RNAlib-2.4.17
default.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_PARAMS_DEFAULT_H
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#define VIENNA_RNA_PACKAGE_PARAMS_DEFAULT_H
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#include <
ViennaRNA/params/constants.h
>
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#define PUBLIC
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extern
double
lxc37;
/* parameter for logarithmic loop
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energy extrapolation */
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extern
int
stack37[
NBPAIRS
+1][
NBPAIRS
+1];
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extern
int
stackdH[
NBPAIRS
+1][
NBPAIRS
+1];
/* stack enthalpies */
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extern
int
hairpin37[31];
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extern
int
hairpindH[31];
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extern
int
bulge37[31];
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extern
int
bulgedH[31];
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extern
int
internal_loop37[31];
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extern
int
internal_loopdH[31];
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extern
int
mismatchI37[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatchIdH[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch1nI37[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch23I37[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch1nIdH[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatch23IdH[
NBPAIRS
+1][5][5];
/* interior loop mismatches */
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extern
int
mismatchH37[
NBPAIRS
+1][5][5];
/* same for hairpins */
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extern
int
mismatchM37[
NBPAIRS
+1][5][5];
/* same for multiloops */
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extern
int
mismatchHdH[
NBPAIRS
+1][5][5];
/* same for hairpins */
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extern
int
mismatchMdH[
NBPAIRS
+1][5][5];
/* same for multiloops */
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extern
int
mismatchExt37[
NBPAIRS
+1][5][5];
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extern
int
mismatchExtdH[
NBPAIRS
+1][5][5];
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extern
int
dangle5_37[
NBPAIRS
+1][5];
/* 5' dangle exterior of pair */
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extern
int
dangle3_37[
NBPAIRS
+1][5];
/* 3' dangle */
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extern
int
dangle3_dH[
NBPAIRS
+1][5];
/* corresponding enthalpies */
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extern
int
dangle5_dH[
NBPAIRS
+1][5];
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extern
int
int11_37[
NBPAIRS
+1][
NBPAIRS
+1][5][5];
/* 1x1 interior loops */
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extern
int
int11_dH[
NBPAIRS
+1][
NBPAIRS
+1][5][5];
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extern
int
int21_37[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5];
/* 2x1 interior loops */
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extern
int
int21_dH[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5];
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extern
int
int22_37[
NBPAIRS
+1][
NBPAIRS
+1][5][5][5][5];
/* 2x2 interior loops */
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extern
int
int22_dH[
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;
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extern
int
ML_BASEdH;
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extern
int
ML_closing37;
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extern
int
ML_closingdH;
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extern
int
ML_intern37;
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extern
int
ML_interndH;
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extern
int
TripleC37;
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extern
int
TripleCdH;
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extern
int
MultipleCA37;
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extern
int
MultipleCAdH;
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extern
int
MultipleCB37;
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extern
int
MultipleCBdH;
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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;
/* maximum correction */
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extern
int
ninio37;
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extern
int
niniodH;
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/* penalty for helices terminated by AU (actually not GC) */
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extern
int
TerminalAU37;
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extern
int
TerminalAUdH;
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/* penalty for forming bi-molecular duplex */
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extern
int
DuplexInit37;
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extern
int
DuplexInitdH;
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/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
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extern
char
Tetraloops[281];
/* string containing the special tetraloops */
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extern
int
Tetraloop37[40];
/* Bonus energy for special tetraloops */
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extern
int
TetraloopdH[40];
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extern
char
Triloops[241];
/* string containing the special triloops */
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extern
int
Triloop37[40];
/* Bonus energy for special Triloops */
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extern
int
TriloopdH[40];
/* Bonus energy for special Triloops */
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extern
char
Hexaloops[361];
/* string containing the special triloops */
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extern
int
Hexaloop37[40];
/* Bonus energy for special Triloops */
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extern
int
HexaloopdH[40];
/* Bonus energy for special Triloops */
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extern
int
GQuadAlpha37;
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extern
int
GQuadAlphadH;
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extern
int
GQuadBeta37;
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extern
int
GQuadBetadH;
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extern
int
GQuadLayerMismatch37;
/* penalty per incompatible gquad layer in a sub-alignment (applied twice for inner layers) */
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extern
int
GQuadLayerMismatchH;
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extern
int
GQuadLayerMismatchMax;
/* maximum number of mismatching sequences in the alignment when gquad should be formed */
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extern
double
Tmeasure;
/* temperature of param measurements */
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#endif
constants.h
Energy parameter constants.
NBPAIRS
#define NBPAIRS
Definition:
constants.h:25
ViennaRNA
params
default.h
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