binaries/src/ViennaRNA/doc/html/params_8h_source.html

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  68 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h</h1><a href="params_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_PARAMS_H__</span>
  69 <a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_PARAMS_H__</span>
  70 <a name="l00003"></a>00003 <span class="preprocessor"></span>
  71 <a name="l00004"></a>00004 <span class="preprocessor">#include &quot;<a class="code" href="energy__const_8h.html">energy_const.h</a>&quot;</span>
  72 <a name="l00005"></a>00005 <span class="preprocessor">#include &quot;<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>&quot;</span>
  73 <a name="l00006"></a>00006
  74 <a name="l00007"></a>00007 <span class="preprocessor">#ifdef __GNUC__</span>
  75 <a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span>
  76 <a name="l00009"></a>00009 <span class="preprocessor"></span><span class="preprocessor">#else</span>
  77 <a name="l00010"></a>00010 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span>
  78 <a name="l00011"></a>00011 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
  79 <a name="l00012"></a>00012 <span class="preprocessor"></span>
  80 <a name="l00036"></a>00036 <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>);
  81 <a name="l00037"></a>00037
  82 <a name="l00052"></a>00052 <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,
  83 <a name="l00053"></a>00053                               <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);
  84 <a name="l00054"></a>00054
  85 <a name="l00055"></a>00055 <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);
  86 <a name="l00056"></a>00056
  87 <a name="l00063"></a>00063 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gab85f6b6da051f380371deb0d8921bdba">get_scaled_pf_parameters</a>(<span class="keywordtype">void</span>);
  88 <a name="l00064"></a>00064
  89 <a name="l00088"></a>00088 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions...">get_boltzmann_factors</a>( <span class="keywordtype">double</span> temperature,
  90 <a name="l00089"></a>00089                                   <span class="keywordtype">double</span> betaScale,
  91 <a name="l00090"></a>00090                                   <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,
  92 <a name="l00091"></a>00091                                   <span class="keywordtype">double</span> pf_scale);
  93 <a name="l00092"></a>00092
  94 <a name="l00101"></a>00101 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">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...">pf_paramT</a> *parameters);
  95 <a name="l00102"></a>00102
  96 <a name="l00108"></a>00108 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gaa6a4297a2b91d6f7ae47dd61ca1862a0" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions...">get_scaled_alipf_parameters</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq);
  97 <a name="l00109"></a>00109
  98 <a name="l00116"></a>00116 PUBLIC <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *<a class="code" href="group__energy__parameters.html#gaf0c74574b40f2778556535bf9d382828" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions...">get_boltzmann_factors_ali</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq,
  99 <a name="l00117"></a>00117                                             <span class="keywordtype">double</span> temperature,
 100 <a name="l00118"></a>00118                                             <span class="keywordtype">double</span> betaScale,
 101 <a name="l00119"></a>00119                                             <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,
 102 <a name="l00120"></a>00120                                             <span class="keywordtype">double</span> pf_scale);
 103 <a name="l00121"></a>00121
 104 <a name="l00126"></a>00126 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>));
 105 <a name="l00127"></a>00127 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));
 106 <a name="l00128"></a>00128 DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a>  *scale_pf_parameters(<span class="keywordtype">void</span>));
 107 <a name="l00129"></a>00129 DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a>  *copy_pf_param(<span class="keywordtype">void</span>));
 108 <a name="l00130"></a>00130 DEPRECATED(<a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a>  *set_pf_param(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *dest));
 109 <a name="l00131"></a>00131
 110 <a name="l00132"></a>00132
 111 <a name="l00133"></a>00133
 112 <a name="l00134"></a>00134 <span class="preprocessor">#endif</span>
 113 </pre></div></div>
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