binaries/src/ViennaRNA/doc/html/group__subopt__stochbt.html

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   6 <title>RNAlib-2.1.2: Stochastic backtracking in the Ensemble</title>
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  62   <div class="headertitle">
  63 <div class="title">Stochastic backtracking in the Ensemble</div>  </div>
  64 <div class="ingroups"><a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a></div></div><!--header-->
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  67   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Stochastic backtracking in the Ensemble:</div>
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  71 <center><table><tr><td><img src="group__subopt__stochbt.png" border="0" alt="" usemap="#group____subopt____stochbt"/>
  72 <map name="group____subopt____stochbt" id="group____subopt____stochbt">
  73 <area shape="rect" id="node1" href="group__kl__neighborhood__stochbt.html" title="Contains functions related to stochastic backtracking from a specified distance class." alt="" coords="463,5,665,61"/><area shape="rect" id="node2" href="group__subopt__fold.html" title="Enumerating Suboptimal\l Structures" alt="" coords="5,53,187,94"/><area shape="rect" id="node4" href="group__consensus__stochbt.html" title="Stochastic Backtracking\l of Consensus Structures\l from Sequence Alignment(s)" alt="" coords="459,85,669,141"/></map>
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  76 <table class="memberdecls">
  77 <tr class="heading"><td colspan="2"><h2><a name="groups"></a>
  78 Modules</h2></td></tr>
  79 <tr class="memitem:group__consensus__stochbt"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td></tr>
  80 <tr class="memitem:group__kl__neighborhood__stochbt"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html">Stochastic Backtracking of Structures from Distance Based Partitioning</a></td></tr>
  81 <tr class="memdesc:group__kl__neighborhood__stochbt"><td class="mdescLeft">&#160;</td><td class="mdescRight">Contains functions related to stochastic backtracking from a specified distance class. <br/></td></tr>
  82 </table><table class="memberdecls">
  83 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  84 Functions</h2></td></tr>
  85 <tr class="memitem:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
  86 <tr class="memdesc:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
  87 .  <a href="#gac03ca6db186bb3bf0a2a326d7fb3ba03"></a><br/></td></tr>
  88 <tr class="memitem:ga00474051204ac9ad576b3e45174d03ff"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
  89 <tr class="memdesc:ga00474051204ac9ad576b3e45174d03ff"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.  <a href="#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
  90 </table><table class="memberdecls">
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  92 Variables</h2></td></tr>
  93 <tr class="memitem:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
  94 <tr class="memdesc:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.  <a href="#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
  95 </table>
  96 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
  97 <hr/><h2>Function Documentation</h2>
  98 <a class="anchor" id="gac03ca6db186bb3bf0a2a326d7fb3ba03"></a>
  99 <div class="memitem">
 100 <div class="memproto">
 101       <table class="memname">
 102         <tr>
 103           <td class="memname">char* pbacktrack </td>
 104           <td>(</td>
 105           <td class="paramtype">char *&#160;</td>
 106           <td class="paramname"><em>sequence</em></td><td>)</td>
 107           <td></td>
 108         </tr>
 109       </table>
 110 </div><div class="memdoc">
 111
 112 <p>Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
 113 . </p>
 114 <dl class="section pre"><dt>Precondition:</dt><dd><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function  for a given RNA sequence.">pf_fold_par()</a> or <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a> have to be called first to fill the partition function matrices</dd></dl>
 115 <dl class="params"><dt>Parameters:</dt><dd>
 116   <table class="params">
 117     <tr><td class="paramname">sequence</td><td>The RNA sequence </td></tr>
 118   </table>
 119   </dd>
 120 </dl>
 121 <dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
 122
 123 </div>
 124 </div>
 125 <a class="anchor" id="ga00474051204ac9ad576b3e45174d03ff"></a>
 126 <div class="memitem">
 127 <div class="memproto">
 128       <table class="memname">
 129         <tr>
 130           <td class="memname">char* pbacktrack_circ </td>
 131           <td>(</td>
 132           <td class="paramtype">char *&#160;</td>
 133           <td class="paramname"><em>sequence</em></td><td>)</td>
 134           <td></td>
 135         </tr>
 136       </table>
 137 </div><div class="memdoc">
 138
 139 <p>Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. </p>
 140 <p>This function does the same as <a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack()</a> but assumes the RNA molecule to be circular</p>
 141 <pre class="fragment">\pre    pf_fold_par() or pf_fold_circ() have to be called first to fill the partition function matrices
 142
 143 \param  sequence  The RNA sequence
 144 \return           A sampled secondary structure in dot-bracket notation</pre>
 145 </div>
 146 </div>
 147 <hr/><h2>Variable Documentation</h2>
 148 <a class="anchor" id="gacd79b1a570e6ad9be24cb11fe8cae30a"></a>
 149 <div class="memitem">
 150 <div class="memproto">
 151       <table class="memname">
 152         <tr>
 153           <td class="memname">int st_back</td>
 154         </tr>
 155       </table>
 156 </div><div class="memdoc">
 157
 158 <p>Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. </p>
 159 <p>Set this variable to 1 prior to a call of <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a> to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions</p>
 160 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability ...">pbacktrack()</a>, <a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability...">pbacktrack_circ</a> </dd></dl>
 161
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