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+<div class="title">data_structures.h</div> </div>
+</div><!--header-->
+<div class="contents">
+<a href="data__structures_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_DATA_STRUCTURES_H__</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_DATA_STRUCTURES_H__</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include "<a class="code" href="energy__const_8h.html">energy_const.h</a>"</span></div>
+<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">/* to use floats instead of doubles in pf_fold() comment next line */</span></div>
+<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define LARGE_PF</span></div>
+<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor"></span><span class="preprocessor">#ifdef LARGE_PF</span></div>
+<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor"></span><span class="preprocessor">#define FLT_OR_DBL double</span></div>
+<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
+<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor"></span><span class="preprocessor">#define FLT_OR_DBL float</span></div>
+<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#ifndef NBASES</span></div>
+<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor"></span><span class="preprocessor">#define NBASES 8</span></div>
+<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#ifndef MAXALPHA</span></div>
+<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00026"></a><span class="lineno"><a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379"> 26</a></span> <span class="preprocessor">#define MAXALPHA 20</span></div>
+<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00032"></a><span class="lineno"><a class="code" href="data__structures_8h.html#a5ec740b80afb4906ba4311dbd8ddbd89"> 32</a></span> <span class="preprocessor">#define MAXDOS 1000</span></div>
+<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#define VRNA_GQUAD_MAX_STACK_SIZE 7</span></div>
+<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor"></span><span class="preprocessor">#define VRNA_GQUAD_MIN_STACK_SIZE 2</span></div>
+<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define VRNA_GQUAD_MAX_LINKER_LENGTH 15</span></div>
+<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define VRNA_GQUAD_MIN_LINKER_LENGTH 1</span></div>
+<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span><span class="preprocessor">#define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))</span></div>
+<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor"></span><span class="preprocessor">#define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))</span></div>
+<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
+<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment">* Here are the type definitions of various datastructures</span></div>
+<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment">* shared among the Vienna RNA Package</span></div>
+<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
+<div class="line"><a name="l00052"></a><span class="lineno"><a class="code" href="structplist.html"> 52</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> {</div>
+<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">float</span> p;</div>
+<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">int</span> type;</div>
+<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> } <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a>;</div>
+<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div>
+<div class="line"><a name="l00062"></a><span class="lineno"><a class="code" href="structcpair.html"> 62</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structcpair.html" title="this datastructure is used as input parameter in functions of PS_dot.c">cpair</a> {</div>
+<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">int</span> i,j,mfe;</div>
+<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordtype">float</span> p, hue, sat;</div>
+<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> } <a class="code" href="structcpair.html" title="this datastructure is used as input parameter in functions of PS_dot.c">cpair</a>;</div>
+<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
+<div class="line"><a name="l00071"></a><span class="lineno"><a class="code" href="structCOORDINATE.html"> 71</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">float</span> X; <span class="comment">/* X coords */</span></div>
+<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">float</span> Y; <span class="comment">/* Y coords */</span></div>
+<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> } <a class="code" href="structCOORDINATE.html" title="this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORD...">COORDINATE</a>;</div>
+<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
+<div class="line"><a name="l00079"></a><span class="lineno"><a class="code" href="structsect.html"> 79</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structsect.html" title="Stack of partial structures for backtracking.">sect</a> {</div>
+<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">int</span> ml;</div>
+<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> } <a class="code" href="structsect.html" title="Stack of partial structures for backtracking.">sect</a>;</div>
+<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
+<div class="line"><a name="l00088"></a><span class="lineno"><a class="code" href="structbondT.html"> 88</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structbondT.html" title="Base pair.">bondT</a> {</div>
+<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> } <a class="code" href="structbondT.html" title="Base pair.">bondT</a>;</div>
+<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
+<div class="line"><a name="l00096"></a><span class="lineno"><a class="code" href="structbondTEn.html"> 96</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structbondTEn.html" title="Base pair with associated energy.">bondTEn</a> {</div>
+<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordtype">int</span> energy;</div>
+<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> } <a class="code" href="structbondTEn.html" title="Base pair with associated energy.">bondTEn</a>;</div>
+<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
+<div class="line"><a name="l00106"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html"> 106</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00107"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a89f9df217a4a7f4351a642655976376b"> 107</a></span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a>; </div>
+<div class="line"><a name="l00113"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617"> 113</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617" title="Include special hairpin contributions for tri, tetra and hexaloops.">special_hp</a>; </div>
+<div class="line"><a name="l00114"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a6fb076173d2cbc4259606ce23eedf17d"> 114</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#a6fb076173d2cbc4259606ce23eedf17d" title="Only consider canonical structures, i.e. no 'lonely' base pairs.">noLP</a>; </div>
+<div class="line"><a name="l00115"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a0f982e6904d012e4fe41e99daa797f5d"> 115</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#a0f982e6904d012e4fe41e99daa797f5d" title="Do not allow GU pairs.">noGU</a>; </div>
+<div class="line"><a name="l00116"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#ae9cedf375cd904e5fb8e56cf3f64bcd9"> 116</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#ae9cedf375cd904e5fb8e56cf3f64bcd9" title="Do not allow loops to be closed by GU pair.">noGUclosure</a>; </div>
+<div class="line"><a name="l00117"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a415556dc150e02d108be81ecc5c48e85"> 117</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#a415556dc150e02d108be81ecc5c48e85" title="Use logarithmic scaling for multi loops.">logML</a>; </div>
+<div class="line"><a name="l00118"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#a55f083dad18c216505805a8062e63074"> 118</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#a55f083dad18c216505805a8062e63074" title="Assume molecule to be circular.">circ</a>; </div>
+<div class="line"><a name="l00119"></a><span class="lineno"><a class="code" href="structmodel__detailsT.html#aa1ecdce7bc3f375bd8a9a7b738abc0ea"> 119</a></span>  <span class="keywordtype">int</span> <a class="code" href="structmodel__detailsT.html#aa1ecdce7bc3f375bd8a9a7b738abc0ea" title="Include G-quadruplexes in structure prediction.">gquad</a>; </div>
+<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> } <a class="code" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations.">model_detailsT</a>;</div>
+<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
+<div class="line"><a name="l00125"></a><span class="lineno"><a class="code" href="structparamT.html"> 125</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">int</span> id;</div>
+<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">int</span> stack[<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="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">int</span> hairpin[31];</div>
+<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">int</span> bulge[<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>+1];</div>
+<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">int</span> internal_loop[<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>+1];</div>
+<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">int</span> mismatchExt[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">int</span> mismatchI[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordtype">int</span> mismatch1nI[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">int</span> mismatch23I[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordtype">int</span> mismatchH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordtype">int</span> mismatchM[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordtype">int</span> dangle5[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];</div>
+<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">int</span> dangle3[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];</div>
+<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordtype">int</span> int11[<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="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">int</span> int21[<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="l00141"></a><span class="lineno"> 141</span>  <span class="keywordtype">int</span> int22[<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="l00142"></a><span class="lineno"> 142</span>  <span class="keywordtype">int</span> ninio[5];</div>
+<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">double</span> lxc;</div>
+<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">int</span> MLbase;</div>
+<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">int</span> MLintern[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1];</div>
+<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordtype">int</span> MLclosing;</div>
+<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordtype">int</span> TerminalAU;</div>
+<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordtype">int</span> DuplexInit;</div>
+<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordtype">int</span> Tetraloop_E[200];</div>
+<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordtype">char</span> Tetraloops[1401];</div>
+<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordtype">int</span> Triloop_E[40];</div>
+<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordtype">char</span> Triloops[241];</div>
+<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">int</span> Hexaloop_E[40];</div>
+<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordtype">char</span> Hexaloops[1801];</div>
+<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">int</span> TripleC;</div>
+<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordtype">int</span> MultipleCA;</div>
+<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordtype">int</span> MultipleCB;</div>
+<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a25f2bdcdf56e813d288845484a13d704" title="Allow G-quadruplex formation.">gquad</a> [VRNA_GQUAD_MAX_STACK_SIZE + 1]</div>
+<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];</div>
+<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
+<div class="line"><a name="l00161"></a><span class="lineno"><a class="code" href="structparamT.html#a8ed207b95868d1085bd9c197fbc6924f"> 161</a></span>  <span class="keywordtype">double</span> <a class="code" href="structparamT.html#a8ed207b95868d1085bd9c197fbc6924f" title="Temperature used for loop contribution scaling.">temperature</a>; </div>
+<div class="line"><a name="l00163"></a><span class="lineno"><a class="code" href="structparamT.html#aeb912822ef912705bc202b14f9d71ad9"> 163</a></span>  <a class="code" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations.">model_detailsT</a> <a class="code" href="structparamT.html#aeb912822ef912705bc202b14f9d71ad9" title="Model details to be used in the recursions.">model_details</a>; </div>
+<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> } <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a>;</div>
+<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
+<div class="line"><a name="l00170"></a><span class="lineno"><a class="code" href="structpf__paramT.html"> 170</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordtype">int</span> id;</div>
+<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordtype">double</span> expstack[<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="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">double</span> exphairpin[31];</div>
+<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordtype">double</span> expbulge[<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>+1];</div>
+<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordtype">double</span> expinternal[<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>+1];</div>
+<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordtype">double</span> expmismatchExt[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordtype">double</span> expmismatchI[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordtype">double</span> expmismatch23I[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordtype">double</span> expmismatch1nI[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordtype">double</span> expmismatchH[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">double</span> expmismatchM[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5][5];</div>
+<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordtype">double</span> expdangle5[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];</div>
+<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">double</span> expdangle3[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1][5];</div>
+<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordtype">double</span> expint11[<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="l00185"></a><span class="lineno"> 185</span>  <span class="keywordtype">double</span> expint21[<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="l00186"></a><span class="lineno"> 186</span>  <span class="keywordtype">double</span> expint22[<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="l00187"></a><span class="lineno"> 187</span>  <span class="keywordtype">double</span> expninio[5][<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>+1];</div>
+<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordtype">double</span> lxc;</div>
+<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordtype">double</span> expMLbase;</div>
+<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordtype">double</span> expMLintern[<a class="code" href="energy__const_8h.html#a5e75221c779d618eab81e096f37e32ce">NBPAIRS</a>+1];</div>
+<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">double</span> expMLclosing;</div>
+<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordtype">double</span> expTermAU;</div>
+<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordtype">double</span> expDuplexInit;</div>
+<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordtype">double</span> exptetra[40];</div>
+<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordtype">double</span> exptri[40];</div>
+<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordtype">double</span> exphex[40];</div>
+<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordtype">char</span> Tetraloops[1401];</div>
+<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordtype">double</span> expTriloop[40];</div>
+<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordtype">char</span> Triloops[241];</div>
+<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordtype">char</span> Hexaloops[1801];</div>
+<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordtype">double</span> expTripleC;</div>
+<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordtype">double</span> expMultipleCA;</div>
+<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordtype">double</span> expMultipleCB;</div>
+<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordtype">double</span> expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]</div>
+<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];</div>
+<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
+<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordtype">double</span> kT;</div>
+<div class="line"><a name="l00208"></a><span class="lineno"><a class="code" href="structpf__paramT.html#aef40322e7ca1adbd9b438aeda0352e8f"> 208</a></span>  <span class="keywordtype">double</span> <a class="code" href="structpf__paramT.html#aef40322e7ca1adbd9b438aeda0352e8f" title="Scaling factor to avoid over-/underflows.">pf_scale</a>; </div>
+<div class="line"><a name="l00210"></a><span class="lineno"><a class="code" href="structpf__paramT.html#aa0e11e9f1f6e212640baf40d7195a014"> 210</a></span>  <span class="keywordtype">double</span> <a class="code" href="structpf__paramT.html#aa0e11e9f1f6e212640baf40d7195a014" title="Temperature used for loop contribution scaling.">temperature</a>; </div>
+<div class="line"><a name="l00211"></a><span class="lineno"><a class="code" href="structpf__paramT.html#a3d2af9040acfa08295efb50f0219149d"> 211</a></span>  <span class="keywordtype">double</span> alpha; </div>
+<div class="line"><a name="l00218"></a><span class="lineno"><a class="code" href="structpf__paramT.html#a43ec875779c5e7c8bf5fa7e837ec6d09"> 218</a></span>  <a class="code" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations.">model_detailsT</a> <a class="code" href="structpf__paramT.html#a43ec875779c5e7c8bf5fa7e837ec6d09" title="Model details to be used in the recursions.">model_details</a>; </div>
+<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> } <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a>;</div>
+<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
+<div class="line"><a name="l00222"></a><span class="lineno"> 222</span> </div>
+<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
+<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> <span class="comment">* SUBOPT data structures</span></div>
+<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00228"></a><span class="lineno"> 228</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div>
+<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
+<div class="line"><a name="l00234"></a><span class="lineno"><a class="code" href="structPAIR.html"> 234</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> } <a class="code" href="structPAIR.html" title="Base pair data structure used in subopt.c.">PAIR</a>;</div>
+<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div>
+<div class="line"><a name="l00242"></a><span class="lineno"><a class="code" href="structINTERVAL.html"> 242</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keywordtype">int</span> array_flag;</div>
+<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> } <a class="code" href="structINTERVAL.html" title="Sequence interval stack element used in subopt.c.">INTERVAL</a>;</div>
+<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> </div>
+<div class="line"><a name="l00251"></a><span class="lineno"><a class="code" href="structSOLUTION.html"> 251</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00252"></a><span class="lineno"><a class="code" href="structSOLUTION.html#a4fe8e9027171f2dc4031587d7fab6b87"> 252</a></span>  <span class="keywordtype">float</span> <a class="code" href="structSOLUTION.html#a4fe8e9027171f2dc4031587d7fab6b87" title="Free Energy of structure in kcal/mol.">energy</a>; </div>
+<div class="line"><a name="l00253"></a><span class="lineno"><a class="code" href="structSOLUTION.html#a89ae453dfad0509468c39a62c303a63b"> 253</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structSOLUTION.html#a89ae453dfad0509468c39a62c303a63b" title="Structure in dot-bracket notation.">structure</a>; </div>
+<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> } <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a>;</div>
+<div class="line"><a name="l00255"></a><span class="lineno"> 255</span> </div>
+<div class="line"><a name="l00256"></a><span class="lineno"> 256</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00258"></a><span class="lineno"> 258</span> <span class="comment">* COFOLD data structures</span></div>
+<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> </div>
+<div class="line"><a name="l00265"></a><span class="lineno"><a class="code" href="structcofoldF.html"> 265</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structcofoldF.html">cofoldF</a> {</div>
+<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">/* free energies for: */</span></div>
+<div class="line"><a name="l00267"></a><span class="lineno"><a class="code" href="structcofoldF.html#af6c496438321eb8bb907a21de1915c23"> 267</a></span>  <span class="keywordtype">double</span> <a class="code" href="structcofoldF.html#af6c496438321eb8bb907a21de1915c23" title="Null model without DuplexInit.">F0AB</a>; </div>
+<div class="line"><a name="l00268"></a><span class="lineno"><a class="code" href="structcofoldF.html#a2ae1245ff4a93cd11f882f490f777cb7"> 268</a></span>  <span class="keywordtype">double</span> <a class="code" href="structcofoldF.html#a2ae1245ff4a93cd11f882f490f777cb7" title="all states with DuplexInit correction">FAB</a>; </div>
+<div class="line"><a name="l00269"></a><span class="lineno"><a class="code" href="structcofoldF.html#a4899a4f9b42e416baf46c5fe10751c45"> 269</a></span>  <span class="keywordtype">double</span> <a class="code" href="structcofoldF.html#a4899a4f9b42e416baf46c5fe10751c45" title="true hybrid states only">FcAB</a>; </div>
+<div class="line"><a name="l00270"></a><span class="lineno"><a class="code" href="structcofoldF.html#a460f3ba205c205e6f5ec27cc2e2eb2b2"> 270</a></span>  <span class="keywordtype">double</span> <a class="code" href="structcofoldF.html#a460f3ba205c205e6f5ec27cc2e2eb2b2" title="monomer A">FA</a>; </div>
+<div class="line"><a name="l00271"></a><span class="lineno"><a class="code" href="structcofoldF.html#ad3e5466724f3987be9d6f388b8ee5129"> 271</a></span>  <span class="keywordtype">double</span> <a class="code" href="structcofoldF.html#ad3e5466724f3987be9d6f388b8ee5129" title="monomer B">FB</a>; </div>
+<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> } <a class="code" href="structcofoldF.html">cofoldF</a>;</div>
+<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div>
+<div class="line"><a name="l00277"></a><span class="lineno"><a class="code" href="structConcEnt.html"> 277</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structConcEnt.html">ConcEnt</a> {</div>
+<div class="line"><a name="l00278"></a><span class="lineno"><a class="code" href="structConcEnt.html#adcf4d93c7efeaa4e6c4154b64d367681"> 278</a></span>  <span class="keywordtype">double</span> <a class="code" href="structConcEnt.html#adcf4d93c7efeaa4e6c4154b64d367681" title="start concentration A">A0</a>; </div>
+<div class="line"><a name="l00279"></a><span class="lineno"><a class="code" href="structConcEnt.html#add4c33b94b34e847fbf5838b04cce346"> 279</a></span>  <span class="keywordtype">double</span> <a class="code" href="structConcEnt.html#add4c33b94b34e847fbf5838b04cce346" title="start concentration B">B0</a>; </div>
+<div class="line"><a name="l00280"></a><span class="lineno"><a class="code" href="structConcEnt.html#ac59c07a31d844e7b05bcdc05c4413b19"> 280</a></span>  <span class="keywordtype">double</span> <a class="code" href="structConcEnt.html#ac59c07a31d844e7b05bcdc05c4413b19" title="End concentration AB.">ABc</a>; </div>
+<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordtype">double</span> AAc;</div>
+<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordtype">double</span> BBc;</div>
+<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordtype">double</span> Ac;</div>
+<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordtype">double</span> Bc;</div>
+<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> } <a class="code" href="structConcEnt.html">ConcEnt</a>;</div>
+<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> </div>
+<div class="line"><a name="l00290"></a><span class="lineno"><a class="code" href="structpairpro.html"> 290</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structpairpro.html">pairpro</a>{</div>
+<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *AB;</div>
+<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *AA;</div>
+<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *A;</div>
+<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *B;</div>
+<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keyword">struct </span><a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *BB;</div>
+<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> }<a class="code" href="structpairpro.html">pairpro</a>;</div>
+<div class="line"><a name="l00297"></a><span class="lineno"> 297</span> </div>
+<div class="line"><a name="l00308"></a><span class="lineno"><a class="code" href="structpair__info.html"> 308</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00309"></a><span class="lineno"><a class="code" href="structpair__info.html#a7905e17da6a6cc48230ee6205628ed7f"> 309</a></span>  <span class="keywordtype">unsigned</span> <a class="code" href="structpair__info.html#a7905e17da6a6cc48230ee6205628ed7f" title="nucleotide position i">i</a>; </div>
+<div class="line"><a name="l00310"></a><span class="lineno"><a class="code" href="structpair__info.html#a35665817b5792703ff4325e1bcbe5e21"> 310</a></span>  <span class="keywordtype">unsigned</span> <a class="code" href="structpair__info.html#a35665817b5792703ff4325e1bcbe5e21" title="nucleotide position j">j</a>; </div>
+<div class="line"><a name="l00311"></a><span class="lineno"><a class="code" href="structpair__info.html#af0895ea40ec0c23bfe8aa2c3babf0e80"> 311</a></span>  <span class="keywordtype">float</span> <a class="code" href="structpair__info.html#af0895ea40ec0c23bfe8aa2c3babf0e80" title="Probability.">p</a>; </div>
+<div class="line"><a name="l00312"></a><span class="lineno"><a class="code" href="structpair__info.html#ab3aa7a54e6976f46e69c6ffcddd0e782"> 312</a></span>  <span class="keywordtype">float</span> <a class="code" href="structpair__info.html#ab3aa7a54e6976f46e69c6ffcddd0e782" title="Pseudo entropy for .">ent</a>; </div>
+<div class="line"><a name="l00313"></a><span class="lineno"><a class="code" href="structpair__info.html#a23fc316453d179474bed7f6ed2489723"> 313</a></span>  <span class="keywordtype">short</span> bp[8]; </div>
+<div class="line"><a name="l00314"></a><span class="lineno"><a class="code" href="structpair__info.html#a4da3d6c9042500c16c4b06e0bbc48190"> 314</a></span>  <span class="keywordtype">char</span> <a class="code" href="structpair__info.html#a4da3d6c9042500c16c4b06e0bbc48190" title="1 iff pair is in mfe structure">comp</a>; </div>
+<div class="line"><a name="l00315"></a><span class="lineno"> 315</span> } <a class="code" href="structpair__info.html" title="A base pair info structure.">pair_info</a>;</div>
+<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div>
+<div class="line"><a name="l00317"></a><span class="lineno"> 317</span> </div>
+<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00320"></a><span class="lineno"> 320</span> <span class="comment">* FINDPATH data structures</span></div>
+<div class="line"><a name="l00321"></a><span class="lineno"> 321</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div>
+<div class="line"><a name="l00327"></a><span class="lineno"><a class="code" href="structmove__t.html"> 327</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>move {</div>
+<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="keywordtype">int</span> i; <span class="comment">/* i,j>0 insert; i,j<0 delete */</span></div>
+<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordtype">int</span> when; <span class="comment">/* 0 if still available, else resulting distance from start */</span></div>
+<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordtype">int</span> E;</div>
+<div class="line"><a name="l00332"></a><span class="lineno"> 332</span> } <a class="code" href="structmove__t.html">move_t</a>;</div>
+<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
+<div class="line"><a name="l00337"></a><span class="lineno"><a class="code" href="structintermediate__t.html"> 337</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>intermediate {</div>
+<div class="line"><a name="l00338"></a><span class="lineno"><a class="code" href="structintermediate__t.html#a9a2b6258aa1af06ea3504631de8dadba"> 338</a></span>  <span class="keywordtype">short</span> *<a class="code" href="structintermediate__t.html#a9a2b6258aa1af06ea3504631de8dadba" title="pair table">pt</a>; </div>
+<div class="line"><a name="l00339"></a><span class="lineno"><a class="code" href="structintermediate__t.html#ac44e091915da58927978d54ef59234c7"> 339</a></span>  <span class="keywordtype">int</span> <a class="code" href="structintermediate__t.html#ac44e091915da58927978d54ef59234c7" title="saddle energy so far">Sen</a>; </div>
+<div class="line"><a name="l00340"></a><span class="lineno"><a class="code" href="structintermediate__t.html#af84d640df33aea99e959b2e4f61a7367"> 340</a></span>  <span class="keywordtype">int</span> <a class="code" href="structintermediate__t.html#af84d640df33aea99e959b2e4f61a7367" title="current energy">curr_en</a>; </div>
+<div class="line"><a name="l00341"></a><span class="lineno"><a class="code" href="structintermediate__t.html#a94e947f18273bbfe3dd544085b025a7b"> 341</a></span>  <a class="code" href="structmove__t.html">move_t</a> *<a class="code" href="structintermediate__t.html#a94e947f18273bbfe3dd544085b025a7b" title="remaining moves to target">moves</a>; </div>
+<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> } <a class="code" href="structintermediate__t.html">intermediate_t</a>;</div>
+<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
+<div class="line"><a name="l00347"></a><span class="lineno"><a class="code" href="structpath__t.html"> 347</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>path {</div>
+<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <span class="keywordtype">double</span> en;</div>
+<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordtype">char</span> *s;</div>
+<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> } <a class="code" href="structpath__t.html">path_t</a>;</div>
+<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> </div>
+<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00353"></a><span class="lineno"> 353</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> <span class="comment">* RNAup data structures</span></div>
+<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> </div>
+<div class="line"><a name="l00361"></a><span class="lineno"><a class="code" href="structpu__contrib.html"> 361</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> {</div>
+<div class="line"><a name="l00362"></a><span class="lineno"><a class="code" href="structpu__contrib.html#ac9034ac9a84ed0647587659d6e9be1e8"> 362</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structpu__contrib.html#ac9034ac9a84ed0647587659d6e9be1e8" title="hairpin loops">H</a>; </div>
+<div class="line"><a name="l00363"></a><span class="lineno"><a class="code" href="structpu__contrib.html#a8ca0da20536780589fb3e3472ca0581f"> 363</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structpu__contrib.html#a8ca0da20536780589fb3e3472ca0581f" title="interior loops">I</a>; </div>
+<div class="line"><a name="l00364"></a><span class="lineno"><a class="code" href="structpu__contrib.html#a1222ebf74f426bbcd843dcc325da207b"> 364</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structpu__contrib.html#a1222ebf74f426bbcd843dcc325da207b" title="multi loops">M</a>; </div>
+<div class="line"><a name="l00365"></a><span class="lineno"><a class="code" href="structpu__contrib.html#accb192ba6b4b91a1cb2f8080934fd428"> 365</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structpu__contrib.html#accb192ba6b4b91a1cb2f8080934fd428" title="exterior loop">E</a>; </div>
+<div class="line"><a name="l00366"></a><span class="lineno"><a class="code" href="structpu__contrib.html#a33d5ada6e861db0c81aa3d5b2989262e"> 366</a></span>  <span class="keywordtype">int</span> <a class="code" href="structpu__contrib.html#a33d5ada6e861db0c81aa3d5b2989262e" title="length of the input sequence">length</a>; </div>
+<div class="line"><a name="l00367"></a><span class="lineno"><a class="code" href="structpu__contrib.html#a403c1c7f20beeeffba7632fac0cfcbff"> 367</a></span>  <span class="keywordtype">int</span> <a class="code" href="structpu__contrib.html#a403c1c7f20beeeffba7632fac0cfcbff" title="longest unpaired region">w</a>; </div>
+<div class="line"><a name="l00368"></a><span class="lineno"> 368</span> } <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a>;</div>
+<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> </div>
+<div class="line"><a name="l00373"></a><span class="lineno"><a class="code" href="structinteract.html"> 373</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structinteract.html">interact</a> {</div>
+<div class="line"><a name="l00374"></a><span class="lineno"><a class="code" href="structinteract.html#a1fc8b3860c083f164daa9712690a3a56"> 374</a></span>  <span class="keywordtype">double</span> *<a class="code" href="structinteract.html#a1fc8b3860c083f164daa9712690a3a56" title="probabilities of interaction">Pi</a>; </div>
+<div class="line"><a name="l00375"></a><span class="lineno"><a class="code" href="structinteract.html#a54f8183542fff4c32ab7ace49a16c02c"> 375</a></span>  <span class="keywordtype">double</span> *<a class="code" href="structinteract.html#a54f8183542fff4c32ab7ace49a16c02c" title="free energies of interaction">Gi</a>; </div>
+<div class="line"><a name="l00376"></a><span class="lineno"><a class="code" href="structinteract.html#ad58303190f9e085c3ab59890cbf61223"> 376</a></span>  <span class="keywordtype">double</span> <a class="code" href="structinteract.html#ad58303190f9e085c3ab59890cbf61223" title="full free energy for interaction between [k,i] k<i in longer seq and [j,l] j<l in shorter seq...">Gikjl</a>; </div>
+<div class="line"><a name="l00378"></a><span class="lineno"><a class="code" href="structinteract.html#a41793812abae560805414761fec398fe"> 378</a></span>  <span class="keywordtype">double</span> <a class="code" href="structinteract.html#a41793812abae560805414761fec398fe" title="Gikjl without contributions for prob_unpaired.">Gikjl_wo</a>; </div>
+<div class="line"><a name="l00379"></a><span class="lineno"><a class="code" href="structinteract.html#ab6d031a21388be8763b75ea74c937f17"> 379</a></span>  <span class="keywordtype">int</span> <a class="code" href="structinteract.html#ab6d031a21388be8763b75ea74c937f17" title="k<i in longer seq">i</a>; </div>
+<div class="line"><a name="l00380"></a><span class="lineno"><a class="code" href="structinteract.html#a61e457fbf943d57364be6ddf1b4e7b8a"> 380</a></span>  <span class="keywordtype">int</span> <a class="code" href="structinteract.html#a61e457fbf943d57364be6ddf1b4e7b8a" title="k<i in longer seq">k</a>; </div>
+<div class="line"><a name="l00381"></a><span class="lineno"><a class="code" href="structinteract.html#a7555cb6363d1479341eb72b9c087aa34"> 381</a></span>  <span class="keywordtype">int</span> <a class="code" href="structinteract.html#a7555cb6363d1479341eb72b9c087aa34" title="j<l in shorter seq">j</a>; </div>
+<div class="line"><a name="l00382"></a><span class="lineno"><a class="code" href="structinteract.html#a030ab45056342e12cb3955e4defd3904"> 382</a></span>  <span class="keywordtype">int</span> <a class="code" href="structinteract.html#a030ab45056342e12cb3955e4defd3904" title="j<l in shorter seq">l</a>; </div>
+<div class="line"><a name="l00383"></a><span class="lineno"><a class="code" href="structinteract.html#ac9fcb5dca54ec5faa76e02b6488b9524"> 383</a></span>  <span class="keywordtype">int</span> <a class="code" href="structinteract.html#ac9fcb5dca54ec5faa76e02b6488b9524" title="length of longer sequence">length</a>; </div>
+<div class="line"><a name="l00384"></a><span class="lineno"> 384</span> } <a class="code" href="structinteract.html">interact</a>;</div>
+<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div>
+<div class="line"><a name="l00389"></a><span class="lineno"><a class="code" href="structpu__out.html"> 389</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structpu__out.html" title="Collection of all free_energy of beeing unpaired values for output.">pu_out</a> {</div>
+<div class="line"><a name="l00390"></a><span class="lineno"><a class="code" href="structpu__out.html#a314b8f43c3ee0bf6060afbeced5dbe6c"> 390</a></span>  <span class="keywordtype">int</span> <a class="code" href="structpu__out.html#a314b8f43c3ee0bf6060afbeced5dbe6c" title="sequence length">len</a>; </div>
+<div class="line"><a name="l00391"></a><span class="lineno"><a class="code" href="structpu__out.html#a7697bc7a46cd1b8e37e337e708cb6023"> 391</a></span>  <span class="keywordtype">int</span> <a class="code" href="structpu__out.html#a7697bc7a46cd1b8e37e337e708cb6023" title="number of different -u values">u_vals</a>; </div>
+<div class="line"><a name="l00392"></a><span class="lineno"><a class="code" href="structpu__out.html#a638b0de1837cfd441871d005d3ab2938"> 392</a></span>  <span class="keywordtype">int</span> <a class="code" href="structpu__out.html#a638b0de1837cfd441871d005d3ab2938" title="[-c "SHIME"]">contribs</a>; </div>
+<div class="line"><a name="l00393"></a><span class="lineno"><a class="code" href="structpu__out.html#ac9e9e30b16e7d04c770460b8487fb09d"> 393</a></span>  <span class="keywordtype">char</span> **<a class="code" href="structpu__out.html#ac9e9e30b16e7d04c770460b8487fb09d" title="header line">header</a>; </div>
+<div class="line"><a name="l00394"></a><span class="lineno"><a class="code" href="structpu__out.html#a366edbc4170d5c177908e178ff340828"> 394</a></span>  <span class="keywordtype">double</span> **<a class="code" href="structpu__out.html#a366edbc4170d5c177908e178ff340828" title="(the -u values * [-c "SHIME"]) * seq len">u_values</a>; </div>
+<div class="line"><a name="l00395"></a><span class="lineno"> 395</span> } <a class="code" href="structpu__out.html" title="Collection of all free_energy of beeing unpaired values for output.">pu_out</a>;</div>
+<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> </div>
+<div class="line"><a name="l00400"></a><span class="lineno"><a class="code" href="structconstrain.html"> 400</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structconstrain.html" title="constraints for cofolding">constrain</a>{</div>
+<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordtype">int</span> *indx;</div>
+<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="keywordtype">char</span> *ptype;</div>
+<div class="line"><a name="l00403"></a><span class="lineno"> 403</span> } <a class="code" href="structconstrain.html" title="constraints for cofolding">constrain</a>;</div>
+<div class="line"><a name="l00404"></a><span class="lineno"> 404</span> </div>
+<div class="line"><a name="l00405"></a><span class="lineno"> 405</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> <span class="comment">* RNAduplex data structures</span></div>
+<div class="line"><a name="l00408"></a><span class="lineno"> 408</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00409"></a><span class="lineno"> 409</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> </div>
+<div class="line"><a name="l00414"></a><span class="lineno"><a class="code" href="structduplexT.html"> 414</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keywordtype">int</span> end;</div>
+<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordtype">char</span> *structure;</div>
+<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <span class="keywordtype">double</span> energy;</div>
+<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordtype">double</span> energy_backtrack;</div>
+<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  <span class="keywordtype">double</span> opening_backtrack_x;</div>
+<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordtype">double</span> opening_backtrack_y;</div>
+<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordtype">int</span> offset;</div>
+<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordtype">double</span> dG1;</div>
+<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  <span class="keywordtype">double</span> dG2;</div>
+<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordtype">double</span> ddG;</div>
+<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordtype">int</span> tb;</div>
+<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordtype">int</span> te;</div>
+<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="keywordtype">int</span> qb;</div>
+<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <span class="keywordtype">int</span> qe;</div>
+<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> } <a class="code" href="structduplexT.html">duplexT</a>;</div>
+<div class="line"><a name="l00432"></a><span class="lineno"> 432</span> </div>
+<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00434"></a><span class="lineno"> 434</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> <span class="comment">* RNAsnoop data structures</span></div>
+<div class="line"><a name="l00436"></a><span class="lineno"> 436</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00438"></a><span class="lineno"> 438</span> </div>
+<div class="line"><a name="l00442"></a><span class="lineno"><a class="code" href="structfolden.html"> 442</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>node {</div>
+<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keywordtype">int</span> k;</div>
+<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keywordtype">int</span> energy;</div>
+<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keyword">struct </span>node *next;</div>
+<div class="line"><a name="l00446"></a><span class="lineno"> 446</span> } <a class="code" href="structfolden.html">folden</a>;</div>
+<div class="line"><a name="l00447"></a><span class="lineno"> 447</span> </div>
+<div class="line"><a name="l00451"></a><span class="lineno"><a class="code" href="structsnoopT.html"> 451</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
+<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keywordtype">int</span> u;</div>
+<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  <span class="keywordtype">char</span> *structure;</div>
+<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <span class="keywordtype">float</span> energy;</div>
+<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <span class="keywordtype">float</span> Duplex_El;</div>
+<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="keywordtype">float</span> Duplex_Er;</div>
+<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordtype">float</span> Loop_E;</div>
+<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordtype">float</span> Loop_D;</div>
+<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordtype">float</span> pscd;</div>
+<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keywordtype">float</span> psct;</div>
+<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="keywordtype">float</span> pscg;</div>
+<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordtype">float</span> Duplex_Ol;</div>
+<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordtype">float</span> Duplex_Or;</div>
+<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordtype">float</span> Duplex_Ot;</div>
+<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordtype">float</span> fullStemEnergy;</div>
+<div class="line"><a name="l00468"></a><span class="lineno"> 468</span> } <a class="code" href="structsnoopT.html">snoopT</a>;</div>
+<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div>
+<div class="line"><a name="l00470"></a><span class="lineno"> 470</span> </div>
+<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
+<div class="line"><a name="l00472"></a><span class="lineno"> 472</span> </div>
+<div class="line"><a name="l00473"></a><span class="lineno"> 473</span> </div>
+<div class="line"><a name="l00474"></a><span class="lineno"> 474</span> </div>
+<div class="line"><a name="l00475"></a><span class="lineno"> 475</span> </div>
+<div class="line"><a name="l00476"></a><span class="lineno"> 476</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00477"></a><span class="lineno"> 477</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00478"></a><span class="lineno"> 478</span> <span class="comment">* PKplex data structures</span></div>
+<div class="line"><a name="l00479"></a><span class="lineno"> 479</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00480"></a><span class="lineno"> 480</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00481"></a><span class="lineno"> 481</span> </div>
+<div class="line"><a name="l00485"></a><span class="lineno"><a class="code" href="structdupVar.html"> 485</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structdupVar.html">dupVar</a>{</div>
+<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  <span class="keywordtype">int</span> i;</div>
+<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  <span class="keywordtype">int</span> j;</div>
+<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  <span class="keywordtype">int</span> end;</div>
+<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  <span class="keywordtype">char</span> *pk_helix;</div>
+<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  <span class="keywordtype">char</span> *structure;</div>
+<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <span class="keywordtype">double</span> energy;</div>
+<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="keywordtype">int</span> offset;</div>
+<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  <span class="keywordtype">double</span> dG1;</div>
+<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  <span class="keywordtype">double</span> dG2;</div>
+<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  <span class="keywordtype">double</span> ddG;</div>
+<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  <span class="keywordtype">int</span> tb;</div>
+<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <span class="keywordtype">int</span> te;</div>
+<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <span class="keywordtype">int</span> qb;</div>
+<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="keywordtype">int</span> qe;</div>
+<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordtype">int</span> inactive;</div>
+<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  <span class="keywordtype">int</span> processed;</div>
+<div class="line"><a name="l00502"></a><span class="lineno"> 502</span> } <a class="code" href="structdupVar.html">dupVar</a>;</div>
+<div class="line"><a name="l00503"></a><span class="lineno"> 503</span> </div>
+<div class="line"><a name="l00504"></a><span class="lineno"> 504</span> </div>
+<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> </div>
+<div class="line"><a name="l00506"></a><span class="lineno"> 506</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00508"></a><span class="lineno"> 508</span> <span class="comment">* 2Dfold data structures</span></div>
+<div class="line"><a name="l00509"></a><span class="lineno"> 509</span> <span class="comment">* ############################################################</span></div>
+<div class="line"><a name="l00510"></a><span class="lineno"> 510</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00511"></a><span class="lineno"> 511</span> </div>
+<div class="line"><a name="l00526"></a><span class="lineno"><a class="code" href="structTwoDfold__solution.html"> 526</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00527"></a><span class="lineno"><a class="code" href="structTwoDfold__solution.html#a298767110e07490d361bf7da920fd153"> 527</a></span>  <span class="keywordtype">int</span> <a class="code" href="structTwoDfold__solution.html#a298767110e07490d361bf7da920fd153" title="Distance to first reference.">k</a>; </div>
+<div class="line"><a name="l00528"></a><span class="lineno"><a class="code" href="structTwoDfold__solution.html#a64fb28259cf925c3bba7b8d14592363a"> 528</a></span>  <span class="keywordtype">int</span> <a class="code" href="structTwoDfold__solution.html#a64fb28259cf925c3bba7b8d14592363a" title="Distance to second reference.">l</a>; </div>
+<div class="line"><a name="l00529"></a><span class="lineno"><a class="code" href="structTwoDfold__solution.html#a3f65891d0c931f88440150bb32bcf753"> 529</a></span>  <span class="keywordtype">float</span> <a class="code" href="structTwoDfold__solution.html#a3f65891d0c931f88440150bb32bcf753" title="Free energy in kcal/mol.">en</a>; </div>
+<div class="line"><a name="l00530"></a><span class="lineno"><a class="code" href="structTwoDfold__solution.html#ac87e00bbdb13e0b6ef45c4f65608b416"> 530</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structTwoDfold__solution.html#ac87e00bbdb13e0b6ef45c4f65608b416" title="MFE representative structure in dot-bracket notation.">s</a>; </div>
+<div class="line"><a name="l00531"></a><span class="lineno"> 531</span> } <a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a>;</div>
+<div class="line"><a name="l00532"></a><span class="lineno"> 532</span> </div>
+<div class="line"><a name="l00538"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html"> 538</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00539"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#ada74adef5f24b4b35c0b25da8223fe26"> 539</a></span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *<a class="code" href="structTwoDfold__vars.html#ada74adef5f24b4b35c0b25da8223fe26" title="Precomputed energy parameters and model details.">P</a>; </div>
+<div class="line"><a name="l00540"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#ade5c7e9337a458ae20bac75abdc52d64"> 540</a></span>  <span class="keywordtype">int</span> <a class="code" href="structTwoDfold__vars.html#ade5c7e9337a458ae20bac75abdc52d64" title="Flag whether to do backtracing of the structure(s) or not.">do_backtrack</a>; </div>
+<div class="line"><a name="l00541"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#aedf60b8b26dae05ad266d3e098d18208"> 541</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structTwoDfold__vars.html#aedf60b8b26dae05ad266d3e098d18208" title="Precomputed array of pair types.">ptype</a>; </div>
+<div class="line"><a name="l00542"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a3596f3d4d320318c4b8428e2abc7ab56"> 542</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structTwoDfold__vars.html#a3596f3d4d320318c4b8428e2abc7ab56" title="The input sequence.">sequence</a>; </div>
+<div class="line"><a name="l00543"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#ab9ee459ffbfb5d2c138a033516056cdc"> 543</a></span>  <span class="keywordtype">short</span> *S, *<a class="code" href="structTwoDfold__vars.html#ab9ee459ffbfb5d2c138a033516056cdc" title="The input sequences in numeric form.">S1</a>; </div>
+<div class="line"><a name="l00544"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a621ed2ab02116f3f8f5e7120dec429eb"> 544</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="structTwoDfold__vars.html#a621ed2ab02116f3f8f5e7120dec429eb" title="Maximum allowed base pair distance to first reference.">maxD1</a>; </div>
+<div class="line"><a name="l00545"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a03f198a4abdb3b784486d2ba5c533aa4"> 545</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="structTwoDfold__vars.html#a03f198a4abdb3b784486d2ba5c533aa4" title="Maximum allowed base pair distance to second reference.">maxD2</a>; </div>
+<div class="line"><a name="l00548"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#aa11f5bcd8c4fe70a91c155c877c855d5"> 548</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#aa11f5bcd8c4fe70a91c155c877c855d5" title="Maximum matching matrix, reference struct 1 disallowed.">mm1</a>; </div>
+<div class="line"><a name="l00549"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a2eaa93316b6beb17531f0c078806036c"> 549</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#a2eaa93316b6beb17531f0c078806036c" title="Maximum matching matrix, reference struct 2 disallowed.">mm2</a>; </div>
+<div class="line"><a name="l00551"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a1a20cb06b58b75d1a3dbdbc8bc60d0a7"> 551</a></span>  <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#a1a20cb06b58b75d1a3dbdbc8bc60d0a7" title="Index for moving in quadratic distancy dimensions.">my_iindx</a>; </div>
+<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  <span class="keywordtype">double</span> <a class="code" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a>;</div>
+<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> </div>
+<div class="line"><a name="l00555"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#a536525b98c1b633d4c5f2da4f8d78c18"> 555</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#a536525b98c1b633d4c5f2da4f8d78c18" title="Matrix containing number of basepairs of reference structure1 in interval [i,j].">referenceBPs1</a>; </div>
+<div class="line"><a name="l00556"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#aa7abf73c3114cb5f0dc90e702fa9dd0f"> 556</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#aa7abf73c3114cb5f0dc90e702fa9dd0f" title="Matrix containing number of basepairs of reference structure2 in interval [i,j].">referenceBPs2</a>; </div>
+<div class="line"><a name="l00557"></a><span class="lineno"><a class="code" href="structTwoDfold__vars.html#af1106e1a592e2dccc92b3452340549e0"> 557</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDfold__vars.html#af1106e1a592e2dccc92b3452340549e0" title="Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].">bpdist</a>; </div>
+<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <span class="keywordtype">short</span> *reference_pt1;</div>
+<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <span class="keywordtype">short</span> *reference_pt2;</div>
+<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111" title="backward compatibility variable.. this does not effect anything">circ</a>;</div>
+<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a>;</div>
+<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> seq_length;</div>
+<div class="line"><a name="l00564"></a><span class="lineno"> 564</span> </div>
+<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  <span class="keywordtype">int</span> ***E_F5;</div>
+<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  <span class="keywordtype">int</span> ***E_F3;</div>
+<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <span class="keywordtype">int</span> ***E_C;</div>
+<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  <span class="keywordtype">int</span> ***E_M;</div>
+<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  <span class="keywordtype">int</span> ***E_M1;</div>
+<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  <span class="keywordtype">int</span> ***E_M2;</div>
+<div class="line"><a name="l00571"></a><span class="lineno"> 571</span> </div>
+<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  <span class="keywordtype">int</span> **E_Fc;</div>
+<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <span class="keywordtype">int</span> **E_FcH;</div>
+<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  <span class="keywordtype">int</span> **E_FcI;</div>
+<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  <span class="keywordtype">int</span> **E_FcM;</div>
+<div class="line"><a name="l00576"></a><span class="lineno"> 576</span> </div>
+<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <span class="keywordtype">int</span> **l_min_values;</div>
+<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <span class="keywordtype">int</span> **l_max_values;</div>
+<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <span class="keywordtype">int</span> *k_min_values;</div>
+<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordtype">int</span> *k_max_values;</div>
+<div class="line"><a name="l00581"></a><span class="lineno"> 581</span> </div>
+<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  <span class="keywordtype">int</span> **l_min_values_m;</div>
+<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  <span class="keywordtype">int</span> **l_max_values_m;</div>
+<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordtype">int</span> *k_min_values_m;</div>
+<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <span class="keywordtype">int</span> *k_max_values_m;</div>
+<div class="line"><a name="l00586"></a><span class="lineno"> 586</span> </div>
+<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  <span class="keywordtype">int</span> **l_min_values_m1;</div>
+<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="keywordtype">int</span> **l_max_values_m1;</div>
+<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  <span class="keywordtype">int</span> *k_min_values_m1;</div>
+<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="keywordtype">int</span> *k_max_values_m1;</div>
+<div class="line"><a name="l00591"></a><span class="lineno"> 591</span> </div>
+<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  <span class="keywordtype">int</span> **l_min_values_f;</div>
+<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  <span class="keywordtype">int</span> **l_max_values_f;</div>
+<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  <span class="keywordtype">int</span> *k_min_values_f;</div>
+<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  <span class="keywordtype">int</span> *k_max_values_f;</div>
+<div class="line"><a name="l00596"></a><span class="lineno"> 596</span> </div>
+<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keywordtype">int</span> **l_min_values_f3;</div>
+<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <span class="keywordtype">int</span> **l_max_values_f3;</div>
+<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="keywordtype">int</span> *k_min_values_f3;</div>
+<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <span class="keywordtype">int</span> *k_max_values_f3;</div>
+<div class="line"><a name="l00601"></a><span class="lineno"> 601</span> </div>
+<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  <span class="keywordtype">int</span> **l_min_values_m2;</div>
+<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordtype">int</span> **l_max_values_m2;</div>
+<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  <span class="keywordtype">int</span> *k_min_values_m2;</div>
+<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <span class="keywordtype">int</span> *k_max_values_m2;</div>
+<div class="line"><a name="l00606"></a><span class="lineno"> 606</span> </div>
+<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  <span class="keywordtype">int</span> *l_min_values_fc;</div>
+<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  <span class="keywordtype">int</span> *l_max_values_fc;</div>
+<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="keywordtype">int</span> k_min_values_fc;</div>
+<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keywordtype">int</span> k_max_values_fc;</div>
+<div class="line"><a name="l00611"></a><span class="lineno"> 611</span> </div>
+<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  <span class="keywordtype">int</span> *l_min_values_fcH;</div>
+<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  <span class="keywordtype">int</span> *l_max_values_fcH;</div>
+<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  <span class="keywordtype">int</span> k_min_values_fcH;</div>
+<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  <span class="keywordtype">int</span> k_max_values_fcH;</div>
+<div class="line"><a name="l00616"></a><span class="lineno"> 616</span> </div>
+<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  <span class="keywordtype">int</span> *l_min_values_fcI;</div>
+<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  <span class="keywordtype">int</span> *l_max_values_fcI;</div>
+<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  <span class="keywordtype">int</span> k_min_values_fcI;</div>
+<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  <span class="keywordtype">int</span> k_max_values_fcI;</div>
+<div class="line"><a name="l00621"></a><span class="lineno"> 621</span> </div>
+<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  <span class="keywordtype">int</span> *l_min_values_fcM;</div>
+<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  <span class="keywordtype">int</span> *l_max_values_fcM;</div>
+<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  <span class="keywordtype">int</span> k_min_values_fcM;</div>
+<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordtype">int</span> k_max_values_fcM;</div>
+<div class="line"><a name="l00626"></a><span class="lineno"> 626</span> </div>
+<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  <span class="comment">/* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */</span></div>
+<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  <span class="keywordtype">int</span> *E_F5_rem;</div>
+<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  <span class="keywordtype">int</span> *E_F3_rem;</div>
+<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  <span class="keywordtype">int</span> *E_C_rem;</div>
+<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  <span class="keywordtype">int</span> *E_M_rem;</div>
+<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <span class="keywordtype">int</span> *E_M1_rem;</div>
+<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  <span class="keywordtype">int</span> *E_M2_rem;</div>
+<div class="line"><a name="l00634"></a><span class="lineno"> 634</span> </div>
+<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  <span class="keywordtype">int</span> E_Fc_rem;</div>
+<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  <span class="keywordtype">int</span> E_FcH_rem;</div>
+<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  <span class="keywordtype">int</span> E_FcI_rem;</div>
+<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  <span class="keywordtype">int</span> E_FcM_rem;</div>
+<div class="line"><a name="l00639"></a><span class="lineno"> 639</span> </div>
+<div class="line"><a name="l00640"></a><span class="lineno"> 640</span> <span class="preprocessor">#ifdef COUNT_STATES</span></div>
+<div class="line"><a name="l00641"></a><span class="lineno"> 641</span> <span class="preprocessor"></span> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> ***N_F5;</div>
+<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> ***N_C;</div>
+<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> ***N_M;</div>
+<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> ***N_M1;</div>
+<div class="line"><a name="l00645"></a><span class="lineno"> 645</span> <span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00646"></a><span class="lineno"> 646</span> <span class="preprocessor"></span>} <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a>;</div>
+<div class="line"><a name="l00647"></a><span class="lineno"> 647</span> </div>
+<div class="line"><a name="l00660"></a><span class="lineno"><a class="code" href="structTwoDpfold__solution.html"> 660</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00661"></a><span class="lineno"><a class="code" href="structTwoDpfold__solution.html#a40ad24e311b193866111623dd1331567"> 661</a></span>  <span class="keywordtype">int</span> <a class="code" href="structTwoDpfold__solution.html#a40ad24e311b193866111623dd1331567" title="Distance to first reference.">k</a>; </div>
+<div class="line"><a name="l00662"></a><span class="lineno"><a class="code" href="structTwoDpfold__solution.html#aeaad6adc35413c76a2e2f18d96a6508c"> 662</a></span>  <span class="keywordtype">int</span> <a class="code" href="structTwoDpfold__solution.html#aeaad6adc35413c76a2e2f18d96a6508c" title="Distance to second reference.">l</a>; </div>
+<div class="line"><a name="l00663"></a><span class="lineno"><a class="code" href="structTwoDpfold__solution.html#af0bf3071502b4a4fa81eeb6dfacef94c"> 663</a></span>  FLT_OR_DBL <a class="code" href="structTwoDpfold__solution.html#af0bf3071502b4a4fa81eeb6dfacef94c" title="partition function">q</a>; </div>
+<div class="line"><a name="l00664"></a><span class="lineno"> 664</span> } <a class="code" href="structTwoDpfold__solution.html" title="Solution element returned from TwoDpfoldList.">TwoDpfold_solution</a>;</div>
+<div class="line"><a name="l00665"></a><span class="lineno"> 665</span> </div>
+<div class="line"><a name="l00672"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html"> 672</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span>{</div>
+<div class="line"><a name="l00673"></a><span class="lineno"> 673</span> </div>
+<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> alloc;</div>
+<div class="line"><a name="l00675"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a67f37b8901b8d0a049c216d4c6241b07"> 675</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structTwoDpfold__vars.html#a67f37b8901b8d0a049c216d4c6241b07" title="Precomputed array of pair types.">ptype</a>; </div>
+<div class="line"><a name="l00676"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a32c15a1e31856588259556c9020f32c6"> 676</a></span>  <span class="keywordtype">char</span> *<a class="code" href="structTwoDpfold__vars.html#a32c15a1e31856588259556c9020f32c6" title="The input sequence.">sequence</a>; </div>
+<div class="line"><a name="l00677"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a240311ae1e8e121441651d6101e187ac"> 677</a></span>  <span class="keywordtype">short</span> *S, *<a class="code" href="structTwoDpfold__vars.html#a240311ae1e8e121441651d6101e187ac" title="The input sequences in numeric form.">S1</a>; </div>
+<div class="line"><a name="l00678"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a7292b6cbc1ee5bacf55e842f316c4bef"> 678</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="structTwoDpfold__vars.html#a7292b6cbc1ee5bacf55e842f316c4bef" title="Maximum allowed base pair distance to first reference.">maxD1</a>; </div>
+<div class="line"><a name="l00679"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a8900622d91454d2d037242e290e42834"> 679</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="structTwoDpfold__vars.html#a8900622d91454d2d037242e290e42834" title="Maximum allowed base pair distance to second reference.">maxD2</a>; </div>
+<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  <span class="keywordtype">double</span> <a class="code" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a>; <span class="comment">/* temperature in last call to scale_pf_params */</span></div>
+<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  <span class="keywordtype">double</span> init_temp; <span class="comment">/* temperature in last call to scale_pf_params */</span></div>
+<div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  FLT_OR_DBL *scale;</div>
+<div class="line"><a name="l00684"></a><span class="lineno"> 684</span>  FLT_OR_DBL <a class="code" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a>;</div>
+<div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *pf_params; <span class="comment">/* holds all [unscaled] pf parameters */</span></div>
+<div class="line"><a name="l00686"></a><span class="lineno"> 686</span> </div>
+<div class="line"><a name="l00687"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#ac2d3e6abf0cb0e1df363904fc938076e"> 687</a></span>  <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#ac2d3e6abf0cb0e1df363904fc938076e" title="Index for moving in quadratic distancy dimensions.">my_iindx</a>; </div>
+<div class="line"><a name="l00688"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a0699e194a797532c91b284ab10272384"> 688</a></span>  <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#a0699e194a797532c91b284ab10272384" title="Index for moving in the triangular matrix qm1.">jindx</a>; </div>
+<div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  <span class="keywordtype">short</span> *reference_pt1;</div>
+<div class="line"><a name="l00691"></a><span class="lineno"> 691</span>  <span class="keywordtype">short</span> *reference_pt2;</div>
+<div class="line"><a name="l00692"></a><span class="lineno"> 692</span> </div>
+<div class="line"><a name="l00693"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#aea15706d27b6b0fc19f5773919f43a8a"> 693</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#aea15706d27b6b0fc19f5773919f43a8a" title="Matrix containing number of basepairs of reference structure1 in interval [i,j].">referenceBPs1</a>; </div>
+<div class="line"><a name="l00694"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a1221396d712bf76b7f35297f2ab35a9f"> 694</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#a1221396d712bf76b7f35297f2ab35a9f" title="Matrix containing number of basepairs of reference structure2 in interval [i,j].">referenceBPs2</a>; </div>
+<div class="line"><a name="l00695"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#accef8eaa05fa57ca33aa22cbc7b7aaff"> 695</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#accef8eaa05fa57ca33aa22cbc7b7aaff" title="Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].">bpdist</a>; </div>
+<div class="line"><a name="l00697"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#a7c9e9af6224d4696118e05835441863d"> 697</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#a7c9e9af6224d4696118e05835441863d" title="Maximum matching matrix, reference struct 1 disallowed.">mm1</a>; </div>
+<div class="line"><a name="l00698"></a><span class="lineno"><a class="code" href="structTwoDpfold__vars.html#affb913470783f9edb12a0bfc22466269"> 698</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> *<a class="code" href="structTwoDpfold__vars.html#affb913470783f9edb12a0bfc22466269" title="Maximum matching matrix, reference struct 2 disallowed.">mm2</a>; </div>
+<div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111" title="backward compatibility variable.. this does not effect anything">circ</a>;</div>
+<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a>;</div>
+<div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> seq_length;</div>
+<div class="line"><a name="l00703"></a><span class="lineno"> 703</span> </div>
+<div class="line"><a name="l00704"></a><span class="lineno"> 704</span>  FLT_OR_DBL ***Q;</div>
+<div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  FLT_OR_DBL ***Q_B;</div>
+<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  FLT_OR_DBL ***Q_M;</div>
+<div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  FLT_OR_DBL ***Q_M1;</div>
+<div class="line"><a name="l00708"></a><span class="lineno"> 708</span>  FLT_OR_DBL ***Q_M2;</div>
+<div class="line"><a name="l00709"></a><span class="lineno"> 709</span> </div>
+<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  FLT_OR_DBL **Q_c;</div>
+<div class="line"><a name="l00711"></a><span class="lineno"> 711</span>  FLT_OR_DBL **Q_cH;</div>
+<div class="line"><a name="l00712"></a><span class="lineno"> 712</span>  FLT_OR_DBL **Q_cI;</div>
+<div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  FLT_OR_DBL **Q_cM;</div>
+<div class="line"><a name="l00714"></a><span class="lineno"> 714</span> </div>
+<div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  <span class="keywordtype">int</span> **l_min_values;</div>
+<div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  <span class="keywordtype">int</span> **l_max_values;</div>
+<div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  <span class="keywordtype">int</span> *k_min_values;</div>
+<div class="line"><a name="l00718"></a><span class="lineno"> 718</span>  <span class="keywordtype">int</span> *k_max_values;</div>
+<div class="line"><a name="l00719"></a><span class="lineno"> 719</span> </div>
+<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  <span class="keywordtype">int</span> **l_min_values_b;</div>
+<div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  <span class="keywordtype">int</span> **l_max_values_b;</div>
+<div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  <span class="keywordtype">int</span> *k_min_values_b;</div>
+<div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  <span class="keywordtype">int</span> *k_max_values_b;</div>
+<div class="line"><a name="l00724"></a><span class="lineno"> 724</span> </div>
+<div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  <span class="keywordtype">int</span> **l_min_values_m;</div>
+<div class="line"><a name="l00726"></a><span class="lineno"> 726</span>  <span class="keywordtype">int</span> **l_max_values_m;</div>
+<div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <span class="keywordtype">int</span> *k_min_values_m;</div>
+<div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  <span class="keywordtype">int</span> *k_max_values_m;</div>
+<div class="line"><a name="l00729"></a><span class="lineno"> 729</span> </div>
+<div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  <span class="keywordtype">int</span> **l_min_values_m1;</div>
+<div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  <span class="keywordtype">int</span> **l_max_values_m1;</div>
+<div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  <span class="keywordtype">int</span> *k_min_values_m1;</div>
+<div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  <span class="keywordtype">int</span> *k_max_values_m1;</div>
+<div class="line"><a name="l00734"></a><span class="lineno"> 734</span> </div>
+<div class="line"><a name="l00735"></a><span class="lineno"> 735</span>  <span class="keywordtype">int</span> **l_min_values_m2;</div>
+<div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  <span class="keywordtype">int</span> **l_max_values_m2;</div>
+<div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  <span class="keywordtype">int</span> *k_min_values_m2;</div>
+<div class="line"><a name="l00738"></a><span class="lineno"> 738</span>  <span class="keywordtype">int</span> *k_max_values_m2;</div>
+<div class="line"><a name="l00739"></a><span class="lineno"> 739</span> </div>
+<div class="line"><a name="l00740"></a><span class="lineno"> 740</span>  <span class="keywordtype">int</span> *l_min_values_qc;</div>
+<div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  <span class="keywordtype">int</span> *l_max_values_qc;</div>
+<div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  <span class="keywordtype">int</span> k_min_values_qc;</div>
+<div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  <span class="keywordtype">int</span> k_max_values_qc;</div>
+<div class="line"><a name="l00744"></a><span class="lineno"> 744</span> </div>
+<div class="line"><a name="l00745"></a><span class="lineno"> 745</span>  <span class="keywordtype">int</span> *l_min_values_qcH;</div>
+<div class="line"><a name="l00746"></a><span class="lineno"> 746</span>  <span class="keywordtype">int</span> *l_max_values_qcH;</div>
+<div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  <span class="keywordtype">int</span> k_min_values_qcH;</div>
+<div class="line"><a name="l00748"></a><span class="lineno"> 748</span>  <span class="keywordtype">int</span> k_max_values_qcH;</div>
+<div class="line"><a name="l00749"></a><span class="lineno"> 749</span> </div>
+<div class="line"><a name="l00750"></a><span class="lineno"> 750</span>  <span class="keywordtype">int</span> *l_min_values_qcI;</div>
+<div class="line"><a name="l00751"></a><span class="lineno"> 751</span>  <span class="keywordtype">int</span> *l_max_values_qcI;</div>
+<div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  <span class="keywordtype">int</span> k_min_values_qcI;</div>
+<div class="line"><a name="l00753"></a><span class="lineno"> 753</span>  <span class="keywordtype">int</span> k_max_values_qcI;</div>
+<div class="line"><a name="l00754"></a><span class="lineno"> 754</span> </div>
+<div class="line"><a name="l00755"></a><span class="lineno"> 755</span>  <span class="keywordtype">int</span> *l_min_values_qcM;</div>
+<div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  <span class="keywordtype">int</span> *l_max_values_qcM;</div>
+<div class="line"><a name="l00757"></a><span class="lineno"> 757</span>  <span class="keywordtype">int</span> k_min_values_qcM;</div>
+<div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  <span class="keywordtype">int</span> k_max_values_qcM;</div>
+<div class="line"><a name="l00759"></a><span class="lineno"> 759</span> </div>
+<div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  <span class="comment">/* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */</span></div>
+<div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  FLT_OR_DBL *Q_rem;</div>
+<div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  FLT_OR_DBL *Q_B_rem;</div>
+<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  FLT_OR_DBL *Q_M_rem;</div>
+<div class="line"><a name="l00764"></a><span class="lineno"> 764</span>  FLT_OR_DBL *Q_M1_rem;</div>
+<div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  FLT_OR_DBL *Q_M2_rem;</div>
+<div class="line"><a name="l00766"></a><span class="lineno"> 766</span> </div>
+<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  FLT_OR_DBL Q_c_rem;</div>
+<div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  FLT_OR_DBL Q_cH_rem;</div>
+<div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  FLT_OR_DBL Q_cI_rem;</div>
+<div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  FLT_OR_DBL Q_cM_rem;</div>
+<div class="line"><a name="l00771"></a><span class="lineno"> 771</span> </div>
+<div class="line"><a name="l00772"></a><span class="lineno"> 772</span> } <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a>;</div>
+<div class="line"><a name="l00773"></a><span class="lineno"> 773</span> </div>
+<div class="line"><a name="l00774"></a><span class="lineno"> 774</span> <span class="preprocessor">#endif</span></div>
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