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

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+++ b/docs/modules/txt/RotatableBondsDescriptors.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    RotatableBondsDescriptors
+
+SYNOPSIS
+    use MolecularDescriptors::RotatableBondsDescriptors;
+
+    use MolecularDescriptors::RotatableBondsDescriptors qw(:all);
+
+DESCRIPTION
+    RotatableBondsDescriptors class provides the following methods:
+
+    new, GenerateDescriptors, GetDescriptorNames,
+    StringifyRotatableBondsDescriptors
+
+    RotatableBondsDescriptors is derived from MolecularDescriptors class
+    which in turn is derived from ObjectProperty base class that provides
+    methods not explicitly defined in RotatableBondsDescriptors,
+    MolecularDescriptors 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>();
+
+    A rotatable bond [ Ref 92 ] is defined as any single bond which is not
+    in a ring and involves only non-hydrogen atoms. By default, the
+    following types of single bonds are not considered rotatable bonds:
+
+        o Terminal bonds
+        o Bonds attached to triple bonds
+        o Amide C-N bonds
+        o Thioamide C-N bond bonds
+        o Sulfonamide S-N bonds
+
+  METHODS
+    new
+            $RotatableBondsDescriptors = new MolecularDescriptors::
+                                         RotatableBondsDescriptors(
+                                         %NamesAndValues);
+
+        Using specified *RotatableBondsDescriptors* property names and
+        values hash, new method creates a new object and returns a reference
+        to newly created RotatableBondsDescriptors object. By default, the
+        following properties are initialized:
+
+            Molecule = ''
+            Type = 'RotatableBonds'
+            IgnoreTerminalBonds = 1
+            IgnoreBondsToTripleBonds = 1
+            IgnoreAmideBonds = 1
+            IgnoreThioamideBonds = 1
+            IgnoreSulfonamideBonds = 1
+            @DescriptorNames = ('RotatableBonds')
+            @DescriptorValues = ('None')
+
+        Examples:
+
+            $RotatableBondsDescriptors = new MolecularDescriptors::
+                                         RotatableBondsDescriptors();
+
+            $RotatableBondsDescriptors = new MolecularDescriptors::
+                                         RotatableBondsDescriptors(
+                                         'IgnoreAmideBonds' => 0,
+                                         'IgnoreThioamideBonds' => 0,
+                                         'IgnoreSulfonamideBonds' => 0);
+
+            $RotatableBondsDescriptors->SetMolecule($Molecule);
+            $RotatableBondsDescriptors->GenerateDescriptors();
+            print "RotatableBondsDescriptors: $RotatableBondsDescriptors\n";
+
+    GenerateDescriptors
+            $RotatableBondsDescriptors->GenerateDescriptors();
+
+        Calculates number of rotatable bonds descriptors in a molecule and
+        returns *RotatableBondsDescriptors*.
+
+    GetDescriptorNames
+            @DescriptorNames = $RotatableBondsDescriptors->GetDescriptorNames();
+            @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors::
+                               GetDescriptorNames();
+
+        Returns all available descriptor names as an array.
+
+    StringifyRotatableBondsDescriptors
+            $String = $RotatableBondsDescriptors->StringifyRotatableBondsDescriptors();
+
+        Returns a string containing information about
+        *RotatableBondsDescriptors* object.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    MolecularDescriptors.pm, MolecularDescriptorsGenerator.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.
+