|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:NucleicAcids.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="./MoleculeFileIO.html" title="MoleculeFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ObjectProperty.html" title="ObjectProperty.html">Next</a></td><td width="34%" align="middle"><strong>NucleicAcids.pm</strong></td><td width="33%" align="right"><a href="././code/NucleicAcids.html" title="View source code">Code</a> | <a href="./../pdf/NucleicAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/NucleicAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/NucleicAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/NucleicAcids.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>NucleicAcids</p>
|
|
|
22 <p>
|
|
|
23 </p>
|
|
|
24 <h2>SYNOPSIS</h2>
|
|
|
25 <p>use NucleicAcids;</p>
|
|
|
26 <p>use NucleicAcids qw(:all);</p>
|
|
|
27 <p>
|
|
|
28 </p>
|
|
|
29 <h2>DESCRIPTION</h2>
|
|
|
30 <p><strong>NucleicAcids</strong> module the provides the following functions:</p>
|
|
|
31 <p>GetNucleicAcidPropertiesData, GetNucleicAcidPropertiesNames,
|
|
|
32 GetNucleicAcids, GetNucleicAcidsByType, IsNucleicAcid, IsNucleicAcidProperty,
|
|
|
33 IsNucleicAcidType</p>
|
|
|
34 <p>
|
|
|
35 </p>
|
|
|
36 <h2>Functions</h2>
|
|
|
37 <dl>
|
|
|
38 <dt><strong><a name="getnucleicacids" class="item"><strong>GetNucleicAcids</strong></a></strong></dt>
|
|
|
39 <dd>
|
|
|
40 <div class="OptionsBox">
|
|
|
41 (@Names) = GetNucleicAcids([$NameType]);
|
|
|
42 <br/> $NamesRef = GetNucleicAcids([$NameType]);</div>
|
|
|
43 <p>Returns an array or a reference to an array containing names of nucleic acids
|
|
|
44 as a code or nucleic acid name controlled by optional parameter <em>NameType</em>. By
|
|
|
45 default, nucleic acids names are returned as the code. Possible values for
|
|
|
46 <em>NameType</em>: <em>Code or Name</em>.</p>
|
|
|
47 </dd>
|
|
|
48 <dt><strong><a name="getnucleicacidsbytype" class="item"><strong>GetNucleicAcidsByType</strong></a></strong></dt>
|
|
|
49 <dd>
|
|
|
50 <div class="OptionsBox">
|
|
|
51 (@Names) = GetNucleicAcidsByType([$Type, $NameType]);
|
|
|
52 <br/> $NamesRef = GetNucleicAcidsByType([$Type, $NameType]);</div>
|
|
|
53 <p>Returns an array or a reference to an array containing names of nucleic acids
|
|
|
54 specified by parameter <em>Type</em> as a code or name controlled by optional
|
|
|
55 parameter <em>NameType</em>. Default values for <em>Type</em>: <em>Nucleoside</em>. Default value for
|
|
|
56 <em>NameType</em>: <em>Code</em>. Possible values for <em>Type</em>: <em>Nucleobase, Nucleoside, Deoxynucleoside,
|
|
|
57 Nucleotide, Deoxynucleotide</em>. Possible values for <em>NameType</em>: <em>Code or Name</em>.</p>
|
|
|
58 </dd>
|
|
|
59 <dt><strong><a name="getnucleicacidpropertiesdata" class="item"><strong>GetNucleicAcidPropertiesData</strong></a></strong></dt>
|
|
|
60 <dd>
|
|
|
61 <div class="OptionsBox">
|
|
|
62 $DataHashRef = GetNucleicAcidPropertiesData($NucleicAcidID);</div>
|
|
|
63 <p>Returns a reference to hash containing property names and values for a specified
|
|
|
64 <em>NucleicAcidID</em>.</p>
|
|
|
65 </dd>
|
|
|
66 <dt><strong><a name="getnucleicacidpropertyname" class="item"><strong>GetNucleicAcidPropertyName</strong></a></strong></dt>
|
|
|
67 <dd>
|
|
|
68 <div class="OptionsBox">
|
|
|
69 $Value = GetNucleicAcid<PropertyName>($NucleicAcidID);</div>
|
|
|
70 <p>Returns nucleic acid property value for a specified <em>NucleicAcidID</em>. This function is
|
|
|
71 implemented on-the-fly using Perl's AUTOLOAD functionality.</p>
|
|
|
72 </dd>
|
|
|
73 <dt><strong><a name="getnucleicacidpropertiesnames" class="item"><strong>GetNucleicAcidPropertiesNames</strong></a></strong></dt>
|
|
|
74 <dd>
|
|
|
75 <div class="OptionsBox">
|
|
|
76 @Names = GetNucleicAcidPropertiesNames([$Mode]);
|
|
|
77 <br/> $NamesRef = GetNucleicAcidPropertiesNames([$Mode]);</div>
|
|
|
78 <p>Returns an array or a reference to an array containing names of properties for
|
|
|
79 nucleic acids. Order of nucleic acids properties is controlled by optional parameter
|
|
|
80 <em>Mode</em>. Possible values for <em>Mode</em>: <em>Alphabetical or ByGroup</em>; Default: <em>ByGroup</em>.</p>
|
|
|
81 </dd>
|
|
|
82 <dt><strong><a name="isnucleicacid" class="item"><strong>IsNucleicAcid</strong></a></strong></dt>
|
|
|
83 <dd>
|
|
|
84 <div class="OptionsBox">
|
|
|
85 $Status = IsNucleicAcid($NucleicAcidID);</div>
|
|
|
86 <p>Returns 1 or 0 based on whether it's a known nucleic acid ID.</p>
|
|
|
87 </dd>
|
|
|
88 <dt><strong><a name="isnucleicacidproperty" class="item"><strong>IsNucleicAcidProperty</strong></a></strong></dt>
|
|
|
89 <dd>
|
|
|
90 <div class="OptionsBox">
|
|
|
91 $Status = IsNucleicAcid($PropertyName);</div>
|
|
|
92 <p>Returns 1 or 0 based on whether it's a known nucleic acid property name.</p>
|
|
|
93 </dd>
|
|
|
94 <dt><strong><a name="isnucleicacidtype" class="item"><strong>IsNucleicAcidType</strong></a></strong></dt>
|
|
|
95 <dd>
|
|
|
96 <div class="OptionsBox">
|
|
|
97 $Status = IsNucleicAcidType();</div>
|
|
|
98 <p>Returns 1 or 0 based on whether it's a known nucleic acid type.</p>
|
|
|
99 </dd>
|
|
|
100 </dl>
|
|
|
101 <p>
|
|
|
102 </p>
|
|
|
103 <h2>AUTHOR</h2>
|
|
|
104 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
105 <p>
|
|
|
106 </p>
|
|
|
107 <h2>SEE ALSO</h2>
|
|
|
108 <p><a href="./AminoAcids.html">AminoAcids.pm</a>, <a href="./PeriodicTable.html">PeriodicTable.pm</a>
|
|
|
109 </p>
|
|
|
110 <p>
|
|
|
111 </p>
|
|
|
112 <h2>COPYRIGHT</h2>
|
|
|
113 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
114 <p>This file is part of MayaChemTools.</p>
|
|
|
115 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
116 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
117 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
118 any later version.</p>
|
|
|
119 <p> </p><p> </p><div class="DocNav">
|
|
|
120 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
121 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MoleculeFileIO.html" title="MoleculeFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ObjectProperty.html" title="ObjectProperty.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>NucleicAcids.pm</strong></td></tr>
|
|
|
122 </table>
|
|
|
123 </div>
|
|
|
124 <br />
|
|
|
125 <center>
|
|
|
126 <img src="../../images/h2o2.png">
|
|
|
127 </center>
|
|
|
128 </body>
|
|
|
129 </html>
|
