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-<div class="title">Suboptimal structures within an energy band arround the MFE</div> </div>
-<div class="ingroups"><a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a></div></div><!--header-->
<div class="contents">
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- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Suboptimal structures within an energy band arround the MFE:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+<h1>Suboptimal structures within an energy band arround the MFE<br/>
+<small>
+[<a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a>]</small>
+</h1>
+<p><div class="dynheader">
+Collaboration diagram for Suboptimal structures within an energy band arround the MFE:</div>
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-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:ga700f662506a233e42dd7fda74fafd40e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e">subopt</a> (char *seq, char *structure, int delta, FILE *fp)</td></tr>
-<tr class="memdesc:ga700f662506a233e42dd7fda74fafd40e"><td class="mdescLeft"> </td><td class="mdescRight">Returns list of subopt structures or writes to fp. <a href="#ga700f662506a233e42dd7fda74fafd40e"></a><br/></td></tr>
-<tr class="memitem:ga554dedfcdb249fdf151caade58666e4d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga554dedfcdb249fdf151caade58666e4d"></a>
-<a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga554dedfcdb249fdf151caade58666e4d">subopt_par</a> (char *seq, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</td></tr>
-<tr class="memdesc:ga554dedfcdb249fdf151caade58666e4d"><td class="mdescLeft"> </td><td class="mdescRight">Returns list of subopt structures or writes to fp. <br/></td></tr>
-<tr class="memitem:ga8634516e4740e0b6c9a46d2bae940340"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga8634516e4740e0b6c9a46d2bae940340">subopt_circ</a> (char *seq, char *sequence, int delta, FILE *fp)</td></tr>
-<tr class="memdesc:ga8634516e4740e0b6c9a46d2bae940340"><td class="mdescLeft"> </td><td class="mdescRight">Returns list of circular subopt structures or writes to fp. <a href="#ga8634516e4740e0b6c9a46d2bae940340"></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:ga873cf8ed69e0437f8efa8b1fec854a0e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga873cf8ed69e0437f8efa8b1fec854a0e"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga873cf8ed69e0437f8efa8b1fec854a0e">subopt_sorted</a></td></tr>
-<tr class="memdesc:ga873cf8ed69e0437f8efa8b1fec854a0e"><td class="mdescLeft"> </td><td class="mdescRight">Sort output by energy. <br/></td></tr>
-<tr class="memitem:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e57d914bcb5feeecdf520e25313fcfe"></a>
-double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga5e57d914bcb5feeecdf520e25313fcfe">print_energy</a></td></tr>
-<tr class="memdesc:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="mdescLeft"> </td><td class="mdescRight">printing threshold for use with logML <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"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e">subopt</a> (char *seq, char *structure, int delta, FILE *fp)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns list of subopt structures or writes to fp. <a href="#ga700f662506a233e42dd7fda74fafd40e"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga554dedfcdb249fdf151caade58666e4d"></a><!-- doxytag: member="subopt_wuchty::subopt_par" ref="ga554dedfcdb249fdf151caade58666e4d" args="(char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp)" -->
+<a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga554dedfcdb249fdf151caade58666e4d">subopt_par</a> (char *seq, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns list of subopt structures or writes to fp. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga8634516e4740e0b6c9a46d2bae940340">subopt_circ</a> (char *seq, char *sequence, int delta, FILE *fp)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns list of circular subopt structures or writes to fp. <a href="#ga8634516e4740e0b6c9a46d2bae940340"></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="ga873cf8ed69e0437f8efa8b1fec854a0e"></a><!-- doxytag: member="subopt_wuchty::subopt_sorted" ref="ga873cf8ed69e0437f8efa8b1fec854a0e" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga873cf8ed69e0437f8efa8b1fec854a0e">subopt_sorted</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sort output by energy. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e57d914bcb5feeecdf520e25313fcfe"></a><!-- doxytag: member="subopt_wuchty::print_energy" ref="ga5e57d914bcb5feeecdf520e25313fcfe" args="" -->
+double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga5e57d914bcb5feeecdf520e25313fcfe">print_energy</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">printing threshold for use with logML <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ga700f662506a233e42dd7fda74fafd40e"></a>
+<a class="anchor" id="ga700f662506a233e42dd7fda74fafd40e"></a><!-- doxytag: member="subopt.h::subopt" ref="ga700f662506a233e42dd7fda74fafd40e" args="(char *seq, char *structure, int delta, FILE *fp)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>seq</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>delta</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>delta</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">FILE * </td>
- <td class="paramname"><em>fp</em> </td>
+ <td class="paramtype">FILE * </td>
+ <td class="paramname"> <em>fp</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>Returns list of subopt structures or writes to fp. </p>
<p>This function produces <b>all</b> suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a <a class="el" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> * list terminated by an entry were the 'structure' pointer is NULL.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">seq</td><td></td></tr>
- <tr><td class="paramname">structure</td><td></td></tr>
- <tr><td class="paramname">delta</td><td></td></tr>
- <tr><td class="paramname">fp</td><td></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>seq</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>delta</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fp</em> </td><td></td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
</div>
</div>
-<a class="anchor" id="ga8634516e4740e0b6c9a46d2bae940340"></a>
+<a class="anchor" id="ga8634516e4740e0b6c9a46d2bae940340"></a><!-- doxytag: member="subopt.h::subopt_circ" ref="ga8634516e4740e0b6c9a46d2bae940340" args="(char *seq, char *sequence, int delta, FILE *fp)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt_circ </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>seq</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>sequence</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>sequence</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>delta</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>delta</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">FILE * </td>
- <td class="paramname"><em>fp</em> </td>
+ <td class="paramtype">FILE * </td>
+ <td class="paramname"> <em>fp</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>Returns list of circular subopt structures or writes to fp. </p>
<p>This function is similar to <a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e" title="Returns list of subopt structures or writes to fp.">subopt()</a> but calculates secondary structures assuming the RNA sequence to be circular instead of linear</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">seq</td><td></td></tr>
- <tr><td class="paramname">sequence</td><td></td></tr>
- <tr><td class="paramname">delta</td><td></td></tr>
- <tr><td class="paramname">fp</td><td></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>seq</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>sequence</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>delta</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fp</em> </td><td></td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
</div>
</div>
-</div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
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- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
- </ul>
</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
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