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-<div class="title">loop_energies.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="loop__energies_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_LOOP_ENERGIES_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_LOOP_ENERGIES_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 <stdio.h></span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include <stdlib.h></span></div>
-<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include <math.h></span></div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include <ctype.h></span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include <string.h></span></div>
-<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "<a class="code" href="params_8h.html">params.h</a>"</span></div>
-<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "<a class="code" href="fold__vars_8h.html" title="Here all all declarations of the global variables used throughout RNAlib.">fold_vars.h</a>"</span></div>
-<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "energy_par.h"</span></div>
-<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div>
-<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
-<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor"></span><span class="preprocessor"># define INLINE inline</span></div>
-<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
-<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor"></span><span class="preprocessor"># define INLINE</span></div>
-<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
-<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> INLINE PRIVATE <span class="keywordtype">int</span> E_MLstem( <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);</div>
-<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div>
-<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> INLINE PRIVATE <span class="keywordtype">double</span> exp_E_MLstem(<span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P);</div>
-<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> INLINE PRIVATE <span class="keywordtype">int</span> E_ExtLoop(<span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);</div>
-<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> INLINE PRIVATE <span class="keywordtype">double</span> exp_E_ExtLoop( <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P);</div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
-<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop</a>(<span class="keywordtype">int</span> n1,</div>
-<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordtype">int</span> n2,</div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordtype">int</span> type_2,</div>
-<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">int</span> sp1,</div>
-<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordtype">int</span> sq1,</div>
-<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);</div>
-<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
-<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
-<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin</a>(<span class="keywordtype">int</span> size,</div>
-<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <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>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);</div>
-<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
-<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">E_Stem</a>( <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordtype">int</span> extLoop,</div>
-<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);</div>
-<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
-<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">exp_E_Stem</a>(<span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="keywordtype">int</span> si1,</div>
-<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">int</span> sj1,</div>
-<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordtype">int</span> extLoop,</div>
-<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P);</div>
-<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div>
-<div class="line"><a name="l00280"></a><span class="lineno"> 280</span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin</a>( <span class="keywordtype">int</span> u,</div>
-<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordtype">short</span> si1,</div>
-<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordtype">short</span> sj1,</div>
-<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P);</div>
-<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> </div>
-<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop</a>(<span class="keywordtype">int</span> u1,</div>
-<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keywordtype">int</span> u2,</div>
-<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordtype">int</span> type,</div>
-<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <span class="keywordtype">int</span> type2,</div>
-<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordtype">short</span> si1,</div>
-<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordtype">short</span> sj1,</div>
-<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordtype">short</span> sp1,</div>
-<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keywordtype">short</span> sq1,</div>
-<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P);</div>
-<div class="line"><a name="l00315"></a><span class="lineno"> 315</span> </div>
-<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div>
-<div class="line"><a name="l00317"></a><span class="lineno"> 317</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> <span class="comment">#################################</span></div>
-<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> <span class="comment"># BEGIN OF FUNCTION DEFINITIONS #</span></div>
-<div class="line"><a name="l00320"></a><span class="lineno"> 320</span> <span class="comment">#################################</span></div>
-<div class="line"><a name="l00321"></a><span class="lineno"> 321</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00322"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6"> 322</a></span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin</a>(<span class="keywordtype">int</span> size, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keywordtype">int</span> energy;</div>
-<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> </div>
-<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(<span class="keywordtype">int</span>)(P->lxc*log((size)/30.));</div>
-<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">if</span> (P-><a class="code" href="structparamT.html#aeb912822ef912705bc202b14f9d71ad9" title="Model details to be used in the recursions.">model_details</a>.<a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617" title="Include special hairpin contributions for tri, tetra and hexaloops.">special_hp</a>){</div>
-<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keywordflow">if</span> (size == 4) { <span class="comment">/* check for tetraloop bonus */</span></div>
-<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="keywordtype">char</span> tl[7]={0}, *ts;</div>
-<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  strncpy(tl, <span class="keywordtype">string</span>, 6);</div>
-<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Tetraloops, tl)))</div>
-<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">return</span> (P->Tetraloop_E[(ts - P->Tetraloops)/7]);</div>
-<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
-<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (size == 6) {</div>
-<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordtype">char</span> tl[9]={0}, *ts;</div>
-<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  strncpy(tl, <span class="keywordtype">string</span>, 8);</div>
-<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Hexaloops, tl)))</div>
-<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="keywordflow">return</span> (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);</div>
-<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div>
-<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (size == 3) {</div>
-<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keywordtype">char</span> tl[6]={0,0,0,0,0,0}, *ts;</div>
-<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  strncpy(tl, <span class="keywordtype">string</span>, 5);</div>
-<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Triloops, tl))) {</div>
-<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keywordflow">return</span> (P->Triloop_E[(ts - P->Triloops)/6]);</div>
-<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  }</div>
-<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">return</span> (energy + (type>2 ? P->TerminalAU : 0));</div>
-<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  }</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>  energy += P->mismatchH[type][si1][sj1];</div>
-<div class="line"><a name="l00349"></a><span class="lineno"> 349</span> </div>
-<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> }</div>
-<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> </div>
-<div class="line"><a name="l00353"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd"> 353</a></span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop</a>(<span class="keywordtype">int</span> n1, <span class="keywordtype">int</span> n2, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type_2, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> sp1, <span class="keywordtype">int</span> sq1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="comment">/* compute energy of degree 2 loop (stack bulge or interior) */</span></div>
-<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="keywordtype">int</span> nl, ns, energy;</div>
-<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  energy = <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>;</div>
-<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> </div>
-<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">if</span> (n1>n2) { nl=n1; ns=n2;}</div>
-<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  <span class="keywordflow">else</span> {nl=n2; ns=n1;}</div>
-<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div>
-<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="keywordflow">if</span> (nl == 0)</div>
-<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keywordflow">return</span> P->stack[type][type_2]; <span class="comment">/* stack */</span></div>
-<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> </div>
-<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keywordflow">if</span> (ns==0) { <span class="comment">/* bulge */</span></div>
-<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  energy = (nl<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?P->bulge[nl]:</div>
-<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  (P->bulge[30]+(<span class="keywordtype">int</span>)(P->lxc*log(nl/30.)));</div>
-<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">if</span> (nl==1) energy += P->stack[type][type_2];</div>
-<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">else</span> {</div>
-<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <span class="keywordflow">if</span> (type>2) energy += P->TerminalAU;</div>
-<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordflow">if</span> (type_2>2) energy += P->TerminalAU;</div>
-<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div>
-<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  }</div>
-<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <span class="keywordflow">else</span> { <span class="comment">/* interior loop */</span></div>
-<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordflow">if</span> (ns==1) {</div>
-<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">if</span> (nl==1) <span class="comment">/* 1x1 loop */</span></div>
-<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="keywordflow">return</span> P->int11[type][type_2][si1][sj1];</div>
-<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">if</span> (nl==2) { <span class="comment">/* 2x1 loop */</span></div>
-<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordflow">if</span> (n1==1)</div>
-<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  energy = P->int21[type][type_2][si1][sq1][sj1];</div>
-<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  energy = P->int21[type_2][type][sq1][si1][sp1];</div>
-<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  }</div>
-<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keywordflow">else</span> { <span class="comment">/* 1xn loop */</span></div>
-<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  energy = (nl+1<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));</div>
-<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(MAX_NINIO, (nl-ns)*P->ninio[2]);</div>
-<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];</div>
-<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  }</div>
-<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  }</div>
-<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ns==2) {</div>
-<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="keywordflow">if</span>(nl==2) { <span class="comment">/* 2x2 loop */</span></div>
-<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="keywordflow">return</span> P->int22[type][type_2][si1][sp1][sq1][sj1];}</div>
-<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (nl==3){ <span class="comment">/* 2x3 loop */</span></div>
-<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  energy = P->internal_loop[5]+P->ninio[2];</div>
-<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];</div>
-<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  }</div>
-<div class="line"><a name="l00400"></a><span class="lineno"> 400</span> </div>
-<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  }</div>
-<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  { <span class="comment">/* generic interior loop (no else here!)*/</span></div>
-<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  energy = (n1+n2<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?(P->internal_loop[n1+n2]) : (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));</div>
-<div class="line"><a name="l00404"></a><span class="lineno"> 404</span> </div>
-<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(MAX_NINIO, (nl-ns)*P->ninio[2]);</div>
-<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> </div>
-<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];</div>
-<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  }</div>
-<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  }</div>
-<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00411"></a><span class="lineno"> 411</span> }</div>
-<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> </div>
-<div class="line"><a name="l00413"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819"> 413</a></span> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">E_Stem</a>(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> extLoop, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="keywordtype">int</span> energy = 0;</div>
-<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="keywordtype">int</span> d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;</div>
-<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordtype">int</span> d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;</div>
-<div class="line"><a name="l00417"></a><span class="lineno"> 417</span> </div>
-<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  energy += P->TerminalAU;</div>
-<div class="line"><a name="l00420"></a><span class="lineno"> 420</span> </div>
-<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0)</div>
-<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];</div>
-<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  energy += d5 + d3;</div>
-<div class="line"><a name="l00425"></a><span class="lineno"> 425</span> </div>
-<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordflow">if</span>(!extLoop) energy += P->MLintern[type];</div>
-<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> }</div>
-<div class="line"><a name="l00429"></a><span class="lineno"> 429</span> </div>
-<div class="line"><a name="l00430"></a><span class="lineno"> 430</span> INLINE PRIVATE <span class="keywordtype">int</span> E_ExtLoop(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordtype">int</span> energy = 0;</div>
-<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){</div>
-<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  energy += P->mismatchExt[type][si1][sj1];</div>
-<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  }</div>
-<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (si1 >= 0){</div>
-<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  energy += P->dangle5[type][si1];</div>
-<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  }</div>
-<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sj1 >= 0){</div>
-<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  energy += P->dangle3[type][sj1];</div>
-<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div>
-<div class="line"><a name="l00441"></a><span class="lineno"> 441</span> </div>
-<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  energy += P->TerminalAU;</div>
-<div class="line"><a name="l00444"></a><span class="lineno"> 444</span> </div>
-<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00446"></a><span class="lineno"> 446</span> }</div>
-<div class="line"><a name="l00447"></a><span class="lineno"> 447</span> </div>
-<div class="line"><a name="l00448"></a><span class="lineno"> 448</span> INLINE PRIVATE <span class="keywordtype">int</span> E_MLstem(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keywordtype">int</span> energy = 0;</div>
-<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){</div>
-<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  energy += P->mismatchM[type][si1][sj1];</div>
-<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  }</div>
-<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (si1 >= 0){</div>
-<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  energy += P->dangle5[type][si1];</div>
-<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  }</div>
-<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sj1 >= 0){</div>
-<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  energy += P->dangle3[type][sj1];</div>
-<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  }</div>
-<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div>
-<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  energy += P->TerminalAU;</div>
-<div class="line"><a name="l00462"></a><span class="lineno"> 462</span> </div>
-<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  energy += P->MLintern[type];</div>
-<div class="line"><a name="l00464"></a><span class="lineno"> 464</span> </div>
-<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00466"></a><span class="lineno"> 466</span> }</div>
-<div class="line"><a name="l00467"></a><span class="lineno"> 467</span> </div>
-<div class="line"><a name="l00468"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6"> 468</a></span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin</a>(<span class="keywordtype">int</span> u, <span class="keywordtype">int</span> type, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P){</div>
-<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  <span class="keywordtype">double</span> q, kT;</div>
-<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  kT = P->kT; <span class="comment">/* kT in cal/mol */</span></div>
-<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
-<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <span class="keywordflow">if</span>(u <= 30)</div>
-<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  q = P->exphairpin[u];</div>
-<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);</div>
-<div class="line"><a name="l00476"></a><span class="lineno"> 476</span> </div>
-<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="keywordflow">if</span>(u < 3) <span class="keywordflow">return</span> q; <span class="comment">/* should only be the case when folding alignments */</span></div>
-<div class="line"><a name="l00478"></a><span class="lineno"> 478</span> </div>
-<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">if</span> ((P-><a class="code" href="structpf__paramT.html#a43ec875779c5e7c8bf5fa7e837ec6d09" title="Model details to be used in the recursions.">model_details</a>.<a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617" title="Include special hairpin contributions for tri, tetra and hexaloops.">special_hp</a>)&&(u==4)) {</div>
-<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordtype">char</span> tl[7]={0,0,0,0,0,0,0}, *ts;</div>
-<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  strncpy(tl, <span class="keywordtype">string</span>, 6);</div>
-<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Tetraloops, tl))){</div>
-<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keywordflow">if</span>(type != 7)</div>
-<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <span class="keywordflow">return</span> (P->exptetra[(ts-P->Tetraloops)/7]);</div>
-<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  q *= P->exptetra[(ts-P->Tetraloops)/7];</div>
-<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  }</div>
-<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  }</div>
-<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  <span class="keywordflow">if</span> ((<a class="code" href="fold__vars_8h.html#a4f6265bdf0ead7ff4628a360adbfd77e" title="Include special stabilizing energies for some tri-, tetra- and hexa-loops;.">tetra_loop</a>)&&(u==6)) {</div>
-<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  <span class="keywordtype">char</span> tl[9]={0,0,0,0,0,0,0,0,0}, *ts;</div>
-<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  strncpy(tl, <span class="keywordtype">string</span>, 6);</div>
-<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Hexaloops, tl)))</div>
-<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  <span class="keywordflow">return</span> (P->exphex[(ts-P->Hexaloops)/9]);</div>
-<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  }</div>
-<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  <span class="keywordflow">if</span> (u==3) {</div>
-<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  <span class="keywordtype">char</span> tl[6]={0,0,0,0,0,0}, *ts;</div>
-<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  strncpy(tl, <span class="keywordtype">string</span>, 5);</div>
-<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <span class="keywordflow">if</span> ((ts=strstr(P->Triloops, tl)))</div>
-<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="keywordflow">return</span> (P->exptri[(ts-P->Triloops)/6]);</div>
-<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordflow">if</span> (type>2)</div>
-<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  q *= P->expTermAU;</div>
-<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  }</div>
-<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordflow">else</span> <span class="comment">/* no mismatches for tri-loops */</span></div>
-<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  q *= P->expmismatchH[type][si1][sj1];</div>
-<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> </div>
-<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <span class="keywordflow">return</span> q;</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> </div>
-<div class="line"><a name="l00509"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e"> 509</a></span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop</a>(<span class="keywordtype">int</span> u1, <span class="keywordtype">int</span> u2, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type2, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keywordtype">short</span> sp1, <span class="keywordtype">short</span> sq1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P){</div>
-<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  <span class="keywordtype">int</span> ul, us, no_close = 0;</div>
-<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  <span class="keywordtype">double</span> z = 0.;</div>
-<div class="line"><a name="l00512"></a><span class="lineno"> 512</span> </div>
-<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  <span class="keywordflow">if</span> ((<a class="code" href="fold__vars_8h.html#aa8d1c7b92489179e1eafa562b7bdd259" title="GU allowed only inside stacks if set to 1.">no_closingGU</a>) && ((type2==3)||(type2==4)||(type==3)||(type==4)))</div>
-<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  no_close = 1;</div>
-<div class="line"><a name="l00515"></a><span class="lineno"> 515</span> </div>
-<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  <span class="keywordflow">if</span> (u1>u2) { ul=u1; us=u2;}</div>
-<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  <span class="keywordflow">else</span> {ul=u2; us=u1;}</div>
-<div class="line"><a name="l00518"></a><span class="lineno"> 518</span> </div>
-<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  <span class="keywordflow">if</span> (ul==0) <span class="comment">/* stack */</span></div>
-<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  z = P->expstack[type][type2];</div>
-<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(!no_close){</div>
-<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordflow">if</span> (us==0) { <span class="comment">/* bulge */</span></div>
-<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  z = P->expbulge[ul];</div>
-<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keywordflow">if</span> (ul==1) z *= P->expstack[type][type2];</div>
-<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <span class="keywordflow">else</span> {</div>
-<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  <span class="keywordflow">if</span> (type>2) z *= P->expTermAU;</div>
-<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <span class="keywordflow">if</span> (type2>2) z *= P->expTermAU;</div>
-<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  }</div>
-<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordflow">return</span> z;</div>
-<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  }</div>
-<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (us==1) {</div>
-<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <span class="keywordflow">if</span> (ul==1){ <span class="comment">/* 1x1 loop */</span></div>
-<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <span class="keywordflow">return</span> P->expint11[type][type2][si1][sj1];</div>
-<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  }</div>
-<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keywordflow">if</span> (ul==2) { <span class="comment">/* 2x1 loop */</span></div>
-<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  <span class="keywordflow">if</span> (u1==1)</div>
-<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  <span class="keywordflow">return</span> P->expint21[type][type2][si1][sq1][sj1];</div>
-<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  <span class="keywordflow">return</span> P->expint21[type2][type][sq1][si1][sp1];</div>
-<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  }</div>
-<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  <span class="keywordflow">else</span> { <span class="comment">/* 1xn loop */</span></div>
-<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];</div>
-<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <span class="keywordflow">return</span> z * P->expninio[2][ul-us];</div>
-<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  }</div>
-<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  }</div>
-<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (us==2) {</div>
-<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  <span class="keywordflow">if</span>(ul==2) <span class="comment">/* 2x2 loop */</span></div>
-<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  <span class="keywordflow">return</span> P->expint22[type][type2][si1][sp1][sq1][sj1];</div>
-<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(ul==3){ <span class="comment">/* 2x3 loop */</span></div>
-<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];</div>
-<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  <span class="keywordflow">return</span> z * P->expninio[2][1];</div>
-<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  }</div>
-<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  }</div>
-<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  <span class="comment">/* generic interior loop (no else here!)*/</span></div>
-<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];</div>
-<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keywordflow">return</span> z * P->expninio[2][ul-us];</div>
-<div class="line"><a name="l00557"></a><span class="lineno"> 557</span> </div>
-<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  }</div>
-<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <span class="keywordflow">return</span> z;</div>
-<div class="line"><a name="l00560"></a><span class="lineno"> 560</span> }</div>
-<div class="line"><a name="l00561"></a><span class="lineno"> 561</span> </div>
-<div class="line"><a name="l00562"></a><span class="lineno"><a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21"> 562</a></span> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">exp_E_Stem</a>(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> extLoop, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P){</div>
-<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  <span class="keywordtype">double</span> energy = 1.0;</div>
-<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  <span class="keywordtype">double</span> d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;</div>
-<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  <span class="keywordtype">double</span> d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;</div>
-<div class="line"><a name="l00566"></a><span class="lineno"> 566</span> </div>
-<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  energy *= P->expTermAU;</div>
-<div class="line"><a name="l00569"></a><span class="lineno"> 569</span> </div>
-<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0)</div>
-<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];</div>
-<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  <span class="keywordflow">else</span></div>
-<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  energy *= d5 * d3;</div>
-<div class="line"><a name="l00574"></a><span class="lineno"> 574</span> </div>
-<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  <span class="keywordflow">if</span>(!extLoop) energy *= P->expMLintern[type];</div>
-<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00577"></a><span class="lineno"> 577</span> }</div>
-<div class="line"><a name="l00578"></a><span class="lineno"> 578</span> </div>
-<div class="line"><a name="l00579"></a><span class="lineno"> 579</span> INLINE PRIVATE <span class="keywordtype">double</span> exp_E_MLstem(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P){</div>
-<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordtype">double</span> energy = 1.0;</div>
-<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){</div>
-<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  energy *= P->expmismatchM[type][si1][sj1];</div>
-<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  }</div>
-<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(si1 >= 0){</div>
-<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  energy *= P->expdangle5[type][si1];</div>
-<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  }</div>
-<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(sj1 >= 0){</div>
-<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  energy *= P->expdangle3[type][sj1];</div>
-<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  }</div>
-<div class="line"><a name="l00590"></a><span class="lineno"> 590</span> </div>
-<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  energy *= P->expTermAU;</div>
-<div class="line"><a name="l00593"></a><span class="lineno"> 593</span> </div>
-<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  energy *= P->expMLintern[type];</div>
-<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00596"></a><span class="lineno"> 596</span> }</div>
-<div class="line"><a name="l00597"></a><span class="lineno"> 597</span> </div>
-<div class="line"><a name="l00598"></a><span class="lineno"> 598</span> INLINE PRIVATE <span class="keywordtype">double</span> exp_E_ExtLoop(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *P){</div>
-<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="keywordtype">double</span> energy = 1.0;</div>
-<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){</div>
-<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  energy *= P->expmismatchExt[type][si1][sj1];</div>
-<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  }</div>
-<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(si1 >= 0){</div>
-<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  energy *= P->expdangle5[type][si1];</div>
-<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  }</div>
-<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(sj1 >= 0){</div>
-<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  energy *= P->expdangle3[type][sj1];</div>
-<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  }</div>
-<div class="line"><a name="l00609"></a><span class="lineno"> 609</span> </div>
-<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keywordflow">if</span>(type > 2)</div>
-<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  energy *= P->expTermAU;</div>
-<div class="line"><a name="l00612"></a><span class="lineno"> 612</span> </div>
-<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00614"></a><span class="lineno"> 614</span> }</div>
-<div class="line"><a name="l00615"></a><span class="lineno"> 615</span> </div>
-<div class="line"><a name="l00616"></a><span class="lineno"> 616</span> INLINE PRIVATE <span class="keywordtype">int</span> E_IntLoop_Co(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type_2, <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j, <span class="keywordtype">int</span> p, <span class="keywordtype">int</span> q, <span class="keywordtype">int</span> cutpoint, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keywordtype">short</span> sp1, <span class="keywordtype">short</span> sq1, <span class="keywordtype">int</span> dangles, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){</div>
-<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  <span class="keywordtype">int</span> energy = 0;</div>
-<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  <span class="keywordflow">if</span>(type > 2) energy += P->TerminalAU;</div>
-<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  <span class="keywordflow">if</span>(type_2 > 2) energy += P->TerminalAU;</div>
-<div class="line"><a name="l00620"></a><span class="lineno"> 620</span> </div>
-<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  <span class="keywordflow">if</span>(!dangles) <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00622"></a><span class="lineno"> 622</span> </div>
-<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  <span class="keywordtype">int</span> ci = (i>=cutpoint)||((i+1)<cutpoint);</div>
-<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  <span class="keywordtype">int</span> cj = ((j-1)>=cutpoint)||(j<cutpoint);</div>
-<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordtype">int</span> cp = ((p-1)>=cutpoint)||(p<cutpoint);</div>
-<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  <span class="keywordtype">int</span> cq = (q>=cutpoint)||((q+1)<cutpoint);</div>
-<div class="line"><a name="l00627"></a><span class="lineno"> 627</span> </div>
-<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  <span class="keywordtype">int</span> d3 = ci ? P->dangle3[type][si1] : 0;</div>
-<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  <span class="keywordtype">int</span> d5 = cj ? P->dangle5[type][sj1] : 0;</div>
-<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  <span class="keywordtype">int</span> d5_2 = cp ? P->dangle5[type_2][sp1] : 0;</div>
-<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  <span class="keywordtype">int</span> d3_2 = cq ? P->dangle3[type_2][sq1] : 0;</div>
-<div class="line"><a name="l00632"></a><span class="lineno"> 632</span> </div>
-<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  <span class="keywordtype">int</span> tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;</div>
-<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  <span class="keywordtype">int</span> tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;</div>
-<div class="line"><a name="l00635"></a><span class="lineno"> 635</span> </div>
-<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  <span class="keywordflow">if</span>(dangles == 2) <span class="keywordflow">return</span> energy + tmm + tmm_2;</div>
-<div class="line"><a name="l00637"></a><span class="lineno"> 637</span> </div>
-<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  <span class="comment">/* now we may have non-double dangles only */</span></div>
-<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  <span class="keywordflow">if</span>(i+2 < p){</div>
-<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  <span class="keywordflow">if</span>(q+2 < j){ energy += tmm + tmm_2;}</div>
-<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){ energy += (cj && cq) ? <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}</div>
-<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  <span class="keywordflow">else</span> energy += d3 + d5_2;</div>
-<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  }</div>
-<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(i+2 == p){</div>
-<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  <span class="keywordflow">if</span>(q+2 < j){ energy += (ci && cp) ? <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}</div>
-<div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){</div>
-<div class="line"><a name="l00647"></a><span class="lineno"> 647</span>  energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm, <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm_2, <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d5 + d5_2, d3 + d3_2)));</div>
-<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  }</div>
-<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  <span class="keywordflow">else</span> energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d3, d5_2);</div>
-<div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  }</div>
-<div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  <span class="keywordflow">else</span>{</div>
-<div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  <span class="keywordflow">if</span>(q+2 < j){ energy += d5 + d3_2;}</div>
-<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){ energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d5, d3_2);}</div>
-<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  }</div>
-<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  <span class="keywordflow">return</span> energy;</div>
-<div class="line"><a name="l00656"></a><span class="lineno"> 656</span> }</div>
-<div class="line"><a name="l00657"></a><span class="lineno"> 657</span> </div>
-<div class="line"><a name="l00658"></a><span class="lineno"> 658</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="loop__energies_8h.html">loop_energies.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/loop_energies.h</h1><a href="loop__energies_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_LOOP_ENERGIES_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00004"></a>00004 <span class="preprocessor">#include <stdio.h></span>
+<a name="l00005"></a>00005 <span class="preprocessor">#include <stdlib.h></span>
+<a name="l00006"></a>00006 <span class="preprocessor">#include <math.h></span>
+<a name="l00007"></a>00007 <span class="preprocessor">#include <ctype.h></span>
+<a name="l00008"></a>00008 <span class="preprocessor">#include <string.h></span>
+<a name="l00009"></a>00009 <span class="preprocessor">#include "<a class="code" href="params_8h.html">params.h</a>"</span>
+<a name="l00010"></a>00010 <span class="preprocessor">#include "<a class="code" href="fold__vars_8h.html" title="Here all all declarations of the global variables used throughout RNAlib.">fold_vars.h</a>"</span>
+<a name="l00011"></a>00011 <span class="preprocessor">#include "energy_par.h"</span>
+<a name="l00012"></a>00012
+<a name="l00013"></a>00013 <span class="preprocessor">#ifdef __GNUC__</span>
+<a name="l00014"></a>00014 <span class="preprocessor"></span><span class="preprocessor"># define INLINE inline</span>
+<a name="l00015"></a>00015 <span class="preprocessor"></span><span class="preprocessor">#else</span>
+<a name="l00016"></a>00016 <span class="preprocessor"></span><span class="preprocessor"># define INLINE</span>
+<a name="l00017"></a>00017 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00018"></a>00018 <span class="preprocessor"></span>
+<a name="l00054"></a>00054 INLINE PRIVATE <span class="keywordtype">int</span> E_MLstem( <span class="keywordtype">int</span> type,
+<a name="l00055"></a>00055 <span class="keywordtype">int</span> si1,
+<a name="l00056"></a>00056 <span class="keywordtype">int</span> sj1,
+<a name="l00057"></a>00057 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);
+<a name="l00058"></a>00058
+<a name="l00065"></a>00065 INLINE PRIVATE <span class="keywordtype">double</span> exp_E_MLstem(<span class="keywordtype">int</span> type,
+<a name="l00066"></a>00066 <span class="keywordtype">int</span> si1,
+<a name="l00067"></a>00067 <span class="keywordtype">int</span> sj1,
+<a name="l00068"></a>00068 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P);
+<a name="l00069"></a>00069
+<a name="l00089"></a>00089 INLINE PRIVATE <span class="keywordtype">int</span> E_ExtLoop(<span class="keywordtype">int</span> type,
+<a name="l00090"></a>00090 <span class="keywordtype">int</span> si1,
+<a name="l00091"></a>00091 <span class="keywordtype">int</span> sj1,
+<a name="l00092"></a>00092 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);
+<a name="l00093"></a>00093
+<a name="l00100"></a>00100 INLINE PRIVATE <span class="keywordtype">double</span> exp_E_ExtLoop( <span class="keywordtype">int</span> type,
+<a name="l00101"></a>00101 <span class="keywordtype">int</span> si1,
+<a name="l00102"></a>00102 <span class="keywordtype">int</span> sj1,
+<a name="l00103"></a>00103 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P);
+<a name="l00104"></a>00104
+<a name="l00149"></a>00149 INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop</a>(<span class="keywordtype">int</span> n1,
+<a name="l00150"></a>00150 <span class="keywordtype">int</span> n2,
+<a name="l00151"></a>00151 <span class="keywordtype">int</span> type,
+<a name="l00152"></a>00152 <span class="keywordtype">int</span> type_2,
+<a name="l00153"></a>00153 <span class="keywordtype">int</span> si1,
+<a name="l00154"></a>00154 <span class="keywordtype">int</span> sj1,
+<a name="l00155"></a>00155 <span class="keywordtype">int</span> sp1,
+<a name="l00156"></a>00156 <span class="keywordtype">int</span> sq1,
+<a name="l00157"></a>00157 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);
+<a name="l00158"></a>00158
+<a name="l00159"></a>00159
+<a name="l00191"></a>00191 INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin</a>(<span class="keywordtype">int</span> size,
+<a name="l00192"></a>00192 <span class="keywordtype">int</span> type,
+<a name="l00193"></a>00193 <span class="keywordtype">int</span> si1,
+<a name="l00194"></a>00194 <span class="keywordtype">int</span> sj1,
+<a name="l00195"></a>00195 <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00196"></a>00196 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);
+<a name="l00197"></a>00197
+<a name="l00243"></a>00243 INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">E_Stem</a>( <span class="keywordtype">int</span> type,
+<a name="l00244"></a>00244 <span class="keywordtype">int</span> si1,
+<a name="l00245"></a>00245 <span class="keywordtype">int</span> sj1,
+<a name="l00246"></a>00246 <span class="keywordtype">int</span> extLoop,
+<a name="l00247"></a>00247 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P);
+<a name="l00248"></a>00248
+<a name="l00257"></a>00257 INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">exp_E_Stem</a>(<span class="keywordtype">int</span> type,
+<a name="l00258"></a>00258 <span class="keywordtype">int</span> si1,
+<a name="l00259"></a>00259 <span class="keywordtype">int</span> sj1,
+<a name="l00260"></a>00260 <span class="keywordtype">int</span> extLoop,
+<a name="l00261"></a>00261 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P);
+<a name="l00262"></a>00262
+<a name="l00280"></a>00280 INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin</a>( <span class="keywordtype">int</span> u,
+<a name="l00281"></a>00281 <span class="keywordtype">int</span> type,
+<a name="l00282"></a>00282 <span class="keywordtype">short</span> si1,
+<a name="l00283"></a>00283 <span class="keywordtype">short</span> sj1,
+<a name="l00284"></a>00284 <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00285"></a>00285 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P);
+<a name="l00286"></a>00286
+<a name="l00306"></a>00306 INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop</a>(<span class="keywordtype">int</span> u1,
+<a name="l00307"></a>00307 <span class="keywordtype">int</span> u2,
+<a name="l00308"></a>00308 <span class="keywordtype">int</span> type,
+<a name="l00309"></a>00309 <span class="keywordtype">int</span> type2,
+<a name="l00310"></a>00310 <span class="keywordtype">short</span> si1,
+<a name="l00311"></a>00311 <span class="keywordtype">short</span> sj1,
+<a name="l00312"></a>00312 <span class="keywordtype">short</span> sp1,
+<a name="l00313"></a>00313 <span class="keywordtype">short</span> sq1,
+<a name="l00314"></a>00314 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P);
+<a name="l00315"></a>00315
+<a name="l00316"></a>00316
+<a name="l00317"></a>00317 <span class="comment">/*</span>
+<a name="l00318"></a>00318 <span class="comment">#################################</span>
+<a name="l00319"></a>00319 <span class="comment"># BEGIN OF FUNCTION DEFINITIONS #</span>
+<a name="l00320"></a>00320 <span class="comment">#################################</span>
+<a name="l00321"></a>00321 <span class="comment">*/</span>
+<a name="l00322"></a><a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">00322</a> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin</a>(<span class="keywordtype">int</span> size, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00323"></a>00323 <span class="keywordtype">int</span> energy;
+<a name="l00324"></a>00324
+<a name="l00325"></a>00325 energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(<span class="keywordtype">int</span>)(P->lxc*log((size)/30.));
+<a name="l00326"></a>00326 <span class="keywordflow">if</span> (P-><a class="code" href="structparamT.html#aeb912822ef912705bc202b14f9d71ad9" title="Model details to be used in the recursions.">model_details</a>.<a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617" title="Include special hairpin contributions for tri, tetra and hexaloops.">special_hp</a>){
+<a name="l00327"></a>00327 <span class="keywordflow">if</span> (size == 4) { <span class="comment">/* check for tetraloop bonus */</span>
+<a name="l00328"></a>00328 <span class="keywordtype">char</span> tl[7]={0}, *ts;
+<a name="l00329"></a>00329 strncpy(tl, <span class="keywordtype">string</span>, 6);
+<a name="l00330"></a>00330 <span class="keywordflow">if</span> ((ts=strstr(P->Tetraloops, tl)))
+<a name="l00331"></a>00331 <span class="keywordflow">return</span> (P->Tetraloop_E[(ts - P->Tetraloops)/7]);
+<a name="l00332"></a>00332 }
+<a name="l00333"></a>00333 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (size == 6) {
+<a name="l00334"></a>00334 <span class="keywordtype">char</span> tl[9]={0}, *ts;
+<a name="l00335"></a>00335 strncpy(tl, <span class="keywordtype">string</span>, 8);
+<a name="l00336"></a>00336 <span class="keywordflow">if</span> ((ts=strstr(P->Hexaloops, tl)))
+<a name="l00337"></a>00337 <span class="keywordflow">return</span> (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);
+<a name="l00338"></a>00338 }
+<a name="l00339"></a>00339 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (size == 3) {
+<a name="l00340"></a>00340 <span class="keywordtype">char</span> tl[6]={0,0,0,0,0,0}, *ts;
+<a name="l00341"></a>00341 strncpy(tl, <span class="keywordtype">string</span>, 5);
+<a name="l00342"></a>00342 <span class="keywordflow">if</span> ((ts=strstr(P->Triloops, tl))) {
+<a name="l00343"></a>00343 <span class="keywordflow">return</span> (P->Triloop_E[(ts - P->Triloops)/6]);
+<a name="l00344"></a>00344 }
+<a name="l00345"></a>00345 <span class="keywordflow">return</span> (energy + (type>2 ? P->TerminalAU : 0));
+<a name="l00346"></a>00346 }
+<a name="l00347"></a>00347 }
+<a name="l00348"></a>00348 energy += P->mismatchH[type][si1][sj1];
+<a name="l00349"></a>00349
+<a name="l00350"></a>00350 <span class="keywordflow">return</span> energy;
+<a name="l00351"></a>00351 }
+<a name="l00352"></a>00352
+<a name="l00353"></a><a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">00353</a> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop</a>(<span class="keywordtype">int</span> n1, <span class="keywordtype">int</span> n2, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type_2, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> sp1, <span class="keywordtype">int</span> sq1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00354"></a>00354 <span class="comment">/* compute energy of degree 2 loop (stack bulge or interior) */</span>
+<a name="l00355"></a>00355 <span class="keywordtype">int</span> nl, ns, energy;
+<a name="l00356"></a>00356 energy = <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>;
+<a name="l00357"></a>00357
+<a name="l00358"></a>00358 <span class="keywordflow">if</span> (n1>n2) { nl=n1; ns=n2;}
+<a name="l00359"></a>00359 <span class="keywordflow">else</span> {nl=n2; ns=n1;}
+<a name="l00360"></a>00360
+<a name="l00361"></a>00361 <span class="keywordflow">if</span> (nl == 0)
+<a name="l00362"></a>00362 <span class="keywordflow">return</span> P->stack[type][type_2]; <span class="comment">/* stack */</span>
+<a name="l00363"></a>00363
+<a name="l00364"></a>00364 <span class="keywordflow">if</span> (ns==0) { <span class="comment">/* bulge */</span>
+<a name="l00365"></a>00365 energy = (nl<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?P->bulge[nl]:
+<a name="l00366"></a>00366 (P->bulge[30]+(<span class="keywordtype">int</span>)(P->lxc*log(nl/30.)));
+<a name="l00367"></a>00367 <span class="keywordflow">if</span> (nl==1) energy += P->stack[type][type_2];
+<a name="l00368"></a>00368 <span class="keywordflow">else</span> {
+<a name="l00369"></a>00369 <span class="keywordflow">if</span> (type>2) energy += P->TerminalAU;
+<a name="l00370"></a>00370 <span class="keywordflow">if</span> (type_2>2) energy += P->TerminalAU;
+<a name="l00371"></a>00371 }
+<a name="l00372"></a>00372 <span class="keywordflow">return</span> energy;
+<a name="l00373"></a>00373 }
+<a name="l00374"></a>00374 <span class="keywordflow">else</span> { <span class="comment">/* interior loop */</span>
+<a name="l00375"></a>00375 <span class="keywordflow">if</span> (ns==1) {
+<a name="l00376"></a>00376 <span class="keywordflow">if</span> (nl==1) <span class="comment">/* 1x1 loop */</span>
+<a name="l00377"></a>00377 <span class="keywordflow">return</span> P->int11[type][type_2][si1][sj1];
+<a name="l00378"></a>00378 <span class="keywordflow">if</span> (nl==2) { <span class="comment">/* 2x1 loop */</span>
+<a name="l00379"></a>00379 <span class="keywordflow">if</span> (n1==1)
+<a name="l00380"></a>00380 energy = P->int21[type][type_2][si1][sq1][sj1];
+<a name="l00381"></a>00381 <span class="keywordflow">else</span>
+<a name="l00382"></a>00382 energy = P->int21[type_2][type][sq1][si1][sp1];
+<a name="l00383"></a>00383 <span class="keywordflow">return</span> energy;
+<a name="l00384"></a>00384 }
+<a name="l00385"></a>00385 <span class="keywordflow">else</span> { <span class="comment">/* 1xn loop */</span>
+<a name="l00386"></a>00386 energy = (nl+1<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));
+<a name="l00387"></a>00387 energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(MAX_NINIO, (nl-ns)*P->ninio[2]);
+<a name="l00388"></a>00388 energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];
+<a name="l00389"></a>00389 <span class="keywordflow">return</span> energy;
+<a name="l00390"></a>00390 }
+<a name="l00391"></a>00391 }
+<a name="l00392"></a>00392 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ns==2) {
+<a name="l00393"></a>00393 <span class="keywordflow">if</span>(nl==2) { <span class="comment">/* 2x2 loop */</span>
+<a name="l00394"></a>00394 <span class="keywordflow">return</span> P->int22[type][type_2][si1][sp1][sq1][sj1];}
+<a name="l00395"></a>00395 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (nl==3){ <span class="comment">/* 2x3 loop */</span>
+<a name="l00396"></a>00396 energy = P->internal_loop[5]+P->ninio[2];
+<a name="l00397"></a>00397 energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];
+<a name="l00398"></a>00398 <span class="keywordflow">return</span> energy;
+<a name="l00399"></a>00399 }
+<a name="l00400"></a>00400
+<a name="l00401"></a>00401 }
+<a name="l00402"></a>00402 { <span class="comment">/* generic interior loop (no else here!)*/</span>
+<a name="l00403"></a>00403 energy = (n1+n2<=<a class="code" href="energy__const_8h.html#ad1bd6eabac419670ddd3c9ed82145988">MAXLOOP</a>)?(P->internal_loop[n1+n2]) : (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));
+<a name="l00404"></a>00404
+<a name="l00405"></a>00405 energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(MAX_NINIO, (nl-ns)*P->ninio[2]);
+<a name="l00406"></a>00406
+<a name="l00407"></a>00407 energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];
+<a name="l00408"></a>00408 }
+<a name="l00409"></a>00409 }
+<a name="l00410"></a>00410 <span class="keywordflow">return</span> energy;
+<a name="l00411"></a>00411 }
+<a name="l00412"></a>00412
+<a name="l00413"></a><a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">00413</a> INLINE PRIVATE <span class="keywordtype">int</span> <a class="code" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">E_Stem</a>(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> extLoop, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00414"></a>00414 <span class="keywordtype">int</span> energy = 0;
+<a name="l00415"></a>00415 <span class="keywordtype">int</span> d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;
+<a name="l00416"></a>00416 <span class="keywordtype">int</span> d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;
+<a name="l00417"></a>00417
+<a name="l00418"></a>00418 <span class="keywordflow">if</span>(type > 2)
+<a name="l00419"></a>00419 energy += P->TerminalAU;
+<a name="l00420"></a>00420
+<a name="l00421"></a>00421 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0)
+<a name="l00422"></a>00422 energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];
+<a name="l00423"></a>00423 <span class="keywordflow">else</span>
+<a name="l00424"></a>00424 energy += d5 + d3;
+<a name="l00425"></a>00425
+<a name="l00426"></a>00426 <span class="keywordflow">if</span>(!extLoop) energy += P->MLintern[type];
+<a name="l00427"></a>00427 <span class="keywordflow">return</span> energy;
+<a name="l00428"></a>00428 }
+<a name="l00429"></a>00429
+<a name="l00430"></a>00430 INLINE PRIVATE <span class="keywordtype">int</span> E_ExtLoop(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00431"></a>00431 <span class="keywordtype">int</span> energy = 0;
+<a name="l00432"></a>00432 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){
+<a name="l00433"></a>00433 energy += P->mismatchExt[type][si1][sj1];
+<a name="l00434"></a>00434 }
+<a name="l00435"></a>00435 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (si1 >= 0){
+<a name="l00436"></a>00436 energy += P->dangle5[type][si1];
+<a name="l00437"></a>00437 }
+<a name="l00438"></a>00438 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sj1 >= 0){
+<a name="l00439"></a>00439 energy += P->dangle3[type][sj1];
+<a name="l00440"></a>00440 }
+<a name="l00441"></a>00441
+<a name="l00442"></a>00442 <span class="keywordflow">if</span>(type > 2)
+<a name="l00443"></a>00443 energy += P->TerminalAU;
+<a name="l00444"></a>00444
+<a name="l00445"></a>00445 <span class="keywordflow">return</span> energy;
+<a name="l00446"></a>00446 }
+<a name="l00447"></a>00447
+<a name="l00448"></a>00448 INLINE PRIVATE <span class="keywordtype">int</span> E_MLstem(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00449"></a>00449 <span class="keywordtype">int</span> energy = 0;
+<a name="l00450"></a>00450 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){
+<a name="l00451"></a>00451 energy += P->mismatchM[type][si1][sj1];
+<a name="l00452"></a>00452 }
+<a name="l00453"></a>00453 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (si1 >= 0){
+<a name="l00454"></a>00454 energy += P->dangle5[type][si1];
+<a name="l00455"></a>00455 }
+<a name="l00456"></a>00456 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sj1 >= 0){
+<a name="l00457"></a>00457 energy += P->dangle3[type][sj1];
+<a name="l00458"></a>00458 }
+<a name="l00459"></a>00459
+<a name="l00460"></a>00460 <span class="keywordflow">if</span>(type > 2)
+<a name="l00461"></a>00461 energy += P->TerminalAU;
+<a name="l00462"></a>00462
+<a name="l00463"></a>00463 energy += P->MLintern[type];
+<a name="l00464"></a>00464
+<a name="l00465"></a>00465 <span class="keywordflow">return</span> energy;
+<a name="l00466"></a>00466 }
+<a name="l00467"></a>00467
+<a name="l00468"></a><a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">00468</a> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin</a>(<span class="keywordtype">int</span> u, <span class="keywordtype">int</span> type, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P){
+<a name="l00469"></a>00469 <span class="keywordtype">double</span> q, kT;
+<a name="l00470"></a>00470 kT = P->kT; <span class="comment">/* kT in cal/mol */</span>
+<a name="l00471"></a>00471
+<a name="l00472"></a>00472 <span class="keywordflow">if</span>(u <= 30)
+<a name="l00473"></a>00473 q = P->exphairpin[u];
+<a name="l00474"></a>00474 <span class="keywordflow">else</span>
+<a name="l00475"></a>00475 q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);
+<a name="l00476"></a>00476
+<a name="l00477"></a>00477 <span class="keywordflow">if</span>(u < 3) <span class="keywordflow">return</span> q; <span class="comment">/* should only be the case when folding alignments */</span>
+<a name="l00478"></a>00478
+<a name="l00479"></a>00479 <span class="keywordflow">if</span> ((P-><a class="code" href="structpf__paramT.html#a43ec875779c5e7c8bf5fa7e837ec6d09" title="Model details to be used in the recursions.">model_details</a>.<a class="code" href="structmodel__detailsT.html#a9d73fde17b0465311a80f607faa85617" title="Include special hairpin contributions for tri, tetra and hexaloops.">special_hp</a>)&&(u==4)) {
+<a name="l00480"></a>00480 <span class="keywordtype">char</span> tl[7]={0,0,0,0,0,0,0}, *ts;
+<a name="l00481"></a>00481 strncpy(tl, <span class="keywordtype">string</span>, 6);
+<a name="l00482"></a>00482 <span class="keywordflow">if</span> ((ts=strstr(P->Tetraloops, tl))){
+<a name="l00483"></a>00483 <span class="keywordflow">if</span>(type != 7)
+<a name="l00484"></a>00484 <span class="keywordflow">return</span> (P->exptetra[(ts-P->Tetraloops)/7]);
+<a name="l00485"></a>00485 <span class="keywordflow">else</span>
+<a name="l00486"></a>00486 q *= P->exptetra[(ts-P->Tetraloops)/7];
+<a name="l00487"></a>00487 }
+<a name="l00488"></a>00488 }
+<a name="l00489"></a>00489 <span class="keywordflow">if</span> ((<a class="code" href="fold__vars_8h.html#a4f6265bdf0ead7ff4628a360adbfd77e" title="Include special stabilizing energies for some tri-, tetra- and hexa-loops;.">tetra_loop</a>)&&(u==6)) {
+<a name="l00490"></a>00490 <span class="keywordtype">char</span> tl[9]={0,0,0,0,0,0,0,0,0}, *ts;
+<a name="l00491"></a>00491 strncpy(tl, <span class="keywordtype">string</span>, 6);
+<a name="l00492"></a>00492 <span class="keywordflow">if</span> ((ts=strstr(P->Hexaloops, tl)))
+<a name="l00493"></a>00493 <span class="keywordflow">return</span> (P->exphex[(ts-P->Hexaloops)/9]);
+<a name="l00494"></a>00494 }
+<a name="l00495"></a>00495 <span class="keywordflow">if</span> (u==3) {
+<a name="l00496"></a>00496 <span class="keywordtype">char</span> tl[6]={0,0,0,0,0,0}, *ts;
+<a name="l00497"></a>00497 strncpy(tl, <span class="keywordtype">string</span>, 5);
+<a name="l00498"></a>00498 <span class="keywordflow">if</span> ((ts=strstr(P->Triloops, tl)))
+<a name="l00499"></a>00499 <span class="keywordflow">return</span> (P->exptri[(ts-P->Triloops)/6]);
+<a name="l00500"></a>00500 <span class="keywordflow">if</span> (type>2)
+<a name="l00501"></a>00501 q *= P->expTermAU;
+<a name="l00502"></a>00502 }
+<a name="l00503"></a>00503 <span class="keywordflow">else</span> <span class="comment">/* no mismatches for tri-loops */</span>
+<a name="l00504"></a>00504 q *= P->expmismatchH[type][si1][sj1];
+<a name="l00505"></a>00505
+<a name="l00506"></a>00506 <span class="keywordflow">return</span> q;
+<a name="l00507"></a>00507 }
+<a name="l00508"></a>00508
+<a name="l00509"></a><a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">00509</a> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop</a>(<span class="keywordtype">int</span> u1, <span class="keywordtype">int</span> u2, <span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type2, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keywordtype">short</span> sp1, <span class="keywordtype">short</span> sq1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P){
+<a name="l00510"></a>00510 <span class="keywordtype">int</span> ul, us, no_close = 0;
+<a name="l00511"></a>00511 <span class="keywordtype">double</span> z = 0.;
+<a name="l00512"></a>00512
+<a name="l00513"></a>00513 <span class="keywordflow">if</span> ((<a class="code" href="fold__vars_8h.html#aa8d1c7b92489179e1eafa562b7bdd259" title="GU allowed only inside stacks if set to 1.">no_closingGU</a>) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
+<a name="l00514"></a>00514 no_close = 1;
+<a name="l00515"></a>00515
+<a name="l00516"></a>00516 <span class="keywordflow">if</span> (u1>u2) { ul=u1; us=u2;}
+<a name="l00517"></a>00517 <span class="keywordflow">else</span> {ul=u2; us=u1;}
+<a name="l00518"></a>00518
+<a name="l00519"></a>00519 <span class="keywordflow">if</span> (ul==0) <span class="comment">/* stack */</span>
+<a name="l00520"></a>00520 z = P->expstack[type][type2];
+<a name="l00521"></a>00521 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(!no_close){
+<a name="l00522"></a>00522 <span class="keywordflow">if</span> (us==0) { <span class="comment">/* bulge */</span>
+<a name="l00523"></a>00523 z = P->expbulge[ul];
+<a name="l00524"></a>00524 <span class="keywordflow">if</span> (ul==1) z *= P->expstack[type][type2];
+<a name="l00525"></a>00525 <span class="keywordflow">else</span> {
+<a name="l00526"></a>00526 <span class="keywordflow">if</span> (type>2) z *= P->expTermAU;
+<a name="l00527"></a>00527 <span class="keywordflow">if</span> (type2>2) z *= P->expTermAU;
+<a name="l00528"></a>00528 }
+<a name="l00529"></a>00529 <span class="keywordflow">return</span> z;
+<a name="l00530"></a>00530 }
+<a name="l00531"></a>00531 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (us==1) {
+<a name="l00532"></a>00532 <span class="keywordflow">if</span> (ul==1){ <span class="comment">/* 1x1 loop */</span>
+<a name="l00533"></a>00533 <span class="keywordflow">return</span> P->expint11[type][type2][si1][sj1];
+<a name="l00534"></a>00534 }
+<a name="l00535"></a>00535 <span class="keywordflow">if</span> (ul==2) { <span class="comment">/* 2x1 loop */</span>
+<a name="l00536"></a>00536 <span class="keywordflow">if</span> (u1==1)
+<a name="l00537"></a>00537 <span class="keywordflow">return</span> P->expint21[type][type2][si1][sq1][sj1];
+<a name="l00538"></a>00538 <span class="keywordflow">else</span>
+<a name="l00539"></a>00539 <span class="keywordflow">return</span> P->expint21[type2][type][sq1][si1][sp1];
+<a name="l00540"></a>00540 }
+<a name="l00541"></a>00541 <span class="keywordflow">else</span> { <span class="comment">/* 1xn loop */</span>
+<a name="l00542"></a>00542 z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];
+<a name="l00543"></a>00543 <span class="keywordflow">return</span> z * P->expninio[2][ul-us];
+<a name="l00544"></a>00544 }
+<a name="l00545"></a>00545 }
+<a name="l00546"></a>00546 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (us==2) {
+<a name="l00547"></a>00547 <span class="keywordflow">if</span>(ul==2) <span class="comment">/* 2x2 loop */</span>
+<a name="l00548"></a>00548 <span class="keywordflow">return</span> P->expint22[type][type2][si1][sp1][sq1][sj1];
+<a name="l00549"></a>00549 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(ul==3){ <span class="comment">/* 2x3 loop */</span>
+<a name="l00550"></a>00550 z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];
+<a name="l00551"></a>00551 <span class="keywordflow">return</span> z * P->expninio[2][1];
+<a name="l00552"></a>00552 }
+<a name="l00553"></a>00553 }
+<a name="l00554"></a>00554 <span class="comment">/* generic interior loop (no else here!)*/</span>
+<a name="l00555"></a>00555 z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];
+<a name="l00556"></a>00556 <span class="keywordflow">return</span> z * P->expninio[2][ul-us];
+<a name="l00557"></a>00557
+<a name="l00558"></a>00558 }
+<a name="l00559"></a>00559 <span class="keywordflow">return</span> z;
+<a name="l00560"></a>00560 }
+<a name="l00561"></a>00561
+<a name="l00562"></a><a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">00562</a> INLINE PRIVATE <span class="keywordtype">double</span> <a class="code" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">exp_E_Stem</a>(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <span class="keywordtype">int</span> extLoop, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P){
+<a name="l00563"></a>00563 <span class="keywordtype">double</span> energy = 1.0;
+<a name="l00564"></a>00564 <span class="keywordtype">double</span> d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;
+<a name="l00565"></a>00565 <span class="keywordtype">double</span> d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;
+<a name="l00566"></a>00566
+<a name="l00567"></a>00567 <span class="keywordflow">if</span>(type > 2)
+<a name="l00568"></a>00568 energy *= P->expTermAU;
+<a name="l00569"></a>00569
+<a name="l00570"></a>00570 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0)
+<a name="l00571"></a>00571 energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];
+<a name="l00572"></a>00572 <span class="keywordflow">else</span>
+<a name="l00573"></a>00573 energy *= d5 * d3;
+<a name="l00574"></a>00574
+<a name="l00575"></a>00575 <span class="keywordflow">if</span>(!extLoop) energy *= P->expMLintern[type];
+<a name="l00576"></a>00576 <span class="keywordflow">return</span> energy;
+<a name="l00577"></a>00577 }
+<a name="l00578"></a>00578
+<a name="l00579"></a>00579 INLINE PRIVATE <span class="keywordtype">double</span> exp_E_MLstem(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P){
+<a name="l00580"></a>00580 <span class="keywordtype">double</span> energy = 1.0;
+<a name="l00581"></a>00581 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){
+<a name="l00582"></a>00582 energy *= P->expmismatchM[type][si1][sj1];
+<a name="l00583"></a>00583 }
+<a name="l00584"></a>00584 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(si1 >= 0){
+<a name="l00585"></a>00585 energy *= P->expdangle5[type][si1];
+<a name="l00586"></a>00586 }
+<a name="l00587"></a>00587 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(sj1 >= 0){
+<a name="l00588"></a>00588 energy *= P->expdangle3[type][sj1];
+<a name="l00589"></a>00589 }
+<a name="l00590"></a>00590
+<a name="l00591"></a>00591 <span class="keywordflow">if</span>(type > 2)
+<a name="l00592"></a>00592 energy *= P->expTermAU;
+<a name="l00593"></a>00593
+<a name="l00594"></a>00594 energy *= P->expMLintern[type];
+<a name="l00595"></a>00595 <span class="keywordflow">return</span> energy;
+<a name="l00596"></a>00596 }
+<a name="l00597"></a>00597
+<a name="l00598"></a>00598 INLINE PRIVATE <span class="keywordtype">double</span> exp_E_ExtLoop(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> si1, <span class="keywordtype">int</span> sj1, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *P){
+<a name="l00599"></a>00599 <span class="keywordtype">double</span> energy = 1.0;
+<a name="l00600"></a>00600 <span class="keywordflow">if</span>(si1 >= 0 && sj1 >= 0){
+<a name="l00601"></a>00601 energy *= P->expmismatchExt[type][si1][sj1];
+<a name="l00602"></a>00602 }
+<a name="l00603"></a>00603 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(si1 >= 0){
+<a name="l00604"></a>00604 energy *= P->expdangle5[type][si1];
+<a name="l00605"></a>00605 }
+<a name="l00606"></a>00606 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(sj1 >= 0){
+<a name="l00607"></a>00607 energy *= P->expdangle3[type][sj1];
+<a name="l00608"></a>00608 }
+<a name="l00609"></a>00609
+<a name="l00610"></a>00610 <span class="keywordflow">if</span>(type > 2)
+<a name="l00611"></a>00611 energy *= P->expTermAU;
+<a name="l00612"></a>00612
+<a name="l00613"></a>00613 <span class="keywordflow">return</span> energy;
+<a name="l00614"></a>00614 }
+<a name="l00615"></a>00615
+<a name="l00616"></a>00616 INLINE PRIVATE <span class="keywordtype">int</span> E_IntLoop_Co(<span class="keywordtype">int</span> type, <span class="keywordtype">int</span> type_2, <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j, <span class="keywordtype">int</span> p, <span class="keywordtype">int</span> q, <span class="keywordtype">int</span> cutpoint, <span class="keywordtype">short</span> si1, <span class="keywordtype">short</span> sj1, <span class="keywordtype">short</span> sp1, <span class="keywordtype">short</span> sq1, <span class="keywordtype">int</span> dangles, <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *P){
+<a name="l00617"></a>00617 <span class="keywordtype">int</span> energy = 0;
+<a name="l00618"></a>00618 <span class="keywordflow">if</span>(type > 2) energy += P->TerminalAU;
+<a name="l00619"></a>00619 <span class="keywordflow">if</span>(type_2 > 2) energy += P->TerminalAU;
+<a name="l00620"></a>00620
+<a name="l00621"></a>00621 <span class="keywordflow">if</span>(!dangles) <span class="keywordflow">return</span> energy;
+<a name="l00622"></a>00622
+<a name="l00623"></a>00623 <span class="keywordtype">int</span> ci = (i>=cutpoint)||((i+1)<cutpoint);
+<a name="l00624"></a>00624 <span class="keywordtype">int</span> cj = ((j-1)>=cutpoint)||(j<cutpoint);
+<a name="l00625"></a>00625 <span class="keywordtype">int</span> cp = ((p-1)>=cutpoint)||(p<cutpoint);
+<a name="l00626"></a>00626 <span class="keywordtype">int</span> cq = (q>=cutpoint)||((q+1)<cutpoint);
+<a name="l00627"></a>00627
+<a name="l00628"></a>00628 <span class="keywordtype">int</span> d3 = ci ? P->dangle3[type][si1] : 0;
+<a name="l00629"></a>00629 <span class="keywordtype">int</span> d5 = cj ? P->dangle5[type][sj1] : 0;
+<a name="l00630"></a>00630 <span class="keywordtype">int</span> d5_2 = cp ? P->dangle5[type_2][sp1] : 0;
+<a name="l00631"></a>00631 <span class="keywordtype">int</span> d3_2 = cq ? P->dangle3[type_2][sq1] : 0;
+<a name="l00632"></a>00632
+<a name="l00633"></a>00633 <span class="keywordtype">int</span> tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;
+<a name="l00634"></a>00634 <span class="keywordtype">int</span> tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;
+<a name="l00635"></a>00635
+<a name="l00636"></a>00636 <span class="keywordflow">if</span>(dangles == 2) <span class="keywordflow">return</span> energy + tmm + tmm_2;
+<a name="l00637"></a>00637
+<a name="l00638"></a>00638 <span class="comment">/* now we may have non-double dangles only */</span>
+<a name="l00639"></a>00639 <span class="keywordflow">if</span>(i+2 < p){
+<a name="l00640"></a>00640 <span class="keywordflow">if</span>(q+2 < j){ energy += tmm + tmm_2;}
+<a name="l00641"></a>00641 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){ energy += (cj && cq) ? <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}
+<a name="l00642"></a>00642 <span class="keywordflow">else</span> energy += d3 + d5_2;
+<a name="l00643"></a>00643 }
+<a name="l00644"></a>00644 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(i+2 == p){
+<a name="l00645"></a>00645 <span class="keywordflow">if</span>(q+2 < j){ energy += (ci && cp) ? <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}
+<a name="l00646"></a>00646 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){
+<a name="l00647"></a>00647 energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm, <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(tmm_2, <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d5 + d5_2, d3 + d3_2)));
+<a name="l00648"></a>00648 }
+<a name="l00649"></a>00649 <span class="keywordflow">else</span> energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d3, d5_2);
+<a name="l00650"></a>00650 }
+<a name="l00651"></a>00651 <span class="keywordflow">else</span>{
+<a name="l00652"></a>00652 <span class="keywordflow">if</span>(q+2 < j){ energy += d5 + d3_2;}
+<a name="l00653"></a>00653 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(q+2 == j){ energy += <a class="code" href="utils_8h.html#ae0b9cd0ce090bd69b951aa73e8fa4f7d">MIN2</a>(d5, d3_2);}
+<a name="l00654"></a>00654 }
+<a name="l00655"></a>00655 <span class="keywordflow">return</span> energy;
+<a name="l00656"></a>00656 }
+<a name="l00657"></a>00657
+<a name="l00658"></a>00658 <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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