binaries/src/ViennaRNA/doc/latex/loop__energies_8h_source.tex

   1 \hypertarget{loop__energies_8h_source}{
   2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\-energies.h}
   3 }
   4
   5
   6 \begin{footnotesize}\begin{alltt}
   7 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
   8 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_LOOP\_ENERGIES\_H\_\_}
   9 00003 \textcolor{preprocessor}{}
  10 00004 \textcolor{preprocessor}{#include <stdio.h>}
  11 00005 \textcolor{preprocessor}{#include <stdlib.h>}
  12 00006 \textcolor{preprocessor}{#include <math.h>}
  13 00007 \textcolor{preprocessor}{#include <ctype.h>}
  14 00008 \textcolor{preprocessor}{#include <string.h>}
  15 00009 \textcolor{preprocessor}{#include "\hyperlink{params_8h}{params.h}"}
  16 00010 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold_vars.h}"}
  17 00011 \textcolor{preprocessor}{#include "energy\_par.h"}
  18 00012
  19 00013 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  20 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline}
  21 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  22 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE}
  23 00017 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  24 00018 \textcolor{preprocessor}{}
  25 00054 INLINE  PRIVATE \textcolor{keywordtype}{int} E\_MLstem( \textcolor{keywordtype}{int} type,
  26 00055                               \textcolor{keywordtype}{int} si1,
  27 00056                               \textcolor{keywordtype}{int} sj1,
  28 00057                               \hyperlink{structparamT}{paramT} *P);
  29 00058
  30 00065 INLINE  PRIVATE \textcolor{keywordtype}{double} exp\_E\_MLstem(\textcolor{keywordtype}{int} type,
  31 00066                                     \textcolor{keywordtype}{int} si1,
  32 00067                                     \textcolor{keywordtype}{int} sj1,
  33 00068                                     \hyperlink{structpf__paramT}{pf_paramT} *P);
  34 00069
  35 00089 INLINE  PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type,
  36 00090                               \textcolor{keywordtype}{int} si1,
  37 00091                               \textcolor{keywordtype}{int} sj1,
  38 00092                               \hyperlink{structparamT}{paramT} *P);
  39 00093
  40 00100 INLINE  PRIVATE \textcolor{keywordtype}{double} exp\_E\_ExtLoop( \textcolor{keywordtype}{int} type,
  41 00101                                       \textcolor{keywordtype}{int} si1,
  42 00102                                       \textcolor{keywordtype}{int} sj1,
  43 00103                                       \hyperlink{structpf__paramT}{pf_paramT} *P);
  44 00104
  45 00149 INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E_IntLoop}(\textcolor{keywordtype}{int} n1,
  46 00150                               \textcolor{keywordtype}{int} n2,
  47 00151                               \textcolor{keywordtype}{int} type,
  48 00152                               \textcolor{keywordtype}{int} type\_2,
  49 00153                               \textcolor{keywordtype}{int} si1,
  50 00154                               \textcolor{keywordtype}{int} sj1,
  51 00155                               \textcolor{keywordtype}{int} sp1,
  52 00156                               \textcolor{keywordtype}{int} sq1,
  53 00157                               \hyperlink{structparamT}{paramT} *P);
  54 00158
  55 00159
  56 00191 INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E_Hairpin}(\textcolor{keywordtype}{int} size,
  57 00192                               \textcolor{keywordtype}{int} type,
  58 00193                               \textcolor{keywordtype}{int} si1,
  59 00194                               \textcolor{keywordtype}{int} sj1,
  60 00195                               \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  61 00196                               \hyperlink{structparamT}{paramT} *P);
  62 00197
  63 00243 INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_af5a6594eba9b2622cb47076650c69819}{E_Stem}( \textcolor{keywordtype}{int} type,
  64 00244                             \textcolor{keywordtype}{int} si1,
  65 00245                             \textcolor{keywordtype}{int} sj1,
  66 00246                             \textcolor{keywordtype}{int} extLoop,
  67 00247                             \hyperlink{structparamT}{paramT} *P);
  68 00248
  69 00257 INLINE  PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a76cc24ec96199e04beddad13e7891e21}{exp_E_Stem}(\textcolor{keywordtype}{int} type,
  70 00258                                   \textcolor{keywordtype}{int} si1,
  71 00259                                   \textcolor{keywordtype}{int} sj1,
  72 00260                                   \textcolor{keywordtype}{int} extLoop,
  73 00261                                   \hyperlink{structpf__paramT}{pf_paramT} *P);
  74 00262
  75 00280 INLINE  PRIVATE \textcolor{keywordtype}{double} \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp_E_Hairpin}( \textcolor{keywordtype}{int} u,
  76 00281                                       \textcolor{keywordtype}{int} type,
  77 00282                                       \textcolor{keywordtype}{short} si1,
  78 00283                                       \textcolor{keywordtype}{short} sj1,
  79 00284                                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  80 00285                                       \hyperlink{structpf__paramT}{pf_paramT} *P);
  81 00286
  82 00306 INLINE  PRIVATE \textcolor{keywordtype}{double}  \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp_E_IntLoop}(\textcolor{keywordtype}{int} u1,
  83 00307                                       \textcolor{keywordtype}{int} u2,
  84 00308                                       \textcolor{keywordtype}{int} type,
  85 00309                                       \textcolor{keywordtype}{int} type2,
  86 00310                                       \textcolor{keywordtype}{short} si1,
  87 00311                                       \textcolor{keywordtype}{short} sj1,
  88 00312                                       \textcolor{keywordtype}{short} sp1,
  89 00313                                       \textcolor{keywordtype}{short} sq1,
  90 00314                                       \hyperlink{structpf__paramT}{pf_paramT} *P);
  91 00315
  92 00316
  93 00317 \textcolor{comment}{/*}
  94 00318 \textcolor{comment}{#################################}
  95 00319 \textcolor{comment}{# BEGIN OF FUNCTION DEFINITIONS #}
  96 00320 \textcolor{comment}{#################################}
  97 00321 \textcolor{comment}{*/}
  98 \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}{s
  99       tring}, \hyperlink{structparamT}{paramT} *P)\{
 100 00323   \textcolor{keywordtype}{int} energy;
 101 00324
 102 00325   energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(\textcolor{keywordtype}{int})(P->lxc*log((siz
 103       e)/30.));
 104 00326   \textcolor{keywordflow}{if} (P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special_hp})\{
 105 00327     \textcolor{keywordflow}{if} (size == 4) \{ \textcolor{comment}{/* check for tetraloop bonus */}
 106 00328       \textcolor{keywordtype}{char} tl[7]=\{0\}, *ts;
 107 00329       strncpy(tl, \textcolor{keywordtype}{string}, 6);
 108 00330       \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))
 109 00331         \textcolor{keywordflow}{return} (P->Tetraloop\_E[(ts - P->Tetraloops)/7]);
 110 00332     \}
 111 00333     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 6) \{
 112 00334       \textcolor{keywordtype}{char} tl[9]=\{0\}, *ts;
 113 00335       strncpy(tl, \textcolor{keywordtype}{string}, 8);
 114 00336       \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
 115 00337         \textcolor{keywordflow}{return} (energy = P->Hexaloop\_E[(ts - P->Hexaloops)/9]);
 116 00338     \}
 117 00339     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (size == 3) \{
 118 00340       \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
 119 00341       strncpy(tl, \textcolor{keywordtype}{string}, 5);
 120 00342       \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl))) \{
 121 00343         \textcolor{keywordflow}{return} (P->Triloop\_E[(ts - P->Triloops)/6]);
 122 00344       \}
 123 00345       \textcolor{keywordflow}{return} (energy + (type>2 ? P->TerminalAU : 0));
 124 00346     \}
 125 00347   \}
 126 00348   energy += P->mismatchH[type][si1][sj1];
 127 00349
 128 00350   \textcolor{keywordflow}{return} energy;
 129 00351 \}
 130 00352
 131 \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}
 132       sj1, \textcolor{keywordtype}{int} sp1, \textcolor{keywordtype}{int} sq1, \hyperlink{structparamT}{paramT} *P)\{
 133 00354   \textcolor{comment}{/* compute energy of degree 2 loop (stack bulge or interior) */}
 134 00355   \textcolor{keywordtype}{int} nl, ns, energy;
 135 00356   energy = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF};
 136 00357
 137 00358   \textcolor{keywordflow}{if} (n1>n2) \{ nl=n1; ns=n2;\}
 138 00359   \textcolor{keywordflow}{else} \{nl=n2; ns=n1;\}
 139 00360
 140 00361   \textcolor{keywordflow}{if} (nl == 0)
 141 00362     \textcolor{keywordflow}{return} P->stack[type][type\_2];  \textcolor{comment}{/* stack */}
 142 00363
 143 00364   \textcolor{keywordflow}{if} (ns==0) \{                      \textcolor{comment}{/* bulge */}
 144 00365     energy = (nl<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?P->bulge[nl]:
 145 00366       (P->bulge[30]+(\textcolor{keywordtype}{int})(P->lxc*log(nl/30.)));
 146 00367     \textcolor{keywordflow}{if} (nl==1) energy += P->stack[type][type\_2];
 147 00368     \textcolor{keywordflow}{else} \{
 148 00369       \textcolor{keywordflow}{if} (type>2) energy += P->TerminalAU;
 149 00370       \textcolor{keywordflow}{if} (type\_2>2) energy += P->TerminalAU;
 150 00371     \}
 151 00372     \textcolor{keywordflow}{return} energy;
 152 00373   \}
 153 00374   \textcolor{keywordflow}{else} \{                            \textcolor{comment}{/* interior loop */}
 154 00375     \textcolor{keywordflow}{if} (ns==1) \{
 155 00376       \textcolor{keywordflow}{if} (nl==1)                    \textcolor{comment}{/* 1x1 loop */}
 156 00377         \textcolor{keywordflow}{return} P->int11[type][type\_2][si1][sj1];
 157 00378       \textcolor{keywordflow}{if} (nl==2) \{                  \textcolor{comment}{/* 2x1 loop */}
 158 00379         \textcolor{keywordflow}{if} (n1==1)
 159 00380           energy = P->int21[type][type\_2][si1][sq1][sj1];
 160 00381         \textcolor{keywordflow}{else}
 161 00382           energy = P->int21[type\_2][type][sq1][si1][sp1];
 162 00383         \textcolor{keywordflow}{return} energy;
 163 00384       \}
 164 00385       \textcolor{keywordflow}{else} \{  \textcolor{comment}{/* 1xn loop */}
 165 00386         energy = (nl+1<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[nl+1]) : (P->internal\_loop[30]
 166       +(int)(P->lxc*log((nl+1)/30.)));
 167 00387         energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
 168 00388         energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type\_2][sq1][sp
 169       1];
 170 00389         \textcolor{keywordflow}{return} energy;
 171 00390       \}
 172 00391     \}
 173 00392     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (ns==2) \{
 174 00393       \textcolor{keywordflow}{if}(nl==2)      \{              \textcolor{comment}{/* 2x2 loop */}
 175 00394         \textcolor{keywordflow}{return} P->int22[type][type\_2][si1][sp1][sq1][sj1];\}
 176 00395       \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (nl==3)\{              \textcolor{comment}{/* 2x3 loop */}
 177 00396         energy = P->internal\_loop[5]+P->ninio[2];
 178 00397         energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type\_2][sq1][sp
 179       1];
 180 00398         \textcolor{keywordflow}{return} energy;
 181 00399       \}
 182 00400
 183 00401     \}
 184 00402     \{ \textcolor{comment}{/* generic interior loop (no else here!)*/}
 185 00403       energy = (n1+n2<=\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP})?(P->internal\_loop[n1+n2]) : (P->internal\_loop[30]
 186       +(int)(P->lxc*log((n1+n2)/30.)));
 187 00404
 188 00405       energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(MAX\_NINIO, (nl-ns)*P->ninio[2]);
 189 00406
 190 00407       energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type\_2][sq1][sp1];
 191 00408     \}
 192 00409   \}
 193 00410   \textcolor{keywordflow}{return} energy;
 194 00411 \}
 195 00412
 196 \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)\{
 197 00414   \textcolor{keywordtype}{int} energy = 0;
 198 00415   \textcolor{keywordtype}{int} d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;
 199 00416   \textcolor{keywordtype}{int} d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;
 200 00417
 201 00418   \textcolor{keywordflow}{if}(type > 2)
 202 00419     energy += P->TerminalAU;
 203 00420
 204 00421   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
 205 00422     energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1
 206       ][sj1];
 207 00423   \textcolor{keywordflow}{else}
 208 00424     energy += d5 + d3;
 209 00425
 210 00426   \textcolor{keywordflow}{if}(!extLoop) energy += P->MLintern[type];
 211 00427   \textcolor{keywordflow}{return} energy;
 212 00428 \}
 213 00429
 214 00430 INLINE  PRIVATE \textcolor{keywordtype}{int} E\_ExtLoop(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
 215 00431   \textcolor{keywordtype}{int} energy = 0;
 216 00432   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
 217 00433     energy += P->mismatchExt[type][si1][sj1];
 218 00434   \}
 219 00435   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
 220 00436     energy += P->dangle5[type][si1];
 221 00437   \}
 222 00438   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
 223 00439     energy += P->dangle3[type][sj1];
 224 00440   \}
 225 00441
 226 00442   \textcolor{keywordflow}{if}(type > 2)
 227 00443     energy += P->TerminalAU;
 228 00444
 229 00445   \textcolor{keywordflow}{return} energy;
 230 00446 \}
 231 00447
 232 00448 INLINE  PRIVATE \textcolor{keywordtype}{int} E\_MLstem(\textcolor{keywordtype}{int} type, \textcolor{keywordtype}{int} si1, \textcolor{keywordtype}{int} sj1, \hyperlink{structparamT}{paramT} *P)\{
 233 00449   \textcolor{keywordtype}{int} energy = 0;
 234 00450   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
 235 00451     energy += P->mismatchM[type][si1][sj1];
 236 00452   \}
 237 00453   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (si1 >= 0)\{
 238 00454     energy += P->dangle5[type][si1];
 239 00455   \}
 240 00456   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (sj1 >= 0)\{
 241 00457     energy += P->dangle3[type][sj1];
 242 00458   \}
 243 00459
 244 00460   \textcolor{keywordflow}{if}(type > 2)
 245 00461     energy += P->TerminalAU;
 246 00462
 247 00463   energy += P->MLintern[type];
 248 00464
 249 00465   \textcolor{keywordflow}{return} energy;
 250 00466 \}
 251 00467
 252 \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
 253       } \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, \hyperlink{structpf__paramT}{pf_paramT} *P)\{
 254 00469   \textcolor{keywordtype}{double} q, kT;
 255 00470   kT = P->kT;   \textcolor{comment}{/* kT in cal/mol  */}
 256 00471
 257 00472   \textcolor{keywordflow}{if}(u <= 30)
 258 00473     q = P->exphairpin[u];
 259 00474   \textcolor{keywordflow}{else}
 260 00475     q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);
 261 00476
 262 00477   \textcolor{keywordflow}{if}(u < 3) \textcolor{keywordflow}{return} q; \textcolor{comment}{/* should only be the case when folding alignments */}
 263 00478
 264 00479   \textcolor{keywordflow}{if} ((P->\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model_details}.\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special_hp})&&(u==4)) \{
 265 00480     \textcolor{keywordtype}{char} tl[7]=\{0,0,0,0,0,0,0\}, *ts;
 266 00481     strncpy(tl, \textcolor{keywordtype}{string}, 6);
 267 00482     \textcolor{keywordflow}{if} ((ts=strstr(P->Tetraloops, tl)))\{
 268 00483       \textcolor{keywordflow}{if}(type != 7)
 269 00484         \textcolor{keywordflow}{return} (P->exptetra[(ts-P->Tetraloops)/7]);
 270 00485       \textcolor{keywordflow}{else}
 271 00486         q *= P->exptetra[(ts-P->Tetraloops)/7];
 272 00487     \}
 273 00488   \}
 274 00489   \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra_loop})&&(u==6)) \{
 275 00490     \textcolor{keywordtype}{char} tl[9]=\{0,0,0,0,0,0,0,0,0\}, *ts;
 276 00491     strncpy(tl, \textcolor{keywordtype}{string}, 6);
 277 00492     \textcolor{keywordflow}{if} ((ts=strstr(P->Hexaloops, tl)))
 278 00493       \textcolor{keywordflow}{return}  (P->exphex[(ts-P->Hexaloops)/9]);
 279 00494   \}
 280 00495   \textcolor{keywordflow}{if} (u==3) \{
 281 00496     \textcolor{keywordtype}{char} tl[6]=\{0,0,0,0,0,0\}, *ts;
 282 00497     strncpy(tl, \textcolor{keywordtype}{string}, 5);
 283 00498     \textcolor{keywordflow}{if} ((ts=strstr(P->Triloops, tl)))
 284 00499       \textcolor{keywordflow}{return} (P->exptri[(ts-P->Triloops)/6]);
 285 00500     \textcolor{keywordflow}{if} (type>2)
 286 00501       q *= P->expTermAU;
 287 00502   \}
 288 00503   \textcolor{keywordflow}{else} \textcolor{comment}{/* no mismatches for tri-loops */}
 289 00504     q *= P->expmismatchH[type][si1][sj1];
 290 00505
 291 00506   \textcolor{keywordflow}{return} q;
 292 00507 \}
 293 00508
 294 \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} s
 295       i1, \textcolor{keywordtype}{short} sj1, \textcolor{keywordtype}{short} sp1, \textcolor{keywordtype}{short} sq1, \hyperlink{structpf__paramT}{pf_paramT} *P)\{
 296 00510   \textcolor{keywordtype}{int} ul, us, no\_close = 0;
 297 00511   \textcolor{keywordtype}{double} z = 0.;
 298 00512
 299 00513   \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no_closingGU}) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
 300 00514     no\_close = 1;
 301 00515
 302 00516   \textcolor{keywordflow}{if} (u1>u2) \{ ul=u1; us=u2;\}
 303 00517   \textcolor{keywordflow}{else} \{ul=u2; us=u1;\}
 304 00518
 305 00519   \textcolor{keywordflow}{if} (ul==0) \textcolor{comment}{/* stack */}
 306 00520     z = P->expstack[type][type2];
 307 00521   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(!no\_close)\{
 308 00522     \textcolor{keywordflow}{if} (us==0) \{                      \textcolor{comment}{/* bulge */}
 309 00523       z = P->expbulge[ul];
 310 00524       \textcolor{keywordflow}{if} (ul==1) z *= P->expstack[type][type2];
 311 00525       \textcolor{keywordflow}{else} \{
 312 00526         \textcolor{keywordflow}{if} (type>2) z *= P->expTermAU;
 313 00527         \textcolor{keywordflow}{if} (type2>2) z *= P->expTermAU;
 314 00528       \}
 315 00529       \textcolor{keywordflow}{return} z;
 316 00530     \}
 317 00531     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==1) \{
 318 00532       \textcolor{keywordflow}{if} (ul==1)\{                    \textcolor{comment}{/* 1x1 loop */}
 319 00533         \textcolor{keywordflow}{return} P->expint11[type][type2][si1][sj1];
 320 00534       \}
 321 00535       \textcolor{keywordflow}{if} (ul==2) \{                  \textcolor{comment}{/* 2x1 loop */}
 322 00536         \textcolor{keywordflow}{if} (u1==1)
 323 00537           \textcolor{keywordflow}{return} P->expint21[type][type2][si1][sq1][sj1];
 324 00538         \textcolor{keywordflow}{else}
 325 00539           \textcolor{keywordflow}{return} P->expint21[type2][type][sq1][si1][sp1];
 326 00540       \}
 327 00541       \textcolor{keywordflow}{else} \{  \textcolor{comment}{/* 1xn loop */}
 328 00542         z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmis
 329       match1nI[type2][sq1][sp1];
 330 00543         \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
 331 00544       \}
 332 00545     \}
 333 00546     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (us==2) \{
 334 00547       \textcolor{keywordflow}{if}(ul==2) \textcolor{comment}{/* 2x2 loop */}
 335 00548         \textcolor{keywordflow}{return} P->expint22[type][type2][si1][sp1][sq1][sj1];
 336 00549       \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(ul==3)\{              \textcolor{comment}{/* 2x3 loop */}
 337 00550         z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I
 338       [type2][sq1][sp1];
 339 00551         \textcolor{keywordflow}{return} z * P->expninio[2][1];
 340 00552       \}
 341 00553     \}
 342 00554     \textcolor{comment}{/* generic interior loop (no else here!)*/}
 343 00555     z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI
 344       [type2][sq1][sp1];
 345 00556     \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
 346 00557
 347 00558   \}
 348 00559   \textcolor{keywordflow}{return} z;
 349 00560 \}
 350 00561
 351 \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,
 352       \hyperlink{structpf__paramT}{pf_paramT} *P)\{
 353 00563   \textcolor{keywordtype}{double} energy = 1.0;
 354 00564   \textcolor{keywordtype}{double} d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;
 355 00565   \textcolor{keywordtype}{double} d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;
 356 00566
 357 00567   \textcolor{keywordflow}{if}(type > 2)
 358 00568     energy *= P->expTermAU;
 359 00569
 360 00570   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)
 361 00571     energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[typ
 362       e][si1][sj1];
 363 00572   \textcolor{keywordflow}{else}
 364 00573     energy *= d5 * d3;
 365 00574
 366 00575   \textcolor{keywordflow}{if}(!extLoop) energy *= P->expMLintern[type];
 367 00576   \textcolor{keywordflow}{return} energy;
 368 00577 \}
 369 00578
 370 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)\{
 371 00580   \textcolor{keywordtype}{double} energy = 1.0;
 372 00581   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
 373 00582     energy *= P->expmismatchM[type][si1][sj1];
 374 00583   \}
 375 00584   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
 376 00585     energy *= P->expdangle5[type][si1];
 377 00586   \}
 378 00587   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
 379 00588     energy *= P->expdangle3[type][sj1];
 380 00589   \}
 381 00590
 382 00591   \textcolor{keywordflow}{if}(type > 2)
 383 00592     energy *= P->expTermAU;
 384 00593
 385 00594   energy *= P->expMLintern[type];
 386 00595   \textcolor{keywordflow}{return} energy;
 387 00596 \}
 388 00597
 389 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)\{
 390 00599   \textcolor{keywordtype}{double} energy = 1.0;
 391 00600   \textcolor{keywordflow}{if}(si1 >= 0 && sj1 >= 0)\{
 392 00601     energy *= P->expmismatchExt[type][si1][sj1];
 393 00602   \}
 394 00603   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(si1 >= 0)\{
 395 00604     energy *= P->expdangle5[type][si1];
 396 00605   \}
 397 00606   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(sj1 >= 0)\{
 398 00607     energy *= P->expdangle3[type][sj1];
 399 00608   \}
 400 00609
 401 00610   \textcolor{keywordflow}{if}(type > 2)
 402 00611     energy *= P->expTermAU;
 403 00612
 404 00613   \textcolor{keywordflow}{return} energy;
 405 00614 \}
 406 00615
 407 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}{i
 408       nt} 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,
 409       \hyperlink{structparamT}{paramT} *P)\{
 410 00617   \textcolor{keywordtype}{int} energy = 0;
 411 00618   \textcolor{keywordflow}{if}(type > 2)   energy += P->TerminalAU;
 412 00619   \textcolor{keywordflow}{if}(type\_2 > 2) energy += P->TerminalAU;
 413 00620
 414 00621   \textcolor{keywordflow}{if}(!dangles) \textcolor{keywordflow}{return} energy;
 415 00622
 416 00623   \textcolor{keywordtype}{int} ci = (i>=cutpoint)||((i+1)<cutpoint);
 417 00624   \textcolor{keywordtype}{int} cj = ((j-1)>=cutpoint)||(j<cutpoint);
 418 00625   \textcolor{keywordtype}{int} cp = ((p-1)>=cutpoint)||(p<cutpoint);
 419 00626   \textcolor{keywordtype}{int} cq = (q>=cutpoint)||((q+1)<cutpoint);
 420 00627
 421 00628   \textcolor{keywordtype}{int} d3    = ci  ? P->dangle3[type][si1]   : 0;
 422 00629   \textcolor{keywordtype}{int} d5    = cj  ? P->dangle5[type][sj1]   : 0;
 423 00630   \textcolor{keywordtype}{int} d5\_2  = cp  ? P->dangle5[type\_2][sp1] : 0;
 424 00631   \textcolor{keywordtype}{int} d3\_2  = cq  ? P->dangle3[type\_2][sq1] : 0;
 425 00632
 426 00633   \textcolor{keywordtype}{int} tmm   = (cj && ci) ? P->mismatchExt[type][sj1][si1]   : d5 + d3;
 427 00634   \textcolor{keywordtype}{int} tmm\_2 = (cp && cq) ? P->mismatchExt[type\_2][sp1][sq1] : d5\_2 + d3\_2;
 428 00635
 429 00636   \textcolor{keywordflow}{if}(dangles == 2) \textcolor{keywordflow}{return} energy + tmm + tmm\_2;
 430 00637
 431 00638   \textcolor{comment}{/* now we may have non-double dangles only */}
 432 00639   \textcolor{keywordflow}{if}(i+2 < p)\{
 433 00640     \textcolor{keywordflow}{if}(q+2 < j)\{ energy += tmm + tmm\_2;\}
 434 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
 435       + tmm\_2;\}
 436 00642     \textcolor{keywordflow}{else} energy += d3 + d5\_2;
 437 00643   \}
 438 00644   \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(i+2 == p)\{
 439 00645     \textcolor{keywordflow}{if}(q+2 < j)\{ energy += (ci && cp) ? \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(tmm + d3\_2, tmm\_2 + d5) : tmm + tmm\_
 440       2;\}
 441 00646     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{
 442 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)));
 443 00648     \}
 444 00649     \textcolor{keywordflow}{else} energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d3, d5\_2);
 445 00650   \}
 446 00651   \textcolor{keywordflow}{else}\{
 447 00652     \textcolor{keywordflow}{if}(q+2 < j)\{ energy += d5 + d3\_2;\}
 448 00653     \textcolor{keywordflow}{else} \textcolor{keywordflow}{if}(q+2 == j)\{ energy += \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(d5, d3\_2);\}
 449 00654   \}
 450 00655   \textcolor{keywordflow}{return} energy;
 451 00656 \}
 452 00657
 453 00658 \textcolor{preprocessor}{#endif}
 454 \end{alltt}\end{footnotesize}