--- /dev/null
+\hypertarget{loop__energies_8h}{\section{loop\-\_\-energies.\-h}
+\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}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
+00003 \textcolor{preprocessor}{}
+00004 \textcolor{preprocessor}{#include <stdio.h>}
+00005 \textcolor{preprocessor}{#include <stdlib.h>}
+00006 \textcolor{preprocessor}{#include <math.h>}
+00007 \textcolor{preprocessor}{#include <ctype.h>}
+00008 \textcolor{preprocessor}{#include <string.h>}
+00009 \textcolor{preprocessor}{#include "\hyperlink{params_8h}{params.h}"}
+00010 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
+00011 \textcolor{preprocessor}{#include "energy\_par.h"}
+00012
+00013 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
+00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline}
+00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
+00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE}
+00017 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00018 \textcolor{preprocessor}{}
+00054 INLINE PRIVATE \textcolor{keywordtype}{int} E\_MLstem( \textcolor{keywordtype}{int} type,
+00055 \textcolor{keywordtype}{int} si1,
+00056 \textcolor{keywordtype}{int} sj1,
+00057 \hyperlink{structparamT}{paramT} *P);
+00058
+00065 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_MLstem(\textcolor{keywordtype}{int} type,
+00066 \textcolor{keywordtype}{int} si1,
+00067 \textcolor{keywordtype}{int} sj1,
+00068 \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00069
+00089 INLINE PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type,
+00090 \textcolor{keywordtype}{int} si1,
+00091 \textcolor{keywordtype}{int} sj1,
+00092 \hyperlink{structparamT}{paramT} *P);
+00093
+00100 INLINE PRIVATE \textcolor{keywordtype}{double} exp\_E\_ExtLoop( \textcolor{keywordtype}{int} type,
+00101 \textcolor{keywordtype}{int} si1,
+00102 \textcolor{keywordtype}{int} sj1,
+00103 \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00104
+00149 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_IntLoop}(\textcolor{keywordtype}{int} n1,
+00150 \textcolor{keywordtype}{int} n2,
+00151 \textcolor{keywordtype}{int} type,
+00152 \textcolor{keywordtype}{int} type\_2,
+00153 \textcolor{keywordtype}{int} si1,
+00154 \textcolor{keywordtype}{int} sj1,
+00155 \textcolor{keywordtype}{int} sp1,
+00156 \textcolor{keywordtype}{int} sq1,
+00157 \hyperlink{structparamT}{paramT} *P);
+00158
+00159
+00191 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_Hairpin}(\textcolor{keywordtype}{int} size,
+00192 \textcolor{keywordtype}{int} type,
+00193 \textcolor{keywordtype}{int} si1,
+00194 \textcolor{keywordtype}{int} sj1,
+00195 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00196 \hyperlink{structparamT}{paramT} *P);
+00197
+00243 INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{E\_Stem}( \textcolor{keywordtype}{int} type,
+00244 \textcolor{keywordtype}{int} si1,
+00245 \textcolor{keywordtype}{int} sj1,
+00246 \textcolor{keywordtype}{int} extLoop,
+00247 \hyperlink{structparamT}{paramT} *P);
+00248
+00257 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{exp\_E\_Stem}(\textcolor{keywordtype}{int} type,
+00258 \textcolor{keywordtype}{int} si1,
+00259 \textcolor{keywordtype}{int} sj1,
+00260 \textcolor{keywordtype}{int} extLoop,
+00261 \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00262
+00280 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\_E\_Hairpin}( \textcolor{keywordtype}{int} u,
+00281 \textcolor{keywordtype}{int} type,
+00282 \textcolor{keywordtype}{short} si1,
+00283 \textcolor{keywordtype}{short} sj1,
+00284 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00285 \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00286
+00306 INLINE PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\_E\_IntLoop}(\textcolor{keywordtype}{int} u1,
+00307 \textcolor{keywordtype}{int} u2,
+00308 \textcolor{keywordtype}{int} type,
+00309 \textcolor{keywordtype}{int} type2,
+00310 \textcolor{keywordtype}{short} si1,
+00311 \textcolor{keywordtype}{short} sj1,
+00312 \textcolor{keywordtype}{short} sp1,
+00313 \textcolor{keywordtype}{short} sq1,
+00314 \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00315
+00316
+00317 \textcolor{comment}{/*}
+00318 \textcolor{comment}{#################################}
+00319 \textcolor{comment}{# BEGIN OF FUNCTION DEFINITIONS #}
+00320 \textcolor{comment}{#################################}
+00321 \textcolor{comment}{*/}
+\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},
+ \hyperlink{structparamT}{paramT} *P)\{
+00323 \textcolor{keywordtype}{int} energy;
+00324
+00325 energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(\textcolor{keywordtype}{int})(P->lxc*log((size)/30.));
+00326 \textcolor{keywordflow}{if} (P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp})\{
+00327 \textcolor{keywordflow}{if} (size == 4) \{ \textcolor{comment}{/* check for tetraloop bonus */}
+00328 \textcolor{keywordtype}{char} tl[7]=\{0\}, *ts;
+00329 strncpy(tl, \textcolor{keywordtype}{string}, 6);
+00330 \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))
+00331 \textcolor{keywordflow}{return} (P->Tetraloop\_E[(ts - P->Tetraloops)/7]);
+00332 \}
+00333 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 6) \{
+00334 \textcolor{keywordtype}{char} tl[9]=\{0\}, *ts;
+00335 strncpy(tl, \textcolor{keywordtype}{string}, 8);
+00336 \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
+00337 \textcolor{keywordflow}{return} (energy = P->Hexaloop\_E[(ts - P->Hexaloops)/9]);
+00338 \}
+00339 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 3) \{
+00340 \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
+00341 strncpy(tl, \textcolor{keywordtype}{string}, 5);
+00342 \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl))) \{
+00343 \textcolor{keywordflow}{return} (P->Triloop\_E[(ts - P->Triloops)/6]);
+00344 \}
+00345 \textcolor{keywordflow}{return} (energy + (type>2 ? P->TerminalAU : 0));
+00346 \}
+00347 \}
+00348 energy += P->mismatchH[type][si1][sj1];
+00349
+00350 \textcolor{keywordflow}{return} energy;
+00351 \}
+00352
+\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}
+ sq1, \hyperlink{structparamT}{paramT} *P)\{
+00354 \textcolor{comment}{/* compute energy of degree 2 loop (stack bulge or interior) */}
+00355 \textcolor{keywordtype}{int} nl, ns, energy;
+00356 energy = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
+00357
+00358 \textcolor{keywordflow}{if} (n1>n2) \{ nl=n1; ns=n2;\}
+00359 \textcolor{keywordflow}{else} \{nl=n2; ns=n1;\}
+00360
+00361 \textcolor{keywordflow}{if} (nl == 0)
+00362 \textcolor{keywordflow}{return} P->stack[type][type\_2]; \textcolor{comment}{/* stack */}
+00363
+00364 \textcolor{keywordflow}{if} (ns==0) \{ \textcolor{comment}{/* bulge */}
+00365 energy = (nl<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?P->bulge[nl]:
+00366 (P->bulge[30]+(\textcolor{keywordtype}{int})(P->lxc*log(nl/30.)));
+00367 \textcolor{keywordflow}{if} (nl==1) energy += P->stack[type][type\_2];
+00368 \textcolor{keywordflow}{else} \{
+00369 \textcolor{keywordflow}{if} (type>2) energy += P->TerminalAU;
+00370 \textcolor{keywordflow}{if} (type\_2>2) energy += P->TerminalAU;
+00371 \}
+00372 \textcolor{keywordflow}{return} energy;
+00373 \}
+00374 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* interior loop */}
+00375 \textcolor{keywordflow}{if} (ns==1) \{
+00376 \textcolor{keywordflow}{if} (nl==1) \textcolor{comment}{/* 1x1 loop */}
+00377 \textcolor{keywordflow}{return} P->int11[type][type\_2][si1][sj1];
+00378 \textcolor{keywordflow}{if} (nl==2) \{ \textcolor{comment}{/* 2x1 loop */}
+00379 \textcolor{keywordflow}{if} (n1==1)
+00380 energy = P->int21[type][type\_2][si1][sq1][sj1];
+00381 \textcolor{keywordflow}{else}
+00382 energy = P->int21[type\_2][type][sq1][si1][sp1];
+00383 \textcolor{keywordflow}{return} energy;
+00384 \}
+00385 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* 1xn loop */}
+00386 energy = (nl+1<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[nl+1]) : (P->internal\_loop[30]+(int)(P->lxc*log((
+ nl+1)/30.)));
+00387 energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
+00388 energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type\_2][sq1][sp1];
+00389 \textcolor{keywordflow}{return} energy;
+00390 \}
+00391 \}
+00392 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (ns==2) \{
+00393 \textcolor{keywordflow}{if}(nl==2) \{ \textcolor{comment}{/* 2x2 loop */}
+00394 \textcolor{keywordflow}{return} P->int22[type][type\_2][si1][sp1][sq1][sj1];\}
+00395 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (nl==3)\{ \textcolor{comment}{/* 2x3 loop */}
+00396 energy = P->internal\_loop[5]+P->ninio[2];
+00397 energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type\_2][sq1][sp1];
+00398 \textcolor{keywordflow}{return} energy;
+00399 \}
+00400
+00401 \}
+00402 \{ \textcolor{comment}{/* generic interior loop (no else here!)*/}
+00403 energy = (n1+n2<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[n1+n2]) : (P->internal\_loop[30]+(int)(P->lxc*log((
+ n1+n2)/30.)));
+00404
+00405 energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
+00406
+00407 energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type\_2][sq1][sp1];
+00408 \}
+00409 \}
+00410 \textcolor{keywordflow}{return} energy;
+00411 \}
+00412
+\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)\{
+00414 \textcolor{keywordtype}{int} energy = 0;
+00415 \textcolor{keywordtype}{int} d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;
+00416 \textcolor{keywordtype}{int} d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;
+00417
+00418 \textcolor{keywordflow}{if}(type > 2)
+00419 energy += P->TerminalAU;
+00420
+00421 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
+00422 energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];
+00423 \textcolor{keywordflow}{else}
+00424 energy += d5 + d3;
+00425
+00426 \textcolor{keywordflow}{if}(!extLoop) energy += P->MLintern[type];
+00427 \textcolor{keywordflow}{return} energy;
+00428 \}
+00429
+00430 INLINE PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
+00431 \textcolor{keywordtype}{int} energy = 0;
+00432 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
+00433 energy += P->mismatchExt[type][si1][sj1];
+00434 \}
+00435 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
+00436 energy += P->dangle5[type][si1];
+00437 \}
+00438 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
+00439 energy += P->dangle3[type][sj1];
+00440 \}
+00441
+00442 \textcolor{keywordflow}{if}(type > 2)
+00443 energy += P->TerminalAU;
+00444
+00445 \textcolor{keywordflow}{return} energy;
+00446 \}
+00447
+00448 INLINE PRIVATE \textcolor{keywordtype}{int} E\_MLstem(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
+00449 \textcolor{keywordtype}{int} energy = 0;
+00450 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
+00451 energy += P->mismatchM[type][si1][sj1];
+00452 \}
+00453 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
+00454 energy += P->dangle5[type][si1];
+00455 \}
+00456 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
+00457 energy += P->dangle3[type][sj1];
+00458 \}
+00459
+00460 \textcolor{keywordflow}{if}(type > 2)
+00461 energy += P->TerminalAU;
+00462
+00463 energy += P->MLintern[type];
+00464
+00465 \textcolor{keywordflow}{return} energy;
+00466 \}
+00467
+\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}
+ , \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
+00469 \textcolor{keywordtype}{double} q, kT;
+00470 kT = P->kT; \textcolor{comment}{/* kT in cal/mol */}
+00471
+00472 \textcolor{keywordflow}{if}(u <= 30)
+00473 q = P->exphairpin[u];
+00474 \textcolor{keywordflow}{else}
+00475 q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);
+00476
+00477 \textcolor{keywordflow}{if}(u < 3) \textcolor{keywordflow}{return} q; \textcolor{comment}{/* should only be the case when folding alignments */}
+00478
+00479 \textcolor{keywordflow}{if} ((P->\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model\_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp})&&(u==4)) \{
+00480 \textcolor{keywordtype}{char} tl[7]=\{0,0,0,0,0,0,0\}, *ts;
+00481 strncpy(tl, \textcolor{keywordtype}{string}, 6);
+00482 \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))\{
+00483 \textcolor{keywordflow}{if}(type != 7)
+00484 \textcolor{keywordflow}{return} (P->exptetra[(ts-P->Tetraloops)/7]);
+00485 \textcolor{keywordflow}{else}
+00486 q *= P->exptetra[(ts-P->Tetraloops)/7];
+00487 \}
+00488 \}
+00489 \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\_loop})&&(u==6)) \{
+00490 \textcolor{keywordtype}{char} tl[9]=\{0,0,0,0,0,0,0,0,0\}, *ts;
+00491 strncpy(tl, \textcolor{keywordtype}{string}, 6);
+00492 \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
+00493 \textcolor{keywordflow}{return} (P->exphex[(ts-P->Hexaloops)/9]);
+00494 \}
+00495 \textcolor{keywordflow}{if} (u==3) \{
+00496 \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
+00497 strncpy(tl, \textcolor{keywordtype}{string}, 5);
+00498 \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl)))
+00499 \textcolor{keywordflow}{return} (P->exptri[(ts-P->Triloops)/6]);
+00500 \textcolor{keywordflow}{if} (type>2)
+00501 q *= P->expTermAU;
+00502 \}
+00503 \textcolor{keywordflow}{else} \textcolor{comment}{/* no mismatches for tri-loops */}
+00504 q *= P->expmismatchH[type][si1][sj1];
+00505
+00506 \textcolor{keywordflow}{return} q;
+00507 \}
+00508
+\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
+ , \textcolor{keywordtype}{short} sp1, \textcolor{keywordtype}{short} sq1, \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
+00510 \textcolor{keywordtype}{int} ul, us, no\_close = 0;
+00511 \textcolor{keywordtype}{double} z = 0.;
+00512
+00513 \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\_closingGU}) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
+00514 no\_close = 1;
+00515
+00516 \textcolor{keywordflow}{if} (u1>u2) \{ ul=u1; us=u2;\}
+00517 \textcolor{keywordflow}{else} \{ul=u2; us=u1;\}
+00518
+00519 \textcolor{keywordflow}{if} (ul==0) \textcolor{comment}{/* stack */}
+00520 z = P->expstack[type][type2];
+00521 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(!no\_close)\{
+00522 \textcolor{keywordflow}{if} (us==0) \{ \textcolor{comment}{/* bulge */}
+00523 z = P->expbulge[ul];
+00524 \textcolor{keywordflow}{if} (ul==1) z *= P->expstack[type][type2];
+00525 \textcolor{keywordflow}{else} \{
+00526 \textcolor{keywordflow}{if} (type>2) z *= P->expTermAU;
+00527 \textcolor{keywordflow}{if} (type2>2) z *= P->expTermAU;
+00528 \}
+00529 \textcolor{keywordflow}{return} z;
+00530 \}
+00531 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==1) \{
+00532 \textcolor{keywordflow}{if} (ul==1)\{ \textcolor{comment}{/* 1x1 loop */}
+00533 \textcolor{keywordflow}{return} P->expint11[type][type2][si1][sj1];
+00534 \}
+00535 \textcolor{keywordflow}{if} (ul==2) \{ \textcolor{comment}{/* 2x1 loop */}
+00536 \textcolor{keywordflow}{if} (u1==1)
+00537 \textcolor{keywordflow}{return} P->expint21[type][type2][si1][sq1][sj1];
+00538 \textcolor{keywordflow}{else}
+00539 \textcolor{keywordflow}{return} P->expint21[type2][type][sq1][si1][sp1];
+00540 \}
+00541 \textcolor{keywordflow}{else} \{ \textcolor{comment}{/* 1xn loop */}
+00542 z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];
+00543 \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
+00544 \}
+00545 \}
+00546 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==2) \{
+00547 \textcolor{keywordflow}{if}(ul==2) \textcolor{comment}{/* 2x2 loop */}
+00548 \textcolor{keywordflow}{return} P->expint22[type][type2][si1][sp1][sq1][sj1];
+00549 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(ul==3)\{ \textcolor{comment}{/* 2x3 loop */}
+00550 z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];
+00551 \textcolor{keywordflow}{return} z * P->expninio[2][1];
+00552 \}
+00553 \}
+00554 \textcolor{comment}{/* generic interior loop (no else here!)*/}
+00555 z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];
+00556 \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
+00557
+00558 \}
+00559 \textcolor{keywordflow}{return} z;
+00560 \}
+00561
+\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,
+ \hyperlink{structpf__paramT}{pf\_paramT} *P)\{
+00563 \textcolor{keywordtype}{double} energy = 1.0;
+00564 \textcolor{keywordtype}{double} d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;
+00565 \textcolor{keywordtype}{double} d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;
+00566
+00567 \textcolor{keywordflow}{if}(type > 2)
+00568 energy *= P->expTermAU;
+00569
+00570 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
+00571 energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];
+00572 \textcolor{keywordflow}{else}
+00573 energy *= d5 * d3;
+00574
+00575 \textcolor{keywordflow}{if}(!extLoop) energy *= P->expMLintern[type];
+00576 \textcolor{keywordflow}{return} energy;
+00577 \}
+00578
+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)\{
+00580 \textcolor{keywordtype}{double} energy = 1.0;
+00581 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
+00582 energy *= P->expmismatchM[type][si1][sj1];
+00583 \}
+00584 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
+00585 energy *= P->expdangle5[type][si1];
+00586 \}
+00587 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
+00588 energy *= P->expdangle3[type][sj1];
+00589 \}
+00590
+00591 \textcolor{keywordflow}{if}(type > 2)
+00592 energy *= P->expTermAU;
+00593
+00594 energy *= P->expMLintern[type];
+00595 \textcolor{keywordflow}{return} energy;
+00596 \}
+00597
+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)\{
+00599 \textcolor{keywordtype}{double} energy = 1.0;
+00600 \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
+00601 energy *= P->expmismatchExt[type][si1][sj1];
+00602 \}
+00603 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
+00604 energy *= P->expdangle5[type][si1];
+00605 \}
+00606 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
+00607 energy *= P->expdangle3[type][sj1];
+00608 \}
+00609
+00610 \textcolor{keywordflow}{if}(type > 2)
+00611 energy *= P->expTermAU;
+00612
+00613 \textcolor{keywordflow}{return} energy;
+00614 \}
+00615
+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}
+ si1, \textcolor{keywordtype}{short} sj1, \textcolor{keywordtype}{short} sp1, \textcolor{keywordtype}{short} sq1, \textcolor{keywordtype}{int} dangles, \hyperlink{structparamT}{paramT} *P)\{
+00617 \textcolor{keywordtype}{int} energy = 0;
+00618 \textcolor{keywordflow}{if}(type > 2) energy += P->TerminalAU;
+00619 \textcolor{keywordflow}{if}(type\_2 > 2) energy += P->TerminalAU;
+00620
+00621 \textcolor{keywordflow}{if}(!dangles) \textcolor{keywordflow}{return} energy;
+00622
+00623 \textcolor{keywordtype}{int} ci = (i>=cutpoint)||((i+1)<cutpoint);
+00624 \textcolor{keywordtype}{int} cj = ((j-1)>=cutpoint)||(j<cutpoint);
+00625 \textcolor{keywordtype}{int} cp = ((p-1)>=cutpoint)||(p<cutpoint);
+00626 \textcolor{keywordtype}{int} cq = (q>=cutpoint)||((q+1)<cutpoint);
+00627
+00628 \textcolor{keywordtype}{int} d3 = ci ? P->dangle3[type][si1] : 0;
+00629 \textcolor{keywordtype}{int} d5 = cj ? P->dangle5[type][sj1] : 0;
+00630 \textcolor{keywordtype}{int} d5\_2 = cp ? P->dangle5[type\_2][sp1] : 0;
+00631 \textcolor{keywordtype}{int} d3\_2 = cq ? P->dangle3[type\_2][sq1] : 0;
+00632
+00633 \textcolor{keywordtype}{int} tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;
+00634 \textcolor{keywordtype}{int} tmm\_2 = (cp && cq) ? P->mismatchExt[type\_2][sp1][sq1] : d5\_2 + d3\_2;
+00635
+00636 \textcolor{keywordflow}{if}(dangles == 2) \textcolor{keywordflow}{return} energy + tmm + tmm\_2;
+00637
+00638 \textcolor{comment}{/* now we may have non-double dangles only */}
+00639 \textcolor{keywordflow}{if}(i+2 < p)\{
+00640 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += tmm + tmm\_2;\}
+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;\}
+00642 \textcolor{keywordflow}{else} energy += d3 + d5\_2;
+00643 \}
+00644 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(i+2 == p)\{
+00645 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += (ci && cp) ? \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm + d3\_2, tmm\_2 + d5) : tmm + tmm\_2;\}
+00646 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{
+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)));
+00648 \}
+00649 \textcolor{keywordflow}{else} energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d3, d5\_2);
+00650 \}
+00651 \textcolor{keywordflow}{else}\{
+00652 \textcolor{keywordflow}{if}(q+2 < j)\{ energy += d5 + d3\_2;\}
+00653 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{ energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d5, d3\_2);\}
+00654 \}
+00655 \textcolor{keywordflow}{return} energy;
+00656 \}
+00657
+00658 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff