1 #ifndef VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H
2 #define VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H
5 #include "ViennaRNA/energy_par.h"
11 # define INLINE inline
20 #define ON_SAME_STRAND(I,J,C) (((I)>=(C))||((J)<(C)))
115 PRIVATE INLINE
int E_IntLoop_Co(
int type,
152 ubf_eval_int_loop(
int i,
165 unsigned char type_2,
177 if((cp < 0) || (ON_SAME_STRAND(i, p, cp) && ON_SAME_STRAND(q, j, cp))){
178 energy =
E_IntLoop(u1, u2, type, type_2, si, sj, sp, sq, P);
181 Si = ON_SAME_STRAND(i, i1, cp) ? si : -1;
182 Sj = ON_SAME_STRAND(j1, j, cp) ? sj : -1;
183 energy = E_IntLoop_Co(rtype[type], rtype[type_2],
228 ubf_eval_ext_int_loop(
int i,
241 unsigned char type_2,
246 int energy, u1, u2, u3;
252 energy =
E_IntLoop(u2, u1 + u3, type, type_2, si, sj, sp, sq, P);
262 if(u1 + u2 + u3 == 0)
288 int nl, ns, u, energy;
291 if (n1>n2) { nl=n1; ns=n2;}
295 return P->stack[type][type_2];
298 energy = (nl<=
MAXLOOP)?P->bulge[nl]:
299 (P->bulge[30]+(
int)(P->lxc*log(nl/30.)));
300 if (nl==1) energy += P->stack[type][type_2];
302 if (type>2) energy += P->TerminalAU;
303 if (type_2>2) energy += P->TerminalAU;
310 return P->int11[type][type_2][si1][sj1];
313 energy = P->int21[type][type_2][si1][sq1][sj1];
315 energy = P->int21[type_2][type][sq1][si1][sp1];
319 energy = (nl+1<=
MAXLOOP)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));
320 energy +=
MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);
321 energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];
327 return P->int22[type][type_2][si1][sp1][sq1][sj1];}
329 energy = P->internal_loop[5]+P->ninio[2];
330 energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];
337 energy = (u <=
MAXLOOP) ? (P->internal_loop[u]) : (P->internal_loop[30]+(int)(P->lxc*log((u)/30.)));
339 energy +=
MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);
341 energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];
358 int ul, us, no_close = 0;
361 if ((
no_closingGU) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
364 if (u1>u2) { ul=u1; us=u2;}
368 z = P->expstack[type][type2];
372 if (ul==1) z *= P->expstack[type][type2];
374 if (type>2) z *= P->expTermAU;
375 if (type2>2) z *= P->expTermAU;
381 return (
FLT_OR_DBL)(P->expint11[type][type2][si1][sj1]);
385 return (
FLT_OR_DBL)(P->expint21[type][type2][si1][sq1][sj1]);
387 return (
FLT_OR_DBL)(P->expint21[type2][type][sq1][si1][sp1]);
390 z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];
391 return (
FLT_OR_DBL)(z * P->expninio[2][ul-us]);
396 return (
FLT_OR_DBL)(P->expint22[type][type2][si1][sp1][sq1][sj1]);
398 z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];
403 z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];
404 return (
FLT_OR_DBL)(z * P->expninio[2][ul-us]);
411 E_IntLoop_Co(
int type,
425 int energy, ci, cj, cp, cq, d3, d5, d5_2, d3_2, tmm, tmm_2;
428 if(type > 2) energy += P->TerminalAU;
429 if(type_2 > 2) energy += P->TerminalAU;
431 if(!dangles)
return energy;
433 ci = ON_SAME_STRAND(i, i + 1, cutpoint);
434 cj = ON_SAME_STRAND(j - 1, j, cutpoint);
435 cp = ON_SAME_STRAND(p - 1, p, cutpoint);
436 cq = ON_SAME_STRAND(q, q + 1, cutpoint);
438 d3 = ci ? P->dangle3[type][si1] : 0;
439 d5 = cj ? P->dangle5[type][sj1] : 0;
440 d5_2 = cp ? P->dangle5[type_2][sp1] : 0;
441 d3_2 = cq ? P->dangle3[type_2][sq1] : 0;
443 tmm = (cj && ci) ? P->mismatchExt[type][sj1][si1] : d5 + d3;
444 tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;
446 if(dangles == 2)
return energy + tmm + tmm_2;
450 if(q+2 < j){ energy += tmm + tmm_2;}
451 else if(q+2 == j){ energy += (cj && cq) ?
MIN2(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}
452 else energy += d3 + d5_2;
455 if(q+2 < j){ energy += (ci && cp) ?
MIN2(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}
457 energy +=
MIN2(tmm,
MIN2(tmm_2,
MIN2(d5 + d5_2, d3 + d3_2)));
459 else energy +=
MIN2(d3, d5_2);
462 if(q+2 < j){ energy += d5 + d3_2;}
463 else if(q+2 == j){ energy +=
MIN2(d5, d3_2);}
515 E_IntLoop_Co(
int type,
PRIVATE int E_IntLoop(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, vrna_param_t *P)
Definition: interior_loops.h:277
#define MAXLOOP
Definition: energy_const.h:28
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:88
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
int * energy_stack
Pseudo Energy contribution per base pair involved in a stack.
Definition: constraints_soft.h:117
#define MIN2(A, B)
Get the minimum of two comparable values.
Definition: utils.h:112
PRIVATE FLT_OR_DBL exp_E_IntLoop(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, vrna_exp_param_t *P)
Definition: interior_loops.h:348
vrna_callback_sc_energy * f
A function pointer used for pseudo energy contribution in MFE calculations.
Definition: constraints_soft.h:121
General utility- and helper-functions used throughout the ViennaRNA Package.
The soft constraints data structure.
Definition: constraints_soft.h:111
#define INF
Definition: energy_const.h:16
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
int ** energy_up
Energy contribution for stretches of unpaired nucleotides.
Definition: constraints_soft.h:112
#define VRNA_DECOMP_PAIR_IL
Indicator for interior loop decomposition step.
Definition: constraints.h:80
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:190
Base pair stack element.
Definition: data_structures.h:192
Functions and data structures for constraining secondary structure predictions and evaluation...
int * energy_bp
Energy contribution for base pairs.
Definition: constraints_soft.h:113
int vrna_BT_stack(vrna_fold_compound_t *vc, int *i, int *j, int *en, vrna_bp_stack_t *bp_stack, int *stack_count)
Backtrack a stacked pair closed by .
int no_closingGU
GU allowed only inside stacks if set to 1.
int vrna_BT_int_loop(vrna_fold_compound_t *vc, int *i, int *j, int en, vrna_bp_stack_t *bp_stack, int *stack_count)
Backtrack an interior loop closed by .
int E_stack(int i, int j, vrna_fold_compound_t *vc)
Evaluate energy of a base pair stack closed by (i,j)
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
void * data
A pointer to the data object provided for for pseudo energy contribution functions of the generic sof...
Definition: constraints_soft.h:138