binaries/src/ViennaRNA/doc/latex/energy__par_8h_source.tex

   1 \hypertarget{energy__par_8h}{\section{energy\-\_\-par.\-h}
   2 \label{energy__par_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-par.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-par.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{comment}{/*}
   7 00002 \textcolor{comment}{   prototypes for energy\_par.c}
   8 00003 \textcolor{comment}{*/}
   9 00004
  10 00005 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_}
  11 00006 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_}
  12 00007 \textcolor{preprocessor}{}
  13 00008 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy\_const.h}"}
  14 00009
  15 00010 \textcolor{preprocessor}{#define PUBLIC}
  16 00011 \textcolor{preprocessor}{}
  17 00012
  18 00013 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} lxc37;   \textcolor{comment}{/* parameter for logarithmic loop}
  19 00014 \textcolor{comment}{        energy extrapolation            */}
  20 00015
  21 00016 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} stack37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1];
  22 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 */}
  23 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 */}
  24 00019
  25 00020 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpin37[31];
  26 00021 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpindH[31];
  27 00022 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulge37[31];
  28 00023 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulgedH[31];
  29 00024 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loop37[31];
  30 00025 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loopdH[31];
  31 00026 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal2\_energy;
  32 00027 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} old\_mismatch\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  33 00028 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  34 00029 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  35 00030 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  36 00031 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23I37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  37 00032 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  38 00033 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23IdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* interior loop mismatches */}
  39 00034 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchH37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for hairpins */}
  40 00035 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchM37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for multiloops */}
  41 00036 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchHdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for hairpins */}
  42 00037 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchMdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];  \textcolor{comment}{/* same for multiloops */}
  43 00038 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExt37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  44 00039 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExtdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
  45 00040
  46 00041 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];      \textcolor{comment}{/* 5' dangle exterior of pair */}
  47 00042 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];      \textcolor{comment}{/* 3' dangle */}
  48 00043 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];       \textcolor{comment}{/* corresponding enthalpies */}
  49 00044 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5];
  50 00045
  51 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 */}
  52 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];
  53 00048
  54 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 */}
  55 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];
  56 00051
  57 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 */}
  58 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];
  59 00054
  60 00055 \textcolor{comment}{/* constants for linearly destabilizing contributions for multi-loops}
  61 00056 \textcolor{comment}{   F = ML\_closing + ML\_intern*(k-1) + ML\_BASE*u  */}
  62 00057 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASE37;
  63 00058 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASEdH;
  64 00059 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closing37;
  65 00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closingdH;
  66 00061 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_intern37;
  67 00062 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_interndH;
  68 00063
  69 00064 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleC37;
  70 00065 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleCdH;
  71 00066 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCA37;
  72 00067 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCAdH;
  73 00068 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCB37;
  74 00069 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCBdH;
  75 00070
  76 00071 \textcolor{comment}{/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */}
  77 00072 \textcolor{comment}{/*    ninio\_energy = min\{max\_ninio, |n1-n2|*F\_ninio[min\{4.0, n1, n2\}] \} */}
  78 00073 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  MAX\_NINIO;                   \textcolor{comment}{/* maximum correction */}
  79 00074 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ninio37;
  80 00075 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} niniodH;
  81 00076 \textcolor{comment}{/* penalty for helices terminated by AU (actually not GC) */}
  82 00077 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAU37;
  83 00078 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAUdH;
  84 00079 \textcolor{comment}{/* penalty for forming bi-molecular duplex */}
  85 00080 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInit37;
  86 00081 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInitdH;
  87 00082 \textcolor{comment}{/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */}
  88 00083 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Tetraloops[];  \textcolor{comment}{/* string containing the special tetraloops */}
  89 00084 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Tetraloop37[];  \textcolor{comment}{/* Bonus energy for special tetraloops */}
  90 00085 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  TetraloopdH[];
  91 00086 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Triloops[];    \textcolor{comment}{/* string containing the special triloops */}
  92 00087 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Triloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
  93 00088 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  TriloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
  94 00089 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Hexaloops[];    \textcolor{comment}{/* string containing the special triloops */}
  95 00090 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  Hexaloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
  96 00091 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}  HexaloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */}
  97 00092
  98 00093 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlpha37;
  99 00094 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlphadH;
 100 00095 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBeta37;
 101 00096 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBetadH;
 102 00097
 103 00098 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} Tmeasure;       \textcolor{comment}{/* temperature of param measurements */}
 104 00099
 105 00100 \textcolor{preprocessor}{#endif}
 106 \end{DoxyCode}