binaries/src/ViennaRNA/doc/html/energy__par_8h_source.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 <title>RNAlib-2.1.2: /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy_par.h Source File</title>
   6 <link href="tabs.css" rel="stylesheet" type="text/css"/>
   7 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
   8 </head>
   9 <body>
  10 <!-- Generated by Doxygen 1.6.1 -->
  11 <script type="text/javascript">
  12 <!--
  13 function changeDisplayState (e){
  14   var num=this.id.replace(/[^[0-9]/g,'');
  15   var button=this.firstChild;
  16   var sectionDiv=document.getElementById('dynsection'+num);
  17   if (sectionDiv.style.display=='none'||sectionDiv.style.display==''){
  18     sectionDiv.style.display='block';
  19     button.src='open.gif';
  20   }else{
  21     sectionDiv.style.display='none';
  22     button.src='closed.gif';
  23   }
  24 }
  25 function initDynSections(){
  26   var divs=document.getElementsByTagName('div');
  27   var sectionCounter=1;
  28   for(var i=0;i<divs.length-1;i++){
  29     if(divs[i].className=='dynheader'&&divs[i+1].className=='dynsection'){
  30       var header=divs[i];
  31       var section=divs[i+1];
  32       var button=header.firstChild;
  33       if (button!='IMG'){
  34         divs[i].insertBefore(document.createTextNode(' '),divs[i].firstChild);
  35         button=document.createElement('img');
  36         divs[i].insertBefore(button,divs[i].firstChild);
  37       }
  38       header.style.cursor='pointer';
  39       header.onclick=changeDisplayState;
  40       header.id='dynheader'+sectionCounter;
  41       button.src='closed.gif';
  42       section.id='dynsection'+sectionCounter;
  43       section.style.display='none';
  44       section.style.marginLeft='14px';
  45       sectionCounter++;
  46     }
  47   }
  48 }
  49 window.onload = initDynSections;
  50 -->
  51 </script>
  52 <div class="navigation" id="top">
  53   <div class="tabs">
  54     <ul>
  55       <li><a href="main.html"><span>Main&nbsp;Page</span></a></li>
  56       <li><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
  57       <li><a href="modules.html"><span>Modules</span></a></li>
  58       <li><a href="annotated.html"><span>Data&nbsp;Structures</span></a></li>
  59       <li class="current"><a href="files.html"><span>Files</span></a></li>
  60     </ul>
  61   </div>
  62   <div class="tabs">
  63     <ul>
  64       <li><a href="files.html"><span>File&nbsp;List</span></a></li>
  65       <li><a href="globals.html"><span>Globals</span></a></li>
  66     </ul>
  67   </div>
  68 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy_par.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
  69 <a name="l00002"></a>00002 <span class="comment">   prototypes for energy_par.c</span>
  70 <a name="l00003"></a>00003 <span class="comment">*/</span>
  71 <a name="l00004"></a>00004
  72 <a name="l00005"></a>00005 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__</span>
  73 <a name="l00006"></a>00006 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__</span>
  74 <a name="l00007"></a>00007 <span class="preprocessor"></span>
  75 <a name="l00008"></a>00008 <span class="preprocessor">#include &quot;<a class="code" href="energy__const_8h.html">energy_const.h</a>&quot;</span>
  76 <a name="l00009"></a>00009
  77 <a name="l00010"></a>00010 <span class="preprocessor">#define PUBLIC</span>
  78 <a name="l00011"></a>00011 <span class="preprocessor"></span>
  79 <a name="l00012"></a>00012
  80 <a name="l00013"></a>00013 <span class="keyword">extern</span> <span class="keywordtype">double</span> lxc37;   <span class="comment">/* parameter for logarithmic loop</span>
  81 <a name="l00014"></a>00014 <span class="comment">        energy extrapolation            */</span>
  82 <a name="l00015"></a>00015
  83 <a name="l00016"></a>00016 <span class="keyword">extern</span> <span class="keywordtype">int</span> stack37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1];
  84 <a name="l00017"></a>00017 <span class="keyword">extern</span> <span class="keywordtype">int</span> stackdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1]; <span class="comment">/* stack enthalpies */</span>
  85 <a name="l00018"></a>00018 <span class="keyword">extern</span> <span class="keywordtype">int</span> entropies[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1];  <span class="comment">/* not used anymore */</span>
  86 <a name="l00019"></a>00019
  87 <a name="l00020"></a>00020 <span class="keyword">extern</span> <span class="keywordtype">int</span> hairpin37[31];
  88 <a name="l00021"></a>00021 <span class="keyword">extern</span> <span class="keywordtype">int</span> hairpindH[31];
  89 <a name="l00022"></a>00022 <span class="keyword">extern</span> <span class="keywordtype">int</span> bulge37[31];
  90 <a name="l00023"></a>00023 <span class="keyword">extern</span> <span class="keywordtype">int</span> bulgedH[31];
  91 <a name="l00024"></a>00024 <span class="keyword">extern</span> <span class="keywordtype">int</span> internal_loop37[31];
  92 <a name="l00025"></a>00025 <span class="keyword">extern</span> <span class="keywordtype">int</span> internal_loopdH[31];
  93 <a name="l00026"></a>00026 <span class="keyword">extern</span> <span class="keywordtype">int</span> internal2_energy;
  94 <a name="l00027"></a>00027 <span class="keyword">extern</span> <span class="keywordtype">int</span> old_mismatch_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];
  95 <a name="l00028"></a>00028 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchI37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
  96 <a name="l00029"></a>00029 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchIdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
  97 <a name="l00030"></a>00030 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatch1nI37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
  98 <a name="l00031"></a>00031 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatch23I37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
  99 <a name="l00032"></a>00032 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatch1nIdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
 100 <a name="l00033"></a>00033 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatch23IdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* interior loop mismatches */</span>
 101 <a name="l00034"></a>00034 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchH37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* same for hairpins */</span>
 102 <a name="l00035"></a>00035 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchM37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* same for multiloops */</span>
 103 <a name="l00036"></a>00036 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchHdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* same for hairpins */</span>
 104 <a name="l00037"></a>00037 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchMdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];  <span class="comment">/* same for multiloops */</span>
 105 <a name="l00038"></a>00038 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchExt37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];
 106 <a name="l00039"></a>00039 <span class="keyword">extern</span> <span class="keywordtype">int</span> mismatchExtdH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];
 107 <a name="l00040"></a>00040
 108 <a name="l00041"></a>00041 <span class="keyword">extern</span> <span class="keywordtype">int</span> dangle5_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];      <span class="comment">/* 5&apos; dangle exterior of pair */</span>
 109 <a name="l00042"></a>00042 <span class="keyword">extern</span> <span class="keywordtype">int</span> dangle3_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];      <span class="comment">/* 3&apos; dangle */</span>
 110 <a name="l00043"></a>00043 <span class="keyword">extern</span> <span class="keywordtype">int</span> dangle3_dH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];       <span class="comment">/* corresponding enthalpies */</span>
 111 <a name="l00044"></a>00044 <span class="keyword">extern</span> <span class="keywordtype">int</span> dangle5_dH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];
 112 <a name="l00045"></a>00045
 113 <a name="l00046"></a>00046 <span class="keyword">extern</span> <span class="keywordtype">int</span> int11_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5]; <span class="comment">/* 1x1 interior loops */</span>
 114 <a name="l00047"></a>00047 <span class="keyword">extern</span> <span class="keywordtype">int</span> int11_dH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];
 115 <a name="l00048"></a>00048
 116 <a name="l00049"></a>00049 <span class="keyword">extern</span> <span class="keywordtype">int</span> int21_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5][5]; <span class="comment">/* 2x1 interior loops */</span>
 117 <a name="l00050"></a>00050 <span class="keyword">extern</span> <span class="keywordtype">int</span> int21_dH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5][5];
 118 <a name="l00051"></a>00051
 119 <a name="l00052"></a>00052 <span class="keyword">extern</span> <span class="keywordtype">int</span> int22_37[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5][5][5]; <span class="comment">/* 2x2 interior loops */</span>
 120 <a name="l00053"></a>00053 <span class="keyword">extern</span> <span class="keywordtype">int</span> int22_dH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5][5][5];
 121 <a name="l00054"></a>00054
 122 <a name="l00055"></a>00055 <span class="comment">/* constants for linearly destabilizing contributions for multi-loops</span>
 123 <a name="l00056"></a>00056 <span class="comment">   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */</span>
 124 <a name="l00057"></a>00057 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_BASE37;
 125 <a name="l00058"></a>00058 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_BASEdH;
 126 <a name="l00059"></a>00059 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_closing37;
 127 <a name="l00060"></a>00060 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_closingdH;
 128 <a name="l00061"></a>00061 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_intern37;
 129 <a name="l00062"></a>00062 <span class="keyword">extern</span> <span class="keywordtype">int</span> ML_interndH;
 130 <a name="l00063"></a>00063
 131 <a name="l00064"></a>00064 <span class="keyword">extern</span> <span class="keywordtype">int</span> TripleC37;
 132 <a name="l00065"></a>00065 <span class="keyword">extern</span> <span class="keywordtype">int</span> TripleCdH;
 133 <a name="l00066"></a>00066 <span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCA37;
 134 <a name="l00067"></a>00067 <span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCAdH;
 135 <a name="l00068"></a>00068 <span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCB37;
 136 <a name="l00069"></a>00069 <span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCBdH;
 137 <a name="l00070"></a>00070
 138 <a name="l00071"></a>00071 <span class="comment">/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */</span>
 139 <a name="l00072"></a>00072 <span class="comment">/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */</span>
 140 <a name="l00073"></a>00073 <span class="keyword">extern</span> <span class="keywordtype">int</span>  MAX_NINIO;                   <span class="comment">/* maximum correction */</span>
 141 <a name="l00074"></a>00074 <span class="keyword">extern</span> <span class="keywordtype">int</span> ninio37;
 142 <a name="l00075"></a>00075 <span class="keyword">extern</span> <span class="keywordtype">int</span> niniodH;
 143 <a name="l00076"></a>00076 <span class="comment">/* penalty for helices terminated by AU (actually not GC) */</span>
 144 <a name="l00077"></a>00077 <span class="keyword">extern</span> <span class="keywordtype">int</span> TerminalAU37;
 145 <a name="l00078"></a>00078 <span class="keyword">extern</span> <span class="keywordtype">int</span> TerminalAUdH;
 146 <a name="l00079"></a>00079 <span class="comment">/* penalty for forming bi-molecular duplex */</span>
 147 <a name="l00080"></a>00080 <span class="keyword">extern</span> <span class="keywordtype">int</span> DuplexInit37;
 148 <a name="l00081"></a>00081 <span class="keyword">extern</span> <span class="keywordtype">int</span> DuplexInitdH;
 149 <a name="l00082"></a>00082 <span class="comment">/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */</span>
 150 <a name="l00083"></a>00083 <span class="keyword">extern</span> <span class="keywordtype">char</span> Tetraloops[];  <span class="comment">/* string containing the special tetraloops */</span>
 151 <a name="l00084"></a>00084 <span class="keyword">extern</span> <span class="keywordtype">int</span>  Tetraloop37[];  <span class="comment">/* Bonus energy for special tetraloops */</span>
 152 <a name="l00085"></a>00085 <span class="keyword">extern</span> <span class="keywordtype">int</span>  TetraloopdH[];
 153 <a name="l00086"></a>00086 <span class="keyword">extern</span> <span class="keywordtype">char</span> Triloops[];    <span class="comment">/* string containing the special triloops */</span>
 154 <a name="l00087"></a>00087 <span class="keyword">extern</span> <span class="keywordtype">int</span>  Triloop37[]; <span class="comment">/* Bonus energy for special Triloops */</span>
 155 <a name="l00088"></a>00088 <span class="keyword">extern</span> <span class="keywordtype">int</span>  TriloopdH[]; <span class="comment">/* Bonus energy for special Triloops */</span>
 156 <a name="l00089"></a>00089 <span class="keyword">extern</span> <span class="keywordtype">char</span> Hexaloops[];    <span class="comment">/* string containing the special triloops */</span>
 157 <a name="l00090"></a>00090 <span class="keyword">extern</span> <span class="keywordtype">int</span>  Hexaloop37[]; <span class="comment">/* Bonus energy for special Triloops */</span>
 158 <a name="l00091"></a>00091 <span class="keyword">extern</span> <span class="keywordtype">int</span>  HexaloopdH[]; <span class="comment">/* Bonus energy for special Triloops */</span>
 159 <a name="l00092"></a>00092
 160 <a name="l00093"></a>00093 <span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadAlpha37;
 161 <a name="l00094"></a>00094 <span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadAlphadH;
 162 <a name="l00095"></a>00095 <span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadBeta37;
 163 <a name="l00096"></a>00096 <span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadBetadH;
 164 <a name="l00097"></a>00097
 165 <a name="l00098"></a>00098 <span class="keyword">extern</span> <span class="keywordtype">double</span> Tmeasure;       <span class="comment">/* temperature of param measurements */</span>
 166 <a name="l00099"></a>00099
 167 <a name="l00100"></a>00100 <span class="preprocessor">#endif</span>
 168 </pre></div></div>
 169 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 170 <a href="http://www.doxygen.org/index.html">
 171 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 172 </body>
 173 </html>