1 \hypertarget{loop__energies_8h}{\section{loop\-\_\-energies.\-h}
2 \label{loop__energies_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/loop\-\_\-energies.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/loop\-\_\-energies.\-h}}
6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
8 00003 \textcolor{preprocessor}{}
9 00004 \textcolor{preprocessor}{#include <stdio.h>}
10 00005 \textcolor{preprocessor}{#include <stdlib.h>}
11 00006 \textcolor{preprocessor}{#include <math.h>}
12 00007 \textcolor{preprocessor}{#include <ctype.h>}
13 00008 \textcolor{preprocessor}{#include <string.h>}
14 00009 \textcolor{preprocessor}{#include "\hyperlink{params_8h}{params.h}"}
15 00010 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
16 00011 \textcolor{preprocessor}{#include "energy\_par.h"}
18 00013 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
19 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline}
20 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
21 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE}
22 00017 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
23 00018 \textcolor{preprocessor}{}
24 00054 INLINE PRIVATE \textcolor{keywordtype}{int} E\_MLstem( \textcolor{keywordtype}{int} type,
25 00055 \textcolor{keywordtype}{int} si1,
26 00056 \textcolor{keywordtype}{int} sj1,
27 00057 \hyperlink{structparamT}{paramT} *P);
29 00065 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_MLstem(\textcolor{keywordtype}{int} type,
30 00066 \textcolor{keywordtype}{int} si1,
31 00067 \textcolor{keywordtype}{int} sj1,
32 00068 \hyperlink{structpf__paramT}{pf\_paramT} *P);
34 00089 INLINE PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type,
35 00090 \textcolor{keywordtype}{int} si1,
36 00091 \textcolor{keywordtype}{int} sj1,
37 00092 \hyperlink{structparamT}{paramT} *P);
39 00100 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_ExtLoop( \textcolor{keywordtype}{int} type,
40 00101 \textcolor{keywordtype}{int} si1,
41 00102 \textcolor{keywordtype}{int} sj1,
42 00103 \hyperlink{structpf__paramT}{pf\_paramT} *P);
44 00149 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_IntLoop}(\textcolor{keywordtype}{int} n1,
45 00150 \textcolor{keywordtype}{int} n2,
46 00151 \textcolor{keywordtype}{int} type,
47 00152 \textcolor{keywordtype}{int} type\_2,
48 00153 \textcolor{keywordtype}{int} si1,
49 00154 \textcolor{keywordtype}{int} sj1,
50 00155 \textcolor{keywordtype}{int} sp1,
51 00156 \textcolor{keywordtype}{int} sq1,
52 00157 \hyperlink{structparamT}{paramT} *P);
55 00191 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_Hairpin}(\textcolor{keywordtype}{int} size,
56 00192 \textcolor{keywordtype}{int} type,
57 00193 \textcolor{keywordtype}{int} si1,
58 00194 \textcolor{keywordtype}{int} sj1,
59 00195 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
60 00196 \hyperlink{structparamT}{paramT} *P);
62 00243 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{E\_Stem}( \textcolor{keywordtype}{int} type,
63 00244 \textcolor{keywordtype}{int} si1,
64 00245 \textcolor{keywordtype}{int} sj1,
65 00246 \textcolor{keywordtype}{int} extLoop,
66 00247 \hyperlink{structparamT}{paramT} *P);
68 00257 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{exp\_E\_Stem}(\textcolor{keywordtype}{int} type,
69 00258 \textcolor{keywordtype}{int} si1,
70 00259 \textcolor{keywordtype}{int} sj1,
71 00260 \textcolor{keywordtype}{int} extLoop,
72 00261 \hyperlink{structpf__paramT}{pf\_paramT} *P);
74 00280 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\_E\_Hairpin}( \textcolor{keywordtype}{int} u,
75 00281 \textcolor{keywordtype}{int} type,
76 00282 \textcolor{keywordtype}{short} si1,
77 00283 \textcolor{keywordtype}{short} sj1,
78 00284 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
79 00285 \hyperlink{structpf__paramT}{pf\_paramT} *P);
81 00306 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\_E\_IntLoop}(\textcolor{keywordtype}{int} u1,
82 00307 \textcolor{keywordtype}{int} u2,
83 00308 \textcolor{keywordtype}{int} type,
84 00309 \textcolor{keywordtype}{int} type2,
85 00310 \textcolor{keywordtype}{short} si1,
86 00311 \textcolor{keywordtype}{short} sj1,
87 00312 \textcolor{keywordtype}{short} sp1,
88 00313 \textcolor{keywordtype}{short} sq1,
89 00314 \hyperlink{structpf__paramT}{pf\_paramT} *P);
92 00317 \textcolor{comment}{/*}
93 00318 \textcolor{comment}{#################################}
94 00319 \textcolor{comment}{# BEGIN OF FUNCTION DEFINITIONS #}
95 00320 \textcolor{comment}{#################################}
96 00321 \textcolor{comment}{*/}
97 \hypertarget{loop__energies_8h_source_l00322}{}\hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{00322} INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_Hairpin}(\textcolor{keywordtype}{int} size, \textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
98 \hyperlink{structparamT}{paramT} *P)\{
99 00323 \textcolor{keywordtype}{int} energy;
101 00325 energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(\textcolor{keywordtype}{int})(P->lxc*log((size)/30.));
102 00326 \textcolor{keywordflow}{if} (P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp})\{
103 00327 \textcolor{keywordflow}{if} (size == 4) \{ \textcolor{comment}{/* check for tetraloop bonus */}
104 00328 \textcolor{keywordtype}{char} tl[7]=\{0\}, *ts;
105 00329 strncpy(tl, \textcolor{keywordtype}{string}, 6);
106 00330 \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))
107 00331 \textcolor{keywordflow}{return} (P->Tetraloop\_E[(ts - P->Tetraloops)/7]);
109 00333 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 6) \{
110 00334 \textcolor{keywordtype}{char} tl[9]=\{0\}, *ts;
111 00335 strncpy(tl, \textcolor{keywordtype}{string}, 8);
112 00336 \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
113 00337 \textcolor{keywordflow}{return} (energy = P->Hexaloop\_E[(ts - P->Hexaloops)/9]);
115 00339 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 3) \{
116 00340 \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
117 00341 strncpy(tl, \textcolor{keywordtype}{string}, 5);
118 00342 \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl))) \{
119 00343 \textcolor{keywordflow}{return} (P->Triloop\_E[(ts - P->Triloops)/6]);
121 00345 \textcolor{keywordflow}{return} (energy + (type>2 ? P->TerminalAU : 0));
124 00348 energy += P->mismatchH[type][si1][sj1];
126 00350 \textcolor{keywordflow}{return} energy;
129 \hypertarget{loop__energies_8h_source_l00353}{}\hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{00353} INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_IntLoop}(\textcolor{keywordtype}{int} n1, \textcolor{keywordtype}{int} n2, \textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} type\_2, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \textcolor{keywordtype}{int} sp1, \textcolor{keywordtype}{int}
130 sq1, \hyperlink{structparamT}{paramT} *P)\{
131 00354 \textcolor{comment}{/* compute energy of degree 2 loop (stack bulge or interior) */}
132 00355 \textcolor{keywordtype}{int} nl, ns, energy;
133 00356 energy = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
135 00358 \textcolor{keywordflow}{if} (n1>n2) \{ nl=n1; ns=n2;\}
136 00359 \textcolor{keywordflow}{else} \{nl=n2; ns=n1;\}
138 00361 \textcolor{keywordflow}{if} (nl == 0)
139 00362 \textcolor{keywordflow}{return} P->stack[type][type\_2]; \textcolor{comment}{/* stack */}
141 00364 \textcolor{keywordflow}{if} (ns==0) \{ \textcolor{comment}{/* bulge */}
142 00365 energy = (nl<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?P->bulge[nl]:
143 00366 (P->bulge[30]+(\textcolor{keywordtype}{int})(P->lxc*log(nl/30.)));
144 00367 \textcolor{keywordflow}{if} (nl==1) energy += P->stack[type][type\_2];
145 00368 \textcolor{keywordflow}{else} \{
146 00369 \textcolor{keywordflow}{if} (type>2) energy += P->TerminalAU;
147 00370 \textcolor{keywordflow}{if} (type\_2>2) energy += P->TerminalAU;
149 00372 \textcolor{keywordflow}{return} energy;
151 00374 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* interior loop */}
152 00375 \textcolor{keywordflow}{if} (ns==1) \{
153 00376 \textcolor{keywordflow}{if} (nl==1) \textcolor{comment}{/* 1x1 loop */}
154 00377 \textcolor{keywordflow}{return} P->int11[type][type\_2][si1][sj1];
155 00378 \textcolor{keywordflow}{if} (nl==2) \{ \textcolor{comment}{/* 2x1 loop */}
156 00379 \textcolor{keywordflow}{if} (n1==1)
157 00380 energy = P->int21[type][type\_2][si1][sq1][sj1];
158 00381 \textcolor{keywordflow}{else}
159 00382 energy = P->int21[type\_2][type][sq1][si1][sp1];
160 00383 \textcolor{keywordflow}{return} energy;
162 00385 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* 1xn loop */}
163 00386 energy = (nl+1<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[nl+1]) : (P->internal\_loop[30]+(int)(P->lxc*log((
165 00387 energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
166 00388 energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type\_2][sq1][sp1];
167 00389 \textcolor{keywordflow}{return} energy;
170 00392 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (ns==2) \{
171 00393 \textcolor{keywordflow}{if}(nl==2) \{ \textcolor{comment}{/* 2x2 loop */}
172 00394 \textcolor{keywordflow}{return} P->int22[type][type\_2][si1][sp1][sq1][sj1];\}
173 00395 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (nl==3)\{ \textcolor{comment}{/* 2x3 loop */}
174 00396 energy = P->internal\_loop[5]+P->ninio[2];
175 00397 energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type\_2][sq1][sp1];
176 00398 \textcolor{keywordflow}{return} energy;
180 00402 \{ \textcolor{comment}{/* generic interior loop (no else here!)*/}
181 00403 energy = (n1+n2<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[n1+n2]) : (P->internal\_loop[30]+(int)(P->lxc*log((
184 00405 energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
186 00407 energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type\_2][sq1][sp1];
189 00410 \textcolor{keywordflow}{return} energy;
192 \hypertarget{loop__energies_8h_source_l00413}{}\hyperlink{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{00413} INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{E\_Stem}(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \textcolor{keywordtype}{int} extLoop, \hyperlink{structparamT}{paramT} *P)\{
193 00414 \textcolor{keywordtype}{int} energy = 0;
194 00415 \textcolor{keywordtype}{int} d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;
195 00416 \textcolor{keywordtype}{int} d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;
197 00418 \textcolor{keywordflow}{if}(type > 2)
198 00419 energy += P->TerminalAU;
200 00421 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
201 00422 energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];
202 00423 \textcolor{keywordflow}{else}
203 00424 energy += d5 + d3;
205 00426 \textcolor{keywordflow}{if}(!extLoop) energy += P->MLintern[type];
206 00427 \textcolor{keywordflow}{return} energy;
209 00430 INLINE PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
210 00431 \textcolor{keywordtype}{int} energy = 0;
211 00432 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
212 00433 energy += P->mismatchExt[type][si1][sj1];
214 00435 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
215 00436 energy += P->dangle5[type][si1];
217 00438 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
218 00439 energy += P->dangle3[type][sj1];
221 00442 \textcolor{keywordflow}{if}(type > 2)
222 00443 energy += P->TerminalAU;
224 00445 \textcolor{keywordflow}{return} energy;
227 00448 INLINE PRIVATE \textcolor{keywordtype}{int} E\_MLstem(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
228 00449 \textcolor{keywordtype}{int} energy = 0;
229 00450 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
230 00451 energy += P->mismatchM[type][si1][sj1];
232 00453 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
233 00454 energy += P->dangle5[type][si1];
235 00456 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
236 00457 energy += P->dangle3[type][sj1];
239 00460 \textcolor{keywordflow}{if}(type > 2)
240 00461 energy += P->TerminalAU;
242 00463 energy += P->MLintern[type];
244 00465 \textcolor{keywordflow}{return} energy;
247 \hypertarget{loop__energies_8h_source_l00468}{}\hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{00468} INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\_E\_Hairpin}(\textcolor{keywordtype}{int} u, \textcolor{keywordtype}{int} type, \textcolor{keywordtype}{short} si1, \textcolor{keywordtype}{short} sj1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}
248 , \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
249 00469 \textcolor{keywordtype}{double} q, kT;
250 00470 kT = P->kT; \textcolor{comment}{/* kT in cal/mol */}
252 00472 \textcolor{keywordflow}{if}(u <= 30)
253 00473 q = P->exphairpin[u];
254 00474 \textcolor{keywordflow}{else}
255 00475 q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);
257 00477 \textcolor{keywordflow}{if}(u < 3) \textcolor{keywordflow}{return} q; \textcolor{comment}{/* should only be the case when folding alignments */}
259 00479 \textcolor{keywordflow}{if} ((P->\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model\_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp})&&(u==4)) \{
260 00480 \textcolor{keywordtype}{char} tl[7]=\{0,0,0,0,0,0,0\}, *ts;
261 00481 strncpy(tl, \textcolor{keywordtype}{string}, 6);
262 00482 \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))\{
263 00483 \textcolor{keywordflow}{if}(type != 7)
264 00484 \textcolor{keywordflow}{return} (P->exptetra[(ts-P->Tetraloops)/7]);
265 00485 \textcolor{keywordflow}{else}
266 00486 q *= P->exptetra[(ts-P->Tetraloops)/7];
269 00489 \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\_loop})&&(u==6)) \{
270 00490 \textcolor{keywordtype}{char} tl[9]=\{0,0,0,0,0,0,0,0,0\}, *ts;
271 00491 strncpy(tl, \textcolor{keywordtype}{string}, 6);
272 00492 \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
273 00493 \textcolor{keywordflow}{return} (P->exphex[(ts-P->Hexaloops)/9]);
275 00495 \textcolor{keywordflow}{if} (u==3) \{
276 00496 \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
277 00497 strncpy(tl, \textcolor{keywordtype}{string}, 5);
278 00498 \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl)))
279 00499 \textcolor{keywordflow}{return} (P->exptri[(ts-P->Triloops)/6]);
280 00500 \textcolor{keywordflow}{if} (type>2)
281 00501 q *= P->expTermAU;
283 00503 \textcolor{keywordflow}{else} \textcolor{comment}{/* no mismatches for tri-loops */}
284 00504 q *= P->expmismatchH[type][si1][sj1];
286 00506 \textcolor{keywordflow}{return} q;
289 \hypertarget{loop__energies_8h_source_l00509}{}\hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{00509} INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\_E\_IntLoop}(\textcolor{keywordtype}{int} u1, \textcolor{keywordtype}{int} u2, \textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} type2, \textcolor{keywordtype}{short} si1, \textcolor{keywordtype}{short} sj1
290 , \textcolor{keywordtype}{short} sp1, \textcolor{keywordtype}{short} sq1, \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
291 00510 \textcolor{keywordtype}{int} ul, us, no\_close = 0;
292 00511 \textcolor{keywordtype}{double} z = 0.;
294 00513 \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\_closingGU}) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
297 00516 \textcolor{keywordflow}{if} (u1>u2) \{ ul=u1; us=u2;\}
298 00517 \textcolor{keywordflow}{else} \{ul=u2; us=u1;\}
300 00519 \textcolor{keywordflow}{if} (ul==0) \textcolor{comment}{/* stack */}
301 00520 z = P->expstack[type][type2];
302 00521 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(!no\_close)\{
303 00522 \textcolor{keywordflow}{if} (us==0) \{ \textcolor{comment}{/* bulge */}
304 00523 z = P->expbulge[ul];
305 00524 \textcolor{keywordflow}{if} (ul==1) z *= P->expstack[type][type2];
306 00525 \textcolor{keywordflow}{else} \{
307 00526 \textcolor{keywordflow}{if} (type>2) z *= P->expTermAU;
308 00527 \textcolor{keywordflow}{if} (type2>2) z *= P->expTermAU;
310 00529 \textcolor{keywordflow}{return} z;
312 00531 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==1) \{
313 00532 \textcolor{keywordflow}{if} (ul==1)\{ \textcolor{comment}{/* 1x1 loop */}
314 00533 \textcolor{keywordflow}{return} P->expint11[type][type2][si1][sj1];
316 00535 \textcolor{keywordflow}{if} (ul==2) \{ \textcolor{comment}{/* 2x1 loop */}
317 00536 \textcolor{keywordflow}{if} (u1==1)
318 00537 \textcolor{keywordflow}{return} P->expint21[type][type2][si1][sq1][sj1];
319 00538 \textcolor{keywordflow}{else}
320 00539 \textcolor{keywordflow}{return} P->expint21[type2][type][sq1][si1][sp1];
322 00541 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* 1xn loop */}
323 00542 z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];
324 00543 \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
327 00546 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==2) \{
328 00547 \textcolor{keywordflow}{if}(ul==2) \textcolor{comment}{/* 2x2 loop */}
329 00548 \textcolor{keywordflow}{return} P->expint22[type][type2][si1][sp1][sq1][sj1];
330 00549 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(ul==3)\{ \textcolor{comment}{/* 2x3 loop */}
331 00550 z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];
332 00551 \textcolor{keywordflow}{return} z * P->expninio[2][1];
335 00554 \textcolor{comment}{/* generic interior loop (no else here!)*/}
336 00555 z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];
337 00556 \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
340 00559 \textcolor{keywordflow}{return} z;
343 \hypertarget{loop__energies_8h_source_l00562}{}\hyperlink{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{00562} INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{exp\_E\_Stem}(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \textcolor{keywordtype}{int} extLoop,
344 \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
345 00563 \textcolor{keywordtype}{double} energy = 1.0;
346 00564 \textcolor{keywordtype}{double} d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;
347 00565 \textcolor{keywordtype}{double} d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;
349 00567 \textcolor{keywordflow}{if}(type > 2)
350 00568 energy *= P->expTermAU;
352 00570 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
353 00571 energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];
354 00572 \textcolor{keywordflow}{else}
355 00573 energy *= d5 * d3;
357 00575 \textcolor{keywordflow}{if}(!extLoop) energy *= P->expMLintern[type];
358 00576 \textcolor{keywordflow}{return} energy;
361 00579 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_MLstem(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
362 00580 \textcolor{keywordtype}{double} energy = 1.0;
363 00581 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
364 00582 energy *= P->expmismatchM[type][si1][sj1];
366 00584 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
367 00585 energy *= P->expdangle5[type][si1];
369 00587 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
370 00588 energy *= P->expdangle3[type][sj1];
373 00591 \textcolor{keywordflow}{if}(type > 2)
374 00592 energy *= P->expTermAU;
376 00594 energy *= P->expMLintern[type];
377 00595 \textcolor{keywordflow}{return} energy;
380 00598 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_ExtLoop(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
381 00599 \textcolor{keywordtype}{double} energy = 1.0;
382 00600 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
383 00601 energy *= P->expmismatchExt[type][si1][sj1];
385 00603 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
386 00604 energy *= P->expdangle5[type][si1];
388 00606 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
389 00607 energy *= P->expdangle3[type][sj1];
392 00610 \textcolor{keywordflow}{if}(type > 2)
393 00611 energy *= P->expTermAU;
395 00613 \textcolor{keywordflow}{return} energy;
398 00616 INLINE PRIVATE \textcolor{keywordtype}{int} E\_IntLoop\_Co(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} type\_2, \textcolor{keywordtype}{int} i, \textcolor{keywordtype}{int} j, \textcolor{keywordtype}{int} p, \textcolor{keywordtype}{int} q, \textcolor{keywordtype}{int} cutpoint, \textcolor{keywordtype}{short}
399 si1, \textcolor{keywordtype}{short} sj1, \textcolor{keywordtype}{short} sp1, \textcolor{keywordtype}{short} sq1, \textcolor{keywordtype}{int} dangles, \hyperlink{structparamT}{paramT} *P)\{
400 00617 \textcolor{keywordtype}{int} energy = 0;
401 00618 \textcolor{keywordflow}{if}(type > 2) energy += P->TerminalAU;
402 00619 \textcolor{keywordflow}{if}(type\_2 > 2) energy += P->TerminalAU;
404 00621 \textcolor{keywordflow}{if}(!dangles) \textcolor{keywordflow}{return} energy;
406 00623 \textcolor{keywordtype}{int} ci = (i>=cutpoint)||((i+1)<cutpoint);
407 00624 \textcolor{keywordtype}{int} cj = ((j-1)>=cutpoint)||(j<cutpoint);
408 00625 \textcolor{keywordtype}{int} cp = ((p-1)>=cutpoint)||(p<cutpoint);
409 00626 \textcolor{keywordtype}{int} cq = (q>=cutpoint)||((q+1)<cutpoint);
411 00628 \textcolor{keywordtype}{int} d3 = ci ? P->dangle3[type][si1] : 0;
412 00629 \textcolor{keywordtype}{int} d5 = cj ? P->dangle5[type][sj1] : 0;
413 00630 \textcolor{keywordtype}{int} d5\_2 = cp ? P->dangle5[type\_2][sp1] : 0;
414 00631 \textcolor{keywordtype}{int} d3\_2 = cq ? P->dangle3[type\_2][sq1] : 0;
416 00633 \textcolor{keywordtype}{int} tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;
417 00634 \textcolor{keywordtype}{int} tmm\_2 = (cp && cq) ? P->mismatchExt[type\_2][sp1][sq1] : d5\_2 + d3\_2;
419 00636 \textcolor{keywordflow}{if}(dangles == 2) \textcolor{keywordflow}{return} energy + tmm + tmm\_2;
421 00638 \textcolor{comment}{/* now we may have non-double dangles only */}
422 00639 \textcolor{keywordflow}{if}(i+2 < p)\{
423 00640 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += tmm + tmm\_2;\}
424 00641 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{ energy += (cj && cq) ? \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm + d5\_2, tmm\_2 + d3) : tmm + tmm\_2;\}
425 00642 \textcolor{keywordflow}{else} energy += d3 + d5\_2;
427 00644 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(i+2 == p)\{
428 00645 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += (ci && cp) ? \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm + d3\_2, tmm\_2 + d5) : tmm + tmm\_2;\}
429 00646 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{
430 00647 energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm, \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm\_2, \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d5 + d5\_2, d3 + d3\_2)));
432 00649 \textcolor{keywordflow}{else} energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d3, d5\_2);
434 00651 \textcolor{keywordflow}{else}\{
435 00652 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += d5 + d3\_2;\}
436 00653 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{ energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d5, d3\_2);\}
438 00655 \textcolor{keywordflow}{return} energy;
441 00658 \textcolor{preprocessor}{#endif}