externals.h
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/*
externals.h 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.
*/
#ifndef NUPACK_SHARED_EXTERNALS_H
#define NUPACK_SHARED_EXTERNALS_H
#include <stddef.h>
#include "constants.h"
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#ifdef NUPACK_SAMPLE
extern int nupack_sample;
extern int nupack_num_samples;
extern char ** nupack_sample_list;
extern int nupack_random_seed;
#endif // NUPACK_SAMPLE
extern int NUPACK_VALIDATE;
extern int mfe_sort_method; // A constant to allow forced sort-by-structure
extern int NupackShowHelp;
extern DBL_TYPE Stack[36];
extern DBL_TYPE loop37[90];
extern int tloops[6*4096];//has tetra loop sequences+cp, (6 extern ints per tetra loop)
extern DBL_TYPE tloop_energy[ 4096]; //energies of tetraloops
extern int triloops[5*1024]; //triloops equences + closing pairs
extern DBL_TYPE triloop_energy[ 2048]; //number of triloops
//Mismatch energies (see functions.h)
extern DBL_TYPE MMEnergiesHP[6*16];
extern DBL_TYPE MMEnergiesIL[256];
extern DBL_TYPE IL_SInt2[16*36]; //Symmetric extern interior Loops, size 2
extern DBL_TYPE IL_SInt4[256*36]; // Symmetric extern interior Loops, size 4
extern DBL_TYPE IL_AsInt1x2[64*36]; // Asymmetric extern interior Loop, size 3
extern DBL_TYPE dangle_energy[48]; // Dangle Energies
extern DBL_TYPE asymmetry_penalty[4]; // Asymmetric loop penalties
extern DBL_TYPE max_asymmetry;
extern long int maxGapIndex;
extern DBL_TYPE *sizeTerm;
extern DBL_TYPE *pairPr;
extern DBL_TYPE *EXTERN_Q;
extern DBL_TYPE *EXTERN_QB;
extern DBL_TYPE BIMOLECULAR;
extern DBL_TYPE AT_PENALTY;
extern DBL_TYPE POLYC3;
extern DBL_TYPE POLYCSLOPE;
extern DBL_TYPE POLYCINT;
extern DBL_TYPE ALPHA_1; //multiloop penalties
extern DBL_TYPE ALPHA_2;
extern DBL_TYPE ALPHA_3;
extern DBL_TYPE BETA_1; //pseudoknot penalties
extern DBL_TYPE BETA_2;
extern DBL_TYPE BETA_3;
extern DBL_TYPE BETA_1M;
extern DBL_TYPE BETA_1P;
extern DBL_TYPE SODIUM_CONC;
extern DBL_TYPE MAGNESIUM_CONC;
extern int USE_LONG_HELIX_FOR_SALT_CORRECTION;
extern DBL_TYPE SALT_CORRECTION;
extern DBL_TYPE TEMP_K;
extern int DANGLETYPE;
extern int DNARNACOUNT;
extern int DO_PSEUDOKNOTS;
extern int ONLY_ONE_MFE;
extern int USE_MFE;
extern char PARAM_FILE[MAX_FILENAME_LEN];
extern unsigned int seqHash;
extern char NUPACK_VERSION[200];
extern char COMMAND_PATH[MAX_FILENAME_LEN];
#ifdef __cplusplus
}
#endif /* __cplusplus */
#endif // NUPACK_SHARED_EXTERNALS_H