--- /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/part_func_co.h File 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="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('part__func__co_8h.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+ <div class="summary">
+<a href="#func-members">Functions</a> |
+<a href="#var-members">Variables</a> </div>
+ <div class="headertitle">
+<div class="title">part_func_co.h File Reference<div class="ingroups"><a class="el" href="group__pf__cofold.html">Partition Function for two hybridized Sequences</a></div></div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>Partition function for two RNA sequences.
+<a href="#details">More...</a></p>
+<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for part_func_co.h:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="part__func__co_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func__co_8h" alt=""/></div>
+<map name="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func__co_8h" id="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func__co_8h">
+<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="42,109,176,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="49,184,169,211"/></map>
+</div>
+</div>
+<p><a href="part__func__co_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:gaa86a5f998789ed71813d23d7307a791b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b">co_pf_fold</a> (char *sequence, char *structure)</td></tr>
+<tr class="memdesc:gaa86a5f998789ed71813d23d7307a791b"><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b"></a><br/></td></tr>
+<tr class="memitem:gabd873b450832ab5f21101fc5ab354d21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21">co_pf_fold_par</a> (char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained)</td></tr>
+<tr class="memdesc:gabd873b450832ab5f21101fc5ab354d21"><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21"></a><br/></td></tr>
+<tr class="memitem:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">export_co_bppm</a> (void)</td></tr>
+<tr class="memdesc:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability array. <a href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c"></a><br/></td></tr>
+<tr class="memitem:gade3ce34ae8214811374b1d28a40dc247"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gade3ce34ae8214811374b1d28a40dc247"></a>
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">free_co_pf_arrays</a> (void)</td></tr>
+<tr class="memdesc:gade3ce34ae8214811374b1d28a40dc247"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a> <br/></td></tr>
+<tr class="memitem:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">update_co_pf_params</a> (int length)</td></tr>
+<tr class="memdesc:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a><br/></td></tr>
+<tr class="memitem:ga117d880df45bef444d5e2785ffa40a53"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53">update_co_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
+<tr class="memdesc:ga117d880df45bef444d5e2785ffa40a53"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53"></a><br/></td></tr>
+<tr class="memitem:ga15ae04ac5ab84e876dcf0093120cb617"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617">compute_probabilities</a> (double FAB, double FEA, double FEB, struct <a class="el" href="structplist.html">plist</a> *prAB, struct <a class="el" href="structplist.html">plist</a> *prA, struct <a class="el" href="structplist.html">plist</a> *prB, int Alength)</td></tr>
+<tr class="memdesc:ga15ae04ac5ab84e876dcf0093120cb617"><td class="mdescLeft"> </td><td class="mdescRight">Compute Boltzmann probabilities of dimerization without homodimers. <a href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617"></a><br/></td></tr>
+<tr class="memitem:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structConcEnt.html">ConcEnt</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7">get_concentrations</a> (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</td></tr>
+<tr class="memdesc:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="mdescLeft"> </td><td class="mdescRight">Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. <a href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7"></a><br/></td></tr>
+<tr class="memitem:a334de3c96e2186abfbdc0eaea6d08b14"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structplist.html">plist</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a> (struct <a class="el" href="structplist.html">plist</a> *pl, int length, double cut_off)</td></tr>
+<tr class="memitem:aa12dda9dd6179cdd22bcce87c0682c07"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a> (int length)</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr class="memitem:gaff27888c4088cc1f60fd59cbd589474c"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaff27888c4088cc1f60fd59cbd589474c"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c">mirnatog</a></td></tr>
+<tr class="memdesc:gaff27888c4088cc1f60fd59cbd589474c"><td class="mdescLeft"> </td><td class="mdescRight">Toggles no intrabp in 2nd mol. <br/></td></tr>
+<tr class="memitem:gac2d1851a710a8561390861155ca988fe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac2d1851a710a8561390861155ca988fe"></a>
+double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe">F_monomer</a> [2]</td></tr>
+<tr class="memdesc:gac2d1851a710a8561390861155ca988fe"><td class="mdescLeft"> </td><td class="mdescRight">Free energies of the two monomers. <br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>Partition function for two RNA sequences. </p>
+<p>As for folding one RNA molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global <a class="el" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a> variable to avoid overflows.</p>
+<p>To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed.</p>
+<p>After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway.</p>
+<p>Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers AB, AA, and BB one can compute the equilibrium concentrations, given input concentrations of A and B, see e.g. Dimitrov & Zuker (2004) </p>
+</div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a334de3c96e2186abfbdc0eaea6d08b14"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname"><a class="el" href="structplist.html">plist</a>* get_plist </td>
+ <td>(</td>
+ <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> * </td>
+ <td class="paramname"><em>pl</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>length</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">double </td>
+ <td class="paramname"><em>cut_off</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>DO NOT USE THIS FUNCTION ANYMORE </p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000016">Deprecated:</a></b></dt><dd>{ This function is deprecated and will be removed soon!} use <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr()</a> instead! </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="aa12dda9dd6179cdd22bcce87c0682c07"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">void init_co_pf_fold </td>
+ <td>(</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>length</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>DO NOT USE THIS FUNCTION ANYMORE </p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000017">Deprecated:</a></b></dt><dd>{ This function is deprecated and will be removed soon!} </dd></dl>
+
+</div>
+</div>
+</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="part__func__co_8h.html">part_func_co.h</a></li>
+ <li class="footer">Generated on Wed Jul 24 2013 13:38:58 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