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

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

diff --git a/binaries/src/ViennaRNA/H/energy_const.h b/binaries/src/ViennaRNA/H/energy_const.h
new file mode 100644 (file)
index 0000000..e677f58
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/energy_const.h
@@ -0,0 +1,33 @@
+#ifndef __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__
+#define __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__
+
+#include <limits.h>
+
+/**
+ *  \file energy_const.h
+ *  energy constants
+ */
+
+/** The gas constant */
+#define GASCONST 1.98717  /* in [cal/K] */
+/** 0 deg Celsius in Kelvin */
+#define K0  273.15
+/** Infinity as used in minimization routines */
+#define INF 10000000 /* (INT_MAX/10) */
+
+#define EMAX (INF/10)
+/** forbidden */
+#define FORBIDDEN 9999
+/** bonus contribution */
+#define BONUS 10000
+/** The number of distinguishable base pairs */
+#define NBPAIRS 7
+/** The minimum loop length */
+#define TURN 3
+/** The maximum loop length */
+#define MAXLOOP 30
+
+#define   VRNA_GQUAD_MISMATCH_PENALTY   300   /* penalty for incompatible nucleotides in an alignment that destruct a gquad layer */
+#define   VRNA_GQUAD_MISMATCH_NUM_ALI   1   /* maximum number of mismatching sequences in the alignment when gquad should be formed */
+
+#endif