binaries/src/ViennaRNA/doc/html/part__func_8h.html

   1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
   2 <html xmlns="http://www.w3.org/1999/xhtml">
   3 <head>
   4 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
   5 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
   6 <title>RNAlib-2.1.2: /home/mescalin/ronny/public_html/programs/ViennaRNA/H/part_func.h File Reference</title>
   7 <link href="tabs.css" rel="stylesheet" type="text/css"/>
   8 <script type="text/javascript" src="jquery.js"></script>
   9 <script type="text/javascript" src="dynsections.js"></script>
  10 <link href="navtree.css" rel="stylesheet" type="text/css"/>
  11 <script type="text/javascript" src="resize.js"></script>
  12 <script type="text/javascript" src="navtree.js"></script>
  13 <script type="text/javascript">
  14   $(document).ready(initResizable);
  15 </script>
  16 <link href="doxygen.css" rel="stylesheet" type="text/css" />
  17 </head>
  18 <body>
  19 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
  20 <div id="titlearea">
  21 <table cellspacing="0" cellpadding="0">
  22  <tbody>
  23  <tr style="height: 56px;">
  24   <td style="padding-left: 0.5em;">
  25    <div id="projectname">RNAlib-2.1.2
  26    </div>
  27   </td>
  28  </tr>
  29  </tbody>
  30 </table>
  31 </div>
  32 <!-- end header part -->
  33 <!-- Generated by Doxygen 1.8.1.1 -->
  34   <div id="navrow1" class="tabs">
  35     <ul class="tablist">
  36       <li><a href="index.html"><span>Main&#160;Page</span></a></li>
  37       <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
  38       <li><a href="modules.html"><span>Modules</span></a></li>
  39       <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
  40       <li class="current"><a href="files.html"><span>Files</span></a></li>
  41     </ul>
  42   </div>
  43   <div id="navrow2" class="tabs2">
  44     <ul class="tablist">
  45       <li><a href="files.html"><span>File&#160;List</span></a></li>
  46       <li><a href="globals.html"><span>Globals</span></a></li>
  47     </ul>
  48   </div>
  49 </div><!-- top -->
  50 <div id="side-nav" class="ui-resizable side-nav-resizable">
  51   <div id="nav-tree">
  52     <div id="nav-tree-contents">
  53     </div>
  54   </div>
  55   <div id="splitbar" style="-moz-user-select:none;"
  56        class="ui-resizable-handle">
  57   </div>
  58 </div>
  59 <script type="text/javascript">
  60 $(document).ready(function(){initNavTree('part__func_8h.html','');});
  61 </script>
  62 <div id="doc-content">
  63 <div class="header">
  64   <div class="summary">
  65 <a href="#func-members">Functions</a> &#124;
  66 <a href="#var-members">Variables</a>  </div>
  67   <div class="headertitle">
  68 <div class="title">part_func.h File Reference<div class="ingroups"><a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a></div></div>  </div>
  69 </div><!--header-->
  70 <div class="contents">
  71
  72 <p>Partition function of single RNA sequences.
  73 <a href="#details">More...</a></p>
  74 <div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
  75   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for part_func.h:</div>
  76 <div id="dynsection-0-summary" class="dynsummary" style="display:block;">
  77 </div>
  78 <div id="dynsection-0-content" class="dyncontent" style="display:none;">
  79 <div class="center"><img src="part__func_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func_8h" alt=""/></div>
  80 <map name="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func_8h" id="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2part__func_8h">
  81 <area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="31,109,165,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="39,184,159,211"/></map>
  82 </div>
  83 </div>
  84 <p><a href="part__func_8h_source.html">Go to the source code of this file.</a></p>
  85 <table class="memberdecls">
  86 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  87 Functions</h2></td></tr>
  88 <tr class="memitem:ga1839c61275760944b3a007c41d5c0823"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823">pf_fold_par</a> (const char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
  89 <tr class="memdesc:ga1839c61275760944b3a007c41d5c0823"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> for a given RNA sequence.  <a href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823"></a><br/></td></tr>
  90 <tr class="memitem:gadc3db3d98742427e7001a7fd36ef28c2"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2">pf_fold</a> (const char *sequence, char *structure)</td></tr>
  91 <tr class="memdesc:gadc3db3d98742427e7001a7fd36ef28c2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> of an RNA sequence.  <a href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2"></a><br/></td></tr>
  92 <tr class="memitem:ga819ce5fca8984004ac81c4a3b04cb735"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735">pf_circ_fold</a> (const char *sequence, char *structure)</td></tr>
  93 <tr class="memdesc:ga819ce5fca8984004ac81c4a3b04cb735"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute the partition function of a circular RNA sequence.  <a href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735"></a><br/></td></tr>
  94 <tr class="memitem:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
  95 <tr class="memdesc:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
  96 .  <a href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03"></a><br/></td></tr>
  97 <tr class="memitem:ga00474051204ac9ad576b3e45174d03ff"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
  98 <tr class="memdesc:ga00474051204ac9ad576b3e45174d03ff"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.  <a href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
  99 <tr class="memitem:gae73db3f49a94f0f72e067ecd12681dbd"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd">free_pf_arrays</a> (void)</td></tr>
 100 <tr class="memdesc:gae73db3f49a94f0f72e067ecd12681dbd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Free arrays for the partition function recursions.  <a href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd"></a><br/></td></tr>
 101 <tr class="memitem:ga384e927890f9c034ff09fa66da102d28"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28">update_pf_params</a> (int length)</td></tr>
 102 <tr class="memdesc:ga384e927890f9c034ff09fa66da102d28"><td class="mdescLeft">&#160;</td><td class="mdescRight">Recalculate energy parameters.  <a href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28"></a><br/></td></tr>
 103 <tr class="memitem:ga0733527a94de3b79eee3c3c03c99c1bc"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga0733527a94de3b79eee3c3c03c99c1bc"></a>
 104 void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc">update_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
 105 <tr class="memdesc:ga0733527a94de3b79eee3c3c03c99c1bc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
 106 <tr class="memitem:ga6d463707d5f64bdc4d21515b7dd9b115"><td class="memItemLeft" align="right" valign="top">double *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115">export_bppm</a> (void)</td></tr>
 107 <tr class="memdesc:ga6d463707d5f64bdc4d21515b7dd9b115"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i,j) is achieved by.  <a href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115"></a><br/></td></tr>
 108 <tr class="memitem:ga03e15e831a31b1154855ab47edbdb019"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr</a> (<a class="el" href="structplist.html">plist</a> **pl, double *probs, int length, double cutoff)</td></tr>
 109 <tr class="memdesc:ga03e15e831a31b1154855ab47edbdb019"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a plist from a probability matrix.  <a href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019"></a><br/></td></tr>
 110 <tr class="memitem:ga18607e79e106cad827f482eedd2f632e"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e">get_pf_arrays</a> (short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</td></tr>
 111 <tr class="memdesc:ga18607e79e106cad827f482eedd2f632e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the pointers to (almost) all relavant computation arrays used in partition function computation.  <a href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e"></a><br/></td></tr>
 112 <tr class="memitem:a189e2a1ec6cc32c53ea72f7543b0441e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a189e2a1ec6cc32c53ea72f7543b0441e"></a>
 113 double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e">get_subseq_F</a> (int i, int j)</td></tr>
 114 <tr class="memdesc:a189e2a1ec6cc32c53ea72f7543b0441e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the free energy of a subsequence from the q[] array. <br/></td></tr>
 115 <tr class="memitem:ga9aba0ba1433a6d259331e0fe9fc4a9a6"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6">get_centroid_struct_pl</a> (int length, double *dist, <a class="el" href="structplist.html">plist</a> *pl)</td></tr>
 116 <tr class="memdesc:ga9aba0ba1433a6d259331e0fe9fc4a9a6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the centroid structure of the ensemble.  <a href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6"></a><br/></td></tr>
 117 <tr class="memitem:gacdabece4aa1e20c9eaa97acb4c4dcc38"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38">get_centroid_struct_pr</a> (int length, double *dist, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
 118 <tr class="memdesc:gacdabece4aa1e20c9eaa97acb4c4dcc38"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the centroid structure of the ensemble.  <a href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38"></a><br/></td></tr>
 119 <tr class="memitem:ga79cbc375af65f11609feb6b055269e7d"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance</a> (int length)</td></tr>
 120 <tr class="memdesc:ga79cbc375af65f11609feb6b055269e7d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the mean base pair distance of the last partition function computation.  <a href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d"></a><br/></td></tr>
 121 <tr class="memitem:ga72d84525f0afd3a9d60d830a2f501fa5"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5">mean_bp_distance_pr</a> (int length, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
 122 <tr class="memdesc:ga72d84525f0afd3a9d60d830a2f501fa5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the mean base pair distance in the thermodynamic ensemble.  <a href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5"></a><br/></td></tr>
 123 <tr class="memitem:a1f562d463c14d4703d9656056200eb38"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1f562d463c14d4703d9656056200eb38"></a>
 124 void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38">bppm_to_structure</a> (char *structure, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>, unsigned int length)</td></tr>
 125 <tr class="memdesc:a1f562d463c14d4703d9656056200eb38"><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a dot-bracket like structure string from base pair probability matrix. <br/></td></tr>
 126 <tr class="memitem:a49962ad6242b8c628de6ca16bb831c1d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a49962ad6242b8c628de6ca16bb831c1d"></a>
 127 char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d">bppm_symbol</a> (const float *x)</td></tr>
 128 <tr class="memdesc:a49962ad6242b8c628de6ca16bb831c1d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get a pseudo dot bracket notation for a given probability information. <br/></td></tr>
 129 <tr class="memitem:a15176e23eceeff8c7d14eabcfec8a2af"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">init_pf_fold</a> (int length)</td></tr>
 130 <tr class="memdesc:a15176e23eceeff8c7d14eabcfec8a2af"><td class="mdescLeft">&#160;</td><td class="mdescRight">Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a>  <a href="#a15176e23eceeff8c7d14eabcfec8a2af"></a><br/></td></tr>
 131 <tr class="memitem:ae89a63bd83e75a80b2ba36d20b31ce81"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a> (int length, double *dist)</td></tr>
 132 <tr class="memitem:ae9556ba7ded44fe2321b6f67c3fc02a3"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a> (int length)</td></tr>
 133 <tr class="memitem:a68ba6f3a48e08ca131ab54621ce3a2d7"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a> (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</td></tr>
 134 <tr class="memitem:a7b6ab474cc80accc48010ccfcc59f96b"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a> (int u, int type, short si1, short sj1, const char *string)</td></tr>
 135 </table><table class="memberdecls">
 136 <tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
 137 Variables</h2></td></tr>
 138 <tr class="memitem:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
 139 <tr class="memdesc:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.  <a href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
 140 </table>
 141 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 142 <div class="textblock"><p>Partition function of single RNA sequences. </p>
 143 <p>This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to Partion function folding... </p>
 144 </div><hr/><h2>Function Documentation</h2>
 145 <a class="anchor" id="a15176e23eceeff8c7d14eabcfec8a2af"></a>
 146 <div class="memitem">
 147 <div class="memproto">
 148       <table class="memname">
 149         <tr>
 150           <td class="memname">void init_pf_fold </td>
 151           <td>(</td>
 152           <td class="paramtype">int&#160;</td>
 153           <td class="paramname"><em>length</em></td><td>)</td>
 154           <td></td>
 155         </tr>
 156       </table>
 157 </div><div class="memdoc">
 158
 159 <p>Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a> </p>
 160 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000011">Deprecated:</a></b></dt><dd>This function is obsolete and will be removed soon! </dd></dl>
 161
 162 </div>
 163 </div>
 164 <a class="anchor" id="ae89a63bd83e75a80b2ba36d20b31ce81"></a>
 165 <div class="memitem">
 166 <div class="memproto">
 167       <table class="memname">
 168         <tr>
 169           <td class="memname">char* centroid </td>
 170           <td>(</td>
 171           <td class="paramtype">int&#160;</td>
 172           <td class="paramname"><em>length</em>, </td>
 173         </tr>
 174         <tr>
 175           <td class="paramkey"></td>
 176           <td></td>
 177           <td class="paramtype">double *&#160;</td>
 178           <td class="paramname"><em>dist</em>&#160;</td>
 179         </tr>
 180         <tr>
 181           <td></td>
 182           <td>)</td>
 183           <td></td><td></td>
 184         </tr>
 185       </table>
 186 </div><div class="memdoc">
 187 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000012">Deprecated:</a></b></dt><dd>This function is deprecated and should not be used anymore as it is not threadsafe! </dd></dl>
 188 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl()</a>, <a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr()</a> </dd></dl>
 189
 190 </div>
 191 </div>
 192 <a class="anchor" id="ae9556ba7ded44fe2321b6f67c3fc02a3"></a>
 193 <div class="memitem">
 194 <div class="memproto">
 195       <table class="memname">
 196         <tr>
 197           <td class="memname">double mean_bp_dist </td>
 198           <td>(</td>
 199           <td class="paramtype">int&#160;</td>
 200           <td class="paramname"><em>length</em></td><td>)</td>
 201           <td></td>
 202         </tr>
 203       </table>
 204 </div><div class="memdoc">
 205 <p>get the mean pair distance of ensemble</p>
 206 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000013">Deprecated:</a></b></dt><dd>This function is not threadsafe and should not be used anymore. Use <a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance()</a> instead! </dd></dl>
 207
 208 </div>
 209 </div>
 210 <a class="anchor" id="a68ba6f3a48e08ca131ab54621ce3a2d7"></a>
 211 <div class="memitem">
 212 <div class="memproto">
 213       <table class="memname">
 214         <tr>
 215           <td class="memname">double expLoopEnergy </td>
 216           <td>(</td>
 217           <td class="paramtype">int&#160;</td>
 218           <td class="paramname"><em>u1</em>, </td>
 219         </tr>
 220         <tr>
 221           <td class="paramkey"></td>
 222           <td></td>
 223           <td class="paramtype">int&#160;</td>
 224           <td class="paramname"><em>u2</em>, </td>
 225         </tr>
 226         <tr>
 227           <td class="paramkey"></td>
 228           <td></td>
 229           <td class="paramtype">int&#160;</td>
 230           <td class="paramname"><em>type</em>, </td>
 231         </tr>
 232         <tr>
 233           <td class="paramkey"></td>
 234           <td></td>
 235           <td class="paramtype">int&#160;</td>
 236           <td class="paramname"><em>type2</em>, </td>
 237         </tr>
 238         <tr>
 239           <td class="paramkey"></td>
 240           <td></td>
 241           <td class="paramtype">short&#160;</td>
 242           <td class="paramname"><em>si1</em>, </td>
 243         </tr>
 244         <tr>
 245           <td class="paramkey"></td>
 246           <td></td>
 247           <td class="paramtype">short&#160;</td>
 248           <td class="paramname"><em>sj1</em>, </td>
 249         </tr>
 250         <tr>
 251           <td class="paramkey"></td>
 252           <td></td>
 253           <td class="paramtype">short&#160;</td>
 254           <td class="paramname"><em>sp1</em>, </td>
 255         </tr>
 256         <tr>
 257           <td class="paramkey"></td>
 258           <td></td>
 259           <td class="paramtype">short&#160;</td>
 260           <td class="paramname"><em>sq1</em>&#160;</td>
 261         </tr>
 262         <tr>
 263           <td></td>
 264           <td>)</td>
 265           <td></td><td></td>
 266         </tr>
 267       </table>
 268 </div><div class="memdoc">
 269 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000014">Deprecated:</a></b></dt><dd>Use <a class="el" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd></dl>
 270
 271 </div>
 272 </div>
 273 <a class="anchor" id="a7b6ab474cc80accc48010ccfcc59f96b"></a>
 274 <div class="memitem">
 275 <div class="memproto">
 276       <table class="memname">
 277         <tr>
 278           <td class="memname">double expHairpinEnergy </td>
 279           <td>(</td>
 280           <td class="paramtype">int&#160;</td>
 281           <td class="paramname"><em>u</em>, </td>
 282         </tr>
 283         <tr>
 284           <td class="paramkey"></td>
 285           <td></td>
 286           <td class="paramtype">int&#160;</td>
 287           <td class="paramname"><em>type</em>, </td>
 288         </tr>
 289         <tr>
 290           <td class="paramkey"></td>
 291           <td></td>
 292           <td class="paramtype">short&#160;</td>
 293           <td class="paramname"><em>si1</em>, </td>
 294         </tr>
 295         <tr>
 296           <td class="paramkey"></td>
 297           <td></td>
 298           <td class="paramtype">short&#160;</td>
 299           <td class="paramname"><em>sj1</em>, </td>
 300         </tr>
 301         <tr>
 302           <td class="paramkey"></td>
 303           <td></td>
 304           <td class="paramtype">const char *&#160;</td>
 305           <td class="paramname"><em>string</em>&#160;</td>
 306         </tr>
 307         <tr>
 308           <td></td>
 309           <td>)</td>
 310           <td></td><td></td>
 311         </tr>
 312       </table>
 313 </div><div class="memdoc">
 314 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000015">Deprecated:</a></b></dt><dd>Use <a class="el" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd></dl>
 315
 316 </div>
 317 </div>
 318 </div><!-- contents -->
 319 </div><!-- doc-content -->
 320 <!-- start footer part -->
 321 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
 322   <ul>
 323     <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="part__func_8h.html">part_func.h</a></li>
 324     <li class="footer">Generated on Wed Jul 24 2013 13:38:58 for RNAlib-2.1.2 by
 325     <a href="http://www.doxygen.org/index.html">
 326     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
 327   </ul>
 328 </div>
 329 </body>
 330 </html>