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+<div class="title">2Dpfold.h</div> </div>
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+<div class="contents">
+<a href="2Dpfold_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="comment">/*</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> minimum free energy</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> RNA secondary structure with</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> basepair distance d to reference structure prediction</span></div>
+<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"></span></div>
+<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__</span></div>
+<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00010"></a><span class="lineno"> 10</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="l00011"></a><span class="lineno"> 11</span> </div>
+<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
+<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
+<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
+<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
+<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *<a class="code" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64" title="Get a datastructure containing all necessary attributes and global folding switches.">get_TwoDpfold_variables</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *seq,</div>
+<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure1,</div>
+<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">char</span> *structure2,</div>
+<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">int</span> circ);</div>
+<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
+<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *<a class="code" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216" title="Get the datastructure containing all necessary attributes and global folding switches from a pre-fill...">get_TwoDpfold_variables_from_MFE</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *mfe_vars);</div>
+<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div>
+<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keywordtype">void</span> <a class="code" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15" title="Free all memory occupied by a TwoDpfold_vars datastructure.">destroy_TwoDpfold_variables</a>(<a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *vars);</div>
+<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
+<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <a class="code" href="structTwoDpfold__solution.html" title="Solution element returned from TwoDpfoldList.">TwoDpfold_solution</a> *<a class="code" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList</a>( <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *vars,</div>
+<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordtype">int</span> maxDistance1,</div>
+<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordtype">int</span> maxDistance2);</div>
+<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">/* End of group kl_neighborhood_pf */</span></div>
+<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
+<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="keywordtype">char</span> *<a class="code" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71" title="Sample secondary structure representatives from a set of distance classes according to their Boltzman...">TwoDpfold_pbacktrack</a>(<a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *vars,</div>
+<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">int</span> d1,</div>
+<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">int</span> d2);</div>
+<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
+<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="keywordtype">char</span> *<a class="code" href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7" title="Sample secondary structure representatives with a specified length from a set of distance classes acc...">TwoDpfold_pbacktrack5</a>( <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *vars,</div>
+<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordtype">int</span> d1,</div>
+<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordtype">int</span> d2,</div>
+<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length);</div>
+<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">/* End of group kl_neighborhood_stochbt */</span></div>
+<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
+<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> DEPRECATED(FLT_OR_DBL **TwoDpfold(<a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *our_variables,</div>
+<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">int</span> maxDistance1,</div>
+<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordtype">int</span> maxDistance2));</div>
+<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
+<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(</div>
+<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <a class="code" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> *our_variables,</div>
+<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordtype">int</span> maxDistance1,</div>
+<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">int</span> maxDistance2));</div>
+<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
+<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div>
+<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> <span class="preprocessor">#endif</span></div>
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