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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / loop__energies_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/loop__energies_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/loop__energies_8h_source.tex
index d6c8dbc..d9b3354 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/loop__energies_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/loop__energies_8h_source.tex
@@ -1,8 +1,9 @@
-\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}}
+\hypertarget{loop__energies_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\-energies.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 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}{}
@@ -12,7 +13,7 @@
 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}"}
+00010 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold_vars.h}"}
 00011 \textcolor{preprocessor}{#include "energy\_par.h"}
 00012 
 00013 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
@@ -29,7 +30,7 @@
 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);
+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,
@@ -39,9 +40,9 @@
 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);
+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,
+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,
@@ -52,33 +53,33 @@
 00157                               \hyperlink{structparamT}{paramT} *P);
 00158 
 00159 
-00191 INLINE  PRIVATE \textcolor{keywordtype}{int} \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_Hairpin}(\textcolor{keywordtype}{int} size,
+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,
+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,
+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);
+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,
+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);
+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,
+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,
@@ -86,7 +87,7 @@
 00311                                       \textcolor{keywordtype}{short} sj1,
 00312                                       \textcolor{keywordtype}{short} sp1,
 00313                                       \textcolor{keywordtype}{short} sq1,
-00314                                       \hyperlink{structpf__paramT}{pf\_paramT} *P);
+00314                                       \hyperlink{structpf__paramT}{pf_paramT} *P);
 00315 
 00316 
 00317 \textcolor{comment}{/*}
@@ -94,12 +95,13 @@
 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)\{
+\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
+      tring}, \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})\{
+00325   energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(\textcolor{keywordtype}{int})(P->lxc*log((siz
+      e)/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);
@@ -126,8 +128,8 @@
 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)\{
+\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};
@@ -160,10 +162,11 @@
 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.)));
+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];
+00388         energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type\_2][sq1][sp
+      1];
 00389         \textcolor{keywordflow}{return} energy;
 00390       \}
 00391     \}
@@ -172,14 +175,15 @@
 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];
+00397         energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type\_2][sq1][sp
+      1];
 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.)));
+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 
@@ -189,7 +193,7 @@
 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)\{
+\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;
@@ -198,7 +202,8 @@
 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];
+00422     energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1
+      ][sj1];
 00423   \textcolor{keywordflow}{else}
 00424     energy += d5 + d3;
 00425 
@@ -244,8 +249,8 @@
 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)\{
+\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 
@@ -256,7 +261,7 @@
 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)) \{
+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)))\{
@@ -266,7 +271,7 @@
 00486         q *= P->exptetra[(ts-P->Tetraloops)/7];
 00487     \}
 00488   \}
-00489   \textcolor{keywordflow}{if} ((\hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\_loop})&&(u==6)) \{
+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)))
@@ -286,12 +291,12 @@
 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)\{
+\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
+      i1, \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)))
+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;\}
@@ -320,7 +325,8 @@
 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];
+00542         z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmis
+      match1nI[type2][sq1][sp1];
 00543         \textcolor{keywordflow}{return} z * P->expninio[2][ul-us];
 00544       \}
 00545     \}
@@ -328,20 +334,22 @@
 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];
+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];
+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)\{
+\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.;
@@ -350,7 +358,8 @@
 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];
+00571     energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[typ
+      e][si1][sj1];
 00572   \textcolor{keywordflow}{else}
 00573     energy *= d5 * d3;
 00574 
@@ -358,7 +367,7 @@
 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)\{
+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];
@@ -377,7 +386,7 @@
 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)\{
+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];
@@ -395,8 +404,9 @@
 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)\{
+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
+      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, 
+      \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;
@@ -421,11 +431,13 @@
 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;\}
+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;\}
+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     \}
@@ -439,4 +451,4 @@
 00656 \}
 00657 
 00658 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}