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  66 <a href="#pub-attribs">Data Fields</a>  </div>
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  68 <div class="title">model_detailsT Struct Reference</div>  </div>
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  71
  72 <p>The data structure that contains the complete model details used throughout the calculations.
  73  <a href="structmodel__detailsT.html#details">More...</a></p>
  74 <table class="memberdecls">
  75 <tr class="heading"><td colspan="2"><h2><a name="pub-attribs"></a>
  76 Data Fields</h2></td></tr>
  77 <tr class="memitem:a89f9df217a4a7f4351a642655976376b"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a89f9df217a4a7f4351a642655976376b">dangles</a></td></tr>
  78 <tr class="memdesc:a89f9df217a4a7f4351a642655976376b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Specifies the dangle model used in any energy evaluation (0,1,2 or 3)  <a href="#a89f9df217a4a7f4351a642655976376b"></a><br/></td></tr>
  79 <tr class="memitem:a9d73fde17b0465311a80f607faa85617"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a9d73fde17b0465311a80f607faa85617"></a>
  80 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617">special_hp</a></td></tr>
  81 <tr class="memdesc:a9d73fde17b0465311a80f607faa85617"><td class="mdescLeft">&#160;</td><td class="mdescRight">Include special hairpin contributions for tri, tetra and hexaloops. <br/></td></tr>
  82 <tr class="memitem:a6fb076173d2cbc4259606ce23eedf17d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6fb076173d2cbc4259606ce23eedf17d"></a>
  83 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a6fb076173d2cbc4259606ce23eedf17d">noLP</a></td></tr>
  84 <tr class="memdesc:a6fb076173d2cbc4259606ce23eedf17d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Only consider canonical structures, i.e. no 'lonely' base pairs. <br/></td></tr>
  85 <tr class="memitem:a0f982e6904d012e4fe41e99daa797f5d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a0f982e6904d012e4fe41e99daa797f5d"></a>
  86 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a0f982e6904d012e4fe41e99daa797f5d">noGU</a></td></tr>
  87 <tr class="memdesc:a0f982e6904d012e4fe41e99daa797f5d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Do not allow GU pairs. <br/></td></tr>
  88 <tr class="memitem:ae9cedf375cd904e5fb8e56cf3f64bcd9"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ae9cedf375cd904e5fb8e56cf3f64bcd9"></a>
  89 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#ae9cedf375cd904e5fb8e56cf3f64bcd9">noGUclosure</a></td></tr>
  90 <tr class="memdesc:ae9cedf375cd904e5fb8e56cf3f64bcd9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Do not allow loops to be closed by GU pair. <br/></td></tr>
  91 <tr class="memitem:a415556dc150e02d108be81ecc5c48e85"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a415556dc150e02d108be81ecc5c48e85"></a>
  92 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a415556dc150e02d108be81ecc5c48e85">logML</a></td></tr>
  93 <tr class="memdesc:a415556dc150e02d108be81ecc5c48e85"><td class="mdescLeft">&#160;</td><td class="mdescRight">Use logarithmic scaling for multi loops. <br/></td></tr>
  94 <tr class="memitem:a55f083dad18c216505805a8062e63074"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a55f083dad18c216505805a8062e63074"></a>
  95 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#a55f083dad18c216505805a8062e63074">circ</a></td></tr>
  96 <tr class="memdesc:a55f083dad18c216505805a8062e63074"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assume molecule to be circular. <br/></td></tr>
  97 <tr class="memitem:aa1ecdce7bc3f375bd8a9a7b738abc0ea"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa1ecdce7bc3f375bd8a9a7b738abc0ea"></a>
  98 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmodel__detailsT.html#aa1ecdce7bc3f375bd8a9a7b738abc0ea">gquad</a></td></tr>
  99 <tr class="memdesc:aa1ecdce7bc3f375bd8a9a7b738abc0ea"><td class="mdescLeft">&#160;</td><td class="mdescRight">Include G-quadruplexes in structure prediction. <br/></td></tr>
 100 </table>
 101 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 102 <div class="textblock"><p>The data structure that contains the complete model details used throughout the calculations. </p>
 103 </div><hr/><h2>Field Documentation</h2>
 104 <a class="anchor" id="a89f9df217a4a7f4351a642655976376b"></a>
 105 <div class="memitem">
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 108         <tr>
 109           <td class="memname">int model_detailsT::dangles</td>
 110         </tr>
 111       </table>
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 113
 114 <p>Specifies the dangle model used in any energy evaluation (0,1,2 or 3) </p>
 115 <dl class="section note"><dt>Note:</dt><dd>Some function do not implement all dangle model but only a subset of (0,1,2,3). Read the documentaion of the particular recurrences or energy evaluation function for information about the provided dangle model. </dd></dl>
 116
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