diff docs/modules/txt/EStateIndiciesFingerprints.txt @ 0:4816e4a8ae95 draft default tip

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+NAME
+    EStateIndiciesFingerprints
+
+SYNOPSIS
+    use Fingerprints::EStateIndiciesFingerprints;
+
+    use Fingerprints::EStateIndiciesFingerprints qw(:all);
+
+DESCRIPTION
+    EStateIndiciesFingerprints [ Ref 75-78 ] class provides the following
+    methods:
+
+    new, GenerateFingerprints, GetDescription, 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:
+
+        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...
+
+  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*.
+
+    GetDescription
+            $Description = $EStateIndiciesFingerprints->GetDescription();
+
+        Returns a string containing description of EState keys fingerprints.
+
+    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 <[e-mail]>
+
+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
+
+COPYRIGHT
+    Copyright (C) 2015 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.
+