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

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+++ b/docs/modules/txt/TPSADescriptors.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    TPSADescriptors
+
+SYNOPSIS
+    use MolecularDescriptors::TPSADescriptors;
+
+    use MolecularDescriptors::TPSADescriptors qw(:all);
+
+DESCRIPTION
+    TPSADescriptors class provides the following methods:
+
+    new, GenerateDescriptors, GetDescriptorNames, StringifyTPSADescriptors
+
+    TPSADescriptors is derived from MolecularDescriptors class which in turn
+    is derived from ObjectProperty base class that provides methods not
+    explicitly defined in TPSADescriptors, 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>();
+
+    After Topological Polar Surface Area (TPSA) atom types [ Ref 90-91 ] has
+    been assigned to appropriate atoms in a molecule using
+    AtomTypes::TPSAAtomTypes.pm module, TPSA value is calculated by adding
+    up contributions of each appropriate atom type.
+
+    By default, MayaChemTools only uses nitrogen and oxygen atoms during
+    calculation of TPSA and ignores phosphorous and sulfur atoms. [ Ref 90 -
+    91 ]
+
+  METHODS
+    new
+            $NewTPSADescriptors = new MolecularDescriptors::TPSADescriptors(
+                                                           %NamesAndValues);
+
+        Using specified *TPSADescriptors* property names and values hash,
+        new method creates a new object and returns a reference to newly
+        created TPSADescriptors object. By default, the following properties
+        are initialized:
+
+            Molecule = ''
+            Type = 'TPSA'
+            IgnorePhosphorus = 1
+            IgnoreSulfur = 1
+            @DescriptorNames = ('TPSA')
+            @DescriptorValues = ('None')
+
+        Examples:
+
+            $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
+                                      'Molecule' => $Molecule);
+
+            $TPSADescriptors = new MolecularDescriptors::TPSADescriptors();
+
+            $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
+                                      'IgnorePhosphorus' => 0,
+                                      'IgnoreSulfur' => 0);
+
+            $TPSADescriptors->SetMolecule($Molecule);
+            $TPSADescriptors->GenerateDescriptors();
+            print "TPSADescriptors: $TPSADescriptors\n";
+
+    GenerateDescriptors
+            $TPSADescriptors->GenerateDescriptors();
+
+        Calculate TPSA value for a molecule and returns *TPSADescriptors*.
+
+    GetDescriptorNames
+            @DescriptorNames = $TPSADescriptors->GetDescriptorNames();
+            @DescriptorNames = MolecularDescriptors::TPSADescriptors::
+                               GetDescriptorNames();
+
+        Returns all available descriptor names as an array.
+
+    StringifyTPSADescriptors
+            $String = $TPSADescriptors->StringifyTPSADescriptors();
+
+        Returns a string containing information about *TPSADescriptors*
+        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.
+