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-<div class="title">1.8.4_epars.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="1_88_84__epars_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_OLD_EPARS__</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_OLD_EPARS__</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#define K0 273.15</span></div>
-<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor"></span><span class="preprocessor">#ifdef INF</span></div>
-<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor"></span><span class="preprocessor">#undef INF</span></div>
-<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
-<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor"></span><span class="preprocessor">#define INF 1000000</span></div>
-<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor"></span><span class="preprocessor">#define NBPAIRS 7</span></div>
-<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor"></span><span class="preprocessor">#define NST 0 </span><span class="comment">/* Energy for nonstandard stacked pairs */</span><span class="preprocessor"></span></div>
-<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor"></span><span class="preprocessor">#define DEF -50 </span><span class="comment">/* Default terminal mismatch, used for I */</span><span class="preprocessor"></span></div>
-<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor"></span> <span class="comment">/* and any non_pairing bases */</span></div>
-<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#define NSM 0 </span><span class="comment">/* terminal mismatch for non standard pairs */</span><span class="preprocessor"></span></div>
-<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> PRIVATE <span class="keywordtype">double</span> Tmeasure_184 = 37 + <a class="code" href="energy__const_8h.html#a307c72605e3713972b4f4fb2d53ea20e">K0</a>; <span class="comment">/* temperature of param measurements */</span></div>
-<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> PRIVATE <span class="keywordtype">double</span> lxc37_184 = 107.856; <span class="comment">/* parameter for logarithmic loop</span></div>
-<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="comment"> energy extrapolation */</span></div>
-<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
-<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> PRIVATE <span class="keywordtype">int</span> stack37_184[<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="l00054"></a><span class="lineno"> 54</span> <span class="comment">/* CG GC GU UG AU UA */</span></div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> { { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF},</div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -240, -330, -210, -140, -210, -210, NST},</div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -330, -340, -250, -150, -220, -240, NST},</div>
-<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -250, 130, -50, -140, -130, NST},</div>
-<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -140, -150, -50, 30, -60, -100, NST},</div>
-<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -220, -140, -60, -110, -90, NST},</div>
-<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -240, -130, -100, -90, -130, NST},</div>
-<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, NST, NST, NST, NST, NST, NST, NST}};</div>
-<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
-<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="comment">/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */</span></div>
-<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="comment">/* different from mfold-2.3, which uses values from mfold-2.2 */</span></div>
-<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> PRIVATE <span class="keywordtype">int</span> enthalpies_184[<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="l00067"></a><span class="lineno"> 67</span> <span class="comment">/* CG GC GU UG AU UA */</span></div>
-<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> { { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF},</div>
-<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1060, -1340, -1210, -560, -1050, -1040, NST},</div>
-<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1340, -1490, -1260, -830, -1140, -1240, NST},</div>
-<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1210, -1260, -1460, -1350, -880, -1280, NST},</div>
-<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -560, -830, -1350, -930, -320, -700, NST},</div>
-<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1050, -1140, -880, -320, -940, -680, NST},</div>
-<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1040, -1240, -1280, -700, -680, -770, NST},</div>
-<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, NST, NST, NST, NST, NST, NST, NST}};</div>
-<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
-<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
-<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> <span class="comment">/* old values are here just for comparison */</span></div>
-<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> PRIVATE <span class="keywordtype">int</span> oldhairpin37_184[31] = { <span class="comment">/* from ViennaRNA 1.3 */</span></div>
-<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 410, 490, 440, 470, 500, 510, 520, 531,</div>
-<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  542, 551, 560, 568, 575, 582, 589, 595, 601, 606,</div>
-<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  611, 616, 621, 626, 630, 634, 638, 642, 646, 650};</div>
-<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
-<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> PRIVATE <span class="keywordtype">int</span> hairpin37_184[31] = {</div>
-<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 570, 560, 560, 540, 590, 560, 640, 650,</div>
-<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  660, 670, 678, 686, 694, 701, 707, 713, 719, 725,</div>
-<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  730, 735, 740, 744, 749, 753, 757, 761, 765, 769};</div>
-<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> PRIVATE <span class="keywordtype">int</span> oldbulge37_184[31] = {</div>
-<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,</div>
-<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  565, 574, 583, 591, 598, 605, 612, 618, 624, 630,</div>
-<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  635, 640, 645, 649, 654, 658, 662, 666, 670, 673};</div>
-<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
-<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> PRIVATE <span class="keywordtype">int</span> bulge37_184[31] = {</div>
-<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,</div>
-<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  500, 510, 519, 527, 534, 541, 548, 554, 560, 565,</div>
-<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  571, 576, 580, 585, 589, 594, 598, 602, 605, 609};</div>
-<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
-<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> PRIVATE <span class="keywordtype">int</span> oldinternal_loop37_184[31] = {</div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 410, 510, 490, 530, 570, 587, 601, 614, 625,</div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  635, 645, 653, 661, 669, 676, 682, 688, 694, 700,</div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  705, 710, 715, 720, 724, 728, 732, 736, 740, 744};</div>
-<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> PRIVATE <span class="keywordtype">int</span> internal_loop37_184[31] = {</div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 410, 510, 170, 180, 200, 220, 230, 240, 250,</div>
-<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  260, 270, 278, 286, 294, 301, 307, 313, 319, 325,</div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  330, 335, 340, 345, 349, 353, 357, 361, 365, 369};</div>
-<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
-<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="comment">/* terminal mismatches */</span></div>
-<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="comment">/* mismatch free energies for interior loops at 37C */</span></div>
-<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> PRIVATE <span class="keywordtype">int</span> mismatchI37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =</div>
-<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> { <span class="comment">/* @@ */</span></div>
-<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},</div>
-<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  { <span class="comment">/* CG */</span></div>
-<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  { 0, 0, 0, -110, 0}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  { 0, -110, 0, 0, 0}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  { 0, 0, 0, 0, -70}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  { <span class="comment">/* GC */</span></div>
-<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  { 0, 0, 0, -110, 0}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  { 0, -110, 0, 0, 0}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  { 0, 0, 0, 0, -70}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  { <span class="comment">/* GU */</span></div>
-<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  { <span class="comment">/* UG */</span></div>
-<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  { <span class="comment">/* AU */</span></div>
-<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  { <span class="comment">/* UA */</span></div>
-<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  { <span class="comment">/* @@ */</span></div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},</div>
-<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}</div>
-<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> };</div>
-<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
-<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment">/* mismatch free energies for hairpins at 37C */</span></div>
-<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> PRIVATE <span class="keywordtype">int</span> mismatchH37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =</div>
-<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> { <span class="comment">/* @@ */</span></div>
-<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},</div>
-<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  { <span class="comment">/* CG */</span></div>
-<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  { -90, -150, -150, -140, -180}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  { -90, -100, -90, -290, -80}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  { -90, -220, -200, -160, -110}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  { -90, -170, -140, -180, -200}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  { <span class="comment">/* GC */</span></div>
-<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  { -70, -110, -150, -130, -210}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  { -70, -110, -70, -240, -50}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  { -70, -240, -290, -140, -120}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  { -70, -190, -100, -220, -150}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  { <span class="comment">/* GU */</span></div>
-<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  { 0, 20, -50, -30, -30}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  { 0, -10, -20, -150, -20}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  { 0, -90, -110, -30, 0}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  { 0, -30, -30, -40, -110}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  { <span class="comment">/* UG */</span></div>
-<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  { 0, -50, -30, -60, -50}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  { 0, -20, -10, -170, 0}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  { 0, -80, -120, -30, -70}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  { 0, -60, -10, -60, -80}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  { <span class="comment">/* AU */</span></div>
-<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  { 0, -30, -50, -30, -30}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  { 0, -10, -20, -150, -20}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  { 0, -110, -120, -20, 20}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  { 0, -30, -30, -60, -110}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  { <span class="comment">/* UA */</span></div>
-<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  { 0, -50, -30, -60, -50}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  { 0, -20, -10, -120, -0}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  { 0, -140, -120, -70, -20}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  { 0, -30, -10, -50, -80}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  { <span class="comment">/* @@ */</span></div>
-<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},</div>
-<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}}</div>
-<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> };</div>
-<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
-<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment">/* mismatch energies in multiloops */</span></div>
-<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> PRIVATE <span class="keywordtype">int</span> mismatchM37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
-<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
-<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="comment">/* these are probably junk */</span></div>
-<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="comment">/* mismatch enthalpies for temperature scaling */</span></div>
-<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> PRIVATE <span class="keywordtype">int</span> mism_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =</div>
-<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> { <span class="comment">/* no pair */</span></div>
-<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},</div>
-<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  { <span class="comment">/* CG */</span></div>
-<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  { DEF,-1030, -950,-1030,-1030}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  { DEF, -520, -450, -520, -670}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  { DEF, -940, -940, -940, -940}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  { DEF, -810, -740, -810, -860}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  { <span class="comment">/* GC */</span></div>
-<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  { DEF, -520, -880, -560, -880}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  { DEF, -720, -310, -310, -390}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  { DEF, -710, -740, -620, -740}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  { DEF, -500, -500, -500, -570}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  { <span class="comment">/* GU */</span></div>
-<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  { DEF, -430, -600, -600, -600}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  { DEF, -260, -240, -240, -240}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  { DEF, -340, -690, -690, -690}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  { DEF, -330, -330, -330, -330}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  { <span class="comment">/* UG */</span></div>
-<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  { DEF, -720, -790, -960, -810}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  { DEF, -480, -480, -360, -480}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  { DEF, -660, -810, -920, -810}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  { DEF, -550, -440, -550, -360}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  { <span class="comment">/* AU */</span></div>
-<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  { DEF, -430, -600, -600, -600}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  { DEF, -260, -240, -240, -240}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  { DEF, -340, -690, -690, -690}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  { DEF, -330, -330, -330, -330}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  { <span class="comment">/* UA */</span></div>
-<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span></div>
-<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  { DEF, -400, -630, -890, -590}, <span class="comment">/* A@ AA AC AG AU */</span></div>
-<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  { DEF, -430, -510, -200, -180}, <span class="comment">/* C@ CA CC CG CU */</span></div>
-<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  { DEF, -380, -680, -890, -680}, <span class="comment">/* G@ GA GC GG GU */</span></div>
-<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  { DEF, -280, -140, -280, -140}},<span class="comment">/* U@ UA UC UG UU */</span></div>
-<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  { <span class="comment">/* nonstandard pair */</span></div>
-<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},</div>
-<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}</div>
-<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> };</div>
-<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
-<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> <span class="comment">/* 5' dangling ends (unpaird base stacks on first paired base) */</span></div>
-<div class="line"><a name="l00250"></a><span class="lineno"> 250</span> PRIVATE <span class="keywordtype">int</span> dangle5_37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5]=</div>
-<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> {<span class="comment">/* @ A C G U */</span></div>
-<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF}, <span class="comment">/* no pair */</span></div>
-<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -50, -30, -20, -10}, <span class="comment">/* CG (stacks on C) */</span></div>
-<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -20, -30, -0, -0}, <span class="comment">/* GC (stacks on G) */</span></div>
-<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -30, -40, -20}, <span class="comment">/* GU */</span></div>
-<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -10, -20, -20}, <span class="comment">/* UG */</span></div>
-<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -30, -40, -20}, <span class="comment">/* AU */</span></div>
-<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -10, -20, -20}, <span class="comment">/* UA */</span></div>
-<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  { 0, 0, 0, 0, 0} <span class="comment">/* @ */</span></div>
-<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> };</div>
-<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> </div>
-<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> <span class="comment">/* 3' dangling ends (unpaired base stacks on second paired base */</span></div>
-<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> PRIVATE <span class="keywordtype">int</span> dangle3_37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5]=</div>
-<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> {<span class="comment">/* @ A C G U */</span></div>
-<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF}, <span class="comment">/* no pair */</span></div>
-<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -110, -40, -130, -60}, <span class="comment">/* CG (stacks on G) */</span></div>
-<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -170, -80, -170, -120}, <span class="comment">/* GC */</span></div>
-<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -70, -10, -70, -10}, <span class="comment">/* GU */</span></div>
-<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -80, -50, -80, -60}, <span class="comment">/* UG */</span></div>
-<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -70, -10, -70, -10}, <span class="comment">/* AU */</span></div>
-<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -80, -50, -80, -60}, <span class="comment">/* UA */</span></div>
-<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  { 0, 0, 0, 0, 0} <span class="comment">/* @ */</span></div>
-<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> };</div>
-<div class="line"><a name="l00274"></a><span class="lineno"> 274</span> </div>
-<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> <span class="comment">/* enthalpies for temperature scaling */</span></div>
-<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> PRIVATE <span class="keywordtype">int</span> dangle3_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5] =</div>
-<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> {<span class="comment">/* @ A C G U */</span></div>
-<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF}, <span class="comment">/* no pair */</span></div>
-<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  { 0, -740, -280, -640, -360},</div>
-<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  { 0, -900, -410, -860, -750},</div>
-<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  { 0, -740, -240, -720, -490},</div>
-<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  { 0, -490, -90, -550, -230},</div>
-<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  { 0, -570, -70, -580, -220},</div>
-<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  { 0, -490, -90, -550, -230},</div>
-<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  { 0, 0, 0, 0, 0}</div>
-<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> };</div>
-<div class="line"><a name="l00287"></a><span class="lineno"> 287</span> </div>
-<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> PRIVATE <span class="keywordtype">int</span> dangle5_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5] =</div>
-<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> {<span class="comment">/* @ A C G U */</span></div>
-<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF}, <span class="comment">/* no pair */</span></div>
-<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  { 0, -240, 330, 80, -140},</div>
-<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  { 0, -160, 70, -460, -40},</div>
-<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  { 0, 160, 220, 70, 310},</div>
-<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  { 0, -150, 510, 10, 100},</div>
-<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  { 0, 160, 220, 70, 310},</div>
-<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  { 0, -50, 690, -60, -60},</div>
-<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  { 0, 0, 0, 0, 0}</div>
-<div class="line"><a name="l00298"></a><span class="lineno"> 298</span> };</div>
-<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> </div>
-<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> </div>
-<div class="line"><a name="l00301"></a><span class="lineno"> 301</span> <span class="comment">/* constants for linearly destabilizing contributions for multi-loops</span></div>
-<div class="line"><a name="l00302"></a><span class="lineno"> 302</span> <span class="comment"> F = ML_closing + ML_intern*k + ML_BASE*u */</span></div>
-<div class="line"><a name="l00303"></a><span class="lineno"> 303</span> <span class="comment">/* old versions erroneously used ML_intern*(k-1) */</span></div>
-<div class="line"><a name="l00304"></a><span class="lineno"> 304</span> PRIVATE <span class="keywordtype">int</span> ML_BASE37_184 = 0;</div>
-<div class="line"><a name="l00305"></a><span class="lineno"> 305</span> PRIVATE <span class="keywordtype">int</span> ML_closing37_184 = 340;</div>
-<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> PRIVATE <span class="keywordtype">int</span> ML_intern37_184 = 40;</div>
-<div class="line"><a name="l00307"></a><span class="lineno"> 307</span> </div>
-<div class="line"><a name="l00308"></a><span class="lineno"> 308</span> <span class="comment">/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */</span></div>
-<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> <span class="comment">/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */</span></div>
-<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> PRIVATE <span class="keywordtype">int</span> MAX_NINIO_184 = 300; <span class="comment">/* maximum correction */</span></div>
-<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> PRIVATE <span class="keywordtype">int</span> F_ninio37_184[5] = { 0, 40, 50, 20, 10 }; <span class="comment">/* only F[2] used */</span></div>
-<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> </div>
-<div class="line"><a name="l00313"></a><span class="lineno"> 313</span> <span class="comment">/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */</span></div>
-<div class="line"><a name="l00314"></a><span class="lineno"> 314</span> </div>
-<div class="line"><a name="l00315"></a><span class="lineno"> 315</span> PRIVATE <span class="keywordtype">char</span> Tetraloops_184[1400] = <span class="comment">/* place for up to 200 tetra loops */</span></div>
-<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="stringliteral">"GGGGAC "</span></div>
-<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="stringliteral">"GGUGAC "</span></div>
-<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="stringliteral">"CGAAAG "</span></div>
-<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="stringliteral">"GGAGAC "</span></div>
-<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="stringliteral">"CGCAAG "</span></div>
-<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="stringliteral">"GGAAAC "</span></div>
-<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="stringliteral">"CGGAAG "</span></div>
-<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="stringliteral">"CUUCGG "</span></div>
-<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="stringliteral">"CGUGAG "</span></div>
-<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="stringliteral">"CGAAGG "</span></div>
-<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="stringliteral">"CUACGG "</span></div>
-<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="stringliteral">"GGCAAC "</span></div>
-<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="stringliteral">"CGCGAG "</span></div>
-<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="stringliteral">"UGAGAG "</span></div>
-<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="stringliteral">"CGAGAG "</span></div>
-<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="stringliteral">"AGAAAU "</span></div>
-<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="stringliteral">"CGUAAG "</span></div>
-<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="stringliteral">"CUAACG "</span></div>
-<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="stringliteral">"UGAAAG "</span></div>
-<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="stringliteral">"GGAAGC "</span></div>
-<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="stringliteral">"GGGAAC "</span></div>
-<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="stringliteral">"UGAAAA "</span></div>
-<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <span class="stringliteral">"AGCAAU "</span></div>
-<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="stringliteral">"AGUAAU "</span></div>
-<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="stringliteral">"CGGGAG "</span></div>
-<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="stringliteral">"AGUGAU "</span></div>
-<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="stringliteral">"GGCGAC "</span></div>
-<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="stringliteral">"GGGAGC "</span></div>
-<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="stringliteral">"GUGAAC "</span></div>
-<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="stringliteral">"UGGAAA "</span></div>
-<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> ;</div>
-<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> </div>
-<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> PRIVATE <span class="keywordtype">int</span> TETRA_ENERGY37_184[200] = {</div>
-<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,</div>
-<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,</div>
-<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  -150, -150, -150, -150, -150, -150};</div>
-<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> </div>
-<div class="line"><a name="l00353"></a><span class="lineno"> 353</span> PRIVATE <span class="keywordtype">int</span> TETRA_ENTH37_184 = -400;</div>
-<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> </div>
-<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> PRIVATE <span class="keywordtype">char</span> Triloops_184[241] = <span class="stringliteral">""</span>;</div>
-<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> </div>
-<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> PRIVATE <span class="keywordtype">int</span> Triloop_E37_184[40];</div>
-<div class="line"><a name="l00358"></a><span class="lineno"> 358</span> </div>
-<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> <span class="comment">/* penalty for AU (or GU) terminating helix) */</span></div>
-<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> <span class="comment">/* mismatches already contain these */</span></div>
-<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> PRIVATE <span class="keywordtype">int</span> TerminalAU_184 = 50;</div>
-<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> </div>
-<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> <span class="comment">/* penalty for forming a bi-molecular duplex */</span></div>
-<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> PRIVATE <span class="keywordtype">int</span> DuplexInit_184 = 410;</div>
-<div class="line"><a name="l00365"></a><span class="lineno"> 365</span> </div>
-<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
- <li class="navelem"><a class="el" href="dir_97aefd0d527b934f1d99a682da8fe6a9.html">lib</a></li><li class="navelem"><a class="el" href="1_88_84__epars_8h.html">1.8.4_epars.h</a></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>
- </ul>
-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4_epars.h</h1><a href="1_88_84__epars_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_OLD_EPARS__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_OLD_EPARS__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00038"></a>00038 <span class="preprocessor">#define K0 273.15</span>
+<a name="l00039"></a>00039 <span class="preprocessor"></span><span class="preprocessor">#ifdef INF</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#undef INF</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00042"></a>00042 <span class="preprocessor"></span><span class="preprocessor">#define INF 1000000</span>
+<a name="l00043"></a>00043 <span class="preprocessor"></span><span class="preprocessor">#define NBPAIRS 7</span>
+<a name="l00044"></a>00044 <span class="preprocessor"></span><span class="preprocessor">#define NST 0 </span><span class="comment">/* Energy for nonstandard stacked pairs */</span>
+<a name="l00045"></a>00045 <span class="preprocessor">#define DEF -50 </span><span class="comment">/* Default terminal mismatch, used for I */</span>
+<a name="l00046"></a>00046 <span class="comment">/* and any non_pairing bases */</span>
+<a name="l00047"></a>00047 <span class="preprocessor">#define NSM 0 </span><span class="comment">/* terminal mismatch for non standard pairs */</span>
+<a name="l00048"></a>00048
+<a name="l00049"></a>00049 PRIVATE <span class="keywordtype">double</span> Tmeasure_184 = 37 + <a class="code" href="energy__const_8h.html#a307c72605e3713972b4f4fb2d53ea20e">K0</a>; <span class="comment">/* temperature of param measurements */</span>
+<a name="l00050"></a>00050 PRIVATE <span class="keywordtype">double</span> lxc37_184 = 107.856; <span class="comment">/* parameter for logarithmic loop</span>
+<a name="l00051"></a>00051 <span class="comment"> energy extrapolation */</span>
+<a name="l00052"></a>00052
+<a name="l00053"></a>00053 PRIVATE <span class="keywordtype">int</span> stack37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1] =
+<a name="l00054"></a>00054 <span class="comment">/* CG GC GU UG AU UA */</span>
+<a name="l00055"></a>00055 { { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF, INF, INF, INF},
+<a name="l00056"></a>00056 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -240, -330, -210, -140, -210, -210, NST},
+<a name="l00057"></a>00057 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -330, -340, -250, -150, -220, -240, NST},
+<a name="l00058"></a>00058 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -250, 130, -50, -140, -130, NST},
+<a name="l00059"></a>00059 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -140, -150, -50, 30, -60, -100, NST},
+<a name="l00060"></a>00060 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -220, -140, -60, -110, -90, NST},
+<a name="l00061"></a>00061 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -210, -240, -130, -100, -90, -130, NST},
+<a name="l00062"></a>00062 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, NST, NST, NST, NST, NST, NST, NST}};
+<a name="l00063"></a>00063
+<a name="l00064"></a>00064 <span class="comment">/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */</span>
+<a name="l00065"></a>00065 <span class="comment">/* different from mfold-2.3, which uses values from mfold-2.2 */</span>
+<a name="l00066"></a>00066 PRIVATE <span class="keywordtype">int</span> enthalpies_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1] =
+<a name="l00067"></a>00067 <span class="comment">/* CG GC GU UG AU UA */</span>
+<a name="l00068"></a>00068 { { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF, INF, INF, INF},
+<a name="l00069"></a>00069 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1060, -1340, -1210, -560, -1050, -1040, NST},
+<a name="l00070"></a>00070 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1340, -1490, -1260, -830, -1140, -1240, NST},
+<a name="l00071"></a>00071 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1210, -1260, -1460, -1350, -880, -1280, NST},
+<a name="l00072"></a>00072 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -560, -830, -1350, -930, -320, -700, NST},
+<a name="l00073"></a>00073 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1050, -1140, -880, -320, -940, -680, NST},
+<a name="l00074"></a>00074 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -1040, -1240, -1280, -700, -680, -770, NST},
+<a name="l00075"></a>00075 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, NST, NST, NST, NST, NST, NST, NST}};
+<a name="l00076"></a>00076
+<a name="l00077"></a>00077
+<a name="l00078"></a>00078 <span class="comment">/* old values are here just for comparison */</span>
+<a name="l00079"></a>00079 PRIVATE <span class="keywordtype">int</span> oldhairpin37_184[31] = { <span class="comment">/* from ViennaRNA 1.3 */</span>
+<a name="l00080"></a>00080 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, 410, 490, 440, 470, 500, 510, 520, 531,
+<a name="l00081"></a>00081 542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
+<a name="l00082"></a>00082 611, 616, 621, 626, 630, 634, 638, 642, 646, 650};
+<a name="l00083"></a>00083
+<a name="l00084"></a>00084 PRIVATE <span class="keywordtype">int</span> hairpin37_184[31] = {
+<a name="l00085"></a>00085 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, 570, 560, 560, 540, 590, 560, 640, 650,
+<a name="l00086"></a>00086 660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
+<a name="l00087"></a>00087 730, 735, 740, 744, 749, 753, 757, 761, 765, 769};
+<a name="l00088"></a>00088
+<a name="l00089"></a>00089 PRIVATE <span class="keywordtype">int</span> oldbulge37_184[31] = {
+<a name="l00090"></a>00090 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
+<a name="l00091"></a>00091 565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
+<a name="l00092"></a>00092 635, 640, 645, 649, 654, 658, 662, 666, 670, 673};
+<a name="l00093"></a>00093
+<a name="l00094"></a>00094 PRIVATE <span class="keywordtype">int</span> bulge37_184[31] = {
+<a name="l00095"></a>00095 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
+<a name="l00096"></a>00096 500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
+<a name="l00097"></a>00097 571, 576, 580, 585, 589, 594, 598, 602, 605, 609};
+<a name="l00098"></a>00098
+<a name="l00099"></a>00099 PRIVATE <span class="keywordtype">int</span> oldinternal_loop37_184[31] = {
+<a name="l00100"></a>00100 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 410, 510, 490, 530, 570, 587, 601, 614, 625,
+<a name="l00101"></a>00101 635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
+<a name="l00102"></a>00102 705, 710, 715, 720, 724, 728, 732, 736, 740, 744};
+<a name="l00103"></a>00103
+<a name="l00104"></a>00104 PRIVATE <span class="keywordtype">int</span> internal_loop37_184[31] = {
+<a name="l00105"></a>00105 <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 410, 510, 170, 180, 200, 220, 230, 240, 250,
+<a name="l00106"></a>00106 260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
+<a name="l00107"></a>00107 330, 335, 340, 345, 349, 353, 357, 361, 365, 369};
+<a name="l00108"></a>00108
+<a name="l00109"></a>00109 <span class="comment">/* terminal mismatches */</span>
+<a name="l00110"></a>00110 <span class="comment">/* mismatch free energies for interior loops at 37C */</span>
+<a name="l00111"></a>00111 PRIVATE <span class="keywordtype">int</span> mismatchI37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =
+<a name="l00112"></a>00112 { <span class="comment">/* @@ */</span>
+<a name="l00113"></a>00113 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+<a name="l00114"></a>00114 { <span class="comment">/* CG */</span>
+<a name="l00115"></a>00115 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00116"></a>00116 { 0, 0, 0, -110, 0}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00117"></a>00117 { 0, 0, 0, 0, 0}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00118"></a>00118 { 0, -110, 0, 0, 0}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00119"></a>00119 { 0, 0, 0, 0, -70}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00120"></a>00120 { <span class="comment">/* GC */</span>
+<a name="l00121"></a>00121 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00122"></a>00122 { 0, 0, 0, -110, 0}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00123"></a>00123 { 0, 0, 0, 0, 0}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00124"></a>00124 { 0, -110, 0, 0, 0}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00125"></a>00125 { 0, 0, 0, 0, -70}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00126"></a>00126 { <span class="comment">/* GU */</span>
+<a name="l00127"></a>00127 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00128"></a>00128 { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00129"></a>00129 { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00130"></a>00130 { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00131"></a>00131 { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00132"></a>00132 { <span class="comment">/* UG */</span>
+<a name="l00133"></a>00133 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00134"></a>00134 { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00135"></a>00135 { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00136"></a>00136 { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00137"></a>00137 { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00138"></a>00138 { <span class="comment">/* AU */</span>
+<a name="l00139"></a>00139 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00140"></a>00140 { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00141"></a>00141 { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00142"></a>00142 { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00143"></a>00143 { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00144"></a>00144 { <span class="comment">/* UA */</span>
+<a name="l00145"></a>00145 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00146"></a>00146 { 0, 70, 70, -40, 70}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00147"></a>00147 { 0, 70, 70, 70, 70}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00148"></a>00148 { 0, -40, 70, 70, 70}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00149"></a>00149 { 0, 70, 70, 70, 0}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00150"></a>00150 { <span class="comment">/* @@ */</span>
+<a name="l00151"></a>00151 { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},
+<a name="l00152"></a>00152 { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}
+<a name="l00153"></a>00153 };
+<a name="l00154"></a>00154
+<a name="l00155"></a>00155 <span class="comment">/* mismatch free energies for hairpins at 37C */</span>
+<a name="l00156"></a>00156 PRIVATE <span class="keywordtype">int</span> mismatchH37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =
+<a name="l00157"></a>00157 { <span class="comment">/* @@ */</span>
+<a name="l00158"></a>00158 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+<a name="l00159"></a>00159 { <span class="comment">/* CG */</span>
+<a name="l00160"></a>00160 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00161"></a>00161 { -90, -150, -150, -140, -180}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00162"></a>00162 { -90, -100, -90, -290, -80}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00163"></a>00163 { -90, -220, -200, -160, -110}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00164"></a>00164 { -90, -170, -140, -180, -200}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00165"></a>00165 { <span class="comment">/* GC */</span>
+<a name="l00166"></a>00166 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00167"></a>00167 { -70, -110, -150, -130, -210}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00168"></a>00168 { -70, -110, -70, -240, -50}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00169"></a>00169 { -70, -240, -290, -140, -120}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00170"></a>00170 { -70, -190, -100, -220, -150}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00171"></a>00171 { <span class="comment">/* GU */</span>
+<a name="l00172"></a>00172 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00173"></a>00173 { 0, 20, -50, -30, -30}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00174"></a>00174 { 0, -10, -20, -150, -20}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00175"></a>00175 { 0, -90, -110, -30, 0}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00176"></a>00176 { 0, -30, -30, -40, -110}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00177"></a>00177 { <span class="comment">/* UG */</span>
+<a name="l00178"></a>00178 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00179"></a>00179 { 0, -50, -30, -60, -50}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00180"></a>00180 { 0, -20, -10, -170, 0}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00181"></a>00181 { 0, -80, -120, -30, -70}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00182"></a>00182 { 0, -60, -10, -60, -80}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00183"></a>00183 { <span class="comment">/* AU */</span>
+<a name="l00184"></a>00184 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00185"></a>00185 { 0, -30, -50, -30, -30}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00186"></a>00186 { 0, -10, -20, -150, -20}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00187"></a>00187 { 0, -110, -120, -20, 20}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00188"></a>00188 { 0, -30, -30, -60, -110}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00189"></a>00189 { <span class="comment">/* UA */</span>
+<a name="l00190"></a>00190 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00191"></a>00191 { 0, -50, -30, -60, -50}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00192"></a>00192 { 0, -20, -10, -120, -0}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00193"></a>00193 { 0, -140, -120, -70, -20}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00194"></a>00194 { 0, -30, -10, -50, -80}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00195"></a>00195 { <span class="comment">/* @@ */</span>
+<a name="l00196"></a>00196 { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},
+<a name="l00197"></a>00197 { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}}
+<a name="l00198"></a>00198 };
+<a name="l00199"></a>00199
+<a name="l00200"></a>00200 <span class="comment">/* mismatch energies in multiloops */</span>
+<a name="l00201"></a>00201 PRIVATE <span class="keywordtype">int</span> mismatchM37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];
+<a name="l00202"></a>00202
+<a name="l00203"></a>00203 <span class="comment">/* these are probably junk */</span>
+<a name="l00204"></a>00204 <span class="comment">/* mismatch enthalpies for temperature scaling */</span>
+<a name="l00205"></a>00205 PRIVATE <span class="keywordtype">int</span> mism_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5] =
+<a name="l00206"></a>00206 { <span class="comment">/* no pair */</span>
+<a name="l00207"></a>00207 {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+<a name="l00208"></a>00208 { <span class="comment">/* CG */</span>
+<a name="l00209"></a>00209 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00210"></a>00210 { DEF,-1030, -950,-1030,-1030}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00211"></a>00211 { DEF, -520, -450, -520, -670}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00212"></a>00212 { DEF, -940, -940, -940, -940}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00213"></a>00213 { DEF, -810, -740, -810, -860}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00214"></a>00214 { <span class="comment">/* GC */</span>
+<a name="l00215"></a>00215 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00216"></a>00216 { DEF, -520, -880, -560, -880}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00217"></a>00217 { DEF, -720, -310, -310, -390}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00218"></a>00218 { DEF, -710, -740, -620, -740}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00219"></a>00219 { DEF, -500, -500, -500, -570}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00220"></a>00220 { <span class="comment">/* GU */</span>
+<a name="l00221"></a>00221 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00222"></a>00222 { DEF, -430, -600, -600, -600}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00223"></a>00223 { DEF, -260, -240, -240, -240}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00224"></a>00224 { DEF, -340, -690, -690, -690}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00225"></a>00225 { DEF, -330, -330, -330, -330}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00226"></a>00226 { <span class="comment">/* UG */</span>
+<a name="l00227"></a>00227 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00228"></a>00228 { DEF, -720, -790, -960, -810}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00229"></a>00229 { DEF, -480, -480, -360, -480}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00230"></a>00230 { DEF, -660, -810, -920, -810}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00231"></a>00231 { DEF, -550, -440, -550, -360}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00232"></a>00232 { <span class="comment">/* AU */</span>
+<a name="l00233"></a>00233 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00234"></a>00234 { DEF, -430, -600, -600, -600}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00235"></a>00235 { DEF, -260, -240, -240, -240}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00236"></a>00236 { DEF, -340, -690, -690, -690}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00237"></a>00237 { DEF, -330, -330, -330, -330}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00238"></a>00238 { <span class="comment">/* UA */</span>
+<a name="l00239"></a>00239 { 0, 0, 0, 0, 0}, <span class="comment">/* @@ @A @C @G @U */</span>
+<a name="l00240"></a>00240 { DEF, -400, -630, -890, -590}, <span class="comment">/* A@ AA AC AG AU */</span>
+<a name="l00241"></a>00241 { DEF, -430, -510, -200, -180}, <span class="comment">/* C@ CA CC CG CU */</span>
+<a name="l00242"></a>00242 { DEF, -380, -680, -890, -680}, <span class="comment">/* G@ GA GC GG GU */</span>
+<a name="l00243"></a>00243 { DEF, -280, -140, -280, -140}},<span class="comment">/* U@ UA UC UG UU */</span>
+<a name="l00244"></a>00244 { <span class="comment">/* nonstandard pair */</span>
+<a name="l00245"></a>00245 {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},
+<a name="l00246"></a>00246 {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}
+<a name="l00247"></a>00247 };
+<a name="l00248"></a>00248
+<a name="l00249"></a>00249 <span class="comment">/* 5' dangling ends (unpaird base stacks on first paired base) */</span>
+<a name="l00250"></a>00250 PRIVATE <span class="keywordtype">int</span> dangle5_37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5]=
+<a name="l00251"></a>00251 {<span class="comment">/* @ A C G U */</span>
+<a name="l00252"></a>00252 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF}, <span class="comment">/* no pair */</span>
+<a name="l00253"></a>00253 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -50, -30, -20, -10}, <span class="comment">/* CG (stacks on C) */</span>
+<a name="l00254"></a>00254 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -20, -30, -0, -0}, <span class="comment">/* GC (stacks on G) */</span>
+<a name="l00255"></a>00255 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -30, -40, -20}, <span class="comment">/* GU */</span>
+<a name="l00256"></a>00256 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -10, -20, -20}, <span class="comment">/* UG */</span>
+<a name="l00257"></a>00257 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -30, -40, -20}, <span class="comment">/* AU */</span>
+<a name="l00258"></a>00258 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -30, -10, -20, -20}, <span class="comment">/* UA */</span>
+<a name="l00259"></a>00259 { 0, 0, 0, 0, 0} <span class="comment">/* @ */</span>
+<a name="l00260"></a>00260 };
+<a name="l00261"></a>00261
+<a name="l00262"></a>00262 <span class="comment">/* 3' dangling ends (unpaired base stacks on second paired base */</span>
+<a name="l00263"></a>00263 PRIVATE <span class="keywordtype">int</span> dangle3_37_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5]=
+<a name="l00264"></a>00264 {<span class="comment">/* @ A C G U */</span>
+<a name="l00265"></a>00265 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF}, <span class="comment">/* no pair */</span>
+<a name="l00266"></a>00266 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -110, -40, -130, -60}, <span class="comment">/* CG (stacks on G) */</span>
+<a name="l00267"></a>00267 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -170, -80, -170, -120}, <span class="comment">/* GC */</span>
+<a name="l00268"></a>00268 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -70, -10, -70, -10}, <span class="comment">/* GU */</span>
+<a name="l00269"></a>00269 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -80, -50, -80, -60}, <span class="comment">/* UG */</span>
+<a name="l00270"></a>00270 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -70, -10, -70, -10}, <span class="comment">/* AU */</span>
+<a name="l00271"></a>00271 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, -80, -50, -80, -60}, <span class="comment">/* UA */</span>
+<a name="l00272"></a>00272 { 0, 0, 0, 0, 0} <span class="comment">/* @ */</span>
+<a name="l00273"></a>00273 };
+<a name="l00274"></a>00274
+<a name="l00275"></a>00275 <span class="comment">/* enthalpies for temperature scaling */</span>
+<a name="l00276"></a>00276 PRIVATE <span class="keywordtype">int</span> dangle3_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5] =
+<a name="l00277"></a>00277 {<span class="comment">/* @ A C G U */</span>
+<a name="l00278"></a>00278 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF}, <span class="comment">/* no pair */</span>
+<a name="l00279"></a>00279 { 0, -740, -280, -640, -360},
+<a name="l00280"></a>00280 { 0, -900, -410, -860, -750},
+<a name="l00281"></a>00281 { 0, -740, -240, -720, -490},
+<a name="l00282"></a>00282 { 0, -490, -90, -550, -230},
+<a name="l00283"></a>00283 { 0, -570, -70, -580, -220},
+<a name="l00284"></a>00284 { 0, -490, -90, -550, -230},
+<a name="l00285"></a>00285 { 0, 0, 0, 0, 0}
+<a name="l00286"></a>00286 };
+<a name="l00287"></a>00287
+<a name="l00288"></a>00288 PRIVATE <span class="keywordtype">int</span> dangle5_H_184[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5] =
+<a name="l00289"></a>00289 {<span class="comment">/* @ A C G U */</span>
+<a name="l00290"></a>00290 { <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, INF, INF, INF}, <span class="comment">/* no pair */</span>
+<a name="l00291"></a>00291 { 0, -240, 330, 80, -140},
+<a name="l00292"></a>00292 { 0, -160, 70, -460, -40},
+<a name="l00293"></a>00293 { 0, 160, 220, 70, 310},
+<a name="l00294"></a>00294 { 0, -150, 510, 10, 100},
+<a name="l00295"></a>00295 { 0, 160, 220, 70, 310},
+<a name="l00296"></a>00296 { 0, -50, 690, -60, -60},
+<a name="l00297"></a>00297 { 0, 0, 0, 0, 0}
+<a name="l00298"></a>00298 };
+<a name="l00299"></a>00299
+<a name="l00300"></a>00300
+<a name="l00301"></a>00301 <span class="comment">/* constants for linearly destabilizing contributions for multi-loops</span>
+<a name="l00302"></a>00302 <span class="comment"> F = ML_closing + ML_intern*k + ML_BASE*u */</span>
+<a name="l00303"></a>00303 <span class="comment">/* old versions erroneously used ML_intern*(k-1) */</span>
+<a name="l00304"></a>00304 PRIVATE <span class="keywordtype">int</span> ML_BASE37_184 = 0;
+<a name="l00305"></a>00305 PRIVATE <span class="keywordtype">int</span> ML_closing37_184 = 340;
+<a name="l00306"></a>00306 PRIVATE <span class="keywordtype">int</span> ML_intern37_184 = 40;
+<a name="l00307"></a>00307
+<a name="l00308"></a>00308 <span class="comment">/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */</span>
+<a name="l00309"></a>00309 <span class="comment">/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */</span>
+<a name="l00310"></a>00310 PRIVATE <span class="keywordtype">int</span> MAX_NINIO_184 = 300; <span class="comment">/* maximum correction */</span>
+<a name="l00311"></a>00311 PRIVATE <span class="keywordtype">int</span> F_ninio37_184[5] = { 0, 40, 50, 20, 10 }; <span class="comment">/* only F[2] used */</span>
+<a name="l00312"></a>00312
+<a name="l00313"></a>00313 <span class="comment">/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */</span>
+<a name="l00314"></a>00314
+<a name="l00315"></a>00315 PRIVATE <span class="keywordtype">char</span> Tetraloops_184[1400] = <span class="comment">/* place for up to 200 tetra loops */</span>
+<a name="l00316"></a>00316 <span class="stringliteral">"GGGGAC "</span>
+<a name="l00317"></a>00317 <span class="stringliteral">"GGUGAC "</span>
+<a name="l00318"></a>00318 <span class="stringliteral">"CGAAAG "</span>
+<a name="l00319"></a>00319 <span class="stringliteral">"GGAGAC "</span>
+<a name="l00320"></a>00320 <span class="stringliteral">"CGCAAG "</span>
+<a name="l00321"></a>00321 <span class="stringliteral">"GGAAAC "</span>
+<a name="l00322"></a>00322 <span class="stringliteral">"CGGAAG "</span>
+<a name="l00323"></a>00323 <span class="stringliteral">"CUUCGG "</span>
+<a name="l00324"></a>00324 <span class="stringliteral">"CGUGAG "</span>
+<a name="l00325"></a>00325 <span class="stringliteral">"CGAAGG "</span>
+<a name="l00326"></a>00326 <span class="stringliteral">"CUACGG "</span>
+<a name="l00327"></a>00327 <span class="stringliteral">"GGCAAC "</span>
+<a name="l00328"></a>00328 <span class="stringliteral">"CGCGAG "</span>
+<a name="l00329"></a>00329 <span class="stringliteral">"UGAGAG "</span>
+<a name="l00330"></a>00330 <span class="stringliteral">"CGAGAG "</span>
+<a name="l00331"></a>00331 <span class="stringliteral">"AGAAAU "</span>
+<a name="l00332"></a>00332 <span class="stringliteral">"CGUAAG "</span>
+<a name="l00333"></a>00333 <span class="stringliteral">"CUAACG "</span>
+<a name="l00334"></a>00334 <span class="stringliteral">"UGAAAG "</span>
+<a name="l00335"></a>00335 <span class="stringliteral">"GGAAGC "</span>
+<a name="l00336"></a>00336 <span class="stringliteral">"GGGAAC "</span>
+<a name="l00337"></a>00337 <span class="stringliteral">"UGAAAA "</span>
+<a name="l00338"></a>00338 <span class="stringliteral">"AGCAAU "</span>
+<a name="l00339"></a>00339 <span class="stringliteral">"AGUAAU "</span>
+<a name="l00340"></a>00340 <span class="stringliteral">"CGGGAG "</span>
+<a name="l00341"></a>00341 <span class="stringliteral">"AGUGAU "</span>
+<a name="l00342"></a>00342 <span class="stringliteral">"GGCGAC "</span>
+<a name="l00343"></a>00343 <span class="stringliteral">"GGGAGC "</span>
+<a name="l00344"></a>00344 <span class="stringliteral">"GUGAAC "</span>
+<a name="l00345"></a>00345 <span class="stringliteral">"UGGAAA "</span>
+<a name="l00346"></a>00346 ;
+<a name="l00347"></a>00347
+<a name="l00348"></a>00348 PRIVATE <span class="keywordtype">int</span> TETRA_ENERGY37_184[200] = {
+<a name="l00349"></a>00349 -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
+<a name="l00350"></a>00350 -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
+<a name="l00351"></a>00351 -150, -150, -150, -150, -150, -150};
+<a name="l00352"></a>00352
+<a name="l00353"></a>00353 PRIVATE <span class="keywordtype">int</span> TETRA_ENTH37_184 = -400;
+<a name="l00354"></a>00354
+<a name="l00355"></a>00355 PRIVATE <span class="keywordtype">char</span> Triloops_184[241] = <span class="stringliteral">""</span>;
+<a name="l00356"></a>00356
+<a name="l00357"></a>00357 PRIVATE <span class="keywordtype">int</span> Triloop_E37_184[40];
+<a name="l00358"></a>00358
+<a name="l00359"></a>00359 <span class="comment">/* penalty for AU (or GU) terminating helix) */</span>
+<a name="l00360"></a>00360 <span class="comment">/* mismatches already contain these */</span>
+<a name="l00361"></a>00361 PRIVATE <span class="keywordtype">int</span> TerminalAU_184 = 50;
+<a name="l00362"></a>00362
+<a name="l00363"></a>00363 <span class="comment">/* penalty for forming a bi-molecular duplex */</span>
+<a name="l00364"></a>00364 PRIVATE <span class="keywordtype">int</span> DuplexInit_184 = 410;
+<a name="l00365"></a>00365
+<a name="l00366"></a>00366 <span class="preprocessor">#endif</span>
+</pre></div></div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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