--- /dev/null
+<!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>RNAlib-2.1.2: /home/mescalin/ronny/public_html/programs/ViennaRNA/H/cofold.h Source File</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="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">RNAlib-2.1.2
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="modules.html"><span>Modules</span></a></li>
+ <li><a href="annotated.html"><span>Data Structures</span></a></li>
+ <li class="current"><a href="files.html"><span>Files</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="files.html"><span>File List</span></a></li>
+ <li><a href="globals.html"><span>Globals</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('cofold_8h.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+ <div class="headertitle">
+<div class="title">cofold.h</div> </div>
+</div><!--header-->
+<div class="contents">
+<a href="cofold_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_COFOLD_H__</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>"</span></div>
+<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div>
+<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
+<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
+<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
+<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
+<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">char</span> *structure);</div>
+<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
+<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f" title="Compute the minimum free energy of two interacting RNA molecules.">cofold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
+<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">int</span> is_constrained);</div>
+<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
+<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a" title="Free memory occupied by cofold()">free_co_arrays</a>(<span class="keywordtype">void</span>);</div>
+<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
+<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57" title="Recalculate parameters.">update_cofold_params</a>(<span class="keywordtype">void</span>);</div>
+<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
+<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="keywordtype">void</span> update_cofold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);</div>
+<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
+<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
+<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48" title="Export the arrays of partition function cofold (with gquadruplex support)">export_cofold_arrays_gq</a>( <span class="keywordtype">int</span> **f5_p,</div>
+<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> **c_p,</div>
+<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">int</span> **fML_p,</div>
+<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">int</span> **fM1_p,</div>
+<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">int</span> **fc_p,</div>
+<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">int</span> **ggg_p,</div>
+<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">int</span> **indx_p,</div>
+<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">char</span> **ptype_p);</div>
+<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
+<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482" title="Export the arrays of partition function cofold.">export_cofold_arrays</a>(<span class="keywordtype">int</span> **f5_p,</div>
+<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">int</span> **c_p,</div>
+<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">int</span> **fML_p,</div>
+<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">int</span> **fM1_p,</div>
+<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">int</span> **fc_p,</div>
+<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordtype">int</span> **indx_p,</div>
+<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">char</span> **ptype_p);</div>
+<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
+<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
+<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90" title="Compute Zuker type suboptimal structures.">zukersubopt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>);</div>
+<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
+<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c" title="Compute Zuker type suboptimal structures.">zukersubopt_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);</div>
+<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
+<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79" title="get_monomer_free_energies">get_monomere_mfes</a>( <span class="keywordtype">float</span> *e1,</div>
+<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">float</span> *e2);</div>
+<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
+<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div>
+<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a>(<span class="keywordtype">int</span> length));</div>
+<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
+<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="preprocessor">#endif</span></div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="cofold_8h.html">cofold.h</a></li>
+ <li class="footer">Generated on Wed Jul 24 2013 13:38:55 for RNAlib-2.1.2 by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
+ </ul>
+</div>
+</body>
+</html>
git://source.jalview.org / jabaws.git / blobdiff