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+<div class="title">loop_energies.h</div> </div>
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+<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>
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