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.\" ========================================================================
.\"
.IX Title "ESTATEINDICIESFINGERPRINTS 1"
.TH ESTATEINDICIESFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
EStateIndiciesFingerprints
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use Fingerprints::EStateIndiciesFingerprints;
.PP
use Fingerprints::EStateIndiciesFingerprints qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBEStateIndiciesFingerprints\fR [ Ref 75\-78 ] class provides the following methods:
.PP
new, GenerateFingerprints, GetDescription, SetEStateAtomTypesSetToUse,
SetValuesPrecision, StringifyEStateIndiciesFingerprints
.PP
\&\fBEStateIndiciesFingerprints\fR is derived from \fBFingerprints\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBAtomNeighborhoodsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
\&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
.PP
.Vb 3
\&    Set<PropertyName>(<PropertyValue>);
\&    $PropertyValue = Get<PropertyName>();
\&    Delete<PropertyName>();
.Ve
.PP
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,
\&\fBEStateIndiciesFingerprints\fR constituting sum of E\-state values for E\-sate atom types
are generated.
.PP
Two types of E\-state atom types set size are allowed:
.PP
.Vb 4
\&    ArbitrarySize \- Corresponds to only E\-state atom types detected
\&                    in molecule
\&    FixedSize \- Corresponds to fixed number of E\-state atom types previously
\&                defined
.Ve
.PP
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 \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR, only a
fixed set of E\-state atom types corresponding to specific atom groups [ Appendix \s-1III\s0 in
Ref 77 ] are used for fingerprints.
.PP
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.
.PP
Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
E\-state indicies fingerprints:
.PP
.Vb 1
\&    Type                        EStateAtomTypesSetToUse
\&
\&    EStateIndicies              ArbitrarySize      [ default fingerprints ]
\&    EStateIndicies              FixedSize
.Ve
.PP
The current release of MayaChemTools generates the following types of E\-state
fingerprints vector strings:
.PP
.Vb 4
\&    FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
\&    AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
\&    H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
\&    .024 \-2.270
\&
\&    FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
\&    ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
\&    4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
\&    4.006 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:FixedSize;87;OrderedNumericalValues;
\&    IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
\&    SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
\&    C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
\&    0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435 4.387 0 0 0
\&    0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 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...
.Ve
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 1
\&    $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);
.Ve
.Sp
Using specified \fIEStateIndiciesFingerprints\fR property names and values hash, \fBnew\fR method creates a new object
and returns a reference to newly created \fBPathLengthFingerprints\fR object. By default, the
following properties are initialized:
.Sp
.Vb 4
\&    Molecule = \*(Aq\*(Aq;
\&    Type = \*(AqEStateIndicies\*(Aq
\&    EStateAtomTypesSetToUse = \*(AqArbitrarySize\*(Aq
\&    ValuesPrecision = 3
.Ve
.Sp
Examples:
.Sp
.Vb 4
\&    $EStateIndiciesFingerprints = new AtomTypesFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqEStateAtomTypesSetToUse\*(Aq =>
\&                                              \*(AqArbitrarySize\*(Aq);
\&
\&    $EStateIndiciesFingerprints = new AtomTypesFingerprints(
\&                              \*(AqMolecule\*(Aq => $Molecule,
\&                              \*(AqEStateAtomTypesSetToUse\*(Aq =>
\&                                              \*(AqFixedSize\*(Aq);
\&
\&    $EStateIndiciesFingerprints\->GenerateFingerprints();
\&    print "$EStateIndiciesFingerprints\en";
.Ve
.IP "\fBGenerateFingerprints\fR" 4
.IX Item "GenerateFingerprints"
.Vb 2
\&    $EStateIndiciesFingerprints = $EStateIndiciesFingerprints\->
\&                                  GenerateEStateIndiciesFingerprints();
.Ve
.Sp
Generates EState keys fingerprints and returns \fIEStateIndiciesFingerprints\fR.
.IP "\fBGetDescription\fR" 4
.IX Item "GetDescription"
.Vb 1
\&    $Description = $EStateIndiciesFingerprints\->GetDescription();
.Ve
.Sp
Returns a string containing description of EState keys fingerprints.
.IP "\fBSetEStateAtomTypesSetToUse\fR" 4
.IX Item "SetEStateAtomTypesSetToUse"
.Vb 1
\&    $EStateIndiciesFingerprints\->SetEStateAtomTypesSetToUse($Value);
.Ve
.Sp
Sets \fIValue\fR of \fIEStateAtomTypesSetToUse\fR and returns \fIEStateIndiciesFingerprints\fR.
Possible values: \fIArbitrarySize or FixedSize\fR. Default value: \fIArbitrarySize\fR.
.IP "\fBSetValuesPrecision\fR" 4
.IX Item "SetValuesPrecision"
.Vb 1
\&    $EStateIndiciesFingerprints\->SetValuesPrecision($Precision);
.Ve
.Sp
Sets precesion of E\-state values to use during generation of E\-state indices fingerprints
and returns \fIEStateIndiciesFingerprints\fR. Possible values: \fIPositive integers\fR.
Default value: \fI3\fR.
.IP "\fBStringifyEStateIndiciesFingerprints\fR" 4
.IX Item "StringifyEStateIndiciesFingerprints"
.Vb 1
\&    $String = $EStateIndiciesFingerprints\->StringifyEStateIndiciesFingerprints();
.Ve
.Sp
Returns a string containing information about \fIEStateIndiciesFingerprints\fR object.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
TopologicalPharmacophoreAtomTripletsFingerprints.pm
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.