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-<div class="title">part_func.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="part__func_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_PART_FUNC_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_PART_FUNC_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="l00012"></a><span class="lineno"> 12</span> </div>
-<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a" title="Flag indicating that auxilary arrays are needed throughout the computations. This is essential for st...">st_back</a>;</div>
-<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
-<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment"># PARTITION FUNCTION COMPUTATION #</span></div>
-<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
-<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function for a given RNA sequence.">pf_fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</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="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">int</span> calculate_bppm,</div>
-<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">int</span> is_constrained,</div>
-<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">int</span> is_circular);</div>
-<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
-<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
-<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735" title="Compute the partition function of a circular RNA sequence.">pf_circ_fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
-<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> <span class="keywordtype">char</span> *<a class="code" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability ...">pbacktrack</a>(<span class="keywordtype">char</span> *sequence);</div>
-<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
-<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="keywordtype">char</span> *<a class="code" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability...">pbacktrack_circ</a>(<span class="keywordtype">char</span> *sequence);</div>
-<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
-<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd" title="Free arrays for the partition function recursions.">free_pf_arrays</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
-<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28" title="Recalculate energy parameters.">update_pf_params</a>(<span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
-<div class="line"><a name="l00222"></a><span class="lineno"> 222</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc" title="Recalculate energy parameters.">update_pf_params_par</a>(<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="l00223"></a><span class="lineno"> 223</span> </div>
-<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> FLT_OR_DBL *<a class="code" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115" title="Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i...">export_bppm</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00241"></a><span class="lineno"> 241</span> </div>
-<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> <span class="comment"># OTHER PARTITION FUNCTION RELATED DECLARATIONS #</span></div>
-<div class="line"><a name="l00245"></a><span class="lineno"> 245</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> </div>
-<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019" title="Create a plist from a probability matrix.">assign_plist_from_pr</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="l00266"></a><span class="lineno"> 266</span>  FLT_OR_DBL *probs,</div>
-<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <span class="keywordtype">double</span> cutoff);</div>
-<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> </div>
-<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> <span class="comment">/* this doesn't work if free_pf_arrays() is called before */</span></div>
-<div class="line"><a name="l00271"></a><span class="lineno"> 271</span> <span class="keywordtype">void</span> assign_plist_gquad_from_pr(<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="l00272"></a><span class="lineno"> 272</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordtype">double</span> cut_off);</div>
-<div class="line"><a name="l00274"></a><span class="lineno"> 274</span> </div>
-<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> <span class="keywordtype">char</span> *get_centroid_struct_gquad_pr(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordtype">double</span> *dist);</div>
-<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div>
-<div class="line"><a name="l00293"></a><span class="lineno"> 293</span> <span class="keywordtype">int</span> <a class="code" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e" title="Get the pointers to (almost) all relavant computation arrays used in partition function computation...">get_pf_arrays</a>(<span class="keywordtype">short</span> **S_p,</div>
-<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keywordtype">short</span> **S1_p,</div>
-<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keywordtype">char</span> **ptype_p,</div>
-<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  FLT_OR_DBL **qb_p,</div>
-<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  FLT_OR_DBL **qm_p,</div>
-<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  FLT_OR_DBL **q1k_p,</div>
-<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  FLT_OR_DBL **qln_p);</div>
-<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> </div>
-<div class="line"><a name="l00304"></a><span class="lineno"> 304</span> <span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e" title="Get the free energy of a subsequence from the q[] array.">get_subseq_F</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);</div>
-<div class="line"><a name="l00305"></a><span class="lineno"> 305</span> </div>
-<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> <span class="keywordtype">char</span> *<a class="code" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl</a>(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keywordtype">double</span> *dist,</div>
-<div class="line"><a name="l00324"></a><span class="lineno"> 324</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> *pl);</div>
-<div class="line"><a name="l00325"></a><span class="lineno"> 325</span> </div>
-<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> <span class="keywordtype">char</span> *<a class="code" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr</a>(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keywordtype">double</span> *dist,</div>
-<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  FLT_OR_DBL *pr);</div>
-<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
-<div class="line"><a name="l00358"></a><span class="lineno"> 358</span> <span class="keywordtype">double</span> <a class="code" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d" title="Get the mean base pair distance of the last partition function computation.">mean_bp_distance</a>(<span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> </div>
-<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> <span class="keywordtype">double</span> <a class="code" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5" title="Get the mean base pair distance in the thermodynamic ensemble.">mean_bp_distance_pr</a>(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  FLT_OR_DBL *pr);</div>
-<div class="line"><a name="l00379"></a><span class="lineno"> 379</span> </div>
-<div class="line"><a name="l00383"></a><span class="lineno"> 383</span> <span class="keywordtype">void</span> <a class="code" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38" title="Create a dot-bracket like structure string from base pair probability matrix.">bppm_to_structure</a>(<span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  FLT_OR_DBL *pr,</div>
-<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00386"></a><span class="lineno"> 386</span> </div>
-<div class="line"><a name="l00387"></a><span class="lineno"> 387</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> *stackProb(<span class="keywordtype">double</span> cutoff);</div>
-<div class="line"><a name="l00388"></a><span class="lineno"> 388</span> </div>
-<div class="line"><a name="l00392"></a><span class="lineno"> 392</span> <span class="keywordtype">char</span> <a class="code" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d" title="Get a pseudo dot bracket notation for a given probability information.">bppm_symbol</a>(<span class="keyword">const</span> <span class="keywordtype">float</span> *x);</div>
-<div class="line"><a name="l00393"></a><span class="lineno"> 393</span> </div>
-<div class="line"><a name="l00394"></a><span class="lineno"> 394</span> </div>
-<div class="line"><a name="l00395"></a><span class="lineno"> 395</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> <span class="comment"># DEPRECATED FUNCTIONS #</span></div>
-<div class="line"><a name="l00398"></a><span class="lineno"> 398</span> <span class="comment">#################################################</span></div>
-<div class="line"><a name="l00399"></a><span class="lineno"> 399</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00400"></a><span class="lineno"> 400</span> </div>
-<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af" title="Allocate space for pf_fold()">init_pf_fold</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> </div>
-<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> DEPRECATED(<span class="keywordtype">char</span> *<a class="code" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a>(<span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <span class="keywordtype">double</span> *dist)); <span class="comment">/* mean pair distance of ensemble */</span></div>
-<div class="line"><a name="l00414"></a><span class="lineno"> 414</span> </div>
-<div class="line"><a name="l00420"></a><span class="lineno"> 420</span> DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div>
-<div class="line"><a name="l00425"></a><span class="lineno"> 425</span> DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a>(<span class="keywordtype">int</span> u1,</div>
-<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordtype">int</span> u2,</div>
-<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordtype">int</span> type2,</div>
-<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="keywordtype">short</span> si1,</div>
-<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <span class="keywordtype">short</span> sj1,</div>
-<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordtype">short</span> sp1,</div>
-<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordtype">short</span> sq1));</div>
-<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> </div>
-<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a>( <span class="keywordtype">int</span> u,</div>
-<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keywordtype">short</span> si1,</div>
-<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  <span class="keywordtype">short</span> sj1,</div>
-<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>));</div>
-<div class="line"><a name="l00442"></a><span class="lineno"> 442</span> </div>
-<div class="line"><a name="l00443"></a><span class="lineno"> 443</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="part__func_8h.html">part_func.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/part_func.h</h1><a href="part__func_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_PART_FUNC_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_PART_FUNC_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="l00012"></a>00012
+<a name="l00041"></a>00041 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a" title="Flag indicating that auxilary arrays are needed throughout the computations. This...">st_back</a>;
+<a name="l00042"></a>00042
+<a name="l00043"></a>00043 <span class="comment">/*</span>
+<a name="l00044"></a>00044 <span class="comment">#################################################</span>
+<a name="l00045"></a>00045 <span class="comment"># PARTITION FUNCTION COMPUTATION #</span>
+<a name="l00046"></a>00046 <span class="comment">#################################################</span>
+<a name="l00047"></a>00047 <span class="comment">*/</span>
+<a name="l00048"></a>00048
+<a name="l00087"></a>00087 <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function for a given RNA sequence.">pf_fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00088"></a>00088 <span class="keywordtype">char</span> *structure,
+<a name="l00089"></a>00089 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters,
+<a name="l00090"></a>00090 <span class="keywordtype">int</span> calculate_bppm,
+<a name="l00091"></a>00091 <span class="keywordtype">int</span> is_constrained,
+<a name="l00092"></a>00092 <span class="keywordtype">int</span> is_circular);
+<a name="l00093"></a>00093
+<a name="l00133"></a>00133 <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00134"></a>00134 <span class="keywordtype">char</span> *structure);
+<a name="l00135"></a>00135
+<a name="l00161"></a>00161 <span class="keywordtype">float</span> <a class="code" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735" title="Compute the partition function of a circular RNA sequence.">pf_circ_fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00162"></a>00162 <span class="keywordtype">char</span> *structure);
+<a name="l00163"></a>00163
+<a name="l00173"></a>00173 <span class="keywordtype">char</span> *<a class="code" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability...">pbacktrack</a>(<span class="keywordtype">char</span> *sequence);
+<a name="l00174"></a>00174
+<a name="l00186"></a>00186 <span class="keywordtype">char</span> *<a class="code" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according...">pbacktrack_circ</a>(<span class="keywordtype">char</span> *sequence);
+<a name="l00187"></a>00187
+<a name="l00203"></a>00203 <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd" title="Free arrays for the partition function recursions.">free_pf_arrays</a>(<span class="keywordtype">void</span>);
+<a name="l00204"></a>00204
+<a name="l00214"></a>00214 <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28" title="Recalculate energy parameters.">update_pf_params</a>(<span class="keywordtype">int</span> length);
+<a name="l00215"></a>00215
+<a name="l00222"></a>00222 <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc" title="Recalculate energy parameters.">update_pf_params_par</a>(<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...">pf_paramT</a> *parameters);
+<a name="l00223"></a>00223
+<a name="l00240"></a>00240 FLT_OR_DBL *<a class="code" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115" title="Get a pointer to the base pair probability arrayAccessing the base pair probabilities...">export_bppm</a>(<span class="keywordtype">void</span>);
+<a name="l00241"></a>00241
+<a name="l00242"></a>00242 <span class="comment">/*</span>
+<a name="l00243"></a>00243 <span class="comment">#################################################</span>
+<a name="l00244"></a>00244 <span class="comment"># OTHER PARTITION FUNCTION RELATED DECLARATIONS #</span>
+<a name="l00245"></a>00245 <span class="comment">#################################################</span>
+<a name="l00246"></a>00246 <span class="comment">*/</span>
+<a name="l00247"></a>00247
+<a name="l00265"></a>00265 <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019" title="Create a plist from a probability matrix.">assign_plist_from_pr</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="l00266"></a>00266 FLT_OR_DBL *probs,
+<a name="l00267"></a>00267 <span class="keywordtype">int</span> length,
+<a name="l00268"></a>00268 <span class="keywordtype">double</span> cutoff);
+<a name="l00269"></a>00269
+<a name="l00270"></a>00270 <span class="comment">/* this doesn't work if free_pf_arrays() is called before */</span>
+<a name="l00271"></a>00271 <span class="keywordtype">void</span> assign_plist_gquad_from_pr(<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="l00272"></a>00272 <span class="keywordtype">int</span> length,
+<a name="l00273"></a>00273 <span class="keywordtype">double</span> cut_off);
+<a name="l00274"></a>00274
+<a name="l00275"></a>00275 <span class="keywordtype">char</span> *get_centroid_struct_gquad_pr(<span class="keywordtype">int</span> length,
+<a name="l00276"></a>00276 <span class="keywordtype">double</span> *dist);
+<a name="l00277"></a>00277
+<a name="l00293"></a>00293 <span class="keywordtype">int</span> <a class="code" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e" title="Get the pointers to (almost) all relavant computation arrays used in partition function...">get_pf_arrays</a>(<span class="keywordtype">short</span> **S_p,
+<a name="l00294"></a>00294 <span class="keywordtype">short</span> **S1_p,
+<a name="l00295"></a>00295 <span class="keywordtype">char</span> **ptype_p,
+<a name="l00296"></a>00296 FLT_OR_DBL **qb_p,
+<a name="l00297"></a>00297 FLT_OR_DBL **qm_p,
+<a name="l00298"></a>00298 FLT_OR_DBL **q1k_p,
+<a name="l00299"></a>00299 FLT_OR_DBL **qln_p);
+<a name="l00300"></a>00300
+<a name="l00304"></a>00304 <span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e" title="Get the free energy of a subsequence from the q[] array.">get_subseq_F</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
+<a name="l00305"></a>00305
+<a name="l00322"></a>00322 <span class="keywordtype">char</span> *<a class="code" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl</a>(<span class="keywordtype">int</span> length,
+<a name="l00323"></a>00323 <span class="keywordtype">double</span> *dist,
+<a name="l00324"></a>00324 <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="l00325"></a>00325
+<a name="l00342"></a>00342 <span class="keywordtype">char</span> *<a class="code" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr</a>(<span class="keywordtype">int</span> length,
+<a name="l00343"></a>00343 <span class="keywordtype">double</span> *dist,
+<a name="l00344"></a>00344 FLT_OR_DBL *pr);
+<a name="l00345"></a>00345
+<a name="l00358"></a>00358 <span class="keywordtype">double</span> <a class="code" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d" title="Get the mean base pair distance of the last partition function computation.">mean_bp_distance</a>(<span class="keywordtype">int</span> length);
+<a name="l00359"></a>00359
+<a name="l00377"></a>00377 <span class="keywordtype">double</span> <a class="code" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5" title="Get the mean base pair distance in the thermodynamic ensemble.">mean_bp_distance_pr</a>(<span class="keywordtype">int</span> length,
+<a name="l00378"></a>00378 FLT_OR_DBL *pr);
+<a name="l00379"></a>00379
+<a name="l00383"></a>00383 <span class="keywordtype">void</span> <a class="code" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38" title="Create a dot-bracket like structure string from base pair probability matrix.">bppm_to_structure</a>(<span class="keywordtype">char</span> *structure,
+<a name="l00384"></a>00384 FLT_OR_DBL *pr,
+<a name="l00385"></a>00385 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length);
+<a name="l00386"></a>00386
+<a name="l00387"></a>00387 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> *stackProb(<span class="keywordtype">double</span> cutoff);
+<a name="l00388"></a>00388
+<a name="l00392"></a>00392 <span class="keywordtype">char</span> <a class="code" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d" title="Get a pseudo dot bracket notation for a given probability information.">bppm_symbol</a>(<span class="keyword">const</span> <span class="keywordtype">float</span> *x);
+<a name="l00393"></a>00393
+<a name="l00394"></a>00394
+<a name="l00395"></a>00395 <span class="comment">/*</span>
+<a name="l00396"></a>00396 <span class="comment">#################################################</span>
+<a name="l00397"></a>00397 <span class="comment"># DEPRECATED FUNCTIONS #</span>
+<a name="l00398"></a>00398 <span class="comment">#################################################</span>
+<a name="l00399"></a>00399 <span class="comment">*/</span>
+<a name="l00400"></a>00400
+<a name="l00406"></a>00406 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af" title="Allocate space for pf_fold().">init_pf_fold</a>(<span class="keywordtype">int</span> length));
+<a name="l00407"></a>00407
+<a name="l00412"></a>00412 DEPRECATED(<span class="keywordtype">char</span> *<a class="code" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a>(<span class="keywordtype">int</span> length,
+<a name="l00413"></a>00413 <span class="keywordtype">double</span> *dist)); <span class="comment">/* mean pair distance of ensemble */</span>
+<a name="l00414"></a>00414
+<a name="l00420"></a>00420 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a>(<span class="keywordtype">int</span> length));
+<a name="l00421"></a>00421
+<a name="l00425"></a>00425 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a>(<span class="keywordtype">int</span> u1,
+<a name="l00426"></a>00426 <span class="keywordtype">int</span> u2,
+<a name="l00427"></a>00427 <span class="keywordtype">int</span> type,
+<a name="l00428"></a>00428 <span class="keywordtype">int</span> type2,
+<a name="l00429"></a>00429 <span class="keywordtype">short</span> si1,
+<a name="l00430"></a>00430 <span class="keywordtype">short</span> sj1,
+<a name="l00431"></a>00431 <span class="keywordtype">short</span> sp1,
+<a name="l00432"></a>00432 <span class="keywordtype">short</span> sq1));
+<a name="l00433"></a>00433
+<a name="l00437"></a>00437 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a>( <span class="keywordtype">int</span> u,
+<a name="l00438"></a>00438 <span class="keywordtype">int</span> type,
+<a name="l00439"></a>00439 <span class="keywordtype">short</span> si1,
+<a name="l00440"></a>00440 <span class="keywordtype">short</span> sj1,
+<a name="l00441"></a>00441 <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>));
+<a name="l00442"></a>00442
+<a name="l00443"></a>00443 <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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