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-<div class="title">fold_vars.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="fold__vars_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_FOLD_VARS_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_FOLD_VARS_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="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>"</span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div>
-<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#define PUBLIC</span></div>
-<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor"></span><span class="preprocessor">#define PRIVATE static</span></div>
-<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a0afc287c2464866d94858c39175154af" title="Global switch to activate/deactivate folding with structure constraints.">fold_constrained</a>;</div>
-<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div>
-<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a097eccaabd6ae8b4fef83cccff85bb5d" title="Global switch to avoid/allow helices of length 1.">noLonelyPairs</a>;</div>
-<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div>
-<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="keyword">extern</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="l00051"></a><span class="lineno"> 51</span> </div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#abf380d09e4f1ab94fc6af57cf0ad5d32" title="Global switch to forbid/allow GU base pairs at all.">noGU</a>;</div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div>
-<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#aa8d1c7b92489179e1eafa562b7bdd259" title="GU allowed only inside stacks if set to 1.">no_closingGU</a>;</div>
-<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
-<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a4f6265bdf0ead7ff4628a360adbfd77e" title="Include special stabilizing energies for some tri-, tetra- and hexa-loops;.">tetra_loop</a>;</div>
-<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
-<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#afb1ef1166da85092ae8a325e02dcae71" title="0 = BP; 1=any mit GC; 2=any mit AU-parameter">energy_set</a>;</div>
-<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
-<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">extern</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="l00082"></a><span class="lineno"> 82</span> </div>
-<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af2763d55a74663a5e60652b8880baa5b" title="generate comma seperated output">csv</a>;</div>
-<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
-<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#ac408868ba00671cbc7d1d535105af045">oldAliEn</a>;</div>
-<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a0656afca1d2853f9ee6591172f5638de">ribo</a>; </div>
-<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="keyword">extern</span> <span class="keywordtype">char</span> *<a class="code" href="fold__vars_8h.html#a5dbaa0cca2c8c82048a0f0e38e164944">RibosumFile</a>; </div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
-<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="keyword">extern</span> <span class="keywordtype">char</span> *<a class="code" href="fold__vars_8h.html#a2695d91cc535d09c2eae5c3884e2ec64" title="contains allowed non standard base pairs">nonstandards</a>;</div>
-<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
-<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="keyword">extern</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="l00119"></a><span class="lineno"> 119</span> </div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af349001ad3b4d008d0051d935b1b6261">james_rule</a>;</div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743" title="if nonzero use logarithmic ML energy in energy_of_struct">logML</a>;</div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
-<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="set to first pos of second seq for cofolding">cut_point</a>;</div>
-<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div>
-<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="keyword">extern</span> <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *<a class="code" href="fold__vars_8h.html#a0244a629b5ab4f58b77590c3dfd130dc" title="Contains a list of base pairs after a call to fold().">base_pair</a>;</div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
-<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="keyword">extern</span> FLT_OR_DBL *<a class="code" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52" title="A pointer to the base pair probability matrix.">pr</a>;</div>
-<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
-<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> *<a class="code" href="fold__vars_8h.html#a92089ae3a51b5d75a14ce9cc29cc8317" title="index array to move through pr.">iindx</a>;</div>
-<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
-<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <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="l00179"></a><span class="lineno"> 179</span> </div>
-<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#ad512b5dd4dbec60faccfe137bb474489" title="do backtracking, i.e. compute secondary structures or base pair probabilities">do_backtrack</a>;</div>
-<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
-<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> <span class="keyword">extern</span> <span class="keywordtype">char</span> <a class="code" href="fold__vars_8h.html#a83bdb43472a259c71e69fa9f70f420c3" title="A backtrack array marker for inverse_fold()">backtrack_type</a>;</div>
-<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
-<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a25f2bdcdf56e813d288845484a13d704" title="Allow G-quadruplex formation.">gquad</a>;</div>
-<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> </div>
-<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
-<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="keywordtype">char</span> * option_string(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
-<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="keywordtype">void</span> <a class="code" href="fold__vars_8h.html#a4c3257186a796182462f18a5480ac8b3" title="Set default model details.">set_model_details</a>(<a class="code" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations.">model_detailsT</a> *md);</div>
-<div class="line"><a name="l00216"></a><span class="lineno"> 216</span> </div>
-<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> <span class="preprocessor">#endif</span></div>
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- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="fold__vars_8h.html">fold_vars.h</a></li>
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- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold_vars.h</h1><a href="fold__vars_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00004"></a>00004 <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found...">data_structures.h</a>"</span>
+<a name="l00005"></a>00005
+<a name="l00012"></a>00012 <span class="preprocessor">#define PUBLIC</span>
+<a name="l00013"></a>00013 <span class="preprocessor"></span><span class="preprocessor">#define PRIVATE static</span>
+<a name="l00014"></a>00014 <span class="preprocessor"></span>
+<a name="l00018"></a>00018 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a0afc287c2464866d94858c39175154af" title="Global switch to activate/deactivate folding with structure constraints.">fold_constrained</a>;
+<a name="l00019"></a>00019
+<a name="l00027"></a>00027 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a097eccaabd6ae8b4fef83cccff85bb5d" title="Global switch to avoid/allow helices of length 1.">noLonelyPairs</a>;
+<a name="l00028"></a>00028
+<a name="l00050"></a>00050 <span class="keyword">extern</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>;
+<a name="l00051"></a>00051
+<a name="l00055"></a>00055 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#abf380d09e4f1ab94fc6af57cf0ad5d32" title="Global switch to forbid/allow GU base pairs at all.">noGU</a>;
+<a name="l00056"></a>00056
+<a name="l00060"></a>00060 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#aa8d1c7b92489179e1eafa562b7bdd259" title="GU allowed only inside stacks if set to 1.">no_closingGU</a>;
+<a name="l00061"></a>00061
+<a name="l00067"></a>00067 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a4f6265bdf0ead7ff4628a360adbfd77e" title="Include special stabilizing energies for some tri-, tetra- and hexa-loops;.">tetra_loop</a>;
+<a name="l00068"></a>00068
+<a name="l00076"></a>00076 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#afb1ef1166da85092ae8a325e02dcae71" title="0 = BP; 1=any mit GC; 2=any mit AU-parameter">energy_set</a>;
+<a name="l00077"></a>00077
+<a name="l00081"></a>00081 <span class="keyword">extern</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>;
+<a name="l00082"></a>00082
+<a name="l00086"></a>00086 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af2763d55a74663a5e60652b8880baa5b" title="generate comma seperated output">csv</a>;
+<a name="l00087"></a>00087
+<a name="l00091"></a>00091 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#ac408868ba00671cbc7d1d535105af045">oldAliEn</a>;
+<a name="l00095"></a>00095 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a0656afca1d2853f9ee6591172f5638de">ribo</a>;
+<a name="l00096"></a>00096
+<a name="l00101"></a>00101 <span class="keyword">extern</span> <span class="keywordtype">char</span> *<a class="code" href="fold__vars_8h.html#a5dbaa0cca2c8c82048a0f0e38e164944">RibosumFile</a>;
+<a name="l00102"></a>00102
+<a name="l00110"></a>00110 <span class="keyword">extern</span> <span class="keywordtype">char</span> *<a class="code" href="fold__vars_8h.html#a2695d91cc535d09c2eae5c3884e2ec64" title="contains allowed non standard base pairs">nonstandards</a>;
+<a name="l00111"></a>00111
+<a name="l00118"></a>00118 <span class="keyword">extern</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>;
+<a name="l00119"></a>00119
+<a name="l00124"></a>00124 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#af349001ad3b4d008d0051d935b1b6261">james_rule</a>;
+<a name="l00125"></a>00125
+<a name="l00129"></a>00129 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743" title="if nonzero use logarithmic ML energy in energy_of_struct">logML</a>;
+<a name="l00130"></a>00130
+<a name="l00142"></a>00142 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="set to first pos of second seq for cofolding">cut_point</a>;
+<a name="l00143"></a>00143
+<a name="l00150"></a>00150 <span class="keyword">extern</span> <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *<a class="code" href="fold__vars_8h.html#a0244a629b5ab4f58b77590c3dfd130dc" title="Contains a list of base pairs after a call to fold().">base_pair</a>;
+<a name="l00151"></a>00151
+<a name="l00157"></a>00157 <span class="keyword">extern</span> FLT_OR_DBL *<a class="code" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52" title="A pointer to the base pair probability matrix.">pr</a>;
+<a name="l00158"></a>00158
+<a name="l00165"></a>00165 <span class="keyword">extern</span> <span class="keywordtype">int</span> *<a class="code" href="fold__vars_8h.html#a92089ae3a51b5d75a14ce9cc29cc8317" title="index array to move through pr.">iindx</a>;
+<a name="l00166"></a>00166
+<a name="l00178"></a>00178 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a>;
+<a name="l00179"></a>00179
+<a name="l00186"></a>00186 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#ad512b5dd4dbec60faccfe137bb474489" title="do backtracking, i.e. compute secondary structures or base pair probabilities">do_backtrack</a>;
+<a name="l00187"></a>00187
+<a name="l00195"></a>00195 <span class="keyword">extern</span> <span class="keywordtype">char</span> <a class="code" href="fold__vars_8h.html#a83bdb43472a259c71e69fa9f70f420c3" title="A backtrack array marker for inverse_fold().">backtrack_type</a>;
+<a name="l00196"></a>00196
+<a name="l00200"></a>00200 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold__vars_8h.html#a25f2bdcdf56e813d288845484a13d704" title="Allow G-quadruplex formation.">gquad</a>;
+<a name="l00201"></a>00201
+<a name="l00202"></a>00202
+<a name="l00203"></a>00203 <span class="keywordtype">char</span> * option_string(<span class="keywordtype">void</span>);
+<a name="l00204"></a>00204
+<a name="l00215"></a>00215 <span class="keywordtype">void</span> <a class="code" href="fold__vars_8h.html#a4c3257186a796182462f18a5480ac8b3" title="Set default model details.">set_model_details</a>(<a class="code" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations...">model_detailsT</a> *md);
+<a name="l00216"></a>00216
+<a name="l00217"></a>00217 <span class="preprocessor">#endif</span>
+</pre></div></div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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