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+<div class="title">params.h</div> </div>
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+<div class="contents">
+<a href="params_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_PARAMS_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_PARAMS_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="l00005"></a><span class="lineno"> 5</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="l00006"></a><span class="lineno"> 6</span> </div>
+<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
+<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
+<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
+<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *<a class="code" href="group__energy__parameters.html#ga527ef619cd8210b84d5d53be1e0e29b6" title="Get precomputed energy contributions for all the known loop types.">scale_parameters</a>(<span class="keywordtype">void</span>);</div>
+<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div>
+<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *<a class="code" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters</a>(<span class="keywordtype">double</span> temperature,</div>
+<div class="line"><a name="l00053"></a><span class="lineno"> 53</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> md);</div>
+<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
+<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *get_parameter_copy(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *par);</div>
+<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div>
+<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gab85f6b6da051f380371deb0d8921bdba">get_scaled_pf_parameters</a>(<span class="keywordtype">void</span>);</div>
+<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
+<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...">get_boltzmann_factors</a>( <span class="keywordtype">double</span> temperature,</div>
+<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordtype">double</span> betaScale,</div>
+<div class="line"><a name="l00090"></a><span class="lineno"> 90</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> md,</div>
+<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">double</span> pf_scale);</div>
+<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
+<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gacba212326a051734797e65987260fdd0" title="Get a copy of already precomputed Boltzmann factors.">get_boltzmann_factor_copy</a>(<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="l00102"></a><span class="lineno"> 102</span> </div>
+<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gaa6a4297a2b91d6f7ae47dd61ca1862a0" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant)...">get_scaled_alipf_parameters</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq);</div>
+<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
+<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> PUBLIC <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gaaa049a8c9f1c2ed4398cb1b5a3d65a66" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) w...">get_boltzmann_factors_ali</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq,</div>
+<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordtype">double</span> temperature,</div>
+<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordtype">double</span> betaScale,</div>
+<div class="line"><a name="l00119"></a><span class="lineno"> 119</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> md,</div>
+<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">double</span> pf_scale);</div>
+<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
+<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> DEPRECATED(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *copy_parameters(<span class="keywordtype">void</span>));</div>
+<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> DEPRECATED(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *set_parameters(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *dest));</div>
+<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *scale_pf_parameters(<span class="keywordtype">void</span>));</div>
+<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *copy_pf_param(<span class="keywordtype">void</span>));</div>
+<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *set_pf_param(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *dest));</div>
+<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
+<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> </div>
+<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
+<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="preprocessor">#endif</span></div>
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