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-<div class="title">part_func_co.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="part__func__co_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_PART_FUNC_CO_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_PART_FUNC_CO_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="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
-<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
-<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
-<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor"></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="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c" title="Toggles no intrabp in 2nd mol.">mirnatog</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">double</span> <a class="code" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe" title="Free energies of the two monomers.">F_monomer</a>[2];</div>
-<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
-<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <a class="code" href="structcofoldF.html">cofoldF</a> <a class="code" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold</a>( <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <a class="code" href="structcofoldF.html">cofoldF</a> <a class="code" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21" title="Calculate partition function and base pair probabilities.">co_pf_fold_par</a>( <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters,</div>
-<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">int</span> calculate_bppm,</div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">int</span> is_constrained);</div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
-<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> FLT_OR_DBL *<a class="code" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c" title="Get a pointer to the base pair probability array.">export_co_bppm</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
-<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247" title="Free the memory occupied by co_pf_fold()">free_co_pf_arrays</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5" title="Recalculate energy parameters.">update_co_pf_params</a>(<span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> </div>
-<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53" title="Recalculate energy parameters.">update_co_pf_params_par</a>(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters);</div>
-<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
-<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617" title="Compute Boltzmann probabilities of dimerization without homodimers.">compute_probabilities</a>(<span class="keywordtype">double</span> FAB,</div>
-<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordtype">double</span> FEA,</div>
-<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordtype">double</span> FEB,</div>
-<div class="line"><a name="l00180"></a><span class="lineno"> 180</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> *prAB,</div>
-<div class="line"><a name="l00181"></a><span class="lineno"> 181</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> *prA,</div>
-<div class="line"><a name="l00182"></a><span class="lineno"> 182</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> *prB,</div>
-<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">int</span> Alength);</div>
-<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div>
-<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <a class="code" href="structConcEnt.html">ConcEnt</a> *<a class="code" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7" title="Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...">get_concentrations</a>(<span class="keywordtype">double</span> FEAB,</div>
-<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordtype">double</span> FEAA,</div>
-<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordtype">double</span> FEBB,</div>
-<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordtype">double</span> FEA,</div>
-<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordtype">double</span> FEB,</div>
-<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordtype">double</span> *startconc);</div>
-<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
-<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div>
-<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00216"></a><span class="lineno"> 216</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> <span class="comment"># DEPRECATED FUNCTIONS #</span></div>
-<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
-<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> DEPRECATED(<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 class="code" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a>( <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> *pl,</div>
-<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordtype">double</span> cut_off));</div>
-<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
-<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> <span class="preprocessor">#endif</span></div>
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- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="part__func__co_8h.html">part_func_co.h</a></li>
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- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_co.h</h1><a href="part__func__co_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_PART_FUNC_CO_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_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="l00006"></a>00006 <span class="preprocessor">#ifdef __GNUC__</span>
+<a name="l00007"></a>00007 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span>
+<a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#else</span>
+<a name="l00009"></a>00009 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span>
+<a name="l00010"></a>00010 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00011"></a>00011 <span class="preprocessor"></span>
+<a name="l00055"></a>00055 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c" title="Toggles no intrabp in 2nd mol.">mirnatog</a>;
+<a name="l00056"></a>00056
+<a name="l00060"></a>00060 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe" title="Free energies of the two monomers.">F_monomer</a>[2];
+<a name="l00061"></a>00061
+<a name="l00080"></a>00080 <a class="code" href="structcofoldF.html">cofoldF</a> <a class="code" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold</a>( <span class="keywordtype">char</span> *sequence,
+<a name="l00081"></a>00081 <span class="keywordtype">char</span> *structure);
+<a name="l00082"></a>00082
+<a name="l00100"></a>00100 <a class="code" href="structcofoldF.html">cofoldF</a> <a class="code" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21" title="Calculate partition function and base pair probabilities.">co_pf_fold_par</a>( <span class="keywordtype">char</span> *sequence,
+<a name="l00101"></a>00101 <span class="keywordtype">char</span> *structure,
+<a name="l00102"></a>00102 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters,
+<a name="l00103"></a>00103 <span class="keywordtype">int</span> calculate_bppm,
+<a name="l00104"></a>00104 <span class="keywordtype">int</span> is_constrained);
+<a name="l00105"></a>00105
+<a name="l00115"></a>00115 FLT_OR_DBL *<a class="code" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c" title="Get a pointer to the base pair probability array.">export_co_bppm</a>(<span class="keywordtype">void</span>);
+<a name="l00116"></a>00116
+<a name="l00120"></a>00120 <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247" title="Free the memory occupied by co_pf_fold().">free_co_pf_arrays</a>(<span class="keywordtype">void</span>);
+<a name="l00121"></a>00121
+<a name="l00136"></a>00136 <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5" title="Recalculate energy parameters.">update_co_pf_params</a>(<span class="keywordtype">int</span> length);
+<a name="l00137"></a>00137
+<a name="l00157"></a>00157 <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53" title="Recalculate energy parameters.">update_co_pf_params_par</a>(<span class="keywordtype">int</span> length,
+<a name="l00158"></a>00158 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
+<a name="l00159"></a>00159
+<a name="l00177"></a>00177 <span class="keywordtype">void</span> <a class="code" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617" title="Compute Boltzmann probabilities of dimerization without homodimers.">compute_probabilities</a>(<span class="keywordtype">double</span> FAB,
+<a name="l00178"></a>00178 <span class="keywordtype">double</span> FEA,
+<a name="l00179"></a>00179 <span class="keywordtype">double</span> FEB,
+<a name="l00180"></a>00180 <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> *prAB,
+<a name="l00181"></a>00181 <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> *prA,
+<a name="l00182"></a>00182 <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> *prB,
+<a name="l00183"></a>00183 <span class="keywordtype">int</span> Alength);
+<a name="l00184"></a>00184
+<a name="l00203"></a>00203 <a class="code" href="structConcEnt.html">ConcEnt</a> *<a class="code" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7" title="Given two start monomer concentrations a and b, compute the concentrations in thermodynamic...">get_concentrations</a>(<span class="keywordtype">double</span> FEAB,
+<a name="l00204"></a>00204 <span class="keywordtype">double</span> FEAA,
+<a name="l00205"></a>00205 <span class="keywordtype">double</span> FEBB,
+<a name="l00206"></a>00206 <span class="keywordtype">double</span> FEA,
+<a name="l00207"></a>00207 <span class="keywordtype">double</span> FEB,
+<a name="l00208"></a>00208 <span class="keywordtype">double</span> *startconc);
+<a name="l00209"></a>00209
+<a name="l00210"></a>00210
+<a name="l00215"></a>00215 <span class="comment">/*</span>
+<a name="l00216"></a>00216 <span class="comment">#################################################</span>
+<a name="l00217"></a>00217 <span class="comment"># DEPRECATED FUNCTIONS #</span>
+<a name="l00218"></a>00218 <span class="comment">#################################################</span>
+<a name="l00219"></a>00219 <span class="comment">*/</span>
+<a name="l00220"></a>00220
+<a name="l00226"></a>00226 DEPRECATED(<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 class="code" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a>( <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> *pl,
+<a name="l00227"></a>00227 <span class="keywordtype">int</span> length,
+<a name="l00228"></a>00228 <span class="keywordtype">double</span> cut_off));
+<a name="l00233"></a>00233 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a>(<span class="keywordtype">int</span> length));
+<a name="l00234"></a>00234
+<a name="l00235"></a>00235 <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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