binaries/src/ViennaRNA/doc/html/group__kl__neighborhood__stochbt.html

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  59 <a href="#func-members">Functions</a>  </div>
  60   <div class="headertitle">
  61 <div class="title">Stochastic Backtracking of Structures from Distance Based Partitioning</div>  </div>
  62 <div class="ingroups"><a class="el" href="group__kl__neighborhood.html">Distance based partitioning of the Secondary Structure Space</a> &#124; <a class="el" href="group__subopt__stochbt.html">Stochastic backtracking in the Ensemble</a></div></div><!--header-->
  63 <div class="contents">
  64
  65 <p>Contains functions related to stochastic backtracking from a specified distance class.
  66 <a href="#details">More...</a></p>
  67 <div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
  68   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:</div>
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  72 <center><table><tr><td><img src="group__kl__neighborhood__stochbt.png" border="0" alt="" usemap="#group____kl____neighborhood____stochbt"/>
  73 <map name="group____kl____neighborhood____stochbt" id="group____kl____neighborhood____stochbt">
  74 <area shape="rect" id="node2" href="group__kl__neighborhood.html" title="Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space..." alt="" coords="5,5,248,46"/><area shape="rect" id="node3" href="group__subopt__stochbt.html" title="Stochastic backtracking\l in the Ensemble" alt="" coords="39,70,214,111"/></map>
  75 </td></tr></table></center>
  76 </div>
  77 <table class="memberdecls">
  78 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  79 Functions</h2></td></tr>
  80 <tr class="memitem:gae251288f50dd4ae7d315af0085775f71"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71">TwoDpfold_pbacktrack</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2)</td></tr>
  81 <tr class="memdesc:gae251288f50dd4ae7d315af0085775f71"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.  <a href="#gae251288f50dd4ae7d315af0085775f71"></a><br/></td></tr>
  82 <tr class="memitem:ga13430ac6a7f90df426774f131647d2c7"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7">TwoDpfold_pbacktrack5</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2, unsigned int length)</td></tr>
  83 <tr class="memdesc:ga13430ac6a7f90df426774f131647d2c7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.  <a href="#ga13430ac6a7f90df426774f131647d2c7"></a><br/></td></tr>
  84 </table>
  85 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
  86 <p>Contains functions related to stochastic backtracking from a specified distance class. </p>
  87 <hr/><h2>Function Documentation</h2>
  88 <a class="anchor" id="gae251288f50dd4ae7d315af0085775f71"></a>
  89 <div class="memitem">
  90 <div class="memproto">
  91       <table class="memname">
  92         <tr>
  93           <td class="memname">char* TwoDpfold_pbacktrack </td>
  94           <td>(</td>
  95           <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *&#160;</td>
  96           <td class="paramname"><em>vars</em>, </td>
  97         </tr>
  98         <tr>
  99           <td class="paramkey"></td>
 100           <td></td>
 101           <td class="paramtype">int&#160;</td>
 102           <td class="paramname"><em>d1</em>, </td>
 103         </tr>
 104         <tr>
 105           <td class="paramkey"></td>
 106           <td></td>
 107           <td class="paramtype">int&#160;</td>
 108           <td class="paramname"><em>d2</em>&#160;</td>
 109         </tr>
 110         <tr>
 111           <td></td>
 112           <td>)</td>
 113           <td></td><td></td>
 114         </tr>
 115       </table>
 116 </div><div class="memdoc">
 117
 118 <p>Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. </p>
 119 <p>If the argument 'd1' is set to '-1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.</p>
 120 <dl class="section pre"><dt>Precondition:</dt><dd>The argument 'vars' must contain precalculated partition function matrices, i.e. a call to <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a> preceding this function is mandatory!</dd></dl>
 121 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a></dd></dl>
 122 <dl class="params"><dt>Parameters:</dt><dd>
 123   <table class="params">
 124     <tr><td class="paramdir">[in]</td><td class="paramname">vars</td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
 125     <tr><td class="paramdir">[in]</td><td class="paramname">d1</td><td>the distance to reference1 (may be -1) </td></tr>
 126     <tr><td class="paramdir">[in]</td><td class="paramname">d2</td><td>the distance to reference2 </td></tr>
 127   </table>
 128   </dd>
 129 </dl>
 130 <dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
 131
 132 </div>
 133 </div>
 134 <a class="anchor" id="ga13430ac6a7f90df426774f131647d2c7"></a>
 135 <div class="memitem">
 136 <div class="memproto">
 137       <table class="memname">
 138         <tr>
 139           <td class="memname">char* TwoDpfold_pbacktrack5 </td>
 140           <td>(</td>
 141           <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *&#160;</td>
 142           <td class="paramname"><em>vars</em>, </td>
 143         </tr>
 144         <tr>
 145           <td class="paramkey"></td>
 146           <td></td>
 147           <td class="paramtype">int&#160;</td>
 148           <td class="paramname"><em>d1</em>, </td>
 149         </tr>
 150         <tr>
 151           <td class="paramkey"></td>
 152           <td></td>
 153           <td class="paramtype">int&#160;</td>
 154           <td class="paramname"><em>d2</em>, </td>
 155         </tr>
 156         <tr>
 157           <td class="paramkey"></td>
 158           <td></td>
 159           <td class="paramtype">unsigned int&#160;</td>
 160           <td class="paramname"><em>length</em>&#160;</td>
 161         </tr>
 162         <tr>
 163           <td></td>
 164           <td>)</td>
 165           <td></td><td></td>
 166         </tr>
 167       </table>
 168 </div><div class="memdoc">
 169
 170 <p>Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. </p>
 171 <p>This function does essentially the same as TwoDpfold_pbacktrack with the only difference that partial structures, i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked</p>
 172 <dl class="section note"><dt>Note:</dt><dd>This function does not work (since it makes no sense) for circular RNA sequences! </dd></dl>
 173 <dl class="section pre"><dt>Precondition:</dt><dd>The argument 'vars' must contain precalculated partition function matrices, i.e. a call to <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a> preceding this function is mandatory!</dd></dl>
 174 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71" title="Sample secondary structure representatives from a set of distance classes according to their Boltzman...">TwoDpfold_pbacktrack()</a>, <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a></dd></dl>
 175 <dl class="params"><dt>Parameters:</dt><dd>
 176   <table class="params">
 177     <tr><td class="paramdir">[in]</td><td class="paramname">vars</td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
 178     <tr><td class="paramdir">[in]</td><td class="paramname">d1</td><td>the distance to reference1 (may be -1) </td></tr>
 179     <tr><td class="paramdir">[in]</td><td class="paramname">d2</td><td>the distance to reference2 </td></tr>
 180     <tr><td class="paramdir">[in]</td><td class="paramname">length</td><td>the length of the structure beginning from the 5' end </td></tr>
 181   </table>
 182   </dd>
 183 </dl>
 184 <dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
 185
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