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- <div class="headertitle">
-<div class="title">Searching Sequences for Predefined Structures</div> </div>
-<div class="ingroups"><a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a></div></div><!--header-->
<div class="contents">
-<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 Searching Sequences for Predefined Structures:</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__inverse__fold.png" border="0" alt="" usemap="#group____inverse____fold"/>
-<map name="group____inverse____fold" id="group____inverse____fold">
-<area shape="rect" id="node2" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="6,5,191,46"/></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:inverse_8h"><td class="memItemLeft" align="right" valign="top">file  </td><td class="memItemRight" valign="bottom"><a class="el" href="inverse_8h.html">inverse.h</a></td></tr>
-<tr class="memdesc:inverse_8h"><td class="mdescLeft"> </td><td class="mdescRight">Inverse folding routines. <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:ga7af026de55d4babad879f2c92559cbbc"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7af026de55d4babad879f2c92559cbbc">inverse_fold</a> (char *start, const char *target)</td></tr>
-<tr class="memdesc:ga7af026de55d4babad879f2c92559cbbc"><td class="mdescLeft"> </td><td class="mdescRight">Find sequences with predefined structure. <a href="#ga7af026de55d4babad879f2c92559cbbc"></a><br/></td></tr>
-<tr class="memitem:gaeef52ecbf2a2450ad585a344f9826806"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#gaeef52ecbf2a2450ad585a344f9826806">inverse_pf_fold</a> (char *start, const char *target)</td></tr>
-<tr class="memdesc:gaeef52ecbf2a2450ad585a344f9826806"><td class="mdescLeft"> </td><td class="mdescRight">Find sequence that maximizes probability of a predefined structure. <a href="#gaeef52ecbf2a2450ad585a344f9826806"></a><br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
-Variables</h2></td></tr>
-<tr class="memitem:ga8f791e7740a5a28b9f6fafb4e60301d9"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga8f791e7740a5a28b9f6fafb4e60301d9"></a>
-char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga8f791e7740a5a28b9f6fafb4e60301d9">symbolset</a></td></tr>
-<tr class="memdesc:ga8f791e7740a5a28b9f6fafb4e60301d9"><td class="mdescLeft"> </td><td class="mdescRight">This global variable points to the allowed bases, initially "AUGC". It can be used to design sequences from reduced alphabets. <br/></td></tr>
-<tr class="memitem:ga7f17d3b169af048d32bb185039a9c09c"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7f17d3b169af048d32bb185039a9c09c">final_cost</a></td></tr>
-<tr class="memitem:ga7ec4ba51f86e1717a1e174264e4a75ce"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7ec4ba51f86e1717a1e174264e4a75ce">give_up</a></td></tr>
-<tr class="memitem:gafcfc65fba01b9cca5946726ed9057a63"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#gafcfc65fba01b9cca5946726ed9057a63">inv_verbose</a></td></tr>
+<h1>Searching Sequences for Predefined Structures<br/>
+<small>
+[<a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a>]</small>
+</h1>
+<p><div class="dynheader">
+Collaboration diagram for Searching Sequences for Predefined Structures:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__inverse__fold.png" border="0" alt="" usemap="#group____inverse____fold_map"/>
+<map name="group____inverse____fold_map" id="group____inverse____fold">
+<area shape="rect" id="node2" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="5,5,229,35"/></map></td></tr></table></center>
+</div>
+</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="inverse_8h.html">inverse.h</a></td></tr>
+
+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>Inverse folding routines. </p>
+<br/></td></tr>
+</p>
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7af026de55d4babad879f2c92559cbbc">inverse_fold</a> (char *start, const char *target)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Find sequences with predefined structure. <a href="#ga7af026de55d4babad879f2c92559cbbc"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#gaeef52ecbf2a2450ad585a344f9826806">inverse_pf_fold</a> (char *start, const char *target)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Find sequence that maximizes probability of a predefined structure. <a href="#gaeef52ecbf2a2450ad585a344f9826806"></a><br/></td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga8f791e7740a5a28b9f6fafb4e60301d9"></a><!-- doxytag: member="inverse_fold::symbolset" ref="ga8f791e7740a5a28b9f6fafb4e60301d9" args="" -->
+char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga8f791e7740a5a28b9f6fafb4e60301d9">symbolset</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">This global variable points to the allowed bases, initially "AUGC". It can be used to design sequences from reduced alphabets. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7f17d3b169af048d32bb185039a9c09c">final_cost</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#ga7ec4ba51f86e1717a1e174264e4a75ce">give_up</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__inverse__fold.html#gafcfc65fba01b9cca5946726ed9057a63">inv_verbose</a></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>We provide two functions that search for sequences with a given structure, thereby inverting the folding routines. </p>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ga7af026de55d4babad879f2c92559cbbc"></a>
+<a class="anchor" id="ga7af026de55d4babad879f2c92559cbbc"></a><!-- doxytag: member="inverse.h::inverse_fold" ref="ga7af026de55d4babad879f2c92559cbbc" args="(char *start, const char *target)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float inverse_fold </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>start</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>start</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>target</em> </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>target</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>Find sequences with predefined structure. </p>
<p>This function searches for a sequence with minimum free energy structure provided in the parameter 'target', starting with sequence 'start'. It returns 0 if the search was successful, otherwise a structure distance in terms of the energy difference between the search result and the actual target 'target' is returned. The found sequence is returned in 'start'. If <a class="el" href="group__inverse__fold.html#ga7ec4ba51f86e1717a1e174264e4a75ce">give_up</a> is set to 1, the function will return as soon as it is clear that the search will be unsuccessful, this speeds up the algorithm if you are only interested in exact solutions.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">start</td><td>The start sequence </td></tr>
- <tr><td class="paramname">target</td><td>The target secondary structure in dot-bracket notation </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>start</em> </td><td>The start sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>target</em> </td><td>The target secondary structure in dot-bracket notation </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The distance to the target in case a search was unsuccessful, 0 otherwise </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>The distance to the target in case a search was unsuccessful, 0 otherwise </dd></dl>
</div>
</div>
-<a class="anchor" id="gaeef52ecbf2a2450ad585a344f9826806"></a>
+<a class="anchor" id="gaeef52ecbf2a2450ad585a344f9826806"></a><!-- doxytag: member="inverse.h::inverse_pf_fold" ref="gaeef52ecbf2a2450ad585a344f9826806" args="(char *start, const char *target)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float inverse_pf_fold </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>start</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>start</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>target</em> </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>target</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>Find sequence that maximizes probability of a predefined structure. </p>
<p>This function searches for a sequence with maximum probability to fold into the provided structure 'target' using the partition function algorithm. It returns <img class="formulaInl" alt="$-kT \cdot \log(p)$" src="form_9.png"/> where <img class="formulaInl" alt="$p$" src="form_10.png"/> is the frequency of 'target' in the ensemble of possible structures. This is usually much slower than <a class="el" href="group__inverse__fold.html#ga7af026de55d4babad879f2c92559cbbc" title="Find sequences with predefined structure.">inverse_fold()</a>.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">start</td><td>The start sequence </td></tr>
- <tr><td class="paramname">target</td><td>The target secondary structure in dot-bracket notation </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>start</em> </td><td>The start sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>target</em> </td><td>The target secondary structure in dot-bracket notation </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The distance to the target in case a search was unsuccessful, 0 otherwise </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>The distance to the target in case a search was unsuccessful, 0 otherwise </dd></dl>
</div>
</div>
<hr/><h2>Variable Documentation</h2>
-<a class="anchor" id="ga7f17d3b169af048d32bb185039a9c09c"></a>
+<a class="anchor" id="ga7f17d3b169af048d32bb185039a9c09c"></a><!-- doxytag: member="inverse.h::final_cost" ref="ga7f17d3b169af048d32bb185039a9c09c" args="" -->
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<tr>
- <td class="memname">float final_cost</td>
+ <td class="memname">float <a class="el" href="group__inverse__fold.html#ga7f17d3b169af048d32bb185039a9c09c">final_cost</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>when to stop <a class="el" href="group__inverse__fold.html#gaeef52ecbf2a2450ad585a344f9826806" title="Find sequence that maximizes probability of a predefined structure.">inverse_pf_fold()</a> </p>
</div>
</div>
-<a class="anchor" id="ga7ec4ba51f86e1717a1e174264e4a75ce"></a>
+<a class="anchor" id="ga7ec4ba51f86e1717a1e174264e4a75ce"></a><!-- doxytag: member="inverse.h::give_up" ref="ga7ec4ba51f86e1717a1e174264e4a75ce" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
- <td class="memname">int give_up</td>
+ <td class="memname">int <a class="el" href="group__inverse__fold.html#ga7ec4ba51f86e1717a1e174264e4a75ce">give_up</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>default 0: try to minimize structure distance even if no exact solution can be found </p>
</div>
</div>
-<a class="anchor" id="gafcfc65fba01b9cca5946726ed9057a63"></a>
+<a class="anchor" id="gafcfc65fba01b9cca5946726ed9057a63"></a><!-- doxytag: member="inverse.h::inv_verbose" ref="gafcfc65fba01b9cca5946726ed9057a63" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
- <td class="memname">int inv_verbose</td>
+ <td class="memname">int <a class="el" href="group__inverse__fold.html#gafcfc65fba01b9cca5946726ed9057a63">inv_verbose</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>print out substructure on which <a class="el" href="group__inverse__fold.html#ga7af026de55d4babad879f2c92559cbbc" title="Find sequences with predefined structure.">inverse_fold()</a> fails </p>
</div>
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