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energy_par_RD.h
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/*
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prototypes for energy_par.c
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*/
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#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_RD_H__
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#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_RD_H__
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#include "
energy_const.h
"
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#define PUBLIC
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extern
double
lxc37_RD;
/* parameter for logarithmic loop
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energy extrapolation */
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extern
int
stack37_RD[
NBPAIRS
+1][
NBPAIRS
+1];
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extern
int
stackdH_RD[
NBPAIRS
+1][
NBPAIRS
+1];
/* stack enthalpies */
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extern
int
entropies[
NBPAIRS
+1][
NBPAIRS
+1];
/* not used anymore */
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extern
int
hairpin37_RD[31];
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extern
int
hairpindH_RD[31];
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extern
int
bulge37_RD[31];
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extern
int
bulgedH_RD[31];
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extern
int
internal_loop37_RD[31];
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extern
int
internal_loopdH_RD[31];
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extern
int
internal2_energy_RD;
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extern
int
old_mismatch_37_RD[
NBPAIRS
+1][5][5];
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extern
int
mismatchI37_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatchIdH_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch1nI37_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch23I37_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch1nIdH_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch23IdH_RD[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatchH37_RD[
NBPAIRS
+1][5][5];
/* same for hairpins */
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extern
int
mismatchM37_RD[
NBPAIRS
+1][5][5];
/* same for multiloops */
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extern
int
mismatchHdH_RD[
NBPAIRS
+1][5][5];
/* same for hairpins */
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extern
int
mismatchMdH_RD[
NBPAIRS
+1][5][5];
/* same for multiloops */
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extern
int
mismatchExt37_RD[
NBPAIRS
+1][5][5];
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extern
int
mismatchExtdH_RD[
NBPAIRS
+1][5][5];
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extern
int
dangle5_37_RD[
NBPAIRS
+1][5];
/* 5' dangle exterior of pair */
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extern
int
dangle3_37_RD[
NBPAIRS
+1][5];
/* 3' dangle */
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extern
int
dangle3_dH_RD[
NBPAIRS
+1][5];
/* corresponding enthalpies */
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extern
int
dangle5_dH_RD[
NBPAIRS
+1][5];
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extern
int
int11_37_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5];
/* 1x1 interior loops */
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extern
int
int11_dH_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5];
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extern
int
int21_37_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5];
/* 2x1 interior loops */
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extern
int
int21_dH_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5];
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extern
int
int22_37_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5][5];
/* 2x2 interior loops */
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extern
int
int22_dH_RD[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5][5];
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/* constants for linearly destabilizing contributions for multi-loops
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F = ML_closing + ML_intern*(k-1) + ML_BASE*u */
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extern
int
ML_BASE37_RD;
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extern
int
ML_BASEdH_RD;
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extern
int
ML_closing37_RD;
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extern
int
ML_closingdH_RD;
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extern
int
ML_intern37_RD;
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extern
int
ML_interndH_RD;
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extern
int
TripleC37_RD;
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extern
int
TripleCdH_RD;
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extern
int
MultipleCA37_RD;
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extern
int
MultipleCAdH_RD;
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extern
int
MultipleCB37_RD;
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extern
int
MultipleCBdH_RD;
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/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
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/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
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extern
int
MAX_NINIO_RD;
/* maximum correction */
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extern
int
ninio37_RD;
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extern
int
niniodH_RD;
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/* penalty for helices terminated by AU (actually not GC) */
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extern
int
TerminalAU37_RD;
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extern
int
TerminalAUdH_RD;
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/* penalty for forming bi-molecular duplex */
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extern
int
DuplexInit37_RD;
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extern
int
DuplexInitdH_RD;
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/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
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extern
char
Tetraloops_RD[];
/* string containing the special tetraloops */
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extern
int
Tetraloop37_RD[];
/* Bonus energy for special tetraloops */
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extern
int
TetraloopdH_RD[];
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extern
char
Triloops_RD[];
/* string containing the special triloops */
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extern
int
Triloop37_RD[];
/* Bonus energy for special Triloops */
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extern
int
TriloopdH_RD[];
/* Bonus energy for special Triloops */
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extern
char
Hexaloops_RD[];
/* string containing the special triloops */
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extern
int
Hexaloop37_RD[];
/* Bonus energy for special Triloops */
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extern
int
HexaloopdH_RD[];
/* Bonus energy for special Triloops */
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#endif
energy_const.h
NBPAIRS
#define NBPAIRS
Definition:
energy_const.h:24
H
energy_par_RD.h
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