externals.c.in
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/*
DNAExternals.c is part of the NUPACK software suite
Copyright (c) 2007 Caltech. All rights reserved.
Coded by: Robert Dirks 3/2006, Justin Bois 1/2007
External variables describing fundamental properties of DNA, such as
base types, dangles, etc.
*/
#include <shared/externals.h>
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#ifdef NUPACK_SAMPLE
int nupack_sample;
int nupack_num_samples;
char ** nupack_sample_list;
int nupack_random_seed;
#endif // NUPACK_SAMPLE
int NUPACK_VALIDATE;
int mfe_sort_method; // A constant to allow forced sort-by-structure
int NupackShowHelp;
DBL_TYPE Stack[36];
DBL_TYPE loop37[90];
int tloops[6*4096];//has tetra loop sequences+cp, (6 extern ints per tetra loop)
DBL_TYPE tloop_energy[ 4096]; //energies of tetraloops
int triloops[5*1024]; //triloops equences + closing pairs
DBL_TYPE triloop_energy[ 2048]; //number of triloops
//Mismatch energies (see functions.h)
DBL_TYPE MMEnergiesHP[6*16];
DBL_TYPE MMEnergiesIL[256];
DBL_TYPE IL_SInt2[16*36]; //Symmetric extern interior Loops, size 2
DBL_TYPE IL_SInt4[256*36]; // Symmetric extern interior Loops, size 4
DBL_TYPE IL_AsInt1x2[64*36]; // Asymmetric extern interior Loop, size 3
DBL_TYPE dangle_energy[48]; // Dangle Energies
DBL_TYPE asymmetry_penalty[4]; // Asymmetric loop penalties
DBL_TYPE max_asymmetry;
long int maxGapIndex;
DBL_TYPE *sizeTerm;
DBL_TYPE *pairPrPb = NULL;
DBL_TYPE *pairPr = NULL;
DBL_TYPE *pairPrPbg = NULL;
DBL_TYPE *EXTERN_Q = NULL;
DBL_TYPE *EXTERN_QB = NULL;
DBL_TYPE BIMOLECULAR;
DBL_TYPE AT_PENALTY;
DBL_TYPE POLYC3;
DBL_TYPE POLYCSLOPE;
DBL_TYPE POLYCINT;
DBL_TYPE ALPHA_1; //multiloop penalties
DBL_TYPE ALPHA_2;
DBL_TYPE ALPHA_3;
DBL_TYPE BETA_1; //pseudoknot penalties
DBL_TYPE BETA_2;
DBL_TYPE BETA_3;
DBL_TYPE BETA_1M;
DBL_TYPE BETA_1P;
DBL_TYPE SODIUM_CONC;
DBL_TYPE MAGNESIUM_CONC;
int USE_LONG_HELIX_FOR_SALT_CORRECTION;
DBL_TYPE SALT_CORRECTION;
DBL_TYPE TEMP_K;
int DANGLETYPE;
int DNARNACOUNT;
int DO_PSEUDOKNOTS;
int ONLY_ONE_MFE;
int USE_MFE;
char PARAM_FILE[MAX_FILENAME_LEN];
unsigned int seqHash;
char NUPACK_VERSION[200] = "@NUPACK_VERSION@";
char COMMAND_PATH[MAX_FILENAME_LEN] = "";
#ifdef __cplusplus
}
#endif /* __cplusplus */