Energy evaluation of exterior loops for MFE and partition function calculations. More...
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Functions | |
| int | E_Stem (int type, int si1, int sj1, int extLoop, vrna_param_t *P) |
| Compute the energy contribution of a stem branching off a loop-region. More... | |
| FLT_OR_DBL | exp_E_ExtLoop (int type, int si1, int sj1, vrna_exp_param_t *P) |
| FLT_OR_DBL | exp_E_Stem (int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P) |
Basic free energy interface | |
| int | vrna_E_ext_stem (unsigned int type, int n5d, int n3d, vrna_param_t *p) |
| Evaluate a stem branching off the exterior loop. More... | |
| int | vrna_E_ext_loop (vrna_fold_compound_t *fc, int i, int j) |
| Evaluate the free energy of a base pair in the exterior loop. More... | |
| int | vrna_E_ext_loop_5 (vrna_fold_compound_t *fc) |
| int | vrna_E_ext_loop_3 (vrna_fold_compound_t *fc, int i) |
Boltzmann weight (partition function) interface | |
| typedef struct vrna_mx_pf_aux_el_s * | vrna_mx_pf_aux_el_t |
| Auxiliary helper arrays for fast exterior loop computations. More... | |
| FLT_OR_DBL | vrna_exp_E_ext_stem (unsigned int type, int n5d, int n3d, vrna_exp_param_t *p) |
| Evaluate a stem branching off the exterior loop (Boltzmann factor version) More... | |
| struct vrna_mx_pf_aux_el_s * | vrna_exp_E_ext_fast_init (vrna_fold_compound_t *fc) |
| void | vrna_exp_E_ext_fast_rotate (struct vrna_mx_pf_aux_el_s *aux_mx) |
| void | vrna_exp_E_ext_fast_free (struct vrna_mx_pf_aux_el_s *aux_mx) |
| FLT_OR_DBL | vrna_exp_E_ext_fast (vrna_fold_compound_t *fc, int i, int j, struct vrna_mx_pf_aux_el_s *aux_mx) |
| void | vrna_exp_E_ext_fast_update (vrna_fold_compound_t *fc, int j, struct vrna_mx_pf_aux_el_s *aux_mx) |
Detailed Description
Energy evaluation of exterior loops for MFE and partition function calculations.
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