RNAlib-2.2.7
1.8.4_epars.h
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1 #ifndef VIENNA_RNA_PACKAGE_OLD_EPARS__
2 #define VIENNA_RNA_PACKAGE_OLD_EPARS__
3 
38 #define K0 273.15
39 #ifdef INF
40 #undef INF
41 #endif
42 #define INF 1000000
43 #define NBPAIRS 7
44 #define NST 0 /* Energy for nonstandard stacked pairs */
45 #define DEF -50 /* Default terminal mismatch, used for I */
46  /* and any non_pairing bases */
47 #define NSM 0 /* terminal mismatch for non standard pairs */
48 
49 PRIVATE double Tmeasure_184 = 37 + K0; /* temperature of param measurements */
50 PRIVATE double lxc37_184 = 107.856; /* parameter for logarithmic loop
51  energy extrapolation */
52 
53 PRIVATE int stack37_184[NBPAIRS+1][NBPAIRS+1] =
54 /* CG GC GU UG AU UA */
55 { { INF, INF, INF, INF, INF, INF, INF, INF},
56  { INF, -240, -330, -210, -140, -210, -210, NST},
57  { INF, -330, -340, -250, -150, -220, -240, NST},
58  { INF, -210, -250, 130, -50, -140, -130, NST},
59  { INF, -140, -150, -50, 30, -60, -100, NST},
60  { INF, -210, -220, -140, -60, -110, -90, NST},
61  { INF, -210, -240, -130, -100, -90, -130, NST},
62  { INF, NST, NST, NST, NST, NST, NST, NST}};
63 
64 /* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */
65 /* different from mfold-2.3, which uses values from mfold-2.2 */
66 PRIVATE int enthalpies_184[NBPAIRS+1][NBPAIRS+1] =
67 /* CG GC GU UG AU UA */
68 { { INF, INF, INF, INF, INF, INF, INF, INF},
69  { INF, -1060, -1340, -1210, -560, -1050, -1040, NST},
70  { INF, -1340, -1490, -1260, -830, -1140, -1240, NST},
71  { INF, -1210, -1260, -1460, -1350, -880, -1280, NST},
72  { INF, -560, -830, -1350, -930, -320, -700, NST},
73  { INF, -1050, -1140, -880, -320, -940, -680, NST},
74  { INF, -1040, -1240, -1280, -700, -680, -770, NST},
75  { INF, NST, NST, NST, NST, NST, NST, NST}};
76 
77 
78 /* old values are here just for comparison */
79 PRIVATE int oldhairpin37_184[31] = { /* from ViennaRNA 1.3 */
80  INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531,
81  542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
82  611, 616, 621, 626, 630, 634, 638, 642, 646, 650};
83 
84 PRIVATE int hairpin37_184[31] = {
85  INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650,
86  660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
87  730, 735, 740, 744, 749, 753, 757, 761, 765, 769};
88 
89 PRIVATE int oldbulge37_184[31] = {
90  INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
91  565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
92  635, 640, 645, 649, 654, 658, 662, 666, 670, 673};
93 
94 PRIVATE int bulge37_184[31] = {
95  INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
96  500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
97  571, 576, 580, 585, 589, 594, 598, 602, 605, 609};
98 
99 PRIVATE int oldinternal_loop37_184[31] = {
100  INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625,
101  635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
102  705, 710, 715, 720, 724, 728, 732, 736, 740, 744};
103 
104 PRIVATE int internal_loop37_184[31] = {
105  INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250,
106  260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
107  330, 335, 340, 345, 349, 353, 357, 361, 365, 369};
108 
109 /* terminal mismatches */
110 /* mismatch free energies for interior loops at 37C */
111 PRIVATE int mismatchI37_184[NBPAIRS+1][5][5] =
112 { /* @@ */
113  {{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}},
114  { /* CG */
115  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
116  { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
117  { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
118  { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
119  { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
120  { /* GC */
121  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
122  { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
123  { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
124  { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
125  { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
126  { /* GU */
127  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
128  { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
129  { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
130  { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
131  { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
132  { /* UG */
133  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
134  { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
135  { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
136  { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
137  { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
138  { /* AU */
139  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
140  { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
141  { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
142  { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
143  { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
144  { /* UA */
145  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
146  { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
147  { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
148  { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
149  { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
150  { /* @@ */
151  { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},
152  { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}
153 };
154 
155 /* mismatch free energies for hairpins at 37C */
156 PRIVATE int mismatchH37_184[NBPAIRS+1][5][5] =
157 { /* @@ */
158  {{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}},
159  { /* CG */
160  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
161  { -90, -150, -150, -140, -180}, /* A@ AA AC AG AU */
162  { -90, -100, -90, -290, -80}, /* C@ CA CC CG CU */
163  { -90, -220, -200, -160, -110}, /* G@ GA GC GG GU */
164  { -90, -170, -140, -180, -200}},/* U@ UA UC UG UU */
165  { /* GC */
166  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
167  { -70, -110, -150, -130, -210}, /* A@ AA AC AG AU */
168  { -70, -110, -70, -240, -50}, /* C@ CA CC CG CU */
169  { -70, -240, -290, -140, -120}, /* G@ GA GC GG GU */
170  { -70, -190, -100, -220, -150}},/* U@ UA UC UG UU */
171  { /* GU */
172  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
173  { 0, 20, -50, -30, -30}, /* A@ AA AC AG AU */
174  { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
175  { 0, -90, -110, -30, 0}, /* G@ GA GC GG GU */
176  { 0, -30, -30, -40, -110}},/* U@ UA UC UG UU */
177  { /* UG */
178  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
179  { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
180  { 0, -20, -10, -170, 0}, /* C@ CA CC CG CU */
181  { 0, -80, -120, -30, -70}, /* G@ GA GC GG GU */
182  { 0, -60, -10, -60, -80}},/* U@ UA UC UG UU */
183  { /* AU */
184  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
185  { 0, -30, -50, -30, -30}, /* A@ AA AC AG AU */
186  { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
187  { 0, -110, -120, -20, 20}, /* G@ GA GC GG GU */
188  { 0, -30, -30, -60, -110}},/* U@ UA UC UG UU */
189  { /* UA */
190  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
191  { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
192  { 0, -20, -10, -120, -0}, /* C@ CA CC CG CU */
193  { 0, -140, -120, -70, -20}, /* G@ GA GC GG GU */
194  { 0, -30, -10, -50, -80}},/* U@ UA UC UG UU */
195  { /* @@ */
196  { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},
197  { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}}
198 };
199 
200 /* mismatch energies in multiloops */
201 PRIVATE int mismatchM37_184[NBPAIRS+1][5][5];
202 
203 /* these are probably junk */
204 /* mismatch enthalpies for temperature scaling */
205 PRIVATE int mism_H_184[NBPAIRS+1][5][5] =
206 { /* no pair */
207  {{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}},
208  { /* CG */
209  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
210  { DEF,-1030, -950,-1030,-1030}, /* A@ AA AC AG AU */
211  { DEF, -520, -450, -520, -670}, /* C@ CA CC CG CU */
212  { DEF, -940, -940, -940, -940}, /* G@ GA GC GG GU */
213  { DEF, -810, -740, -810, -860}},/* U@ UA UC UG UU */
214  { /* GC */
215  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
216  { DEF, -520, -880, -560, -880}, /* A@ AA AC AG AU */
217  { DEF, -720, -310, -310, -390}, /* C@ CA CC CG CU */
218  { DEF, -710, -740, -620, -740}, /* G@ GA GC GG GU */
219  { DEF, -500, -500, -500, -570}},/* U@ UA UC UG UU */
220  { /* GU */
221  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
222  { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
223  { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
224  { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
225  { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
226  { /* UG */
227  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
228  { DEF, -720, -790, -960, -810}, /* A@ AA AC AG AU */
229  { DEF, -480, -480, -360, -480}, /* C@ CA CC CG CU */
230  { DEF, -660, -810, -920, -810}, /* G@ GA GC GG GU */
231  { DEF, -550, -440, -550, -360}},/* U@ UA UC UG UU */
232  { /* AU */
233  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
234  { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
235  { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
236  { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
237  { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
238  { /* UA */
239  { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
240  { DEF, -400, -630, -890, -590}, /* A@ AA AC AG AU */
241  { DEF, -430, -510, -200, -180}, /* C@ CA CC CG CU */
242  { DEF, -380, -680, -890, -680}, /* G@ GA GC GG GU */
243  { DEF, -280, -140, -280, -140}},/* U@ UA UC UG UU */
244  { /* nonstandard pair */
245  {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},
246  {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}
247 };
248 
249 /* 5' dangling ends (unpaird base stacks on first paired base) */
250 PRIVATE int dangle5_37_184[NBPAIRS+1][5]=
251 {/* @ A C G U */
252  { INF, INF, INF, INF, INF}, /* no pair */
253  { INF, -50, -30, -20, -10}, /* CG (stacks on C) */
254  { INF, -20, -30, -0, -0}, /* GC (stacks on G) */
255  { INF, -30, -30, -40, -20}, /* GU */
256  { INF, -30, -10, -20, -20}, /* UG */
257  { INF, -30, -30, -40, -20}, /* AU */
258  { INF, -30, -10, -20, -20}, /* UA */
259  { 0, 0, 0, 0, 0} /* @ */
260 };
261 
262 /* 3' dangling ends (unpaired base stacks on second paired base */
263 PRIVATE int dangle3_37_184[NBPAIRS+1][5]=
264 {/* @ A C G U */
265  { INF, INF, INF, INF, INF}, /* no pair */
266  { INF, -110, -40, -130, -60}, /* CG (stacks on G) */
267  { INF, -170, -80, -170, -120}, /* GC */
268  { INF, -70, -10, -70, -10}, /* GU */
269  { INF, -80, -50, -80, -60}, /* UG */
270  { INF, -70, -10, -70, -10}, /* AU */
271  { INF, -80, -50, -80, -60}, /* UA */
272  { 0, 0, 0, 0, 0} /* @ */
273 };
274 
275 /* enthalpies for temperature scaling */
276 PRIVATE int dangle3_H_184[NBPAIRS+1][5] =
277 {/* @ A C G U */
278  { INF, INF, INF, INF, INF}, /* no pair */
279  { 0, -740, -280, -640, -360},
280  { 0, -900, -410, -860, -750},
281  { 0, -740, -240, -720, -490},
282  { 0, -490, -90, -550, -230},
283  { 0, -570, -70, -580, -220},
284  { 0, -490, -90, -550, -230},
285  { 0, 0, 0, 0, 0}
286 };
287 
288 PRIVATE int dangle5_H_184[NBPAIRS+1][5] =
289 {/* @ A C G U */
290  { INF, INF, INF, INF, INF}, /* no pair */
291  { 0, -240, 330, 80, -140},
292  { 0, -160, 70, -460, -40},
293  { 0, 160, 220, 70, 310},
294  { 0, -150, 510, 10, 100},
295  { 0, 160, 220, 70, 310},
296  { 0, -50, 690, -60, -60},
297  { 0, 0, 0, 0, 0}
298 };
299 
300 
301 /* constants for linearly destabilizing contributions for multi-loops
302  F = ML_closing + ML_intern*k + ML_BASE*u */
303 /* old versions erroneously used ML_intern*(k-1) */
304 PRIVATE int ML_BASE37_184 = 0;
305 PRIVATE int ML_closing37_184 = 340;
306 PRIVATE int ML_intern37_184 = 40;
307 
308 /* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
309 /* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
310 PRIVATE int MAX_NINIO_184 = 300; /* maximum correction */
311 PRIVATE int F_ninio37_184[5] = { 0, 40, 50, 20, 10 }; /* only F[2] used */
312 
313 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
314 
315 PRIVATE char Tetraloops_184[1400] = /* place for up to 200 tetra loops */
316  "GGGGAC "
317  "GGUGAC "
318  "CGAAAG "
319  "GGAGAC "
320  "CGCAAG "
321  "GGAAAC "
322  "CGGAAG "
323  "CUUCGG "
324  "CGUGAG "
325  "CGAAGG "
326  "CUACGG "
327  "GGCAAC "
328  "CGCGAG "
329  "UGAGAG "
330  "CGAGAG "
331  "AGAAAU "
332  "CGUAAG "
333  "CUAACG "
334  "UGAAAG "
335  "GGAAGC "
336  "GGGAAC "
337  "UGAAAA "
338  "AGCAAU "
339  "AGUAAU "
340  "CGGGAG "
341  "AGUGAU "
342  "GGCGAC "
343  "GGGAGC "
344  "GUGAAC "
345  "UGGAAA "
346 ;
347 
348 PRIVATE int TETRA_ENERGY37_184[200] = {
349  -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
350  -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
351  -150, -150, -150, -150, -150, -150};
352 
353 PRIVATE int TETRA_ENTH37_184 = -400;
354 
355 PRIVATE char Triloops_184[241] = "";
356 
357 PRIVATE int Triloop_E37_184[40];
358 
359 /* penalty for AU (or GU) terminating helix) */
360 /* mismatches already contain these */
361 PRIVATE int TerminalAU_184 = 50;
362 
363 /* penalty for forming a bi-molecular duplex */
364 PRIVATE int DuplexInit_184 = 410;
365 
366 #endif
#define K0
Definition: energy_const.h:14
#define INF
Definition: energy_const.h:16
#define NBPAIRS
Definition: energy_const.h:24