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+<a href="#func-members">Functions</a> </div>
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+<div class="title">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</div> </div>
+<div class="ingroups"><a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a> | <a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a></div></div><!--header-->
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):</div>
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+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<center><table><tr><td><img src="group__consensus__pf__fold.png" border="0" alt="" usemap="#group____consensus____pf____fold"/>
+<map name="group____consensus____pf____fold" id="group____consensus____pf____fold">
+<area shape="rect" id="node1" href="group__consensus__fold.html" title="compute various properties (consensus MFE structures, partition function, Boltzmann distributed stoch..." alt="" coords="11,5,224,46"/><area shape="rect" id="node3" href="group__pf__fold.html" title="This section provides information about all functions and variables related to the calculation of the..." alt="" coords="6,70,229,111"/></map>
+</td></tr></table></center>
+</div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:ga4d2ff54d8210fc7cceeeff389d4dbd1d"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
+<tr class="memitem:gad32ded7d753ccaf211ab35782d1f42a9"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9">alipf_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr class="memdesc:gad32ded7d753ccaf211ab35782d1f42a9"><td class="mdescLeft"> </td><td class="mdescRight">The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0. <a href="#gad32ded7d753ccaf211ab35782d1f42a9"></a><br/></td></tr>
+<tr class="memitem:ga6b4dde1d43b79ab3753508c46cf50363"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr class="memitem:gadaaf83394216413505e48d913dbc1b4e"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e">export_ali_bppm</a> (void)</td></tr>
+<tr class="memdesc:gadaaf83394216413505e48d913dbc1b4e"><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability array. <a href="#gadaaf83394216413505e48d913dbc1b4e"></a><br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="ga4d2ff54d8210fc7cceeeff389d4dbd1d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float alipf_fold_par </td>
+ <td>(</td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"><em>sequences</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"><em>structure</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype"><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"><a class="el" href="structpf__paramT.html">pf_paramT</a> * </td>
+ <td class="paramname"><em>parameters</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>calculate_bppm</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>is_constrained</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>is_circular</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">sequences</td><td></td></tr>
+ <tr><td class="paramname">structure</td><td></td></tr>
+ <tr><td class="paramname">pl</td><td></td></tr>
+ <tr><td class="paramname">parameters</td><td></td></tr>
+ <tr><td class="paramname">calculate_bppm</td><td></td></tr>
+ <tr><td class="paramname">is_constrained</td><td></td></tr>
+ <tr><td class="paramname">is_circular</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="gad32ded7d753ccaf211ab35782d1f42a9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float alipf_fold </td>
+ <td>(</td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"><em>sequences</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"><em>structure</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype"><a class="el" href="structplist.html">plist</a> ** </td>
+ <td class="paramname"><em>pl</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">sequences</td><td></td></tr>
+ <tr><td class="paramname">structure</td><td></td></tr>
+ <tr><td class="paramname">pl</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="ga6b4dde1d43b79ab3753508c46cf50363"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float alipf_circ_fold </td>
+ <td>(</td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"><em>sequences</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"><em>structure</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype"><a class="el" href="structplist.html">plist</a> ** </td>
+ <td class="paramname"><em>pl</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">sequences</td><td></td></tr>
+ <tr><td class="paramname">structure</td><td></td></tr>
+ <tr><td class="paramname">pl</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="gadaaf83394216413505e48d913dbc1b4e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">double* export_ali_bppm </td>
+ <td>(</td>
+ <td class="paramtype">void </td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Get a pointer to the base pair probability array. </p>
+<p>Accessing the base pair probabilities for a pair (i,j) is achieved by </p>
+<pre class="fragment">FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; </pre><dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...">get_iindx()</a> </dd></dl>
+<dl class="section return"><dt>Returns:</dt><dd>A pointer to the base pair probability array </dd></dl>
+
+</div>
+</div>
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