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+<div class="title">LPfold.h</div> </div>
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+<div class="contents">
+<a href="LPfold_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_LPFOLD_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_LPFOLD_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="l00029"></a><span class="lineno"> 29</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga5a019014d37fe6105131dfc2fc447880">update_pf_paramsLP</a>(<span class="keywordtype">int</span> length);</div>
+<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div>
+<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keywordtype">void</span> update_pf_paramsLP_par(<span class="keywordtype">int</span> length, <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="l00038"></a><span class="lineno"> 38</span> </div>
+<div class="line"><a name="l00076"></a><span class="lineno"> 76</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 class="code" href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777" title="Compute partition functions for locally stable secondary structures.">pfl_fold</a>(<span class="keywordtype">char</span> *sequence,</div>
+<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">int</span> winSize,</div>
+<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">int</span> pairSize,</div>
+<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">float</span> cutoffb,</div>
+<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00081"></a><span class="lineno"> 81</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> **dpp2,</div>
+<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  FILE *pUfp,</div>
+<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  FILE *spup);</div>
+<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
+<div class="line"><a name="l00091"></a><span class="lineno"> 91</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 class="code" href="group__local__pf__fold.html#gab354507e8028f3e1c52ef96bb1eb9df8" title="Compute partition functions for locally stable secondary structures.">pfl_fold_par</a>(<span class="keywordtype">char</span> *sequence,</div>
+<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">int</span> winSize,</div>
+<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordtype">int</span> pairSize,</div>
+<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordtype">float</span> cutoffb,</div>
+<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00096"></a><span class="lineno"> 96</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> **dpp2,</div>
+<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  FILE *pUfp,</div>
+<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  FILE *spup,</div>
+<div class="line"><a name="l00099"></a><span class="lineno"> 99</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="l00100"></a><span class="lineno"> 100</span> </div>
+<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
+<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keywordtype">void</span> putoutpU_prob_par( <span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">int</span> length,</div>
+<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">int</span> ulength,</div>
+<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  FILE *fp,</div>
+<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> energies,</div>
+<div class="line"><a name="l00107"></a><span class="lineno"> 107</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="l00108"></a><span class="lineno"> 108</span> </div>
+<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
+<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3" title="Writes the unpaired probabilities (pU) or opening energies into a file.">putoutpU_prob</a>(<span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">int</span> length,</div>
+<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">int</span> ulength,</div>
+<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  FILE *fp,</div>
+<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">int</span> energies);</div>
+<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
+<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="keywordtype">void</span> putoutpU_prob_bin_par( <span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">int</span> length,</div>
+<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">int</span> ulength,</div>
+<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  FILE *fp,</div>
+<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">int</span> energies,</div>
+<div class="line"><a name="l00135"></a><span class="lineno"> 135</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="l00136"></a><span class="lineno"> 136</span> </div>
+<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75" title="Writes the unpaired probabilities (pU) or opening energies into a binary file.">putoutpU_prob_bin</a>(<span class="keywordtype">double</span> **pU,</div>
+<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordtype">int</span> length,</div>
+<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">int</span> ulength,</div>
+<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  FILE *fp,</div>
+<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">int</span> energies);</div>
+<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
+<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="LPfold_8h.html#ae85bf55053e9fb295208be322e0fa07a">init_pf_foldLP</a>(<span class="keywordtype">int</span> length));</div>
+<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
+<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="preprocessor">#endif</span></div>
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