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-<div class="title">fold.h</div> </div>
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-<a href="fold_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_FOLD_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_FOLD_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="l00061"></a><span class="lineno"> 61</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743" title="if nonzero use logarithmic ML energy in energy_of_struct">logML</a>;</div>
-<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
-<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a6c5655c8b272e3e6cab74dd0f540294f" title="do ML decomposition uniquely (for subopt)">uniq_ML</a>;</div>
-<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
-<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="set to first pos of second seq for cofolding">cut_point</a>;</div>
-<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
-<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5" title="verbose info from energy_of_struct">eos_debug</a>;</div>
-<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
-<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
-<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence.">fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
-<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordtype">int</span> is_constrained,</div>
-<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordtype">int</span> is_circular);</div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
-<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence.">fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div>
-<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423" title="Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...">circfold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
-<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div>
-<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf" title="Calculate the free energy of an already folded RNA using global model detail settings.">energy_of_structure</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div>
-<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
-<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
-<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
-<div class="line"><a name="l00256"></a><span class="lineno"> 256</span> <span class="keywordtype">float</span> <a class="code" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
-<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
-<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> </div>
-<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> <span class="keywordtype">float</span> energy_of_gquad_structure(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> </div>
-<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> <span class="keywordtype">int</span> <a class="code" href="group__eval.html#ga8831445966b761417e713360791299d8" title="Calculate the free energy of an already folded RNA.">energy_of_structure_pt</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordtype">short</span> *ptable,</div>
-<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="keywordtype">short</span> *s1,</div>
-<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00291"></a><span class="lineno"> 291</span> </div>
-<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> <span class="keywordtype">int</span> <a class="code" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordtype">short</span> *ptable,</div>
-<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordtype">short</span> *s1,</div>
-<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
-<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keywordtype">int</span> verbosity_level);</div>
-<div class="line"><a name="l00315"></a><span class="lineno"> 315</span> </div>
-<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7" title="Free arrays for mfe folding.">free_arrays</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div>
-<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> </div>
-<div class="line"><a name="l00330"></a><span class="lineno"> 330</span> <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b" title="Create a dot-backet/parenthesis structure from backtracking stack.">parenthesis_structure</a>(<span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,</div>
-<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
-<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f" title="Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...">parenthesis_zuker</a>( <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,</div>
-<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
-<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> <span class="keywordtype">void</span> letter_structure(<span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,</div>
-<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> </div>
-<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div>
-<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3" title="Recalculate energy parameters.">update_fold_params</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> </div>
-<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> <span class="keywordtype">void</span> update_fold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);</div>
-<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> </div>
-<div class="line"><a name="l00368"></a><span class="lineno"> 368</span> <span class="keywordtype">char</span> *backtrack_fold_from_pair(<span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <span class="keywordtype">int</span> i,</div>
-<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordtype">int</span> j);</div>
-<div class="line"><a name="l00371"></a><span class="lineno"> 371</span> </div>
-<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> <span class="keywordtype">float</span> <a class="code" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b" title="Calculate energy of a move (closing or opening of a base pair)">energy_of_move</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  <span class="keywordtype">int</span> m1,</div>
-<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="keywordtype">int</span> m2);</div>
-<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> </div>
-<div class="line"><a name="l00390"></a><span class="lineno"> 390</span> </div>
-<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f" title="Calculate energy of a move (closing or opening of a base pair)">energy_of_move_pt</a>(<span class="keywordtype">short</span> *pt,</div>
-<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordtype">short</span> *s1,</div>
-<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  <span class="keywordtype">int</span> m1,</div>
-<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordtype">int</span> m2);</div>
-<div class="line"><a name="l00411"></a><span class="lineno"> 411</span> </div>
-<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d" title="Calculate energy of a loop.">loop_energy</a>(<span class="keywordtype">short</span> *ptable,</div>
-<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordtype">short</span> *s1,</div>
-<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordtype">int</span> i);</div>
-<div class="line"><a name="l00425"></a><span class="lineno"> 425</span> </div>
-<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> <span class="keywordtype">void</span> export_fold_arrays(<span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  <span class="keywordtype">char</span> **ptype_p);</div>
-<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div>
-<div class="line"><a name="l00443"></a><span class="lineno"> 443</span> <span class="keywordtype">void</span> export_fold_arrays_par(<span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="keywordtype">char</span> **ptype_p,</div>
-<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> **P_p);</div>
-<div class="line"><a name="l00450"></a><span class="lineno"> 450</span> </div>
-<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> <span class="keywordtype">void</span> export_circfold_arrays(<span class="keywordtype">int</span> *Fc_p,</div>
-<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <span class="keywordtype">int</span> *FcH_p,</div>
-<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="keywordtype">int</span> *FcI_p,</div>
-<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordtype">int</span> *FcM_p,</div>
-<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordtype">int</span> **fM2_p,</div>
-<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordtype">char</span> **ptype_p);</div>
-<div class="line"><a name="l00467"></a><span class="lineno"> 467</span> </div>
-<div class="line"><a name="l00473"></a><span class="lineno"> 473</span> <span class="keywordtype">void</span> export_circfold_arrays_par(<span class="keywordtype">int</span> *Fc_p,</div>
-<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordtype">int</span> *FcH_p,</div>
-<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordtype">int</span> *FcI_p,</div>
-<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordtype">int</span> *FcM_p,</div>
-<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="keywordtype">int</span> **fM2_p,</div>
-<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  <span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keywordtype">char</span> **ptype_p,</div>
-<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> **P_p);</div>
-<div class="line"><a name="l00485"></a><span class="lineno"> 485</span> </div>
-<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> </div>
-<div class="line"><a name="l00504"></a><span class="lineno"> 504</span> <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae" title="Create a plist from a dot-bracket string.">assign_plist_from_db</a>(<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="l00505"></a><span class="lineno"> 505</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *struc,</div>
-<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <span class="keywordtype">float</span> pr);</div>
-<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> </div>
-<div class="line"><a name="l00508"></a><span class="lineno"> 508</span> <span class="comment">/* finally moved the loop energy function declarations to this header... */</span></div>
-<div class="line"><a name="l00509"></a><span class="lineno"> 509</span> <span class="comment">/* BUT: The functions only exist for backward compatibility reasons! */</span></div>
-<div class="line"><a name="l00510"></a><span class="lineno"> 510</span> <span class="comment">/* You better include "loop_energies.h" and call the functions: */</span></div>
-<div class="line"><a name="l00511"></a><span class="lineno"> 511</span> <span class="comment">/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */</span></div>
-<div class="line"><a name="l00512"></a><span class="lineno"> 512</span> <span class="comment">/* a pointer to the energy parameter datastructure as additional argument */</span></div>
-<div class="line"><a name="l00513"></a><span class="lineno"> 513</span> </div>
-<div class="line"><a name="l00518"></a><span class="lineno"> 518</span> DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a>(<span class="keywordtype">int</span> n1,</div>
-<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  <span class="keywordtype">int</span> n2,</div>
-<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="keywordtype">int</span> type_2,</div>
-<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keywordtype">int</span> sp1,</div>
-<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <span class="keywordtype">int</span> sq1));</div>
-<div class="line"><a name="l00526"></a><span class="lineno"> 526</span> </div>
-<div class="line"><a name="l00531"></a><span class="lineno"> 531</span> DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a>(<span class="keywordtype">int</span> size,</div>
-<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>));</div>
-<div class="line"><a name="l00536"></a><span class="lineno"> 536</span> </div>
-<div class="line"><a name="l00542"></a><span class="lineno"> 542</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00543"></a><span class="lineno"> 543</span> </div>
-<div class="line"><a name="l00558"></a><span class="lineno"> 558</span> DEPRECATED(<span class="keywordtype">float</span> <a class="code" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure));</div>
-<div class="line"><a name="l00560"></a><span class="lineno"> 560</span> </div>
-<div class="line"><a name="l00577"></a><span class="lineno"> 577</span> DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <span class="keywordtype">short</span> *ptable,</div>
-<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordtype">short</span> *s1));</div>
-<div class="line"><a name="l00581"></a><span class="lineno"> 581</span> </div>
-<div class="line"><a name="l00596"></a><span class="lineno"> 596</span> DEPRECATED(<span class="keywordtype">float</span> <a class="code" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure));</div>
-<div class="line"><a name="l00598"></a><span class="lineno"> 598</span> </div>
-<div class="line"><a name="l00599"></a><span class="lineno"> 599</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="fold_8h.html">fold.h</a></li>
- <li class="footer">Generated on Wed Jul 24 2013 13:38:56 for RNAlib-2.1.2 by
- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
- </ul>
-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h</h1><a href="fold_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_FOLD_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_FOLD_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="l00061"></a>00061 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743" title="if nonzero use logarithmic ML energy in energy_of_struct">logML</a>;
+<a name="l00062"></a>00062
+<a name="l00064"></a>00064 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a6c5655c8b272e3e6cab74dd0f540294f" title="do ML decomposition uniquely (for subopt)">uniq_ML</a>;
+<a name="l00065"></a>00065
+<a name="l00067"></a>00067 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="set to first pos of second seq for cofolding">cut_point</a>;
+<a name="l00068"></a>00068
+<a name="l00073"></a>00073 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5" title="verbose info from energy_of_struct">eos_debug</a>;
+<a name="l00074"></a>00074
+<a name="l00075"></a>00075
+<a name="l00119"></a>00119 <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence...">fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00120"></a>00120 <span class="keywordtype">char</span> *structure,
+<a name="l00121"></a>00121 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
+<a name="l00122"></a>00122 <span class="keywordtype">int</span> is_constrained,
+<a name="l00123"></a>00123 <span class="keywordtype">int</span> is_circular);
+<a name="l00124"></a>00124
+<a name="l00143"></a>00143 <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence...">fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00144"></a>00144 <span class="keywordtype">char</span> *structure);
+<a name="l00145"></a>00145
+<a name="l00164"></a>00164 <span class="keywordtype">float</span> <a class="code" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423" title="Compute minimum free energy and an appropriate secondary structure of a circular...">circfold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00165"></a>00165 <span class="keywordtype">char</span> *structure);
+<a name="l00166"></a>00166
+<a name="l00167"></a>00167
+<a name="l00195"></a>00195 <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf" title="Calculate the free energy of an already folded RNA using global model detail settings...">energy_of_structure</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00196"></a>00196 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00197"></a>00197 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00198"></a>00198
+<a name="l00214"></a>00214 <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00215"></a>00215 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00216"></a>00216 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
+<a name="l00217"></a>00217 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00218"></a>00218
+<a name="l00237"></a>00237 <span class="keywordtype">float</span> <a class="code" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00238"></a>00238 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00239"></a>00239 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00240"></a>00240
+<a name="l00256"></a>00256 <span class="keywordtype">float</span> <a class="code" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00257"></a>00257 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00258"></a>00258 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
+<a name="l00259"></a>00259 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00260"></a>00260
+<a name="l00261"></a>00261
+<a name="l00262"></a>00262 <span class="keywordtype">float</span> energy_of_gquad_structure(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00263"></a>00263 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00264"></a>00264 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00265"></a>00265
+<a name="l00286"></a>00286 <span class="keywordtype">int</span> <a class="code" href="group__eval.html#ga8831445966b761417e713360791299d8" title="Calculate the free energy of an already folded RNA.">energy_of_structure_pt</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00287"></a>00287 <span class="keywordtype">short</span> *ptable,
+<a name="l00288"></a>00288 <span class="keywordtype">short</span> *s,
+<a name="l00289"></a>00289 <span class="keywordtype">short</span> *s1,
+<a name="l00290"></a>00290 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00291"></a>00291
+<a name="l00309"></a>00309 <span class="keywordtype">int</span> <a class="code" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00310"></a>00310 <span class="keywordtype">short</span> *ptable,
+<a name="l00311"></a>00311 <span class="keywordtype">short</span> *s,
+<a name="l00312"></a>00312 <span class="keywordtype">short</span> *s1,
+<a name="l00313"></a>00313 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
+<a name="l00314"></a>00314 <span class="keywordtype">int</span> verbosity_level);
+<a name="l00315"></a>00315
+<a name="l00322"></a>00322 <span class="keywordtype">void</span> <a class="code" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7" title="Free arrays for mfe folding.">free_arrays</a>(<span class="keywordtype">void</span>);
+<a name="l00323"></a>00323
+<a name="l00324"></a>00324
+<a name="l00330"></a>00330 <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b" title="Create a dot-backet/parenthesis structure from backtracking stack.">parenthesis_structure</a>(<span class="keywordtype">char</span> *structure,
+<a name="l00331"></a>00331 <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,
+<a name="l00332"></a>00332 <span class="keywordtype">int</span> length);
+<a name="l00333"></a>00333
+<a name="l00340"></a>00340 <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f" title="Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker...">parenthesis_zuker</a>( <span class="keywordtype">char</span> *structure,
+<a name="l00341"></a>00341 <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,
+<a name="l00342"></a>00342 <span class="keywordtype">int</span> length);
+<a name="l00343"></a>00343
+<a name="l00344"></a>00344 <span class="keywordtype">void</span> letter_structure(<span class="keywordtype">char</span> *structure,
+<a name="l00345"></a>00345 <a class="code" href="structbondT.html" title="Base pair.">bondT</a> *bp,
+<a name="l00346"></a>00346 <span class="keywordtype">int</span> length);
+<a name="l00347"></a>00347
+<a name="l00348"></a>00348
+<a name="l00354"></a>00354 <span class="keywordtype">void</span> <a class="code" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3" title="Recalculate energy parameters.">update_fold_params</a>(<span class="keywordtype">void</span>);
+<a name="l00355"></a>00355
+<a name="l00361"></a>00361 <span class="keywordtype">void</span> update_fold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);
+<a name="l00362"></a>00362
+<a name="l00368"></a>00368 <span class="keywordtype">char</span> *backtrack_fold_from_pair(<span class="keywordtype">char</span> *sequence,
+<a name="l00369"></a>00369 <span class="keywordtype">int</span> i,
+<a name="l00370"></a>00370 <span class="keywordtype">int</span> j);
+<a name="l00371"></a>00371
+<a name="l00385"></a>00385 <span class="keywordtype">float</span> <a class="code" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b" title="Calculate energy of a move (closing or opening of a base pair).">energy_of_move</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00386"></a>00386 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00387"></a>00387 <span class="keywordtype">int</span> m1,
+<a name="l00388"></a>00388 <span class="keywordtype">int</span> m2);
+<a name="l00389"></a>00389
+<a name="l00390"></a>00390
+<a name="l00406"></a>00406 <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f" title="Calculate energy of a move (closing or opening of a base pair).">energy_of_move_pt</a>(<span class="keywordtype">short</span> *pt,
+<a name="l00407"></a>00407 <span class="keywordtype">short</span> *s,
+<a name="l00408"></a>00408 <span class="keywordtype">short</span> *s1,
+<a name="l00409"></a>00409 <span class="keywordtype">int</span> m1,
+<a name="l00410"></a>00410 <span class="keywordtype">int</span> m2);
+<a name="l00411"></a>00411
+<a name="l00421"></a>00421 <span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d" title="Calculate energy of a loop.">loop_energy</a>(<span class="keywordtype">short</span> *ptable,
+<a name="l00422"></a>00422 <span class="keywordtype">short</span> *s,
+<a name="l00423"></a>00423 <span class="keywordtype">short</span> *s1,
+<a name="l00424"></a>00424 <span class="keywordtype">int</span> i);
+<a name="l00425"></a>00425
+<a name="l00431"></a>00431 <span class="keywordtype">void</span> export_fold_arrays(<span class="keywordtype">int</span> **f5_p,
+<a name="l00432"></a>00432 <span class="keywordtype">int</span> **c_p,
+<a name="l00433"></a>00433 <span class="keywordtype">int</span> **fML_p,
+<a name="l00434"></a>00434 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00435"></a>00435 <span class="keywordtype">int</span> **indx_p,
+<a name="l00436"></a>00436 <span class="keywordtype">char</span> **ptype_p);
+<a name="l00437"></a>00437
+<a name="l00443"></a>00443 <span class="keywordtype">void</span> export_fold_arrays_par(<span class="keywordtype">int</span> **f5_p,
+<a name="l00444"></a>00444 <span class="keywordtype">int</span> **c_p,
+<a name="l00445"></a>00445 <span class="keywordtype">int</span> **fML_p,
+<a name="l00446"></a>00446 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00447"></a>00447 <span class="keywordtype">int</span> **indx_p,
+<a name="l00448"></a>00448 <span class="keywordtype">char</span> **ptype_p,
+<a name="l00449"></a>00449 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> **P_p);
+<a name="l00450"></a>00450
+<a name="l00456"></a>00456 <span class="keywordtype">void</span> export_circfold_arrays(<span class="keywordtype">int</span> *Fc_p,
+<a name="l00457"></a>00457 <span class="keywordtype">int</span> *FcH_p,
+<a name="l00458"></a>00458 <span class="keywordtype">int</span> *FcI_p,
+<a name="l00459"></a>00459 <span class="keywordtype">int</span> *FcM_p,
+<a name="l00460"></a>00460 <span class="keywordtype">int</span> **fM2_p,
+<a name="l00461"></a>00461 <span class="keywordtype">int</span> **f5_p,
+<a name="l00462"></a>00462 <span class="keywordtype">int</span> **c_p,
+<a name="l00463"></a>00463 <span class="keywordtype">int</span> **fML_p,
+<a name="l00464"></a>00464 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00465"></a>00465 <span class="keywordtype">int</span> **indx_p,
+<a name="l00466"></a>00466 <span class="keywordtype">char</span> **ptype_p);
+<a name="l00467"></a>00467
+<a name="l00473"></a>00473 <span class="keywordtype">void</span> export_circfold_arrays_par(<span class="keywordtype">int</span> *Fc_p,
+<a name="l00474"></a>00474 <span class="keywordtype">int</span> *FcH_p,
+<a name="l00475"></a>00475 <span class="keywordtype">int</span> *FcI_p,
+<a name="l00476"></a>00476 <span class="keywordtype">int</span> *FcM_p,
+<a name="l00477"></a>00477 <span class="keywordtype">int</span> **fM2_p,
+<a name="l00478"></a>00478 <span class="keywordtype">int</span> **f5_p,
+<a name="l00479"></a>00479 <span class="keywordtype">int</span> **c_p,
+<a name="l00480"></a>00480 <span class="keywordtype">int</span> **fML_p,
+<a name="l00481"></a>00481 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00482"></a>00482 <span class="keywordtype">int</span> **indx_p,
+<a name="l00483"></a>00483 <span class="keywordtype">char</span> **ptype_p,
+<a name="l00484"></a>00484 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> **P_p);
+<a name="l00485"></a>00485
+<a name="l00486"></a>00486
+<a name="l00504"></a>00504 <span class="keywordtype">void</span> <a class="code" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae" title="Create a plist from a dot-bracket string.">assign_plist_from_db</a>(<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="l00505"></a>00505 <span class="keyword">const</span> <span class="keywordtype">char</span> *struc,
+<a name="l00506"></a>00506 <span class="keywordtype">float</span> pr);
+<a name="l00507"></a>00507
+<a name="l00508"></a>00508 <span class="comment">/* finally moved the loop energy function declarations to this header... */</span>
+<a name="l00509"></a>00509 <span class="comment">/* BUT: The functions only exist for backward compatibility reasons! */</span>
+<a name="l00510"></a>00510 <span class="comment">/* You better include "loop_energies.h" and call the functions: */</span>
+<a name="l00511"></a>00511 <span class="comment">/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */</span>
+<a name="l00512"></a>00512 <span class="comment">/* a pointer to the energy parameter datastructure as additional argument */</span>
+<a name="l00513"></a>00513
+<a name="l00518"></a>00518 DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a>(<span class="keywordtype">int</span> n1,
+<a name="l00519"></a>00519 <span class="keywordtype">int</span> n2,
+<a name="l00520"></a>00520 <span class="keywordtype">int</span> type,
+<a name="l00521"></a>00521 <span class="keywordtype">int</span> type_2,
+<a name="l00522"></a>00522 <span class="keywordtype">int</span> si1,
+<a name="l00523"></a>00523 <span class="keywordtype">int</span> sj1,
+<a name="l00524"></a>00524 <span class="keywordtype">int</span> sp1,
+<a name="l00525"></a>00525 <span class="keywordtype">int</span> sq1));
+<a name="l00526"></a>00526
+<a name="l00531"></a>00531 DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a>(<span class="keywordtype">int</span> size,
+<a name="l00532"></a>00532 <span class="keywordtype">int</span> type,
+<a name="l00533"></a>00533 <span class="keywordtype">int</span> si1,
+<a name="l00534"></a>00534 <span class="keywordtype">int</span> sj1,
+<a name="l00535"></a>00535 <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>));
+<a name="l00536"></a>00536
+<a name="l00542"></a>00542 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a>(<span class="keywordtype">int</span> length));
+<a name="l00543"></a>00543
+<a name="l00558"></a>00558 DEPRECATED(<span class="keywordtype">float</span> <a class="code" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00559"></a>00559 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure));
+<a name="l00560"></a>00560
+<a name="l00577"></a>00577 DEPRECATED(<span class="keywordtype">int</span> <a class="code" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00578"></a>00578 <span class="keywordtype">short</span> *ptable,
+<a name="l00579"></a>00579 <span class="keywordtype">short</span> *s,
+<a name="l00580"></a>00580 <span class="keywordtype">short</span> *s1));
+<a name="l00581"></a>00581
+<a name="l00596"></a>00596 DEPRECATED(<span class="keywordtype">float</span> <a class="code" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00597"></a>00597 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure));
+<a name="l00598"></a>00598
+<a name="l00599"></a>00599 <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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