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WSTester updated to work plus hopefully all the other changes that need to go into...
[jabaws.git] / binaries / src / ViennaRNA / doc / html / energy__par_8h_source.html
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+<div class="title">energy_par.h</div>  </div>
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+<div class="contents">
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">   prototypes for energy_par.c</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*/</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;</div>
+<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__</span></div>
+<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__</span></div>
+<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="preprocessor"></span></div>
+<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="energy__const_8h.html">energy_const.h</a>&quot;</span></div>
+<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;</div>
+<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="preprocessor">#define PUBLIC</span></div>
+<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor"></span></div>
+<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;</div>
+<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">double</span> lxc37;   <span class="comment">/* parameter for logarithmic loop</span></div>
+<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">        energy extrapolation            */</span></div>
+<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;</div>
+<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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];</div>
+<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<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></div>
+<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<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></div>
+<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;</div>
+<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> hairpin37[31];</div>
+<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> hairpindH[31];</div>
+<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> bulge37[31];</div>
+<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> bulgedH[31];</div>
+<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> internal_loop37[31];</div>
+<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> internal_loopdH[31];</div>
+<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> internal2_energy;</div>
+<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<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];</div>
+<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<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></div>
+<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<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></div>
+<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<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></div>
+<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<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></div>
+<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<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></div>
+<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<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></div>
+<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<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></div>
+<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<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></div>
+<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<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></div>
+<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<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></div>
+<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<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];</div>
+<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<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];</div>
+<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
+<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<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&#39; dangle exterior of pair */</span></div>
+<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<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&#39; dangle */</span></div>
+<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<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></div>
+<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<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];</div>
+<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
+<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<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></div>
+<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<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];</div>
+<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
+<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<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></div>
+<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<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];</div>
+<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;</div>
+<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<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></div>
+<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<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];</div>
+<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;</div>
+<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="comment">/* constants for linearly destabilizing contributions for multi-loops</span></div>
+<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="comment">   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */</span></div>
+<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_BASE37;</div>
+<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_BASEdH;</div>
+<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_closing37;</div>
+<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_closingdH;</div>
+<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_intern37;</div>
+<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ML_interndH;</div>
+<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
+<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> TripleC37;</div>
+<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> TripleCdH;</div>
+<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCA37;</div>
+<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCAdH;</div>
+<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCB37;</div>
+<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> MultipleCBdH;</div>
+<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div>
+<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="comment">/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */</span></div>
+<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;<span class="comment">/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */</span></div>
+<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  MAX_NINIO;                   <span class="comment">/* maximum correction */</span></div>
+<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> ninio37;</div>
+<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> niniodH;</div>
+<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;<span class="comment">/* penalty for helices terminated by AU (actually not GC) */</span></div>
+<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> TerminalAU37;</div>
+<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> TerminalAUdH;</div>
+<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="comment">/* penalty for forming bi-molecular duplex */</span></div>
+<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> DuplexInit37;</div>
+<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> DuplexInitdH;</div>
+<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;<span class="comment">/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */</span></div>
+<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">char</span> Tetraloops[];  <span class="comment">/* string containing the special tetraloops */</span></div>
+<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  Tetraloop37[];  <span class="comment">/* Bonus energy for special tetraloops */</span></div>
+<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  TetraloopdH[];</div>
+<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">char</span> Triloops[];    <span class="comment">/* string containing the special triloops */</span></div>
+<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  Triloop37[]; <span class="comment">/* Bonus energy for special Triloops */</span></div>
+<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  TriloopdH[]; <span class="comment">/* Bonus energy for special Triloops */</span></div>
+<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">char</span> Hexaloops[];    <span class="comment">/* string containing the special triloops */</span></div>
+<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  Hexaloop37[]; <span class="comment">/* Bonus energy for special Triloops */</span></div>
+<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span>  HexaloopdH[]; <span class="comment">/* Bonus energy for special Triloops */</span></div>
+<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
+<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadAlpha37;</div>
+<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadAlphadH;</div>
+<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadBeta37;</div>
+<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> GQuadBetadH;</div>
+<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
+<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">double</span> Tmeasure;       <span class="comment">/* temperature of param measurements */</span></div>
+<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
+<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;<span class="preprocessor">#endif</span></div>
+</div><!-- fragment --></div><!-- contents -->
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+    <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><b>energy_par.h</b></li>
+    <li class="footer">Generated on Wed Jul 24 2013 13:38:56 for RNAlib-2.1.2 by
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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