 -1.583 0 0 0 0 5.400 0 7.
418 5.624 0 0 0 0 0 0 0 0 0 19.852 22.984 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

FingerprintsVector;EStateIndicies;87;OrderedNumericalValues;IDsAndValues
String;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3 SdCH2 SssCH2
StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC SssssC SsNH3p SsNH2
SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN SddsN SaasN Sss...
;0 0 0 0 0 0 0 5.387 0 1.737 0 0 0 -3.319 0 0 -1.583 0 0 0 0 5.400 0
7.418 5.624 0 0 0 0 0 0 0 0 0 19.852 22.984 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...

METHODS

new: $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);; Using specified EStateIndiciesFingerprints 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 = 'EStateIndicies'
EStateAtomTypesSetToUse = 'ArbitrarySize'
ValuesPrecision = 3; Examples:; $EStateIndiciesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'EStateAtomTypesSetToUse' => 'ArbitrarySize');; $EStateIndiciesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'EStateAtomTypesSetToUse' => 'FixedSize');; $EStateIndiciesFingerprints->GenerateFingerprints();
print "$EStateIndiciesFingerprints\n";
GenerateFingerprints: $EStateIndiciesFingerprints = $EStateIndiciesFingerprints-> GenerateEStateIndiciesFingerprints();; Generates EState keys fingerprints and returns EStateIndiciesFingerprints.
SetEStateAtomTypesSetToUse: $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($Value);; Sets Value of EStateAtomTypesSetToUse and returns EStateIndiciesFingerprints. Possible values: ArbitrarySize or FixedSize. Default value: ArbitrarySize.
SetValuesPrecision: $EStateIndiciesFingerprints->SetValuesPrecision($Precision);; Sets precesion of E-state values to use during generation of E-state indices fingerprints and returns EStateIndiciesFingerprints. Possible values: Positive integers. Default value: 3.
StringifyEStateIndiciesFingerprints: $String = $EStateIndiciesFingerprints->StringifyEStateIndiciesFingerprints();; Returns a string containing information about EStateIndiciesFingerprints object.

AUTHOR

Manish Sud

COPYRIGHT

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.