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-<div class="title">Partition Function for two hybridized Sequences as a stepwise Process</div> </div>
-<div class="ingroups"><a class="el" href="group__cofold.html">Calculate Secondary Structures of two RNAs upon Dimerization</a> | <a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a></div></div><!--header-->
<div class="contents">
-
+<h1>Partition Function for two hybridized Sequences as a stepwise Process<br/>
+<small>
+[<a class="el" href="group__cofold.html">Calculate Secondary Structures of two RNAs upon Dimerization</a>, <a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a>]</small>
+</h1>
<p>Partition Function Cofolding as a stepwise process.
-<a href="#details">More...</a></p>
-<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Partition Function for two hybridized Sequences as a stepwise Process:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<center><table><tr><td><img src="group__up__cofold.png" border="0" alt="" usemap="#group____up____cofold"/>
-<map name="group____up____cofold" id="group____up____cofold">
-<area shape="rect" id="node2" href="group__pf__fold.html" title="This section provides information about all functions and variables related to the calculation of the..." alt="" coords="6,5,229,46"/><area shape="rect" id="node3" href="group__cofold.html" title="Predict structures formed by two molecules upon hybridization." alt="" coords="31,69,204,125"/></map>
-</td></tr></table></center>
+<a href="#_details">More...</a></p>
+
+<p><div class="dynheader">
+Collaboration diagram for Partition Function for two hybridized Sequences as a stepwise Process:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__up__cofold.png" border="0" alt="" usemap="#group____up____cofold_map"/>
+<map name="group____up____cofold_map" id="group____up____cofold">
+<area shape="rect" id="node2" href="group__pf__fold.html" title="This section provides information about all functions and variables related to the..." alt="" coords="41,5,372,35"/><area shape="rect" id="node3" href="group__cofold.html" title="Predict structures formed by two molecules upon hybridization." alt="" coords="5,58,408,89"/></map></td></tr></table></center>
</div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="files"></a>
-Files</h2></td></tr>
-<tr class="memitem:part__func__up_8h"><td class="memItemLeft" align="right" valign="top">file  </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__up_8h.html">part_func_up.h</a></td></tr>
-<tr class="memdesc:part__func__up_8h"><td class="mdescLeft"> </td><td class="mdescRight">Partition Function Cofolding as stepwise process. <br/></td></tr>
-</table><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="#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="#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>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Files</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__up_8h.html">part_func_up.h</a></td></tr>
+
+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>Partition Function Cofolding as stepwise process. </p>
+<br/></td></tr>
+</p>
+<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="#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="#ga1aa0aa02bc3a724f87360c03097afd00"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gadde308fd5f696dc271b1532aa96fd12f"></a><!-- doxytag: member="up_cofold::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="up_cofold::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>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Partition Function Cofolding as a stepwise process. </p>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ga5b4ee40e190d2f633cd01cf0d2fe93cf"></a>
+<a class="anchor" id="ga5b4ee40e190d2f633cd01cf0d2fe93cf"></a><!-- doxytag: member="part_func_up.h::pf_unstru" ref="ga5b4ee40e190d2f633cd01cf0d2fe93cf" args="(char *sequence, int max_w)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structpu__contrib.html">pu_contrib</a>* pf_unstru </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>sequence</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>sequence</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>max_w</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>max_w</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Calculate the partition function over all unpaired regions of a maximal length. </p>
-<p>You have to call function <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> providing the same sequence before calling <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>. If you want to calculate unpaired regions for a constrained structure, set variable 'structure' in function '<a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>' to the constrain string. It returns a <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> struct containing four arrays of dimension [i = 1 to length(sequence)][j = 0 to u-1] containing all possible contributions to the probabilities of unpaired regions of maximum length u. Each array in <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> contains one of the contributions to the total probability of being unpaired: The probability of being unpaired within an exterior loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->E, the probability of being unpaired within a hairpin loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->H, the probability of being unpaired within an interior loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->I and probability of being unpaired within a multi-loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->M. The total probability of being unpaired is the sum of the four arrays of <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>.</p>
+<p>You have to call function <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> providing the same sequence before calling <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>. If you want to calculate unpaired regions for a constrained structure, set variable 'structure' in function 'pf_fold()' to the <a class="el" href="structconstrain.html" title="constraints for cofolding">constrain</a> string. It returns a <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> struct containing four arrays of dimension [i = 1 to length(sequence)][j = 0 to u-1] containing all possible contributions to the probabilities of unpaired regions of maximum length u. Each array in <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> contains one of the contributions to the total probability of being unpaired: The probability of being unpaired within an exterior loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->E, the probability of being unpaired within a hairpin loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->H, the probability of being unpaired within an interior loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->I and probability of being unpaired within a multi-loop is in array <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>->M. The total probability of being unpaired is the sum of the four arrays of <a class="el" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>.</p>
<p>This function frees everything allocated automatically. To free the output structure call free_pu_contrib().</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequence</td><td></td></tr>
- <tr><td class="paramname">max_w</td><td></td></tr>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>sequence</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>max_w</em> </td><td></td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
</div>
</div>
-<a class="anchor" id="ga1aa0aa02bc3a724f87360c03097afd00"></a>
+<a class="anchor" id="ga1aa0aa02bc3a724f87360c03097afd00"></a><!-- doxytag: member="part_func_up.h::pf_interact" ref="ga1aa0aa02bc3a724f87360c03097afd00" args="(const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structinteract.html">interact</a>* pf_interact </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>s1</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>s1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>s2</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>s2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td>
- <td class="paramname"><em>p_c</em>, </td>
+ <td class="paramtype"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td>
+ <td class="paramname"> <em>p_c</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td>
- <td class="paramname"><em>p_c2</em>, </td>
+ <td class="paramtype"><a class="el" href="structpu__contrib.html">pu_contrib</a> * </td>
+ <td class="paramname"> <em>p_c2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>max_w</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>max_w</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>cstruc</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>cstruc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>incr3</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>incr3</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>incr5</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>incr5</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Calculates the probability of a local interaction between two sequences. </p>
-<p>The function considers the probability that the region of interaction is unpaired within 's1' and 's2'. The longer sequence has to be given as 's1'. The shorter sequence has to be given as 's2'. 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> has to be called for 's1' and 's2', where the probabilities of being unpaired have to be given in 'p_c' and 'p_c2', respectively. If you do not want to include the probabilities of being unpaired for 's2' set 'p_c2' to NULL. If variable 'cstruc' is not NULL, constrained folding is done: The available constrains for intermolecular interaction are: '.' (no constrain), 'x' (the base has no intermolecular interaction) and '|' (the corresponding base has to be paired intermolecularily).<br/>
+<p>The function considers the probability that the region of interaction is unpaired within 's1' and 's2'. The longer sequence has to be given as 's1'. The shorter sequence has to be given as 's2'. 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> has to be called for 's1' and 's2', where the probabilities of being unpaired have to be given in 'p_c' and 'p_c2', respectively. If you do not want to include the probabilities of being unpaired for 's2' set 'p_c2' to NULL. If variable 'cstruc' is not NULL, constrained folding is done: The available constrains for intermolecular interaction are: '.' (no <a class="el" href="structconstrain.html" title="constraints for cofolding">constrain</a>), 'x' (the base has no intermolecular interaction) and '|' (the corresponding base has to be paired intermolecularily).<br/>
The parameter 'w' determines the maximal length of the interaction. The parameters 'incr5' and 'incr3' allows inclusion of unpaired residues left ('incr5') and right ('incr3') of the region of interaction in 's1'. If the 'incr' options are used, 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> has to be called with w=w+incr5+incr3 for the longer sequence 's1'.</p>
<p>It returns a structure of type <a class="el" href="structinteract.html">interact</a> which contains the probability of the best local interaction including residue i in Pi and the minimum free energy in Gi, where i is the position in sequence 's1'. The member Gikjl of structure <a class="el" href="structinteract.html">interact</a> is the best interaction between region [k,i] k<i in longer sequence 's1' and region [j,l] j<l in 's2'. Gikjl_wo is Gikjl without the probability of beeing unpaired.<br/>
Use <a class="el" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f" title="Frees the output of function pf_interact().">free_interact()</a> to free the returned structure, all other stuff is freed inside <a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact()</a>.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">s1</td><td></td></tr>
- <tr><td class="paramname">s2</td><td></td></tr>
- <tr><td class="paramname">p_c</td><td></td></tr>
- <tr><td class="paramname">p_c2</td><td></td></tr>
- <tr><td class="paramname">max_w</td><td></td></tr>
- <tr><td class="paramname">cstruc</td><td></td></tr>
- <tr><td class="paramname">incr3</td><td></td></tr>
- <tr><td class="paramname">incr5</td><td></td></tr>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>s1</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s2</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>p_c</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>p_c2</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>max_w</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>cstruc</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>incr3</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>incr5</em> </td><td></td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
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