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-<div class="title">part_func_up.h File Reference<div class="ingroups"><a class="el" href="group__up__cofold.html">Partition Function for two hybridized Sequences as a stepwise Process</a></div></div> </div>
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_up.h File Reference</h1>
<p>Partition Function Cofolding as stepwise process.
-<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_up.h:</div>
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-<div class="center"><img src="part__func__up_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func__up_8h" alt=""/></div>
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<p><a href="part__func__up_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:ga5b4ee40e190d2f633cd01cf0d2fe93cf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf">pf_unstru</a> (char *sequence, int max_w)</td></tr>
-<tr class="memdesc:ga5b4ee40e190d2f633cd01cf0d2fe93cf"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the partition function over all unpaired regions of a maximal length. <a href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf"></a><br/></td></tr>
-<tr class="memitem:ga1aa0aa02bc3a724f87360c03097afd00"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structinteract.html">interact</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00">pf_interact</a> (const char *s1, const char *s2, <a class="el" href="structpu__contrib.html">pu_contrib</a> *p_c, <a class="el" href="structpu__contrib.html">pu_contrib</a> *p_c2, int max_w, char *cstruc, int incr3, int incr5)</td></tr>
-<tr class="memdesc:ga1aa0aa02bc3a724f87360c03097afd00"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the probability of a local interaction between two sequences. <a href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00"></a><br/></td></tr>
-<tr class="memitem:gadde308fd5f696dc271b1532aa96fd12f"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gadde308fd5f696dc271b1532aa96fd12f"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f">free_interact</a> (<a class="el" href="structinteract.html">interact</a> *pin)</td></tr>
-<tr class="memdesc:gadde308fd5f696dc271b1532aa96fd12f"><td class="mdescLeft"> </td><td class="mdescRight">Frees the output of function <a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact()</a>. <br/></td></tr>
-<tr class="memitem:gac20bd61824981d45ce0dc9934aa56df8"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac20bd61824981d45ce0dc9934aa56df8"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#gac20bd61824981d45ce0dc9934aa56df8">free_pu_contrib_struct</a> (<a class="el" href="structpu__contrib.html">pu_contrib</a> *pu)</td></tr>
-<tr class="memdesc:gac20bd61824981d45ce0dc9934aa56df8"><td class="mdescLeft"> </td><td class="mdescRight">Frees the output of function <a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf" title="Calculate the partition function over all unpaired regions of a maximal length.">pf_unstru()</a>. <br/></td></tr>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf">pf_unstru</a> (char *sequence, int max_w)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the partition function over all unpaired regions of a maximal length. <a href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structinteract.html">interact</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00">pf_interact</a> (const char *s1, const char *s2, <a class="el" href="structpu__contrib.html">pu_contrib</a> *p_c, <a class="el" href="structpu__contrib.html">pu_contrib</a> *p_c2, int max_w, char *cstruc, int incr3, int incr5)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculates the probability of a local interaction between two sequences. <a href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gadde308fd5f696dc271b1532aa96fd12f"></a><!-- doxytag: member="part_func_up.h::free_interact" ref="gadde308fd5f696dc271b1532aa96fd12f" args="(interact *pin)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f">free_interact</a> (<a class="el" href="structinteract.html">interact</a> *pin)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Frees the output of function <a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact()</a>. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac20bd61824981d45ce0dc9934aa56df8"></a><!-- doxytag: member="part_func_up.h::free_pu_contrib_struct" ref="gac20bd61824981d45ce0dc9934aa56df8" args="(pu_contrib *pu)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html#gac20bd61824981d45ce0dc9934aa56df8">free_pu_contrib_struct</a> (<a class="el" href="structpu__contrib.html">pu_contrib</a> *pu)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Frees the output of function <a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf" title="Calculate the partition function over all unpaired regions of a maximal length.">pf_unstru()</a>. <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Partition Function Cofolding as stepwise process. </p>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Partition Function Cofolding as stepwise process. </p>
<p>In this approach to cofolding the interaction between two RNA molecules is seen as a stepwise process. In a first step, the target molecule has to adopt a structure in which a binding site is accessible. In a second step, the ligand molecule will hybridize with a region accessible to an interaction. Consequently the algorithm is designed as a two step process: The first step is the calculation of the probability that a region within the target is unpaired, or equivalently, the calculation of the free energy needed to expose a region. In the second step we compute the free energy of an interaction for every possible binding site. </p>
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