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-<div class="title">Stochastic Backtracking of Structures from Distance Based Partitioning</div> </div>
-<div class="ingroups"><a class="el" href="group__kl__neighborhood.html">Distance based partitioning of the Secondary Structure Space</a> | <a class="el" href="group__subopt__stochbt.html">Stochastic backtracking in the Ensemble</a></div></div><!--header-->
<div class="contents">
-
+<h1>Stochastic Backtracking of Structures from Distance Based Partitioning<br/>
+<small>
+[<a class="el" href="group__kl__neighborhood.html">Distance based partitioning of the Secondary Structure Space</a>, <a class="el" href="group__subopt__stochbt.html">Stochastic backtracking in the Ensemble</a>]</small>
+</h1>
<p>Contains functions related to stochastic backtracking from a specified distance class.
-<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 Stochastic Backtracking of Structures from Distance Based Partitioning:</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__kl__neighborhood__stochbt.png" border="0" alt="" usemap="#group____kl____neighborhood____stochbt"/>
-<map name="group____kl____neighborhood____stochbt" id="group____kl____neighborhood____stochbt">
-<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>
-</td></tr></table></center>
+<a href="#_details">More...</a></p>
+
+<p><div class="dynheader">
+Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__kl__neighborhood__stochbt.png" border="0" alt="" usemap="#group____kl____neighborhood____stochbt_map"/>
+<map name="group____kl____neighborhood____stochbt_map" id="group____kl____neighborhood____stochbt">
+<area shape="rect" id="node2" href="group__kl__neighborhood.html" title="Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary..." alt="" coords="7,5,396,35"/><area shape="rect" id="node3" href="group__subopt__stochbt.html" title="Stochastic backtracking in the Ensemble" alt="" coords="71,58,332,89"/></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:gae251288f50dd4ae7d315af0085775f71"><td class="memItemLeft" align="right" valign="top">char * </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>
-<tr class="memdesc:gae251288f50dd4ae7d315af0085775f71"><td class="mdescLeft"> </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>
-<tr class="memitem:ga13430ac6a7f90df426774f131647d2c7"><td class="memItemLeft" align="right" valign="top">char * </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>
-<tr class="memdesc:ga13430ac6a7f90df426774f131647d2c7"><td class="mdescLeft"> </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>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </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>
+<tr><td class="mdescLeft"> </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>
+<tr><td class="memItemLeft" align="right" valign="top">char * </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>
+<tr><td class="mdescLeft"> </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>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Contains functions related to stochastic backtracking from a specified distance class. </p>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="gae251288f50dd4ae7d315af0085775f71"></a>
+<a class="anchor" id="gae251288f50dd4ae7d315af0085775f71"></a><!-- doxytag: member="2Dpfold.h::TwoDpfold_pbacktrack" ref="gae251288f50dd4ae7d315af0085775f71" args="(TwoDpfold_vars *vars, int d1, int d2)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char* TwoDpfold_pbacktrack </td>
<td>(</td>
- <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td>
- <td class="paramname"><em>vars</em>, </td>
+ <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td>
+ <td class="paramname"> <em>vars</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>d1</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>d1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>d2</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>d2</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>Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. </p>
<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>
-<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>
-<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>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramdir">[in]</td><td class="paramname">vars</td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
- <tr><td class="paramdir">[in]</td><td class="paramname">d1</td><td>the distance to reference1 (may be -1) </td></tr>
- <tr><td class="paramdir">[in]</td><td class="paramname">d2</td><td>the distance to reference2 </td></tr>
+<dl class="pre"><dt><b>Precondition:</b></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>
+<dl class="see"><dt><b>See also:</b></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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>vars</em> </td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>d1</em> </td><td>the distance to reference1 (may be -1) </td></tr>
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>d2</em> </td><td>the distance to reference2 </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
</div>
</div>
-<a class="anchor" id="ga13430ac6a7f90df426774f131647d2c7"></a>
+<a class="anchor" id="ga13430ac6a7f90df426774f131647d2c7"></a><!-- doxytag: member="2Dpfold.h::TwoDpfold_pbacktrack5" ref="ga13430ac6a7f90df426774f131647d2c7" args="(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char* TwoDpfold_pbacktrack5 </td>
<td>(</td>
- <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td>
- <td class="paramname"><em>vars</em>, </td>
+ <td class="paramtype"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td>
+ <td class="paramname"> <em>vars</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>d1</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>d1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>d2</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>d2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">unsigned int </td>
- <td class="paramname"><em>length</em> </td>
+ <td class="paramtype">unsigned int </td>
+ <td class="paramname"> <em>length</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>Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. </p>
<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>
-<dl class="section note"><dt>Note:</dt><dd>This function does not work (since it makes no sense) for circular RNA sequences! </dd></dl>
-<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>
-<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>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramdir">[in]</td><td class="paramname">vars</td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
- <tr><td class="paramdir">[in]</td><td class="paramname">d1</td><td>the distance to reference1 (may be -1) </td></tr>
- <tr><td class="paramdir">[in]</td><td class="paramname">d2</td><td>the distance to reference2 </td></tr>
- <tr><td class="paramdir">[in]</td><td class="paramname">length</td><td>the length of the structure beginning from the 5' end </td></tr>
+<dl class="note"><dt><b>Note:</b></dt><dd>This function does not work (since it makes no sense) for circular RNA sequences! </dd></dl>
+<dl class="pre"><dt><b>Precondition:</b></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>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71" title="Sample secondary structure representatives from a set of distance classes according...">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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>vars</em> </td><td>the datastructure containing all necessary folding attributes and matrices </td></tr>
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>d1</em> </td><td>the distance to reference1 (may be -1) </td></tr>
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>d2</em> </td><td>the distance to reference2 </td></tr>
+ <tr><td valign="top"><tt>[in]</tt> </td><td valign="top"><em>length</em> </td><td>the length of the structure beginning from the 5' end </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
</div>
</div>
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