--- /dev/null
+#ifndef __VIENNA_RNA_PACKAGE_OLD_EPARS__
+#define __VIENNA_RNA_PACKAGE_OLD_EPARS__
+/**
+ \file 1.8.4_epars.h
+ \brief Free energy parameters for parameter file conversion
+
+ This file contains the free energy parameters used in ViennaRNAPackage 1.8.4.
+ They are summarized in:
+
+ D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner
+ "Expanded sequence dependence of thermodynamic parameters improves
+ prediction of RNA secondary structure"
+ JMB, 288, pp 911-940, 1999
+
+ Enthalpies taken from:
+
+ A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker
+ "Coaxial stckaing of helices enhances binding of oligoribonucleotides.."
+ PNAS, 91, pp 9218-9222, 1994
+
+ D.H. Turner, N. Sugimoto, and S.M. Freier.
+ "RNA Structure Prediction",
+ Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.
+
+ John A.Jaeger, Douglas H.Turner, and Michael Zuker.
+ "Improved predictions of secondary structures for RNA",
+ PNAS, 86, 7706-7710, October 1989.
+
+ L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner
+ "Nearest-Neughbor Parameters for GU Mismatches...."
+ Biochemistry 1991, 30 11124-11132
+
+ A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner
+ "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."
+ Biochemistry 1991, 30, 6428--6435
+*/
+
+#define K0 273.15
+#ifdef INF
+#undef INF
+#endif
+#define INF 1000000
+#define NBPAIRS 7
+#define NST 0 /* Energy for nonstandard stacked pairs */
+#define DEF -50 /* Default terminal mismatch, used for I */
+ /* and any non_pairing bases */
+#define NSM 0 /* terminal mismatch for non standard pairs */
+
+PRIVATE double Tmeasure_184 = 37 + K0; /* temperature of param measurements */
+PRIVATE double lxc37_184 = 107.856; /* parameter for logarithmic loop
+ energy extrapolation */
+
+PRIVATE int stack37_184[NBPAIRS+1][NBPAIRS+1] =
+/* CG GC GU UG AU UA */
+{ { INF, INF, INF, INF, INF, INF, INF, INF},
+ { INF, -240, -330, -210, -140, -210, -210, NST},
+ { INF, -330, -340, -250, -150, -220, -240, NST},
+ { INF, -210, -250, 130, -50, -140, -130, NST},
+ { INF, -140, -150, -50, 30, -60, -100, NST},
+ { INF, -210, -220, -140, -60, -110, -90, NST},
+ { INF, -210, -240, -130, -100, -90, -130, NST},
+ { INF, NST, NST, NST, NST, NST, NST, NST}};
+
+/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */
+/* different from mfold-2.3, which uses values from mfold-2.2 */
+PRIVATE int enthalpies_184[NBPAIRS+1][NBPAIRS+1] =
+/* CG GC GU UG AU UA */
+{ { INF, INF, INF, INF, INF, INF, INF, INF},
+ { INF, -1060, -1340, -1210, -560, -1050, -1040, NST},
+ { INF, -1340, -1490, -1260, -830, -1140, -1240, NST},
+ { INF, -1210, -1260, -1460, -1350, -880, -1280, NST},
+ { INF, -560, -830, -1350, -930, -320, -700, NST},
+ { INF, -1050, -1140, -880, -320, -940, -680, NST},
+ { INF, -1040, -1240, -1280, -700, -680, -770, NST},
+ { INF, NST, NST, NST, NST, NST, NST, NST}};
+
+
+/* old values are here just for comparison */
+PRIVATE int oldhairpin37_184[31] = { /* from ViennaRNA 1.3 */
+ INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531,
+ 542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
+ 611, 616, 621, 626, 630, 634, 638, 642, 646, 650};
+
+PRIVATE int hairpin37_184[31] = {
+ INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650,
+ 660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
+ 730, 735, 740, 744, 749, 753, 757, 761, 765, 769};
+
+PRIVATE int oldbulge37_184[31] = {
+ INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
+ 565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
+ 635, 640, 645, 649, 654, 658, 662, 666, 670, 673};
+
+PRIVATE int bulge37_184[31] = {
+ INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
+ 500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
+ 571, 576, 580, 585, 589, 594, 598, 602, 605, 609};
+
+PRIVATE int oldinternal_loop37_184[31] = {
+ INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625,
+ 635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
+ 705, 710, 715, 720, 724, 728, 732, 736, 740, 744};
+
+PRIVATE int internal_loop37_184[31] = {
+ INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250,
+ 260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
+ 330, 335, 340, 345, 349, 353, 357, 361, 365, 369};
+
+/* terminal mismatches */
+/* mismatch free energies for interior loops at 37C */
+PRIVATE int mismatchI37_184[NBPAIRS+1][5][5] =
+{ /* @@ */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
+ { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
+ { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
+ { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
+ { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
+ { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
+ { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* @@ */
+ { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},
+ { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}
+};
+
+/* mismatch free energies for hairpins at 37C */
+PRIVATE int mismatchH37_184[NBPAIRS+1][5][5] =
+{ /* @@ */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { -90, -150, -150, -140, -180}, /* A@ AA AC AG AU */
+ { -90, -100, -90, -290, -80}, /* C@ CA CC CG CU */
+ { -90, -220, -200, -160, -110}, /* G@ GA GC GG GU */
+ { -90, -170, -140, -180, -200}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { -70, -110, -150, -130, -210}, /* A@ AA AC AG AU */
+ { -70, -110, -70, -240, -50}, /* C@ CA CC CG CU */
+ { -70, -240, -290, -140, -120}, /* G@ GA GC GG GU */
+ { -70, -190, -100, -220, -150}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 20, -50, -30, -30}, /* A@ AA AC AG AU */
+ { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
+ { 0, -90, -110, -30, 0}, /* G@ GA GC GG GU */
+ { 0, -30, -30, -40, -110}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
+ { 0, -20, -10, -170, 0}, /* C@ CA CC CG CU */
+ { 0, -80, -120, -30, -70}, /* G@ GA GC GG GU */
+ { 0, -60, -10, -60, -80}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -30, -50, -30, -30}, /* A@ AA AC AG AU */
+ { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
+ { 0, -110, -120, -20, 20}, /* G@ GA GC GG GU */
+ { 0, -30, -30, -60, -110}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
+ { 0, -20, -10, -120, -0}, /* C@ CA CC CG CU */
+ { 0, -140, -120, -70, -20}, /* G@ GA GC GG GU */
+ { 0, -30, -10, -50, -80}},/* U@ UA UC UG UU */
+ { /* @@ */
+ { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}}
+};
+
+/* mismatch energies in multiloops */
+PRIVATE int mismatchM37_184[NBPAIRS+1][5][5];
+
+/* these are probably junk */
+/* mismatch enthalpies for temperature scaling */
+PRIVATE int mism_H_184[NBPAIRS+1][5][5] =
+{ /* no pair */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF,-1030, -950,-1030,-1030}, /* A@ AA AC AG AU */
+ { DEF, -520, -450, -520, -670}, /* C@ CA CC CG CU */
+ { DEF, -940, -940, -940, -940}, /* G@ GA GC GG GU */
+ { DEF, -810, -740, -810, -860}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -520, -880, -560, -880}, /* A@ AA AC AG AU */
+ { DEF, -720, -310, -310, -390}, /* C@ CA CC CG CU */
+ { DEF, -710, -740, -620, -740}, /* G@ GA GC GG GU */
+ { DEF, -500, -500, -500, -570}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
+ { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
+ { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
+ { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -720, -790, -960, -810}, /* A@ AA AC AG AU */
+ { DEF, -480, -480, -360, -480}, /* C@ CA CC CG CU */
+ { DEF, -660, -810, -920, -810}, /* G@ GA GC GG GU */
+ { DEF, -550, -440, -550, -360}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
+ { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
+ { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
+ { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -400, -630, -890, -590}, /* A@ AA AC AG AU */
+ { DEF, -430, -510, -200, -180}, /* C@ CA CC CG CU */
+ { DEF, -380, -680, -890, -680}, /* G@ GA GC GG GU */
+ { DEF, -280, -140, -280, -140}},/* U@ UA UC UG UU */
+ { /* nonstandard pair */
+ {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},
+ {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}
+};
+
+/* 5' dangling ends (unpaird base stacks on first paired base) */
+PRIVATE int dangle5_37_184[NBPAIRS+1][5]=
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { INF, -50, -30, -20, -10}, /* CG (stacks on C) */
+ { INF, -20, -30, -0, -0}, /* GC (stacks on G) */
+ { INF, -30, -30, -40, -20}, /* GU */
+ { INF, -30, -10, -20, -20}, /* UG */
+ { INF, -30, -30, -40, -20}, /* AU */
+ { INF, -30, -10, -20, -20}, /* UA */
+ { 0, 0, 0, 0, 0} /* @ */
+};
+
+/* 3' dangling ends (unpaired base stacks on second paired base */
+PRIVATE int dangle3_37_184[NBPAIRS+1][5]=
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { INF, -110, -40, -130, -60}, /* CG (stacks on G) */
+ { INF, -170, -80, -170, -120}, /* GC */
+ { INF, -70, -10, -70, -10}, /* GU */
+ { INF, -80, -50, -80, -60}, /* UG */
+ { INF, -70, -10, -70, -10}, /* AU */
+ { INF, -80, -50, -80, -60}, /* UA */
+ { 0, 0, 0, 0, 0} /* @ */
+};
+
+/* enthalpies for temperature scaling */
+PRIVATE int dangle3_H_184[NBPAIRS+1][5] =
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { 0, -740, -280, -640, -360},
+ { 0, -900, -410, -860, -750},
+ { 0, -740, -240, -720, -490},
+ { 0, -490, -90, -550, -230},
+ { 0, -570, -70, -580, -220},
+ { 0, -490, -90, -550, -230},
+ { 0, 0, 0, 0, 0}
+};
+
+PRIVATE int dangle5_H_184[NBPAIRS+1][5] =
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { 0, -240, 330, 80, -140},
+ { 0, -160, 70, -460, -40},
+ { 0, 160, 220, 70, 310},
+ { 0, -150, 510, 10, 100},
+ { 0, 160, 220, 70, 310},
+ { 0, -50, 690, -60, -60},
+ { 0, 0, 0, 0, 0}
+};
+
+
+/* constants for linearly destabilizing contributions for multi-loops
+ F = ML_closing + ML_intern*k + ML_BASE*u */
+/* old versions erroneously used ML_intern*(k-1) */
+PRIVATE int ML_BASE37_184 = 0;
+PRIVATE int ML_closing37_184 = 340;
+PRIVATE int ML_intern37_184 = 40;
+
+/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
+/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
+PRIVATE int MAX_NINIO_184 = 300; /* maximum correction */
+PRIVATE int F_ninio37_184[5] = { 0, 40, 50, 20, 10 }; /* only F[2] used */
+
+/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
+
+PRIVATE char Tetraloops_184[1400] = /* place for up to 200 tetra loops */
+ "GGGGAC "
+ "GGUGAC "
+ "CGAAAG "
+ "GGAGAC "
+ "CGCAAG "
+ "GGAAAC "
+ "CGGAAG "
+ "CUUCGG "
+ "CGUGAG "
+ "CGAAGG "
+ "CUACGG "
+ "GGCAAC "
+ "CGCGAG "
+ "UGAGAG "
+ "CGAGAG "
+ "AGAAAU "
+ "CGUAAG "
+ "CUAACG "
+ "UGAAAG "
+ "GGAAGC "
+ "GGGAAC "
+ "UGAAAA "
+ "AGCAAU "
+ "AGUAAU "
+ "CGGGAG "
+ "AGUGAU "
+ "GGCGAC "
+ "GGGAGC "
+ "GUGAAC "
+ "UGGAAA "
+;
+
+PRIVATE int TETRA_ENERGY37_184[200] = {
+ -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
+ -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
+ -150, -150, -150, -150, -150, -150};
+
+PRIVATE int TETRA_ENTH37_184 = -400;
+
+PRIVATE char Triloops_184[241] = "";
+
+PRIVATE int Triloop_E37_184[40];
+
+/* penalty for AU (or GU) terminating helix) */
+/* mismatches already contain these */
+PRIVATE int TerminalAU_184 = 50;
+
+/* penalty for forming a bi-molecular duplex */
+PRIVATE int DuplexInit_184 = 410;
+
+#endif
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