| 1 | /* |
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| 2 | prototypes for energy_par.c |
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| 3 | */ |
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| 4 | |
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| 5 | #include "energy_const.h" |
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| 6 | namespace MXSCARNA { |
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| 7 | extern double lxc37; /* parameter for logarithmic loop |
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| 8 | energy extrapolation */ |
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| 9 | |
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| 10 | extern int stack37[NBPAIRS+1][NBPAIRS+1]; |
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| 11 | extern int enthalpies[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */ |
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| 12 | extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */ |
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| 13 | |
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| 14 | extern int hairpin37[31]; |
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| 15 | extern int bulge37[31]; |
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| 16 | extern int internal_loop37[31]; |
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| 17 | extern int internal2_energy; |
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| 18 | extern int old_mismatch_37[NBPAIRS+1][5][5]; |
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| 19 | extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ |
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| 20 | extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */ |
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| 21 | extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */ |
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| 22 | extern int mism_H[NBPAIRS+1][5][5]; /* mismatch enthalpies */ |
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| 23 | |
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| 24 | extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */ |
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| 25 | extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */ |
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| 26 | extern int dangle3_H[NBPAIRS+1][5]; /* corresponding enthalpies */ |
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| 27 | extern int dangle5_H[NBPAIRS+1][5]; |
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| 28 | |
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| 29 | extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */ |
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| 30 | extern int int11_H[NBPAIRS+1][NBPAIRS+1][5][5]; |
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| 31 | |
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| 32 | extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */ |
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| 33 | extern int int21_H[NBPAIRS+1][NBPAIRS+1][5][5][5]; |
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| 34 | |
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| 35 | extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */ |
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| 36 | extern int int22_H[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; |
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| 37 | |
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| 38 | /* constants for linearly destabilizing contributions for multi-loops |
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| 39 | F = ML_closing + ML_intern*(k-1) + ML_BASE*u */ |
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| 40 | extern int ML_BASE37; |
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| 41 | extern int ML_closing37; |
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| 42 | extern int ML_intern37; |
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| 43 | |
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| 44 | /* Ninio-correction for asymmetric internal loops with branches n1 and n2 */ |
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| 45 | /* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */ |
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| 46 | extern int MAX_NINIO; /* maximum correction */ |
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| 47 | extern int F_ninio37[5]; |
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| 48 | |
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| 49 | /* penalty for helices terminated by AU (actually not GC) */ |
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| 50 | extern int TerminalAU; |
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| 51 | /* penalty for forming bi-molecular duplex */ |
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| 52 | extern int DuplexInit; |
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| 53 | /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */ |
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| 54 | extern char Tetraloops[]; /* string containing the special tetraloops */ |
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| 55 | extern int TETRA_ENERGY37[]; /* Bonus energy for special tetraloops */ |
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| 56 | extern int TETRA_ENTH37; |
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| 57 | extern char Triloops[]; /* string containing the special triloops */ |
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| 58 | extern int Triloop_E37[]; /* Bonus energy for special Triloops */ |
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| 59 | |
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| 60 | extern double Tmeasure; /* temperature of param measurements */ |
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| 61 | } |
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