RNAlib-2.0.7: lib/1.8.4_epars.h Source File

00001 #ifndef __VIENNA_RNA_PACKAGE_OLD_EPARS__
00002 #define __VIENNA_RNA_PACKAGE_OLD_EPARS__
00003 
00038 #define K0        273.15
00039 #ifdef INF
00040 #undef INF
00041 #endif
00042 #define INF       1000000
00043 #define NBPAIRS   7
00044 #define NST       0     /* Energy for nonstandard stacked pairs */
00045 #define DEF       -50   /* Default terminal mismatch, used for I */
00046                         /* and any non_pairing bases */
00047 #define NSM       0     /* terminal mismatch for non standard pairs */
00048 
00049 PRIVATE double Tmeasure_184 = 37 + K0;  /* temperature of param measurements */
00050 PRIVATE double lxc37_184    = 107.856;  /* parameter for logarithmic loop
00051                                            energy extrapolation */
00052 
00053 PRIVATE int stack37_184[NBPAIRS+1][NBPAIRS+1] =
00054 /*          CG     GC     GU     UG     AU     UA  */
00055 { {  INF,   INF,   INF,   INF,   INF,   INF,   INF, INF},
00056   {  INF,  -240,  -330,  -210,  -140,  -210,  -210, NST},
00057   {  INF,  -330,  -340,  -250,  -150,  -220,  -240, NST},
00058   {  INF,  -210,  -250,   130,   -50,  -140,  -130, NST},
00059   {  INF,  -140,  -150,   -50,    30,   -60,  -100, NST},
00060   {  INF,  -210,  -220,  -140,   -60,  -110,   -90, NST},
00061   {  INF,  -210,  -240,  -130,  -100,   -90,  -130, NST},
00062   {  INF,   NST,   NST,   NST,   NST,   NST,   NST, NST}};
00063 
00064 /* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */
00065 /* different from mfold-2.3, which uses values from mfold-2.2 */
00066 PRIVATE int enthalpies_184[NBPAIRS+1][NBPAIRS+1] =
00067 /*          CG     GC     GU     UG     AU     UA  */
00068 { {  INF,   INF,   INF,   INF,   INF,   INF,   INF, INF},
00069   {  INF, -1060, -1340, -1210,  -560, -1050, -1040, NST},
00070   {  INF, -1340, -1490, -1260,  -830, -1140, -1240, NST},
00071   {  INF, -1210, -1260, -1460, -1350,  -880, -1280, NST},
00072   {  INF,  -560,  -830, -1350,  -930,  -320,  -700, NST},
00073   {  INF, -1050, -1140,  -880,  -320,  -940,  -680, NST},
00074   {  INF, -1040, -1240, -1280,  -700,  -680,  -770, NST},
00075   {  INF,   NST,   NST,   NST,   NST,   NST,   NST, NST}};
00076 
00077 
00078 /* old values are here just for comparison */
00079 PRIVATE int oldhairpin37_184[31] = { /* from ViennaRNA 1.3 */
00080   INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531,
00081        542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
00082        611, 616, 621, 626, 630, 634, 638, 642, 646, 650};
00083 
00084 PRIVATE int hairpin37_184[31] = {
00085   INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650,
00086        660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
00087        730, 735, 740, 744, 749, 753, 757, 761, 765, 769};
00088 
00089 PRIVATE int oldbulge37_184[31] = {
00090   INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
00091        565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
00092        635, 640, 645, 649, 654, 658, 662, 666, 670, 673};
00093 
00094 PRIVATE int bulge37_184[31] = {
00095   INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
00096        500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
00097   571, 576, 580, 585, 589, 594, 598, 602, 605, 609};
00098 
00099 PRIVATE int oldinternal_loop37_184[31] = {
00100   INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625,
00101        635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
00102        705, 710, 715, 720, 724, 728, 732, 736, 740, 744};
00103 
00104 PRIVATE int internal_loop37_184[31] = {
00105   INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250,
00106        260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
00107        330, 335, 340, 345, 349, 353, 357, 361, 365, 369};
00108 
00109 /* terminal mismatches */
00110 /* mismatch free energies for interior loops at 37C */
00111 PRIVATE int mismatchI37_184[NBPAIRS+1][5][5] =
00112 { /* @@ */
00113   {{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}},
00114   { /* CG */
00115    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00116    {   0,    0,    0, -110,    0}, /* A@  AA  AC  AG  AU */
00117    {   0,    0,    0,    0,    0}, /* C@  CA  CC  CG  CU */
00118    {   0, -110,    0,    0,    0}, /* G@  GA  GC  GG  GU */
00119    {   0,    0,    0,    0,  -70}},/* U@  UA  UC  UG  UU */
00120   { /* GC */
00121    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00122    {   0,    0,    0, -110,    0}, /* A@  AA  AC  AG  AU */
00123    {   0,    0,    0,    0,    0}, /* C@  CA  CC  CG  CU */
00124    {   0, -110,    0,    0,    0}, /* G@  GA  GC  GG  GU */
00125    {   0,    0,    0,    0,  -70}},/* U@  UA  UC  UG  UU */
00126   { /* GU */
00127    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00128    {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */
00129    {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */
00130    {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */
00131    {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */
00132   { /* UG */
00133    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00134    {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */
00135    {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */
00136    {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */
00137    {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */
00138   { /* AU */
00139    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00140    {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */
00141    {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */
00142    {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */
00143    {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */
00144   { /* UA */
00145    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00146    {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */
00147    {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */
00148    {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */
00149    {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */
00150   { /* @@ */
00151    { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},
00152    { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}
00153 };
00154 
00155 /* mismatch free energies for hairpins at 37C */
00156 PRIVATE int mismatchH37_184[NBPAIRS+1][5][5] =
00157 { /* @@ */
00158   {{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}},
00159   { /* CG */
00160    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00161    { -90, -150, -150, -140, -180}, /* A@  AA  AC  AG  AU */
00162    { -90, -100,  -90, -290,  -80}, /* C@  CA  CC  CG  CU */
00163    { -90, -220, -200, -160, -110}, /* G@  GA  GC  GG  GU */
00164    { -90, -170, -140, -180, -200}},/* U@  UA  UC  UG  UU */
00165   { /* GC */
00166    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00167    { -70, -110, -150, -130, -210}, /* A@  AA  AC  AG  AU */
00168    { -70, -110,  -70, -240,  -50}, /* C@  CA  CC  CG  CU */
00169    { -70, -240, -290, -140, -120}, /* G@  GA  GC  GG  GU */
00170    { -70, -190, -100, -220, -150}},/* U@  UA  UC  UG  UU */
00171   { /* GU */
00172    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00173    {   0,   20,  -50,  -30,  -30}, /* A@  AA  AC  AG  AU */
00174    {   0,  -10,  -20, -150,  -20}, /* C@  CA  CC  CG  CU */
00175    {   0,  -90, -110,  -30,    0}, /* G@  GA  GC  GG  GU */
00176    {   0,  -30,  -30,  -40, -110}},/* U@  UA  UC  UG  UU */
00177   { /* UG */
00178    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00179    {   0,  -50,  -30,  -60,  -50}, /* A@  AA  AC  AG  AU */
00180    {   0,  -20,  -10, -170,    0}, /* C@  CA  CC  CG  CU */
00181    {   0,  -80, -120,  -30,  -70}, /* G@  GA  GC  GG  GU */
00182    {   0,  -60,  -10,  -60,  -80}},/* U@  UA  UC  UG  UU */
00183   { /* AU */
00184    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00185    {   0,  -30,  -50,  -30,  -30}, /* A@  AA  AC  AG  AU */
00186    {   0,  -10,  -20, -150,  -20}, /* C@  CA  CC  CG  CU */
00187    {   0, -110, -120,  -20,   20}, /* G@  GA  GC  GG  GU */
00188    {   0,  -30,  -30,  -60, -110}},/* U@  UA  UC  UG  UU */
00189   { /* UA */
00190    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00191    {   0,  -50,  -30,  -60,  -50}, /* A@  AA  AC  AG  AU */
00192    {   0,  -20,  -10, -120,   -0}, /* C@  CA  CC  CG  CU */
00193    {   0, -140, -120,  -70,  -20}, /* G@  GA  GC  GG  GU */
00194    {   0,  -30,  -10,  -50,  -80}},/* U@  UA  UC  UG  UU */
00195   { /* @@ */
00196    {  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0},
00197    {  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0}}
00198 };
00199 
00200 /* mismatch energies in multiloops */
00201 PRIVATE int mismatchM37_184[NBPAIRS+1][5][5];
00202 
00203 /* these are probably junk */
00204 /* mismatch enthalpies for temperature scaling */
00205 PRIVATE int mism_H_184[NBPAIRS+1][5][5] =
00206 { /* no pair */
00207   {{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}},
00208   { /* CG */
00209    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00210    { DEF,-1030, -950,-1030,-1030}, /* A@  AA  AC  AG  AU */
00211    { DEF, -520, -450, -520, -670}, /* C@  CA  CC  CG  CU */
00212    { DEF, -940, -940, -940, -940}, /* G@  GA  GC  GG  GU */
00213    { DEF, -810, -740, -810, -860}},/* U@  UA  UC  UG  UU */
00214   { /* GC */
00215    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00216    { DEF, -520, -880, -560, -880}, /* A@  AA  AC  AG  AU */
00217    { DEF, -720, -310, -310, -390}, /* C@  CA  CC  CG  CU */
00218    { DEF, -710, -740, -620, -740}, /* G@  GA  GC  GG  GU */
00219    { DEF, -500, -500, -500, -570}},/* U@  UA  UC  UG  UU */
00220   { /* GU */
00221    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00222    { DEF, -430, -600, -600, -600}, /* A@  AA  AC  AG  AU */
00223    { DEF, -260, -240, -240, -240}, /* C@  CA  CC  CG  CU */
00224    { DEF, -340, -690, -690, -690}, /* G@  GA  GC  GG  GU */
00225    { DEF, -330, -330, -330, -330}},/* U@  UA  UC  UG  UU */
00226   { /* UG */
00227    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00228    { DEF, -720, -790, -960, -810}, /* A@  AA  AC  AG  AU */
00229    { DEF, -480, -480, -360, -480}, /* C@  CA  CC  CG  CU */
00230    { DEF, -660, -810, -920, -810}, /* G@  GA  GC  GG  GU */
00231    { DEF, -550, -440, -550, -360}},/* U@  UA  UC  UG  UU */
00232   { /* AU */
00233    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00234    { DEF, -430, -600, -600, -600}, /* A@  AA  AC  AG  AU */
00235    { DEF, -260, -240, -240, -240}, /* C@  CA  CC  CG  CU */
00236    { DEF, -340, -690, -690, -690}, /* G@  GA  GC  GG  GU */
00237    { DEF, -330, -330, -330, -330}},/* U@  UA  UC  UG  UU */
00238   { /* UA */
00239    {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */
00240    { DEF, -400, -630, -890, -590}, /* A@  AA  AC  AG  AU */
00241    { DEF, -430, -510, -200, -180}, /* C@  CA  CC  CG  CU */
00242    { DEF, -380, -680, -890, -680}, /* G@  GA  GC  GG  GU */
00243    { DEF, -280, -140, -280, -140}},/* U@  UA  UC  UG  UU */
00244   { /* nonstandard pair */
00245    {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},
00246    {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}
00247 };
00248 
00249 /* 5' dangling ends (unpaird base stacks on first paired base) */
00250 PRIVATE int dangle5_37_184[NBPAIRS+1][5]=
00251 {/*   @     A     C     G     U   */
00252    { INF,  INF,  INF,  INF,  INF}, /* no pair */
00253    { INF,  -50,  -30,  -20,  -10}, /* CG  (stacks on C) */
00254    { INF,  -20,  -30,   -0,   -0}, /* GC  (stacks on G) */
00255    { INF,  -30,  -30,  -40,  -20}, /* GU */
00256    { INF,  -30,  -10,  -20,  -20}, /* UG */
00257    { INF,  -30,  -30,  -40,  -20}, /* AU */
00258    { INF,  -30,  -10,  -20,  -20}, /* UA */
00259    {   0,    0,     0,    0,   0}  /*  @ */
00260 };
00261 
00262 /* 3' dangling ends (unpaired base stacks on second paired base */
00263 PRIVATE int dangle3_37_184[NBPAIRS+1][5]=
00264 {/*   @     A     C     G     U   */
00265    { INF,  INF,  INF,  INF,  INF},  /* no pair */
00266    { INF, -110,  -40, -130,  -60},  /* CG  (stacks on G) */
00267    { INF, -170,  -80, -170, -120},  /* GC */
00268    { INF,  -70,  -10,  -70,  -10},  /* GU */
00269    { INF,  -80,  -50,  -80,  -60},  /* UG */
00270    { INF,  -70,  -10,  -70,  -10},  /* AU */
00271    { INF,  -80,  -50,  -80,  -60},  /* UA */
00272    {   0,    0,     0,    0,   0}   /*  @ */
00273 };
00274 
00275 /* enthalpies for temperature scaling */
00276 PRIVATE int dangle3_H_184[NBPAIRS+1][5] =
00277 {/*   @     A     C     G     U   */
00278    { INF,  INF,  INF,  INF,  INF},  /* no pair */
00279    {   0, -740, -280, -640, -360},
00280    {   0, -900, -410, -860, -750},
00281    {   0, -740, -240, -720, -490},
00282    {   0, -490,  -90, -550, -230},
00283    {   0, -570,  -70, -580, -220},
00284    {   0, -490,  -90, -550, -230},
00285    {   0,    0,    0,    0,   0}
00286 };
00287 
00288 PRIVATE int dangle5_H_184[NBPAIRS+1][5] =
00289 {/*   @     A     C     G     U   */
00290    { INF,  INF,  INF,  INF,  INF},  /* no pair */
00291    {   0, -240,  330,   80, -140},
00292    {   0, -160,   70, -460,  -40},
00293    {   0,  160,  220,   70,  310},
00294    {   0, -150,  510,   10,  100},
00295    {   0,  160,  220,   70,  310},
00296    {   0,  -50,  690,  -60,  -60},
00297    {   0,    0,    0,    0,   0}
00298 };
00299 
00300 
00301 /* constants for linearly destabilizing contributions for multi-loops
00302    F = ML_closing + ML_intern*k + ML_BASE*u  */
00303 /* old versions erroneously used ML_intern*(k-1) */
00304 PRIVATE int ML_BASE37_184 = 0;
00305 PRIVATE int ML_closing37_184 = 340;
00306 PRIVATE int ML_intern37_184 =  40;
00307 
00308 /* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
00309 /*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
00310 PRIVATE int MAX_NINIO_184 = 300;                   /* maximum correction */
00311 PRIVATE int F_ninio37_184[5] = { 0, 40, 50, 20, 10 };      /* only F[2] used */
00312 
00313 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
00314 
00315 PRIVATE char Tetraloops_184[1400] =  /* place for up to 200 tetra loops */
00316   "GGGGAC "
00317   "GGUGAC "
00318   "CGAAAG "
00319   "GGAGAC "
00320   "CGCAAG "
00321   "GGAAAC "
00322   "CGGAAG "
00323   "CUUCGG "
00324   "CGUGAG "
00325   "CGAAGG "
00326   "CUACGG "
00327   "GGCAAC "
00328   "CGCGAG "
00329   "UGAGAG "
00330   "CGAGAG "
00331   "AGAAAU "
00332   "CGUAAG "
00333   "CUAACG "
00334   "UGAAAG "
00335   "GGAAGC "
00336   "GGGAAC "
00337   "UGAAAA "
00338   "AGCAAU "
00339   "AGUAAU "
00340   "CGGGAG "
00341   "AGUGAU "
00342   "GGCGAC "
00343   "GGGAGC "
00344   "GUGAAC "
00345   "UGGAAA "
00346 ;
00347 
00348 PRIVATE int   TETRA_ENERGY37_184[200] = {
00349   -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
00350   -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
00351   -150, -150, -150, -150, -150, -150};
00352 
00353 PRIVATE int   TETRA_ENTH37_184   = -400;
00354 
00355 PRIVATE char Triloops_184[241] = "";
00356 
00357 PRIVATE int Triloop_E37_184[40];
00358 
00359 /* penalty for AU (or GU) terminating helix) */
00360 /* mismatches already contain these */
00361 PRIVATE int TerminalAU_184 = 50;
00362 
00363 /* penalty for forming a bi-molecular duplex */
00364 PRIVATE int DuplexInit_184 = 410;
00365 
00366 #endif