<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<title>The Gnome Chemistry Utils: gcu::IsotopicPattern Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">The Gnome Chemistry Utils
 <span id="projectnumber">0.14.2</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.1.2 -->
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main Page</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li class="current"><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="annotated.html"><span>Class List</span></a></li>
<li><a href="classes.html"><span>Class Index</span></a></li>
<li><a href="hierarchy.html"><span>Class Hierarchy</span></a></li>
<li><a href="functions.html"><span>Class Members</span></a></li>
</ul>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespacegcu.html">gcu</a></li><li class="navelem"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="classgcu_1_1IsotopicPattern-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">gcu::IsotopicPattern Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p><code>#include <<a class="el" href="isotope_8h_source.html">gcu/isotope.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a62e34589573062f2a9a15d4ec9ba147b"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a62e34589573062f2a9a15d4ec9ba147b">IsotopicPattern</a> ()</td></tr>
<tr class="memitem:aa20e8c062106c001aca794f4fd7c7d06"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#aa20e8c062106c001aca794f4fd7c7d06">IsotopicPattern</a> (int min, int max)</td></tr>
<tr class="memitem:a5bebf0404173ee6ba5bc1dbea6a23629"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a5bebf0404173ee6ba5bc1dbea6a23629">Simplify</a> (void)</td></tr>
<tr class="memitem:a018f28bc6d0f0429655e54a270e97dbe"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a018f28bc6d0f0429655e54a270e97dbe">Multiply</a> (<a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> &pattern)</td></tr>
<tr class="memitem:ae27dc09dbc6c7387eb269e7b89f96d40"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#ae27dc09dbc6c7387eb269e7b89f96d40">Square</a> (void)</td></tr>
<tr class="memitem:a22bdb92b05247ee94ccb45610a92c6ba"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a22bdb92b05247ee94ccb45610a92c6ba">Copy</a> (<a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> &pattern)</td></tr>
<tr class="memitem:a2e6fdfb91b2372f3838ea2aab7238ffa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a2e6fdfb91b2372f3838ea2aab7238ffa">SetValue</a> (int A, double percent)</td></tr>
<tr class="memitem:aed5ce474132328622b693adae969e35a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#aed5ce474132328622b693adae969e35a">Normalize</a> ()</td></tr>
<tr class="memitem:ab0e91cd9e45291bd592e1e3623cde51d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#ab0e91cd9e45291bd592e1e3623cde51d">Clear</a> ()</td></tr>
<tr class="memitem:a279554ce57e78495618d0cbbaac2dcd1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a279554ce57e78495618d0cbbaac2dcd1">Ref</a> ()</td></tr>
<tr class="memitem:a303b0ae1158e85498ae45016b718e821"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a303b0ae1158e85498ae45016b718e821">Unref</a> ()</td></tr>
<tr class="memitem:ae37aefd59db85765c96acb1226c8082c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#ae37aefd59db85765c96acb1226c8082c">GetMinMass</a> ()</td></tr>
<tr class="memitem:ac42a3b171943e8866c3183d9eb60bee2"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#ac42a3b171943e8866c3183d9eb60bee2">GetMonoNuclNb</a> ()</td></tr>
<tr class="memitem:ae6ae8531f3542c9f9a1005736881f4e4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1SimpleValue.html">SimpleValue</a> const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#ae6ae8531f3542c9f9a1005736881f4e4">GetMonoMass</a> ()</td></tr>
<tr class="memitem:a09abfa68359014b1e1efa5348127fbcc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#a09abfa68359014b1e1efa5348127fbcc">SetMonoMass</a> (<a class="el" href="classgcu_1_1SimpleValue.html">SimpleValue</a> mass)</td></tr>
<tr class="memitem:abf8d54eebc7dae33dddd3fcdcac7ce2d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1IsotopicPattern.html#abf8d54eebc7dae33dddd3fcdcac7ce2d">GetValues</a> (double **values)</td></tr>
</table>
<a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Objects of this class represent the isotopic pattern corresponding to a chemical formula. <br/>
The formalism used is similar to polynoms algebra, since calculate the isotopic pattern of the reunion of two fragments is equivalent to a polynomial multiplication. </p>
<p>Definition at line <a class="el" href="isotope_8h_source.html#l00061">61</a> of file <a class="el" href="isotope_8h_source.html">isotope.h</a>.</p>
</div><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a62e34589573062f2a9a15d4ec9ba147b"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">gcu::IsotopicPattern::IsotopicPattern </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Default constructor. Initialize members to nul values. The <a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> is given an initial reference count of 1. </p>
</div>
</div>
<a class="anchor" id="aa20e8c062106c001aca794f4fd7c7d06"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">gcu::IsotopicPattern::IsotopicPattern </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>min</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>max</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Sets the minimum and maximum mass numbers of the pattern, and reserves memory to store the abundances of the mass fragments. The <a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> is given an initial reference count of 1. </p>
</div>
</div>
<h2>Member Function Documentation</h2>
<a class="anchor" id="ab0e91cd9e45291bd592e1e3623cde51d"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::Clear </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Clears the contents of an isotopic pattern for reuse. </p>
</div>
</div>
<a class="anchor" id="a22bdb92b05247ee94ccb45610a92c6ba"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::Copy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> & </td>
<td class="paramname"><em>pattern</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pattern,:</td><td>the isotopic pattern to be copied. Set the values of the isotopic pattern so that it becomes identical to pattern. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a class="anchor" id="ae37aefd59db85765c96acb1226c8082c"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">int gcu::IsotopicPattern::GetMinMass </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<dl class="section return"><dt>Returns</dt><dd>the mass (actually the nucleons number) of the fragment with the lowest mass. This might not be the real minimu, since fragments with very low abundance are discarded during the evaluation. </dd></dl>
<p>Definition at line <a class="el" href="isotope_8h_source.html#l00133">133</a> of file <a class="el" href="isotope_8h_source.html">isotope.h</a>.</p>
</div>
</div>
<a class="anchor" id="ae6ae8531f3542c9f9a1005736881f4e4"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classgcu_1_1SimpleValue.html">SimpleValue</a> const& gcu::IsotopicPattern::GetMonoMass </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<dl class="section return"><dt>Returns</dt><dd>the mass of the fragment made with most abundant isotopes of each element. </dd></dl>
<p>Definition at line <a class="el" href="isotope_8h_source.html#l00143">143</a> of file <a class="el" href="isotope_8h_source.html">isotope.h</a>.</p>
</div>
</div>
<a class="anchor" id="ac42a3b171943e8866c3183d9eb60bee2"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">int gcu::IsotopicPattern::GetMonoNuclNb </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<dl class="section return"><dt>Returns</dt><dd>the nucleons number of the fragment made with most abundant isotopes of each element. </dd></dl>
<p>Definition at line <a class="el" href="isotope_8h_source.html#l00138">138</a> of file <a class="el" href="isotope_8h_source.html">isotope.h</a>.</p>
</div>
</div>
<a class="anchor" id="abf8d54eebc7dae33dddd3fcdcac7ce2d"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int gcu::IsotopicPattern::GetValues </td>
<td>(</td>
<td class="paramtype">double ** </td>
<td class="paramname"><em>values</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">values,:</td><td>where to store the pointer to the abundances of the various mass fragments as a percentage of the most abundant one. The pointer should be freed with g_free when not anymore nedded.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the number of values in the array. </dd></dl>
</div>
</div>
<a class="anchor" id="a018f28bc6d0f0429655e54a270e97dbe"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a>* gcu::IsotopicPattern::Multiply </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a> & </td>
<td class="paramname"><em>pattern</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Effects a polynomial multiplication to calculate the pattern correponding to the reunion of the two fragments. </p>
<dl class="section return"><dt>Returns</dt><dd>the result of the multiplication. </dd></dl>
</div>
</div>
<a class="anchor" id="aed5ce474132328622b693adae969e35a"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::Normalize </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Effects the same multiplication on all abundances so that the largest becomes 100. </p>
</div>
</div>
<a class="anchor" id="a279554ce57e78495618d0cbbaac2dcd1"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::Ref </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Increments the reference count of the pattern. </p>
<p>Definition at line <a class="el" href="isotope_8h_source.html#l00122">122</a> of file <a class="el" href="isotope_8h_source.html">isotope.h</a>.</p>
</div>
</div>
<a class="anchor" id="a09abfa68359014b1e1efa5348127fbcc"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::SetMonoMass </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1SimpleValue.html">SimpleValue</a> </td>
<td class="paramname"><em>mass</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">mass,:</td><td>the mass of the most abundant isotope.</td></tr>
</table>
</dd>
</dl>
<p>This method is used when building an Isotopic Pattern from raw data. To enter the data for each isotope, use <a class="el" href="classgcu_1_1IsotopicPattern.html#a2e6fdfb91b2372f3838ea2aab7238ffa">IsotopicPattern::SetValue</a>. It has no effect if the current monoisotopic mass is not nul. </p>
</div>
</div>
<a class="anchor" id="a2e6fdfb91b2372f3838ea2aab7238ffa"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::SetValue </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>A</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>percent</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">A,:</td><td>the mass number of the isotope. </td></tr>
<tr><td class="paramname">percent,:</td><td>the abundance of the isotope.</td></tr>
</table>
</dd>
</dl>
<p>This method is used when building an Isotopic Pattern from raw data. <a class="el" href="classgcu_1_1IsotopicPattern.html#a09abfa68359014b1e1efa5348127fbcc">IsotopicPattern::SetMonoMass</a> should be called when data for each isotope have been entered. </p>
</div>
</div>
<a class="anchor" id="a5bebf0404173ee6ba5bc1dbea6a23629"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a>* gcu::IsotopicPattern::Simplify </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>This method creates a copy of the original object with abundances normalized as a percentage of the largest value, and removes very small values to save time in subsequent calculations. </p>
<dl class="section return"><dt>Returns</dt><dd>the resulting object. </dd></dl>
</div>
</div>
<a class="anchor" id="ae27dc09dbc6c7387eb269e7b89f96d40"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classgcu_1_1IsotopicPattern.html">IsotopicPattern</a>* gcu::IsotopicPattern::Square </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Squares the original pattern to get the pattern corresponding to twice the original formula. </p>
<dl class="section return"><dt>Returns</dt><dd>the result of the multiplication. </dd></dl>
</div>
</div>
<a class="anchor" id="a303b0ae1158e85498ae45016b718e821"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gcu::IsotopicPattern::Unref </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Decrements the reference count of the pattern. If the reference count becomes 0, the object is destroyed. </p>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="isotope_8h_source.html">isotope.h</a></li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated on Thu Mar 14 2013 17:34:31 for The Gnome Chemistry Utils by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.1.2
</small></address>
</body>
</html>
