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nuc_cruc_santa_lucia.cpp
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nuc_cruc_santa_lucia.cpp
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#include "nuc_cruc.h"
#include <math.h>
// Linear interpolation for missing entropy values
#define INTERPOLATE(S, BEGIN, END, X) ( S[BEGIN] + (S[END] - S[BEGIN])*float(X - BEGIN)/(END - BEGIN) )
void NucCruc::init_param_Santa_Lucia()
{
tm_param = SANTA_LUCIA;
// Initialize all parameters to 0 by default
for(unsigned int i = 0;i < NUM_BASE_PAIR;i++){
memset( param_H[i], 0, NUM_BASE_PAIR*sizeof(float) );
memset( param_S[i], 0, NUM_BASE_PAIR*sizeof(float) );
}
// Initialize forbidden interactions:
//
#define default_enthalpy 100.0f
#define default_entropy 0.0f
for(char i = BASE::A;i <= BASE::I;i++){
for(char j = BASE::A;j <= BASE::I;j++){
// Gap bound to gap is not allowed
int curr = BASE_PAIR(i, j);
int prev = BASE_PAIR(BASE::GAP, BASE::GAP);
param_H[curr][prev] = param_H[prev][curr] = default_enthalpy;
param_S[curr][prev] = param_S[prev][curr] = default_entropy;
// x-/-y is not allowed
curr = BASE_PAIR(i, BASE::GAP);
prev = BASE_PAIR(BASE::GAP, j);
param_H[curr][prev] = param_H[prev][curr] = default_enthalpy;
param_S[curr][prev] = param_S[prev][curr] = default_entropy;
//-x/y- is not allowed
curr = BASE_PAIR(BASE::GAP, i);
prev = BASE_PAIR(j, BASE::GAP);
param_H[curr][prev] = param_H[prev][curr] = default_enthalpy;
param_S[curr][prev] = param_S[prev][curr] = default_entropy;
}
}
// Exact match parameters are from:
// "The thermodynamics of DNA structural motifs"
// J. SantaLucia and D. Hicks
// Annu. Rev. Biophys. Biomol. Struc. 2004. 33:415-440
// Note that this article has an incorrect value for AT_AT
// (it does not agree with all previous published values from the
// same group and does not match the Tm web server provided
// by the SantaLucia group).
// Exact nearest-neighboor matches: Delta H
#define AT_AT -7.9f
#define AT_CG -8.4f
#define AT_GC -7.8f
#define AT_TA -7.2f
#define CG_AT -8.5f
#define CG_CG -8.0f
#define CG_GC -10.6f
#define GC_AT -8.2f
#define GC_CG -9.8f
#define TA_AT -7.2f
param_H[AT][AT] = param_H[TA][TA] = AT_AT; // AA/TT
param_H[AT][CG] = param_H[GC][TA] = AT_CG; // AC/TG
param_H[AT][GC] = param_H[CG][TA] = AT_GC; // AG/TC
param_H[AT][TA] = AT_TA; // AT/TA
param_H[CG][AT] = param_H[TA][GC] = CG_AT; // CA/GT
param_H[CG][CG] = param_H[GC][GC] = CG_CG; // CC/GG
param_H[CG][GC] = CG_GC; // CG/GC
param_H[GC][AT] = param_H[TA][CG] = GC_AT; // GA/CT
param_H[GC][CG] = GC_CG; // GC/CG
param_H[TA][AT] = TA_AT; // TA/AT
param_S[AT][AT] = param_S[TA][TA] = ENTROPY(-1.00f, AT_AT); // AA/TT
param_S[AT][CG] = param_S[GC][TA] = ENTROPY(-1.44f, AT_CG); // AC/TG
param_S[AT][GC] = param_S[CG][TA] = ENTROPY(-1.28f, AT_GC); // AG/TC
param_S[AT][TA] = ENTROPY(-0.88f, AT_TA); // AT/TA
param_S[CG][AT] = param_S[TA][GC] = ENTROPY(-1.45f, CG_AT); // CA/GT
param_S[CG][CG] = param_S[GC][GC] = ENTROPY(-1.84f, CG_CG); // CC/GG
param_S[CG][GC] = ENTROPY(-2.17f, CG_GC); // CG/GC
param_S[GC][AT] = param_S[TA][CG] = ENTROPY(-1.30f, GC_AT); // GA/CT
param_S[GC][CG] = ENTROPY(-2.24f, GC_CG); // GC/CG
param_S[TA][AT] = ENTROPY(-0.58f, TA_AT); // TA/AT
#define AE_AT 0.2f
#define AE_CG -6.3f
#define AE_GC -3.7f
#define AE_TA -2.9f
#define CE_AT 0.6f
#define CE_CG -4.4f
#define CE_GC -4.0f
#define CE_TA -4.1f
#define GE_AT -1.1f
#define GE_CG -5.1f
#define GE_GC -3.9f
#define GE_TA -4.2f
#define TE_AT -6.9f
#define TE_CG -4.0f
#define TE_GC -4.9f
#define TE_TA -0.2f
param_H[AE][AT] = param_H[TA][EA] = AE_AT; // AA/ET
param_H[AE][CG] = param_H[GC][EA] = AE_CG; // AC/EG
param_H[AE][GC] = param_H[CG][EA] = AE_GC; // AG/EC
param_H[AE][TA] = param_H[AT][EA] = AE_TA; // AT/EA
param_H[CE][AT] = param_H[TA][EC] = CE_AT; // CA/ET
param_H[CE][CG] = param_H[GC][EC] = CE_CG; // CC/EG
param_H[CE][GC] = param_H[CG][EC] = CE_GC; // CG/EC
param_H[CE][TA] = param_H[AT][EC] = CE_TA; // CT/EA
param_H[GE][AT] = param_H[TA][EG] = GE_AT; // GA/ET
param_H[GE][CG] = param_H[GC][EG] = GE_CG; // GC/EG
param_H[GE][GC] = param_H[CG][EG] = GE_GC; // GG/EC
param_H[GE][TA] = param_H[AT][EG] = GE_TA; // GT/EA
param_H[TE][AT] = param_H[TA][ET] = TE_AT; // TA/ET
param_H[TE][CG] = param_H[GC][ET] = TE_CG; // TC/EG
param_H[TE][GC] = param_H[CG][ET] = TE_GC; // TG/EC
param_H[TE][TA] = param_H[AT][ET] = TE_TA; // TT/EA
param_S[AE][AT] = param_S[TA][EA] = ENTROPY(-0.51f, AE_AT); // AA/ET
param_S[AE][CG] = param_S[GC][EA] = ENTROPY(-0.96f, AE_CG); // AC/EG
param_S[AE][GC] = param_S[CG][EA] = ENTROPY(-0.58f, AE_GC); // AG/EC
param_S[AE][TA] = param_S[AT][EA] = ENTROPY(-0.5f, AE_TA); // AT/EA
param_S[CE][AT] = param_S[TA][EC] = ENTROPY(-0.42f, CE_AT); // CA/ET
param_S[CE][CG] = param_S[GC][EC] = ENTROPY(-0.52f, CE_CG); // CC/EG
param_S[CE][GC] = param_S[CG][EC] = ENTROPY(-0.34f, CE_GC); // CG/EC
param_S[CE][TA] = param_S[AT][EC] = ENTROPY(-0.02f, CE_TA); // CT/EA
param_S[GE][AT] = param_S[TA][EG] = ENTROPY(-0.62f, GE_AT); // GA/ET
param_S[GE][CG] = param_S[GC][EG] = ENTROPY(-0.72f, GE_CG); // GC/EG
param_S[GE][GC] = param_S[CG][EG] = ENTROPY(-0.56f, GE_GC); // GG/EC
param_S[GE][TA] = param_S[AT][EG] = ENTROPY(0.48f, GE_TA); // GT/EA
param_S[TE][AT] = param_S[TA][ET] = ENTROPY(-0.71f, TE_AT); // TA/ET
param_S[TE][CG] = param_S[GC][ET] = ENTROPY(-0.58f, TE_CG); // TC/EG
param_S[TE][GC] = param_S[CG][ET] = ENTROPY(-0.61f, TE_GC); // TG/EC
param_S[TE][TA] = param_S[AT][ET] = ENTROPY(-0.10f, TE_TA); // TT/EA
#define EA_AT -0.7f
#define EA_CG -2.1f
#define EA_GC -5.9f
#define EA_TA -0.5f
#define EC_AT 4.4f
#define EC_CG -0.2f
#define EC_GC -2.6f
#define EC_TA 4.7f
#define EG_AT -1.6f
#define EG_CG -3.9f
#define EG_GC -3.2f
#define EG_TA -4.1f
#define ET_AT 2.9f
#define ET_CG -4.4f
#define ET_GC -5.2f
#define ET_TA -3.8f
param_H[EA][AT] = param_H[TA][AE] = EA_AT; // EA/AT
param_H[EA][CG] = param_H[GC][AE] = EA_CG; // EC/AG
param_H[EA][GC] = param_H[CG][AE] = EA_GC; // EG/AC
param_H[EA][TA] = param_H[AT][AE] = EA_TA; // ET/AA
param_H[EC][AT] = param_H[TA][CE] = EC_AT; // EA/CT
param_H[EC][CG] = param_H[GC][CE] = EC_CG; // EC/CG
param_H[EC][GC] = param_H[CG][CE] = EC_GC; // EG/CC
param_H[EC][TA] = param_H[AT][CE] = EC_TA; // ET/CA
param_H[EG][AT] = param_H[TA][GE] = EG_AT; // EA/GT
param_H[EG][CG] = param_H[GC][GE] = EG_CG; // EC/GG
param_H[EG][GC] = param_H[CG][GE] = EG_GC; // EG/GC
param_H[EG][TA] = param_H[AT][GE] = EG_TA; // ET/GA
param_H[ET][AT] = param_H[TA][TE] = ET_AT; // EA/TT
param_H[ET][CG] = param_H[GC][TE] = ET_CG; // EC/TG
param_H[ET][GC] = param_H[CG][TE] = ET_GC; // EG/TC
param_H[ET][TA] = param_H[AT][TE] = ET_TA; // ET/TA
param_S[EA][AT] = param_S[TA][AE] = ENTROPY(-0.48f, EA_AT); // EA/AT
param_S[EA][CG] = param_S[GC][AE] = ENTROPY(-0.92f, EA_CG); // EC/AG
param_S[EA][GC] = param_S[CG][AE] = ENTROPY(-0.82f, EA_GC); // EG/AC
param_S[EA][TA] = param_S[AT][AE] = ENTROPY(-0.12f, EA_TA); // ET/AA
param_S[EC][AT] = param_S[TA][CE] = ENTROPY(-0.19f, EC_AT); // EA/CT
param_S[EC][CG] = param_S[GC][CE] = ENTROPY(-0.23f, EC_CG); // EC/CG
param_S[EC][GC] = param_S[CG][CE] = ENTROPY(-0.31f, EC_GC); // EG/CC
param_S[EC][TA] = param_S[AT][CE] = ENTROPY(0.28f, EC_TA); // ET/CA
param_S[EG][AT] = param_S[TA][GE] = ENTROPY(-0.50f, EG_AT); // EA/GT
param_S[EG][CG] = param_S[GC][GE] = ENTROPY(-0.44f, EG_CG); // EC/GG
param_S[EG][GC] = param_S[CG][GE] = ENTROPY(-0.01f, EG_GC); // EG/GC
param_S[EG][TA] = param_S[AT][GE] = ENTROPY(-0.01f, EG_TA); // ET/GA
param_S[ET][AT] = param_S[TA][TE] = ENTROPY(-0.29f, ET_AT); // EA/TT
param_S[ET][CG] = param_S[GC][TE] = ENTROPY(-0.35f, ET_CG); // EC/TG
param_S[ET][GC] = param_S[CG][TE] = ENTROPY(-0.52f, ET_GC); // EG/TC
param_S[ET][TA] = param_S[AT][TE] = ENTROPY(0.13f, ET_TA); // ET/TA
#define AT_AG -0.6f
#define AT_GA -0.7f
#define CG_AG -0.7f
#define CG_GA -4.0f
#define GC_AG -0.6f
#define GC_GA 0.5f
#define TA_AG 0.7f
#define TA_GA 3.0f
// Single G-A mismatch
// Allawi et. al. Biochemistry 1998, 37, 2170-2179
param_H[AT][AG] = param_H[GA][TA] = AT_AG; // Aa/Tg
param_H[AT][GA] = param_H[AG][TA] = AT_GA; // Ag/Ta
param_H[CG][AG] = param_H[GA][GC] = CG_AG; // Ca/Gg
param_H[CG][GA] = param_H[AG][GC] = CG_GA; // Cg/Ga
param_H[GC][AG] = param_H[GA][CG] = GC_AG; // Ga/Cg
param_H[GC][GA] = param_H[AG][CG] = GC_GA; // Gg/Ca
param_H[TA][AG] = param_H[GA][AT] = TA_AG; // Ta/Ag
param_H[TA][GA] = param_H[AG][AT] = TA_GA; // Tg/Aa
param_S[AT][AG] = param_S[GA][TA] = ENTROPY(0.14f, AT_AG); // Aa/Tg
param_S[AT][GA] = param_S[AG][TA] = ENTROPY(0.02f, AT_GA); // Ag/Ta
param_S[CG][AG] = param_S[GA][GC] = ENTROPY(0.03f, CG_AG); // Ca/Gg
param_S[CG][GA] = param_S[AG][GC] = ENTROPY(0.11f, CG_GA); // Cg/Ga
param_S[GC][AG] = param_S[GA][CG] = ENTROPY(-0.25f, GC_AG); // Ga/Cg
param_S[GC][GA] = param_S[AG][CG] = ENTROPY(-0.52f, GC_GA); // Gg/Ca
param_S[TA][AG] = param_S[GA][AT] = ENTROPY(0.42f, TA_AG); // Ta/Ag
param_S[TA][GA] = param_S[AG][AT] = ENTROPY(0.74f, TA_GA); // Tg/Aa
#define AT_CT 0.7f
#define AT_TC -1.2f
#define CG_CT -0.8f
#define CG_TC -1.5f
#define GC_CT 2.3f
#define GC_TC 5.2f
#define TA_CT 1.2f
#define TA_TC 1.0f
// Single C-T mismatch
// Allawi et. al. Nucleic Acids Research, 1998, 26, 11, 2694-2701
param_H[AT][CT] = param_H[TC][TA] = AT_CT; // Ac/Tt
param_H[AT][TC] = param_H[CT][TA] = AT_TC; // At/Tc
param_H[CG][CT] = param_H[TC][GC] = CG_CT; // Cc/Gt
param_H[CG][TC] = param_H[CT][GC] = CG_TC; // Ct/Gc
param_H[GC][CT] = param_H[TC][CG] = GC_CT; // Gc/Ct
param_H[GC][TC] = param_H[CT][CG] = GC_TC; // Gt/Cc
param_H[TA][CT] = param_H[TC][AT] = TA_CT; // Tc/At
param_H[TA][TC] = param_H[CT][AT] = TA_TC; // Tt/Ac
param_S[AT][CT] = param_S[TC][TA] = ENTROPY(0.64f, AT_CT); // Ac/Tt
param_S[AT][TC] = param_S[CT][TA] = ENTROPY(0.73f, AT_TC); // At/Tc
param_S[CG][CT] = param_S[TC][GC] = ENTROPY(0.62f, CG_CT); // Cc/Gt
param_S[CG][TC] = param_S[CT][GC] = ENTROPY(0.40f, CG_TC); // Ct/Gc
param_S[GC][CT] = param_S[TC][CG] = ENTROPY(0.62f, GC_CT); // Gc/Ct
param_S[GC][TC] = param_S[CT][CG] = ENTROPY(0.98f, GC_TC); // Gt/Cc
param_S[TA][CT] = param_S[TC][AT] = ENTROPY(0.97f, TA_CT); // Tc/At
param_S[TA][TC] = param_S[CT][AT] = ENTROPY(0.75f, TA_TC); // Tt/Ac
#define AT_AC 2.3f
#define AT_CA 5.3f
#define CG_AC 1.9f
#define CG_CA 0.6f
#define GC_AC 5.2f
#define GC_CA -0.7f
#define TA_AC 3.4f
#define TA_CA 7.6f
// Single A-C mismatch
// Allawi et. al. Biochemistry 1998, 37, 9435-9444
param_H[AT][AC] = param_H[CA][TA] = AT_AC; // Aa/Tc
param_H[AT][CA] = param_H[AC][TA] = AT_CA; // Ac/Ta
param_H[CG][AC] = param_H[CA][GC] = CG_AC; // Ca/Gc
param_H[CG][CA] = param_H[AC][GC] = CG_CA; // Cc/Ga
param_H[GC][AC] = param_H[CA][CG] = GC_AC; // Ga/Cc
param_H[GC][CA] = param_H[AC][CG] = GC_CA; // Gc/Ca
param_H[TA][AC] = param_H[CA][AT] = TA_AC; // Ta/Ac
param_H[TA][CA] = param_H[AC][AT] = TA_CA; // Tc/Aa
param_S[AT][AC] = param_S[CA][TA] = ENTROPY(0.88f, AT_AC); // Aa/Tc
param_S[AT][CA] = param_S[AC][TA] = ENTROPY(0.77f, AT_CA);// Ac/Ta
param_S[CG][AC] = param_S[CA][GC] = ENTROPY(0.75f, CG_AC); // Ca/Gc
param_S[CG][CA] = param_S[AC][GC] = ENTROPY(0.79f, CG_CA);// Cc/Ga
param_S[GC][AC] = param_S[CA][CG] = ENTROPY(0.81f, GC_AC);// Ga/Cc
param_S[GC][CA] = param_S[AC][CG] = ENTROPY(0.47f, GC_CA);// Gc/Ca
param_S[TA][AC] = param_S[CA][AT] = ENTROPY(0.92f, TA_AC); // Ta/Ac
param_S[TA][CA] = param_S[AC][AT] = ENTROPY(1.33f, TA_CA);// Tc/Aa
#define AT_GT 1.0f
#define AT_TG -2.5f
#define CG_GT -4.1f
#define CG_TG -2.8f
#define GC_GT 3.3f
#define GT_GT 5.8f
#define GC_TG -4.4f
#define GT_TG 4.1f
#define TA_GT -0.1f
#define TG_GT -1.4f
#define TA_TG -1.3f
// Single G-T mismatch
// Allawi et. al. Biochemistry 1997, 36, 10581-10594
param_H[AT][GT] = param_H[TG][TA] = AT_GT; // Ag/Tt
param_H[AT][TG] = param_H[GT][TA] = AT_TG; // At/Tg
param_H[CG][GT] = param_H[TG][GC] = CG_GT; // Cg/Gt
param_H[CG][TG] = param_H[GT][GC] = CG_TG; // Ct/Gg
param_H[GC][GT] = param_H[TG][CG] = GC_GT; // Gg/Ct
param_H[GT][GT] = param_H[TG][TG] = GT_GT; // gg/tt <-- double mismatch!
param_H[GC][TG] = param_H[GT][CG] = GC_TG; // Gt/Cg
param_H[GT][TG] = GT_TG; // gt/tg <-- double mismatch!
param_H[TA][GT] = param_H[TG][AT] = TA_GT; // Tg/At
param_H[TG][GT] = TG_GT; // tg/gt <-- double mismatch!
param_H[TA][TG] = param_H[GT][AT] = TA_TG; // Tt/Ag
param_S[AT][GT] = param_S[TG][TA] = ENTROPY(0.71f, AT_GT); // Ag/Tt
param_S[AT][TG] = param_S[GT][TA] = ENTROPY(0.07f, AT_TG); // At/Tg
param_S[CG][GT] = param_S[TG][GC] = ENTROPY(-0.47f, CG_GT); // Cg/Gt
param_S[CG][TG] = param_S[GT][GC] = ENTROPY(-0.32f, CG_TG); // Ct/Gg
param_S[GC][GT] = param_S[TG][CG] = ENTROPY(0.08f, GC_GT); // Gg/Ct
param_S[GT][GT] = param_S[TG][TG] = ENTROPY(0.74f, GT_GT); // gg/tt <-- double mismatch!
param_S[GC][TG] = param_S[GT][CG] = ENTROPY(-0.59f, GC_TG); // Gt/Cg
param_S[GT][TG] = ENTROPY(1.15f, GT_TG); // gt/tg <-- double mismatch!
param_S[TA][GT] = param_S[TG][AT] = ENTROPY(0.43f, TA_GT); // Tg/At
param_S[TG][GT] = ENTROPY(0.52f, TG_GT); // tg/gt <-- double mismatch!
param_S[TA][TG] = param_S[GT][AT] = ENTROPY(0.34f, TA_TG); // Tt/Ag
#define AT_AA 1.2f
#define CG_AA -0.9f
#define GC_AA -2.9f
#define TA_AA 4.7f
// Single A-A, C-C, G-G or T-T mismatch
// Peyret et. al. Biochemistry 1999, 38, 3468-3477
param_H[AT][AA] = param_H[AA][TA] = AT_AA; // Aa/Ta
param_H[CG][AA] = param_H[AA][GC] = CG_AA; // Ca/Ga
param_H[GC][AA] = param_H[AA][CG] = GC_AA; // Ga/Ca
param_H[TA][AA] = param_H[AA][AT] = TA_AA; // Ta/Aa
param_S[AT][AA] = param_S[AA][TA] = ENTROPY(0.61f, AT_AA); // Aa/Ta
param_S[CG][AA] = param_S[AA][GC] = ENTROPY(0.43f, CG_AA); // Ca/Ga
param_S[GC][AA] = param_S[AA][CG] = ENTROPY(0.17f, GC_AA); // Ga/Ca
param_S[TA][AA] = param_S[AA][AT] = ENTROPY(0.69f, TA_AA); // Ta/Aa
#define AT_CC 0.0f
#define CG_CC -1.5f
#define GC_CC 3.6f
#define TA_CC 6.1f
param_H[AT][CC] = param_H[CC][TA] = AT_CC; // Ac/Tc
param_H[CG][CC] = param_H[CC][GC] = CG_CC; // Cc/Gc
param_H[GC][CC] = param_H[CC][CG] = GC_CC; // Gc/Cc
param_H[TA][CC] = param_H[CC][AT] = TA_CC; // Tc/Ac
param_S[AT][CC] = param_S[CC][TA] = ENTROPY(1.33f, AT_CC); // Ac/Tc
param_S[CG][CC] = param_S[CC][GC] = ENTROPY(0.70f, CG_CC); // Cc/Gc
param_S[GC][CC] = param_S[CC][CG] = ENTROPY(0.79f, GC_CC); // Gc/Cc
param_S[TA][CC] = param_S[CC][AT] = ENTROPY(1.05f, TA_CC); // Tc/Ac
#define AT_GG -3.1f
#define CG_GG -4.9f
#define GC_GG -6.0f
#define TA_GG 1.6f
param_H[AT][GG] = param_H[GG][TA] = AT_GG; // Ag/Tg
param_H[CG][GG] = param_H[GG][GC] = CG_GG; // Cg/Gg
param_H[GC][GG] = param_H[GG][CG] = GC_GG; // Gg/Cg
param_H[TA][GG] = param_H[GG][AT] = TA_GG; // Tg/Ag
param_S[AT][GG] = param_S[GG][TA] = ENTROPY(-0.13f, AT_GG); // Ag/Tg
param_S[CG][GG] = param_S[GG][GC] = ENTROPY(-0.11f, CG_GG); // Cg/Gg
param_S[GC][GG] = param_S[GG][CG] = ENTROPY(-1.11f, GC_GG); // Gg/Cg
param_S[TA][GG] = param_S[GG][AT] = ENTROPY(0.44f, TA_GG); // Tg/Ag
#define AT_TT -2.7f
#define CG_TT -5.0f
#define GC_TT -2.2f
#define TA_TT 0.2f
param_H[AT][TT] = param_H[TT][TA] = AT_TT; // At/Tt
param_H[CG][TT] = param_H[TT][GC] = CG_TT; // Ct/Gt
param_H[GC][TT] = param_H[TT][CG] = GC_TT; // Gt/Ct
param_H[TA][TT] = param_H[TT][AT] = TA_TT; // Tt/At
param_S[AT][TT] = param_S[TT][TA] = ENTROPY(0.69f, AT_TT); // At/Tt
param_S[CG][TT] = param_S[TT][GC] = ENTROPY(-0.12f, CG_TT); // Ct/Gt
param_S[GC][TT] = param_S[TT][CG] = ENTROPY(0.45f, GC_TT); // Gt/Ct
param_S[TA][TT] = param_S[TT][AT] = ENTROPY(0.68f, TA_TT); // Tt/At
// Inosine base-pairs from
// "Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes"
// Norman E. Watkins, Jr and John SantaLucia, Jr
// Nucleic Acids Research, 2005, vol. 33, No. 19 pg. 6258-6267
// Inosine IC pairs: Delta H
#define AT_IC -8.9f
#define TA_IC -5.9f
#define AT_CI -8.8f
#define TA_CI -4.9f
#define CG_IC -5.4f
#define GC_IC -6.8f
#define CG_CI -8.3f
#define GC_CI -5.0f
param_H[AT][IC] = param_H[CI][TA] = AT_IC; // AI/TC
param_H[TA][IC] = param_H[CI][AT] = TA_IC; // TI/AC
param_H[AT][CI] = param_H[IC][TA] = AT_CI; // AC/TI
param_H[TA][CI] = param_H[IC][AT] = TA_CI; // TC/AI
param_H[CG][IC] = param_H[CI][GC] = CG_IC; // CI/GC
param_H[GC][IC] = param_H[CI][CG] = GC_IC; // GI/CC
param_H[CG][CI] = param_H[IC][GC] = CG_CI; // CC/GI
param_H[GC][CI] = param_H[IC][CG] = GC_CI; // GC/CI
param_S[AT][IC] = param_S[CI][TA] = ENTROPY(-0.96f, AT_IC); // AI/TC
param_S[TA][IC] = param_S[CI][AT] = ENTROPY(-0.46f, TA_IC); // AI/TC
param_S[AT][CI] = param_S[IC][TA] = ENTROPY(-0.89f, AT_CI); // AC/TI
param_S[TA][CI] = param_S[IC][AT] = ENTROPY(-0.59f, TA_CI); // TC/AI
param_S[CG][IC] = param_S[CI][GC] = ENTROPY(-1.14f, CG_IC); // CI/GC
param_S[GC][IC] = param_S[CI][CG] = ENTROPY(-0.86f, GC_IC); // GI/CC
param_S[CG][CI] = param_S[IC][GC] = ENTROPY(-0.88f, CG_CI); // CC/GI
param_S[GC][CI] = param_S[IC][CG] = ENTROPY(-1.07f, GC_CI); // GC/CI
// Inosine IA pairs: Delta H
#define AT_IA -8.3f
#define TA_IA -3.4f
#define AT_AI -0.7f
#define TA_AI -1.3f
#define CG_IA 2.6f
#define GC_IA -7.8f
#define CG_AI -7.0f
#define GC_AI -7.6f
param_H[AT][IA] = param_H[AI][TA] = AT_IA; // AI/TA
param_H[TA][IA] = param_H[AI][AT] = TA_IA; // TI/AA
param_H[AT][AI] = param_H[IA][TA] = AT_AI; // AA/TI
param_H[TA][AI] = param_H[IA][AT] = TA_AI; // TA/AI
param_H[CG][IA] = param_H[AI][GC] = CG_IA; // CI/GA
param_H[GC][IA] = param_H[AI][CG] = GC_IA; // GI/CA
param_H[CG][AI] = param_H[IA][GC] = CG_AI; // CA/GI
param_H[GC][AI] = param_H[IA][CG] = GC_AI; // GA/CI
param_S[AT][IA] = param_S[AI][TA] = ENTROPY(-0.51f, AT_IA); // AI/TA
param_S[TA][IA] = param_S[AI][AT] = ENTROPY(0.09f, TA_IA); // TI/AA
param_S[AT][AI] = param_S[IA][TA] = ENTROPY(0.12f, AT_AI); // AA/TI
param_S[TA][AI] = param_S[IA][AT] = ENTROPY(0.12f, TA_AI); // TA/AI
param_S[CG][IA] = param_S[AI][GC] = ENTROPY(-0.18f, CG_IA); // CI/GA
param_S[GC][IA] = param_S[AI][CG] = ENTROPY(-1.24f, GC_IA); // GI/CA
param_S[CG][AI] = param_S[IA][GC] = ENTROPY(-0.77f, CG_AI); // CA/GI
param_S[GC][AI] = param_S[IA][CG] = ENTROPY(-1.33f, GC_AI); // GA/CI
// Inosine IT pairs: Delta H
#define AT_IT 0.49f
#define TA_IT -6.5f
#define AT_TI -5.6f
#define TA_TI -0.8f
#define CG_IT -1.0f
#define GC_IT -3.5f
#define CG_TI 0.1f
#define GC_TI -4.3f
param_H[AT][IT] = param_H[TI][TA] = AT_IT; // AI/TT
param_H[TA][IT] = param_H[TI][AT] = TA_IT; // TI/AT
param_H[AT][TI] = param_H[IT][TA] = AT_TI; // AT/TI
param_H[TA][TI] = param_H[IT][AT] = TA_TI; // TT/AI
param_H[CG][IT] = param_H[TI][GC] = CG_IT; // CI/GT
param_H[GC][IT] = param_H[TI][CG] = GC_IT; // GI/CT
param_H[CG][TI] = param_H[IT][GC] = CG_TI; // CT/GI
param_H[GC][TI] = param_H[IT][CG] = GC_TI; // GT/CI
param_S[AT][IT] = param_S[TI][TA] = ENTROPY(0.71f, AT_IT); // AI/TT
param_S[TA][IT] = param_S[TI][AT] = ENTROPY(0.36f, TA_IT); // TI/AT
param_S[AT][TI] = param_S[IT][TA] = ENTROPY(0.22f, AT_TI); // AT/TI
param_S[TA][TI] = param_S[IT][AT] = ENTROPY(0.54f, TA_TI); // TT/AI
param_S[CG][IT] = param_S[TI][GC] = ENTROPY(-0.26f, CG_IT); // CI/GT
param_S[GC][IT] = param_S[TI][CG] = ENTROPY(-0.19f, GC_IT); // GI/CT
param_S[CG][TI] = param_S[IT][GC] = ENTROPY(0.41f, CG_TI); // CT/GI
param_S[GC][TI] = param_S[IT][CG] = ENTROPY(-0.54f, GC_TI); // GT/CI
// Inosine IG pairs: Delta H
#define AT_IG -4.9f
#define TA_IG -1.9f
#define AT_GI 0.1f
#define TA_GI 1.0f
#define CG_IG 7.1f
#define GC_IG -1.1f
#define CG_GI 5.8f
#define GC_GI -7.6f
param_H[AT][IG] = param_H[GI][TA] = AT_IG; // AI/TG
param_H[TA][IG] = param_H[GI][AT] = TA_IG; // TI/AG
param_H[AT][GI] = param_H[IG][TA] = AT_GI; // AG/TI
param_H[TA][GI] = param_H[IG][AT] = TA_GI; // TG/AI
param_H[CG][IG] = param_H[GI][GC] = CG_IG; // CI/GG
param_H[GC][IG] = param_H[GI][CG] = GC_IG; // GI/CG
param_H[CG][GI] = param_H[IG][GC] = CG_GI; // CG/GI
param_H[GC][GI] = param_H[IG][CG] = GC_GI; // GG/CI
param_S[AT][IG] = param_S[GI][TA] = ENTROPY(0.02f, AT_IG); // AI/TG
param_S[TA][IG] = param_S[GI][AT] = ENTROPY(0.76f, TA_IG); // TI/AG
param_S[AT][GI] = param_S[IG][TA] = ENTROPY(0.65f, AT_GI); // AG/TI
param_S[TA][GI] = param_S[IG][AT] = ENTROPY(0.70f, TA_GI); // TG/AI
param_S[CG][IG] = param_S[GI][GC] = ENTROPY(0.47f, CG_IG); // CI/GG
param_S[GC][IG] = param_S[GI][CG] = ENTROPY(-0.10f, GC_IG); // GI/CG
param_S[CG][GI] = param_S[IG][GC] = ENTROPY(0.54f, CG_GI); // CG/GI
param_S[GC][GI] = param_S[IG][CG] = ENTROPY(-0.74f, GC_GI); // GG/CI
// Inosine II pairs: Delta H
#define AT_II -3.3f
#define TA_II 0.1f
#define CG_II 1.3f
#define GC_II -0.5f
param_H[AT][II] = param_H[II][TA] = AT_II; // AI/TI
param_H[TA][II] = param_H[II][AT] = TA_II; // TI/AI
param_H[CG][II] = param_H[II][GC] = CG_II; // CI/GI
param_H[GC][II] = param_H[II][CG] = GC_II; // GI/CI
param_S[AT][II] = param_S[II][TA] = ENTROPY(0.40f, AT_II); // AI/TI
param_S[TA][II] = param_S[II][AT] = ENTROPY(0.81f, TA_II); // TI/AI
param_S[CG][II] = param_S[II][GC] = ENTROPY(0.36f, CG_II); // CI/GI
param_S[GC][II] = param_S[II][CG] = ENTROPY(-0.09f, GC_II); // GI/CI
// Inosine tandem internal pairs: Delta H
#define IC_IC -9.3f
#define IA_IC -3.1f
#define IC_IA -8.7f
#define IA_IA -2.1f
#define IT_IA 2.3f
#define IG_IA 4.2f
#define IC_IT -14.5f
#define IA_IT -17.8f
#define IT_IT -7.0f
#define IG_IT -19.4f
#define IT_IG 13.3f
#define IG_IG 0.3f // There is a typo in the paper (II/TG should read II/GG)
#define II_II -10.65f // Note that II/II is *not* a two state reaction!
// Two values are published for II/II; -13.8 and -7.5. For
// now, use the average -> -10.65
param_H[IC][IC] = param_H[CI][CI] = IC_IC; // II/CC
param_H[IA][IC] = param_H[CI][AI] = IA_IC; // II/AC
param_H[IC][IA] = param_H[AI][CI] = IC_IA; // II/CA
param_H[IA][IA] = param_H[AI][AI] = IA_IA; // II/AA
param_H[IT][IA] = param_H[AI][TI] = IT_IA; // II/TA
param_H[IG][IA] = param_H[AI][GI] = IG_IA; // II/GA
param_H[IC][IT] = param_H[TI][CI] = IC_IT; // II/CT
param_H[IA][IT] = param_H[TI][AI] = IA_IT; // II/AT
param_H[IT][IT] = param_H[TI][TI] = IT_IT; // II/TT
param_H[IG][IT] = param_H[TI][GI] = IG_IT; // II/GT
param_H[IT][IG] = param_H[GI][TI] = IT_IG; // II/TG
param_H[IG][IG] = param_H[GI][GI] = IG_IG; // II/GG
param_H[II][II] = II_II; // II/II
param_S[IC][IC] = param_S[CI][CI] = ENTROPY(-0.64f, IC_IC); // II/CC
param_S[IA][IC] = param_S[CI][AI] = ENTROPY(0.27f, IA_IC); // II/AC
param_S[IC][IA] = param_S[AI][CI] = ENTROPY(0.44f, IC_IA); // II/CA
param_S[IA][IA] = param_S[AI][AI] = ENTROPY(-0.27f, IA_IA); // II/AA
param_S[IT][IA] = param_S[AI][TI] = ENTROPY(0.83f, IT_IA); // II/TA
param_S[IG][IA] = param_S[AI][GI] = ENTROPY(0.30f, IG_IA); // II/GA
param_S[IC][IT] = param_S[TI][CI] = ENTROPY(0.33f, IC_IT); // II/CT
param_S[IA][IT] = param_S[TI][AI] = ENTROPY(0.19f, IA_IT); // II/AT
param_S[IT][IT] = param_S[TI][TI] = ENTROPY(1.69f, IT_IT); // II/TT
param_S[IG][IT] = param_S[TI][GI] = ENTROPY(0.13f, IG_IT); // II/GT
param_S[IT][IG] = param_S[GI][TI] = ENTROPY(0.03f, IT_IG); // II/TG
param_S[IG][IG] = param_S[GI][GI] = ENTROPY(-1.30f, IG_IG); // II/GG
param_S[II][II] = ENTROPY(0.52f, II_II); // II/II; Not two state!
// Use the average DG:
// (-0.7 and 1.74)
// Inosine "other" tandem mismatch pairs: Delta H
#define IC_CI -12.1f
#define CI_IC -1.8f
#define IA_AI -13.9f
#define AI_IA -9.5f
#define IT_TI -7.6f
#define TI_IT -14.7f
#define IG_GI 3.2f
#define GI_IG -4.2f
param_H[IC][CI] = IC_CI; // IC/CI
param_H[CI][IC] = CI_IC; // CI/IC
param_H[IA][AI] = IA_AI; // IA/AI
param_H[AI][IA] = AI_IA; // AI/IA
param_H[IT][TI] = IT_TI; // IT/TI
param_H[TI][IT] = TI_IT; // TI/IT
param_H[IG][GI] = IG_GI; // IG/GI
param_H[GI][IG] = GI_IG; // GI/IG
param_S[IC][CI] = ENTROPY(-0.85f, IC_CI); // IC/CI
param_S[CI][IC] = ENTROPY(0.06f, CI_IC); // CI/IC
param_S[IA][AI] = ENTROPY(-1.43f, IA_AI); // IA/AI
param_S[AI][IA] = ENTROPY(-0.56f, AI_IA); // AI/IA
param_S[IT][TI] = ENTROPY(2.03f, IT_TI); // IT/TI
param_S[TI][IT] = ENTROPY(0.61f, TI_IT); // TI/IT
param_S[IG][GI] = ENTROPY(1.18f, IG_GI); // IG/GI
param_S[GI][IG] = ENTROPY(1.12f, GI_IG); // GI/IG
///////////////////////////////////////////////////////////////////////
// Internal loop and hairpin terminal mismatch parameters
// These parameters have not been officially published. However, the parameters
// are available from the unafold software package
// (http://frontend.bioinfo.rpi.edu/applications/hybrid/download.php).
for(unsigned int i = 0;i < NUM_BASE_PAIR;i++){
memcpy( param_loop_terminal_H[i], param_H[i], NUM_BASE_PAIR*sizeof(float) );
memcpy( param_loop_terminal_S[i], param_S[i], NUM_BASE_PAIR*sizeof(float) );
memcpy( param_hairpin_terminal_H[i], param_H[i], NUM_BASE_PAIR*sizeof(float) );
memcpy( param_hairpin_terminal_S[i], param_S[i], NUM_BASE_PAIR*sizeof(float) );
}
// ******************************************************************************
// Include a subset of unpublished parameters from the unafold program.
// Please note: Since unafold is not open source software, we can not
// distribute this code outside of LANL!
// ******************************************************************************
//#include "nuc_cruc_santa_lucia_tstacki.cpp"
//#include "nuc_cruc_santa_lucia_tstackh.cpp"
// The following parameters are from:
// "The thermodynamics of DNA structural motifs"
// J. SantaLucia and D. Hicks
// Annu. Rev. Biophys. Biomol. Struc. 2004. 33:415-440
param_init_H = 0.2f;
param_init_S = ENTROPY(1.96f, 0.2f);
param_AT_closing_H = 2.2f;
param_AT_closing_S = ENTROPY(0.05f, 2.2f);
param_symmetry_S = ENTROPY(0.43f, 0.0f);
param_SALT = 0.368e-3f;
param_asymmetric_loop_dS = ENTROPY(0.3f, 0.0f);
param_bulge_AT_closing_S = ENTROPY(0.5f, 0.0f);
///////////////////////////////////////////////////////
// From Table 4 in the above reference:
///////////////////////////////////////////////////////
// Internal Loop
param_loop_S[0] = 0.0f;
param_loop_S[1] = 0.0f;
param_loop_S[2] = 0.0f;
param_loop_S[3] = ENTROPY(3.2f, 0.0f);
param_loop_S[4] = ENTROPY(3.6f, 0.0f);
param_loop_S[5] = ENTROPY(4.0f, 0.0f);
param_loop_S[6] = ENTROPY(4.4f, 0.0f);
param_loop_S[7] = ENTROPY(4.6f, 0.0f);
param_loop_S[8] = ENTROPY(4.8f, 0.0f);
param_loop_S[9] = ENTROPY(4.9f, 0.0f);
param_loop_S[10] = ENTROPY(4.9f, 0.0f);
param_loop_S[12] = ENTROPY(5.2f, 0.0f);
param_loop_S[14] = ENTROPY(5.4f, 0.0f);
param_loop_S[16] = ENTROPY(5.6f, 0.0f);
param_loop_S[18] = ENTROPY(5.8f, 0.0f);
param_loop_S[20] = ENTROPY(5.9f, 0.0f);
param_loop_S[25] = ENTROPY(6.3f, 0.0f);
param_loop_S[30] = ENTROPY(6.6f, 0.0f);
param_loop_S[11] = INTERPOLATE(param_loop_S, 10, 12, 11);
param_loop_S[13] = INTERPOLATE(param_loop_S, 12, 14, 13);
param_loop_S[15] = INTERPOLATE(param_loop_S, 14, 16, 15);
param_loop_S[17] = INTERPOLATE(param_loop_S, 16, 18, 17);
param_loop_S[19] = INTERPOLATE(param_loop_S, 18, 20, 19);
param_loop_S[21] = INTERPOLATE(param_loop_S, 20, 25, 21);
param_loop_S[22] = INTERPOLATE(param_loop_S, 20, 25, 22);
param_loop_S[23] = INTERPOLATE(param_loop_S, 20, 25, 23);
param_loop_S[24] = INTERPOLATE(param_loop_S, 20, 25, 24);
param_loop_S[26] = INTERPOLATE(param_loop_S, 25, 30, 26);
param_loop_S[27] = INTERPOLATE(param_loop_S, 25, 30, 27);
param_loop_S[28] = INTERPOLATE(param_loop_S, 25, 30, 28);
param_loop_S[29] = INTERPOLATE(param_loop_S, 25, 30, 29);
// Jacobson-Stockmayer entropy extrapolation
// dS(n) = dS(x) - 2.44*R*ln(n/x)
#define ANCHOR_LOOP_EXTRAP 30
for(unsigned int i = 31;i < MAX_LOOP_LENGTH;i++){
param_loop_S[i] = param_loop_S[ANCHOR_LOOP_EXTRAP] - 2.44f*NC_R*( log( double(i)/ANCHOR_LOOP_EXTRAP) );
}
///////////////////////////////////////////////////////
// Bulge
param_bulge_S[0] = 0.0f;
param_bulge_S[1] = ENTROPY(4.0f, 0.0f);
param_bulge_S[2] = ENTROPY(2.9f, 0.0f);
param_bulge_S[3] = ENTROPY(3.1f, 0.0f);
param_bulge_S[4] = ENTROPY(3.2f, 0.0f);
param_bulge_S[5] = ENTROPY(3.3f, 0.0f);
param_bulge_S[6] = ENTROPY(3.5f, 0.0f);
param_bulge_S[7] = ENTROPY(3.7f, 0.0f);
param_bulge_S[8] = ENTROPY(3.9f, 0.0f);
param_bulge_S[9] = ENTROPY(4.1f, 0.0f);
param_bulge_S[10] = ENTROPY(4.3f, 0.0f);
param_bulge_S[12] = ENTROPY(4.5f, 0.0f);
param_bulge_S[14] = ENTROPY(4.8f, 0.0f);
param_bulge_S[16] = ENTROPY(5.0f, 0.0f);
param_bulge_S[18] = ENTROPY(5.2f, 0.0f);
param_bulge_S[20] = ENTROPY(5.3f, 0.0f);
param_bulge_S[25] = ENTROPY(5.6f, 0.0f);
param_bulge_S[30] = ENTROPY(5.9f, 0.0f);
param_bulge_S[11] = INTERPOLATE(param_bulge_S, 10, 12, 11);
param_bulge_S[13] = INTERPOLATE(param_bulge_S, 12, 14, 13);
param_bulge_S[15] = INTERPOLATE(param_bulge_S, 14, 16, 15);
param_bulge_S[17] = INTERPOLATE(param_bulge_S, 16, 18, 17);
param_bulge_S[19] = INTERPOLATE(param_bulge_S, 18, 20, 19);
param_bulge_S[21] = INTERPOLATE(param_bulge_S, 20, 25, 21);
param_bulge_S[22] = INTERPOLATE(param_bulge_S, 20, 25, 22);
param_bulge_S[23] = INTERPOLATE(param_bulge_S, 20, 25, 23);
param_bulge_S[24] = INTERPOLATE(param_bulge_S, 20, 25, 24);
param_bulge_S[26] = INTERPOLATE(param_bulge_S, 25, 30, 26);
param_bulge_S[27] = INTERPOLATE(param_bulge_S, 25, 30, 27);
param_bulge_S[28] = INTERPOLATE(param_bulge_S, 25, 30, 28);
param_bulge_S[29] = INTERPOLATE(param_bulge_S, 25, 30, 29);
// Jacobson-Stockmayer entropy extrapolation
// dS(n) = dS(x) - 2.44*R*ln(n/x)
#define ANCHOR_BULGE_EXTRAP 30
for(unsigned int i = 31;i < MAX_BULGE_LENGTH;i++){
param_bulge_S[i] = param_bulge_S[ANCHOR_BULGE_EXTRAP] - 2.44f*NC_R*( log( double(i)/ANCHOR_BULGE_EXTRAP) );
}
///////////////////////////////////////////////////////
// Hairpin loop
param_hairpin_S[0] = 0.0f;
param_hairpin_S[1] = 0.0f;
param_hairpin_S[2] = 0.0f;
param_hairpin_S[3] = ENTROPY(3.5f, 0.0f);
param_hairpin_S[4] = ENTROPY(3.5f, 0.0f);
param_hairpin_S[5] = ENTROPY(3.3f, 0.0f);
param_hairpin_S[6] = ENTROPY(4.0f, 0.0f);
param_hairpin_S[7] = ENTROPY(4.2f, 0.0f);
param_hairpin_S[8] = ENTROPY(4.3f, 0.0f);
param_hairpin_S[9] = ENTROPY(4.5f, 0.0f);
param_hairpin_S[10] = ENTROPY(4.6f, 0.0f);
param_hairpin_S[12] = ENTROPY(5.0f, 0.0f);
param_hairpin_S[14] = ENTROPY(5.1f, 0.0f);
param_hairpin_S[16] = ENTROPY(5.3f, 0.0f);
param_hairpin_S[18] = ENTROPY(5.5f, 0.0f);
param_hairpin_S[20] = ENTROPY(5.7f, 0.0f);
param_hairpin_S[25] = ENTROPY(6.1f, 0.0f);
param_hairpin_S[30] = ENTROPY(6.3f, 0.0f);
// Interpolate the missing values
param_hairpin_S[11] = INTERPOLATE(param_hairpin_S, 10, 12, 11);
param_hairpin_S[13] = INTERPOLATE(param_hairpin_S, 12, 14, 13);
param_hairpin_S[15] = INTERPOLATE(param_hairpin_S, 14, 16, 15);
param_hairpin_S[17] = INTERPOLATE(param_hairpin_S, 16, 18, 17);
param_hairpin_S[19] = INTERPOLATE(param_hairpin_S, 18, 20, 19);
param_hairpin_S[21] = INTERPOLATE(param_hairpin_S, 20, 25, 21);
param_hairpin_S[22] = INTERPOLATE(param_hairpin_S, 20, 25, 22);
param_hairpin_S[23] = INTERPOLATE(param_hairpin_S, 20, 25, 23);
param_hairpin_S[24] = INTERPOLATE(param_hairpin_S, 20, 25, 24);
param_hairpin_S[26] = INTERPOLATE(param_hairpin_S, 25, 30, 26);
param_hairpin_S[27] = INTERPOLATE(param_hairpin_S, 25, 30, 27);
param_hairpin_S[28] = INTERPOLATE(param_hairpin_S, 25, 30, 28);
param_hairpin_S[29] = INTERPOLATE(param_hairpin_S, 25, 30, 29);
// Jacobson-Stockmayer entropy extrapolation
// dS(n) = dS(x) - 2.44*R*ln(n/x)
#define ANCHOR_HAIRPIN_EXTRAP 30
for(unsigned int i = 31;i < MAX_HAIRPIN_LENGTH;i++){
param_hairpin_S[i] = param_hairpin_S[ANCHOR_HAIRPIN_EXTRAP] - 2.44f*NC_R*( log( double(i)/ANCHOR_HAIRPIN_EXTRAP) );
}
// From:
// Supplemental Material: Annu.Rev.Biophs.Biomol.Struct.33:415-40
// doi: 10.1146/annurev.biophys.32.110601.141800
// The Termodynamicso f DNA Structural Motifs
// SantaLucia and Hicks, 2004
// The table has been saved as a text file in: nuc_cruc_santa_lucia_data.txt
// The code below was generated with the command:
// cat nuc_cruc_santa_lucia_data.txt | awk '{print "param_hairpin_special_H["$1"] = "$3";\nparam_hairpin_special_S["$1"] = " ($3-$2)/310.15";\n"}'
//
// This command does *not* append "f" to each number to avoid compiler errors when the number
// is printed as an integer.
param_hairpin_special_H[AAAAAT] = 0.5;
param_hairpin_special_S[AAAAAT] = -0.000644849;
param_hairpin_special_H[AAAACT] = 0.7;
param_hairpin_special_S[AAAACT] = 0.00161212;
param_hairpin_special_H[AAACAT] = 1;
param_hairpin_special_S[AAACAT] = 0.00161212;
param_hairpin_special_H[ACTTGT] = 0;
param_hairpin_special_S[ACTTGT] = 0.00419152;
param_hairpin_special_H[AGAAAT] = -1.1;
param_hairpin_special_S[AGAAAT] = 0.00161212;
param_hairpin_special_H[AGAAT] = -1.5;
param_hairpin_special_S[AGAAT] = 0;
param_hairpin_special_H[AGAGAT] = -1.1;
param_hairpin_special_S[AGAGAT] = 0.00161212;
param_hairpin_special_H[AGATAT] = -1.5;
param_hairpin_special_S[AGATAT] = 0.00161212;
param_hairpin_special_H[AGCAAT] = -1.6;
param_hairpin_special_S[AGCAAT] = 0.00161212;
param_hairpin_special_H[AGCAT] = -1.5;
param_hairpin_special_S[AGCAT] = 0;
param_hairpin_special_H[AGCGAT] = -1.1;
param_hairpin_special_S[AGCGAT] = 0.00161212;
param_hairpin_special_H[AGCTTT] = 0.2;
param_hairpin_special_S[AGCTTT] = 0.00161212;
param_hairpin_special_H[AGGAAT] = -1.1;
param_hairpin_special_S[AGGAAT] = 0.00161212;
param_hairpin_special_H[AGGAT] = -1.5;
param_hairpin_special_S[AGGAT] = 0;
param_hairpin_special_H[AGGGAT] = -1.1;
param_hairpin_special_S[AGGGAT] = 0.00161212;
param_hairpin_special_H[AGGGGT] = 0.5;
param_hairpin_special_S[AGGGGT] = 0.000644849;
param_hairpin_special_H[AGTAAT] = -1.6;
param_hairpin_special_S[AGTAAT] = 0.00161212;
param_hairpin_special_H[AGTAT] = -1.5;
param_hairpin_special_S[AGTAT] = 0;
param_hairpin_special_H[AGTGAT] = -1.1;
param_hairpin_special_S[AGTGAT] = 0.00161212;
param_hairpin_special_H[AGTTCT] = 0.8;
param_hairpin_special_S[AGTTCT] = 0.00161212;
param_hairpin_special_H[ATTCGT] = -0.2;
param_hairpin_special_S[ATTCGT] = 0.00161212;
param_hairpin_special_H[ATTTGT] = 0;
param_hairpin_special_S[ATTTGT] = 0.00161212;
param_hairpin_special_H[ATTTTT] = -0.5;
param_hairpin_special_S[ATTTTT] = 0.00161212;
param_hairpin_special_H[CAAAAG] = 0.5;
param_hairpin_special_S[CAAAAG] = -0.0012897;
param_hairpin_special_H[CAAACG] = 0.7;
param_hairpin_special_S[CAAACG] = 0;
param_hairpin_special_H[CAACAG] = 1;
param_hairpin_special_S[CAACAG] = 0;
param_hairpin_special_H[CAACCG] = 0;
param_hairpin_special_S[CAACCG] = 0;
param_hairpin_special_H[CCTTGG] = 0;
param_hairpin_special_S[CCTTGG] = 0.0025794;
param_hairpin_special_H[CGAAAG] = -1.1;
param_hairpin_special_S[CGAAAG] = 0;
param_hairpin_special_H[CGAAG] = -2.0;
param_hairpin_special_S[CGAAG] = 0;
param_hairpin_special_H[CGAGAG] = -1.1;
param_hairpin_special_S[CGAGAG] = 0;
param_hairpin_special_H[CGATAG] = -1.5;
param_hairpin_special_S[CGATAG] = 0;
param_hairpin_special_H[CGCAAG] = -1.6;
param_hairpin_special_S[CGCAAG] = 0;
param_hairpin_special_H[CGCAG] = -2.0;
param_hairpin_special_S[CGCAG] = 0;
param_hairpin_special_H[CGCGAG] = -1.1;
param_hairpin_special_S[CGCGAG] = 0;
param_hairpin_special_H[CGCTTG] = 0.2;
param_hairpin_special_S[CGCTTG] = 0;
param_hairpin_special_H[CGGAAG] = -1.1;
param_hairpin_special_S[CGGAAG] = 0;
param_hairpin_special_H[CGGAG] = -2.0;
param_hairpin_special_S[CGGAG] = 0;
param_hairpin_special_H[CGGGAG] = -1;
param_hairpin_special_S[CGGGAG] = 0;
param_hairpin_special_H[CGGGGG] = 0.5;
param_hairpin_special_S[CGGGGG] = -0.000967274;
param_hairpin_special_H[CGTAAG] = -1.6;
param_hairpin_special_S[CGTAAG] = 0;
param_hairpin_special_H[CGTAG] = -2.0;
param_hairpin_special_S[CGTAG] = 0;
param_hairpin_special_H[CGTGAG] = -1.1;
param_hairpin_special_S[CGTGAG] = 0;
param_hairpin_special_H[CGTTCG] = 0.8;
param_hairpin_special_S[CGTTCG] = 0;
param_hairpin_special_H[CTTCGG] = -0.2;
param_hairpin_special_S[CTTCGG] = 0;
param_hairpin_special_H[CTTTGG] = 0;
param_hairpin_special_S[CTTTGG] = 0;
param_hairpin_special_H[CTTTTG] = -0.5;
param_hairpin_special_S[CTTTTG] = 0;
param_hairpin_special_H[GAAAAC] = 0.5;
param_hairpin_special_S[GAAAAC] = -0.00322425;
param_hairpin_special_H[GAAAAT] = 0.5;
param_hairpin_special_S[GAAAAT] = -0.00322425;
param_hairpin_special_H[GAAACC] = 0.7;
param_hairpin_special_S[GAAACC] = 0;
param_hairpin_special_H[GAAACT] = 1;
param_hairpin_special_S[GAAACT] = 0;
param_hairpin_special_H[GAACAC] = 1;
param_hairpin_special_S[GAACAC] = 0;
param_hairpin_special_H[GAACAT] = 1;
param_hairpin_special_S[GAACAT] = 0;
param_hairpin_special_H[GCTTGC] = 0;
param_hairpin_special_S[GCTTGC] = 0.0025794;
param_hairpin_special_H[GCTTGT] = 0;
param_hairpin_special_S[GCTTGT] = 0.00161212;
param_hairpin_special_H[GGAAAC] = -1.1;
param_hairpin_special_S[GGAAAC] = 0;
param_hairpin_special_H[GGAAAT] = -1.1;
param_hairpin_special_S[GGAAAT] = 0;
param_hairpin_special_H[GGAAC] = -2.0;
param_hairpin_special_S[GGAAC] = 0;
param_hairpin_special_H[GGAGAC] = -1.1;
param_hairpin_special_S[GGAGAC] = 0;
param_hairpin_special_H[GGAGAT] = -1.1;
param_hairpin_special_S[GGAGAT] = 0;
param_hairpin_special_H[GGATAC] = -1.6;
param_hairpin_special_S[GGATAC] = 0;
param_hairpin_special_H[GGATAT] = -1.6;
param_hairpin_special_S[GGATAT] = 0;
param_hairpin_special_H[GGCAAC] = -1.6;
param_hairpin_special_S[GGCAAC] = 0;
param_hairpin_special_H[GGCAAT] = -1.6;
param_hairpin_special_S[GGCAAT] = 0;
param_hairpin_special_H[GGCAC] = -2.0;
param_hairpin_special_S[GGCAC] = 0;
param_hairpin_special_H[GGCGAC] = -1.1;
param_hairpin_special_S[GGCGAC] = 0;
param_hairpin_special_H[GGCGAT] = -1.1;
param_hairpin_special_S[GGCGAT] = 0;
param_hairpin_special_H[GGCTTC] = 0.2;
param_hairpin_special_S[GGCTTC] = 0;
param_hairpin_special_H[GGCTTT] = -0.1;
param_hairpin_special_S[GGCTTT] = 0;