binaries/src/ViennaRNA/doc/html/group__subopt__wuchty.html

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   6 <title>RNAlib-2.1.2: Suboptimal structures within an energy band arround the MFE</title>
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  59 <a href="#func-members">Functions</a> &#124;
  60 <a href="#var-members">Variables</a>  </div>
  61   <div class="headertitle">
  62 <div class="title">Suboptimal structures within an energy band arround the MFE</div>  </div>
  63 <div class="ingroups"><a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a></div></div><!--header-->
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  66   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Suboptimal structures within an energy band arround the MFE:</div>
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  77 Functions</h2></td></tr>
  78 <tr class="memitem:ga700f662506a233e42dd7fda74fafd40e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</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>
  79 <tr class="memdesc:ga700f662506a233e42dd7fda74fafd40e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of subopt structures or writes to fp.  <a href="#ga700f662506a233e42dd7fda74fafd40e"></a><br/></td></tr>
  80 <tr class="memitem:ga554dedfcdb249fdf151caade58666e4d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga554dedfcdb249fdf151caade58666e4d"></a>
  81 <a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</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>
  82 <tr class="memdesc:ga554dedfcdb249fdf151caade58666e4d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of subopt structures or writes to fp. <br/></td></tr>
  83 <tr class="memitem:ga8634516e4740e0b6c9a46d2bae940340"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</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>
  84 <tr class="memdesc:ga8634516e4740e0b6c9a46d2bae940340"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of circular subopt structures or writes to fp.  <a href="#ga8634516e4740e0b6c9a46d2bae940340"></a><br/></td></tr>
  85 </table><table class="memberdecls">
  86 <tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
  87 Variables</h2></td></tr>
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  89 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga873cf8ed69e0437f8efa8b1fec854a0e">subopt_sorted</a></td></tr>
  90 <tr class="memdesc:ga873cf8ed69e0437f8efa8b1fec854a0e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sort output by energy. <br/></td></tr>
  91 <tr class="memitem:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e57d914bcb5feeecdf520e25313fcfe"></a>
  92 double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga5e57d914bcb5feeecdf520e25313fcfe">print_energy</a></td></tr>
  93 <tr class="memdesc:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="mdescLeft">&#160;</td><td class="mdescRight">printing threshold for use with logML <br/></td></tr>
  94 </table>
  95 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
  96 <hr/><h2>Function Documentation</h2>
  97 <a class="anchor" id="ga700f662506a233e42dd7fda74fafd40e"></a>
  98 <div class="memitem">
  99 <div class="memproto">
 100       <table class="memname">
 101         <tr>
 102           <td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt </td>
 103           <td>(</td>
 104           <td class="paramtype">char *&#160;</td>
 105           <td class="paramname"><em>seq</em>, </td>
 106         </tr>
 107         <tr>
 108           <td class="paramkey"></td>
 109           <td></td>
 110           <td class="paramtype">char *&#160;</td>
 111           <td class="paramname"><em>structure</em>, </td>
 112         </tr>
 113         <tr>
 114           <td class="paramkey"></td>
 115           <td></td>
 116           <td class="paramtype">int&#160;</td>
 117           <td class="paramname"><em>delta</em>, </td>
 118         </tr>
 119         <tr>
 120           <td class="paramkey"></td>
 121           <td></td>
 122           <td class="paramtype">FILE *&#160;</td>
 123           <td class="paramname"><em>fp</em>&#160;</td>
 124         </tr>
 125         <tr>
 126           <td></td>
 127           <td>)</td>
 128           <td></td><td></td>
 129         </tr>
 130       </table>
 131 </div><div class="memdoc">
 132
 133 <p>Returns list of subopt structures or writes to fp. </p>
 134 <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>
 135 <dl class="params"><dt>Parameters:</dt><dd>
 136   <table class="params">
 137     <tr><td class="paramname">seq</td><td></td></tr>
 138     <tr><td class="paramname">structure</td><td></td></tr>
 139     <tr><td class="paramname">delta</td><td></td></tr>
 140     <tr><td class="paramname">fp</td><td></td></tr>
 141   </table>
 142   </dd>
 143 </dl>
 144 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 145
 146 </div>
 147 </div>
 148 <a class="anchor" id="ga8634516e4740e0b6c9a46d2bae940340"></a>
 149 <div class="memitem">
 150 <div class="memproto">
 151       <table class="memname">
 152         <tr>
 153           <td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt_circ </td>
 154           <td>(</td>
 155           <td class="paramtype">char *&#160;</td>
 156           <td class="paramname"><em>seq</em>, </td>
 157         </tr>
 158         <tr>
 159           <td class="paramkey"></td>
 160           <td></td>
 161           <td class="paramtype">char *&#160;</td>
 162           <td class="paramname"><em>sequence</em>, </td>
 163         </tr>
 164         <tr>
 165           <td class="paramkey"></td>
 166           <td></td>
 167           <td class="paramtype">int&#160;</td>
 168           <td class="paramname"><em>delta</em>, </td>
 169         </tr>
 170         <tr>
 171           <td class="paramkey"></td>
 172           <td></td>
 173           <td class="paramtype">FILE *&#160;</td>
 174           <td class="paramname"><em>fp</em>&#160;</td>
 175         </tr>
 176         <tr>
 177           <td></td>
 178           <td>)</td>
 179           <td></td><td></td>
 180         </tr>
 181       </table>
 182 </div><div class="memdoc">
 183
 184 <p>Returns list of circular subopt structures or writes to fp. </p>
 185 <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>
 186 <dl class="params"><dt>Parameters:</dt><dd>
 187   <table class="params">
 188     <tr><td class="paramname">seq</td><td></td></tr>
 189     <tr><td class="paramname">sequence</td><td></td></tr>
 190     <tr><td class="paramname">delta</td><td></td></tr>
 191     <tr><td class="paramname">fp</td><td></td></tr>
 192   </table>
 193   </dd>
 194 </dl>
 195 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 196
 197 </div>
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