\hypertarget{energy__par_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\-par.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{comment}{/*}
00002 \textcolor{comment}{   prototypes for energy\_par.c}
00003 \textcolor{comment}{*/}
00004 
00005 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_}
00006 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_}
00007 \textcolor{preprocessor}{}
00008 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy_const.h}"}
00009 
00010 \textcolor{preprocessor}{#define PUBLIC}
00011 \textcolor{preprocessor}{}
00012 
00013 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} lxc37;   \textcolor{comment}{/* parameter for logarithmic loop}
00014 \textcolor{comment}{        energy extrapolation            */}
00015 
00016 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} stack37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
00017 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} stackdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; \textcolor{comment}{/* stack enthalpies */}
00018 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} entropies[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];  \textcolor{comment}{/* not used anymore */}
00019 
00020 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpin37[31];
00021 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpindH[31];
00022 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulge37[31];
00023 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulgedH[31];
00024 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loop37[31];
00025 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loopdH[31];
00026 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal2\_energy;
00027 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} old\_mismatch\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00028 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00029 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00030 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00031 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23I37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00032 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00033 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23IdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
00034 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchH37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for hairpins */}
00035 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchM37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for multiloops */}
00036 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchHdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for hairpins */}
00037 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchMdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for multiloops */}
00038 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExt37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00039 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExtdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00040 
00041 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];      \textcolor{comment}{/* 5' dangle exterior of pair */}
00042 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];      \textcolor{comment}{/* 3' dangle */}
00043 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];       \textcolor{comment}{/* corresponding enthalpies */}
00044 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
00045 
00046 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int11\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* 1x1 interior loops */}
00047 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int11\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
00048 
00049 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int21\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5]; \textcolor{comment}{/* 2x1 interior loops */}
00050 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int21\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5];
00051 
00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int22\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5]; \textcolor{comment}{/* 2x2 interior loops */}
00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int22\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5];
00054 
00055 \textcolor{comment}{/* constants for linearly destabilizing contributions for multi-loops}
00056 \textcolor{comment}{   F = ML\_closing + ML\_intern*(k-1) + ML\_BASE*u  */}
00057 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASE37;
00058 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASEdH;
00059 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closing37;
00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closingdH;
00061 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_intern37;
00062 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_interndH;
00063 
00064 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleC37;
00065 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleCdH;
00066 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCA37;
00067 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCAdH;
00068 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCB37;
00069 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCBdH;
00070 
00071 \textcolor{comment}{/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */}
00072 \textcolor{comment}{/*    ninio\_energy = min\{max\_ninio, |n1-n2|*F\_ninio[min\{4.0, n1, n2\}] \} */}
00073 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  MAX\_NINIO;                   \textcolor{comment}{/* maximum correction */}
00074 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ninio37;
00075 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} niniodH;
00076 \textcolor{comment}{/* penalty for helices terminated by AU (actually not GC) */}
00077 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAU37;
00078 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAUdH;
00079 \textcolor{comment}{/* penalty for forming bi-molecular duplex */}
00080 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInit37;
00081 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInitdH;
00082 \textcolor{comment}{/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */}
00083 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Tetraloops[];  \textcolor{comment}{/* string containing the special tetraloops */}
00084 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Tetraloop37[];  \textcolor{comment}{/* Bonus energy for special tetraloops */}
00085 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  TetraloopdH[];
00086 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Triloops[];    \textcolor{comment}{/* string containing the special triloops */}
00087 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Triloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
00088 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  TriloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
00089 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Hexaloops[];    \textcolor{comment}{/* string containing the special triloops */}
00090 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Hexaloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
00091 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  HexaloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
00092 
00093 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlpha37;
00094 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlphadH;
00095 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBeta37;
00096 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBetadH;
00097 
00098 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} Tmeasure;       \textcolor{comment}{/* temperature of param measurements */}
00099 
00100 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
