WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / energy_par.h

diff --git a/binaries/src/ViennaRNA/H/energy_par.h b/binaries/src/ViennaRNA/H/energy_par.h
new file mode 100644 (file)
index 0000000..ab67343
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/energy_par.h
@@ -0,0 +1,100 @@
+/*
+   prototypes for energy_par.c
+*/
+
+#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__
+#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__
+
+#include "energy_const.h"
+
+#define PUBLIC
+
+
+extern double lxc37;   /* parameter for logarithmic loop
+                         energy extrapolation            */
+
+extern int stack37[NBPAIRS+1][NBPAIRS+1];
+extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
+extern int entropies[NBPAIRS+1][NBPAIRS+1];  /* not used anymore */
+
+extern int hairpin37[31];
+extern int hairpindH[31];
+extern int bulge37[31];
+extern int bulgedH[31];
+extern int internal_loop37[31];
+extern int internal_loopdH[31];
+extern int internal2_energy;
+extern int old_mismatch_37[NBPAIRS+1][5][5];
+extern int mismatchI37[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatchIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatch1nI37[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatch23I37[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatch1nIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatch23IdH[NBPAIRS+1][5][5];  /* interior loop mismatches */
+extern int mismatchH37[NBPAIRS+1][5][5];  /* same for hairpins */
+extern int mismatchM37[NBPAIRS+1][5][5];  /* same for multiloops */
+extern int mismatchHdH[NBPAIRS+1][5][5];  /* same for hairpins */
+extern int mismatchMdH[NBPAIRS+1][5][5];  /* same for multiloops */
+extern int mismatchExt37[NBPAIRS+1][5][5];
+extern int mismatchExtdH[NBPAIRS+1][5][5];
+
+extern int dangle5_37[NBPAIRS+1][5];      /* 5' dangle exterior of pair */
+extern int dangle3_37[NBPAIRS+1][5];      /* 3' dangle */
+extern int dangle3_dH[NBPAIRS+1][5];       /* corresponding enthalpies */
+extern int dangle5_dH[NBPAIRS+1][5];
+
+extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
+extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];
+
+extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
+extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];
+
+extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
+extern int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
+
+/* constants for linearly destabilizing contributions for multi-loops
+   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */
+extern int ML_BASE37;
+extern int ML_BASEdH;
+extern int ML_closing37;
+extern int ML_closingdH;
+extern int ML_intern37;
+extern int ML_interndH;
+
+extern int TripleC37;
+extern int TripleCdH;
+extern int MultipleCA37;
+extern int MultipleCAdH;
+extern int MultipleCB37;
+extern int MultipleCBdH;
+
+/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
+/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
+extern int  MAX_NINIO;                   /* maximum correction */
+extern int ninio37;
+extern int niniodH;
+/* penalty for helices terminated by AU (actually not GC) */
+extern int TerminalAU37;
+extern int TerminalAUdH;
+/* penalty for forming bi-molecular duplex */
+extern int DuplexInit37;
+extern int DuplexInitdH;
+/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
+extern char Tetraloops[];  /* string containing the special tetraloops */
+extern int  Tetraloop37[];  /* Bonus energy for special tetraloops */
+extern int  TetraloopdH[];
+extern char Triloops[];    /* string containing the special triloops */
+extern int  Triloop37[]; /* Bonus energy for special Triloops */
+extern int  TriloopdH[]; /* Bonus energy for special Triloops */
+extern char Hexaloops[];    /* string containing the special triloops */
+extern int  Hexaloop37[]; /* Bonus energy for special Triloops */
+extern int  HexaloopdH[]; /* Bonus energy for special Triloops */
+
+extern int GQuadAlpha37;
+extern int GQuadAlphadH;
+extern int GQuadBeta37;
+extern int GQuadBetadH;
+
+extern double Tmeasure;       /* temperature of param measurements */
+
+#endif