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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Documentation:MolecularDescriptors::RotatableBondsDescriptors.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
6 </head> | |
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
8 <br/> | |
9 <center> | |
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
11 </center> | |
12 <br/> | |
13 <div class="DocNav"> | |
14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::RotatableBondsDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/RotatableBondsDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/RotatableBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/RotatableBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/RotatableBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/RotatableBondsDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> | |
16 </table> | |
17 </div> | |
18 <p> | |
19 </p> | |
20 <h2>NAME</h2> | |
21 <p>RotatableBondsDescriptors</p> | |
22 <p> | |
23 </p> | |
24 <h2>SYNOPSIS</h2> | |
25 <p>use MolecularDescriptors::RotatableBondsDescriptors;</p> | |
26 <p>use MolecularDescriptors::RotatableBondsDescriptors qw(:all);</p> | |
27 <p> | |
28 </p> | |
29 <h2>DESCRIPTION</h2> | |
30 <p><strong>RotatableBondsDescriptors</strong> class provides the following methods:</p> | |
31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a> | |
32 , <a href="#stringifyrotatablebondsdescriptors">StringifyRotatableBondsDescriptors</a> | |
33 </p><p><strong>RotatableBondsDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn | |
34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined | |
35 in <strong>RotatableBondsDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's | |
36 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> | |
37 <div class="OptionsBox"> | |
38 Set<PropertyName>(<PropertyValue>); | |
39 <br/> $PropertyValue = Get<PropertyName>(); | |
40 <br/> Delete<PropertyName>();</div> | |
41 <p>A rotatable bond [ Ref 92 ] is defined as any single bond which is not in a ring and involves only non-hydrogen | |
42 atoms. By default, the following types of single bonds are not considered rotatable bonds:</p> | |
43 <div class="OptionsBox"> | |
44 o Terminal bonds | |
45 <br/> o Bonds attached to triple bonds | |
46 <br/> o Amide C-N bonds | |
47 <br/> o Thioamide C-N bond bonds | |
48 <br/> o Sulfonamide S-N bonds</div> | |
49 <p> | |
50 </p> | |
51 <h2>METHODS</h2> | |
52 <dl> | |
53 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
54 <dd> | |
55 <div class="OptionsBox"> | |
56 $RotatableBondsDescriptors = new MolecularDescriptors:: | |
57 RotatableBondsDescriptors( | |
58 %NamesAndValues);</div> | |
59 <p>Using specified <em>RotatableBondsDescriptors</em> property names and values hash, <strong>new</strong> | |
60 method creates a new object and returns a reference to newly created <strong>RotatableBondsDescriptors</strong> | |
61 object. By default, the following properties are initialized:</p> | |
62 <div class="OptionsBox"> | |
63 Molecule = '' | |
64 <br/> Type = 'RotatableBonds' | |
65 <br/> IgnoreTerminalBonds = 1 | |
66 <br/> IgnoreBondsToTripleBonds = 1 | |
67 <br/> IgnoreAmideBonds = 1 | |
68 <br/> IgnoreThioamideBonds = 1 | |
69 <br/> IgnoreSulfonamideBonds = 1 | |
70 <br/> @DescriptorNames = ('RotatableBonds') | |
71 <br/> @DescriptorValues = ('None')</div> | |
72 <p>Examples:</p> | |
73 <div class="OptionsBox"> | |
74 $RotatableBondsDescriptors = new MolecularDescriptors:: | |
75 RotatableBondsDescriptors();</div> | |
76 <div class="OptionsBox"> | |
77 $RotatableBondsDescriptors = new MolecularDescriptors:: | |
78 RotatableBondsDescriptors( | |
79 'IgnoreAmideBonds' => 0, | |
80 'IgnoreThioamideBonds' => 0, | |
81 'IgnoreSulfonamideBonds' => 0);</div> | |
82 <div class="OptionsBox"> | |
83 $RotatableBondsDescriptors->SetMolecule($Molecule); | |
84 <br/> $RotatableBondsDescriptors->GenerateDescriptors(); | |
85 <br/> print "RotatableBondsDescriptors: $RotatableBondsDescriptors\n";</div> | |
86 </dd> | |
87 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> | |
88 <dd> | |
89 <div class="OptionsBox"> | |
90 $RotatableBondsDescriptors->GenerateDescriptors();</div> | |
91 <p>Calculates number of rotatable bonds descriptors in a molecule and returns | |
92 <em>RotatableBondsDescriptors</em>.</p> | |
93 </dd> | |
94 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> | |
95 <dd> | |
96 <div class="OptionsBox"> | |
97 @DescriptorNames = $RotatableBondsDescriptors->GetDescriptorNames(); | |
98 <br/> @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors:: | |
99 GetDescriptorNames();</div> | |
100 <p>Returns all available descriptor names as an array.</p> | |
101 </dd> | |
102 <dt><strong><a name="stringifyrotatablebondsdescriptors" class="item"><strong>StringifyRotatableBondsDescriptors</strong></a></strong></dt> | |
103 <dd> | |
104 <div class="OptionsBox"> | |
105 $String = $RotatableBondsDescriptors->StringifyRotatableBondsDescriptors();</div> | |
106 <p>Returns a string containing information about <em>RotatableBondsDescriptors</em> object.</p> | |
107 </dd> | |
108 </dl> | |
109 <p> | |
110 </p> | |
111 <h2>AUTHOR</h2> | |
112 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
113 <p> | |
114 </p> | |
115 <h2>SEE ALSO</h2> | |
116 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> | |
117 </p> | |
118 <p> | |
119 </p> | |
120 <h2>COPYRIGHT</h2> | |
121 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
122 <p>This file is part of MayaChemTools.</p> | |
123 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
124 the terms of the GNU Lesser General Public License as published by the Free | |
125 Software Foundation; either version 3 of the License, or (at your option) | |
126 any later version.</p> | |
127 <p> </p><p> </p><div class="DocNav"> | |
128 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
129 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::RotatableBondsDescriptors.pm</strong></td></tr> | |
130 </table> | |
131 </div> | |
132 <br /> | |
133 <center> | |
134 <img src="../../images/h2o2.png"> | |
135 </center> | |
136 </body> | |
137 </html> |