| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/loops/ |
| H A D | hairpin.c | 115 int u1, u2, e, s, type, n_seq, length, noGUclosure; in vrna_eval_ext_hp_loop() local
123 noGUclosure = md->noGUclosure; in vrna_eval_ext_hp_loop()
141 if (noGUclosure && ((type == 3) || (type == 4))) in vrna_eval_ext_hp_loop()
223 int u, e, s, type, n_seq, en, noGUclosure; in vrna_eval_hp_loop() local
231 noGUclosure = md->noGUclosure; in vrna_eval_hp_loop()
250 if (noGUclosure && ((type == 3) || (type == 4))) in vrna_eval_hp_loop()
313 int u, e, ij, type, *idx, en, noGUclosure; in eval_hp_loop_fake() local
322 noGUclosure = md->noGUclosure; in eval_hp_loop_fake()
337 if (noGUclosure && ((type == 3) || (type == 4))) in eval_hp_loop_fake()
|
| H A D | hairpin_pf.c | 282 int u1, u2, n, type, n_seq, s, noGUclosure; in exp_eval_ext_hp_loop() local
292 noGUclosure = md->noGUclosure; in exp_eval_ext_hp_loop()
312 if (((type == 3) || (type == 4)) && noGUclosure) in exp_eval_ext_hp_loop()
|
| H A D | internal_pf.c | 164 int k, l, kl, last_k, first_l, u1, u2, turn, noGUclosure; in exp_E_int_loop() local
167 noGUclosure = md->noGUclosure; in exp_E_int_loop()
176 noclose = ((noGUclosure) && (type == 3 || type == 4)) ? 1 : 0; in exp_E_int_loop()
273 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in exp_E_int_loop()
355 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in exp_E_int_loop()
451 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in exp_E_int_loop()
|
| H A D | internal.c | 416 int k, l, kl, last_k, first_l, u1, u2, turn, noGUclosure; in E_internal_loop() local
420 noGUclosure = md->noGUclosure; in E_internal_loop()
429 noclose = ((noGUclosure) && (type == 3 || type == 4)) ? 1 : 0; in E_internal_loop()
525 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in E_internal_loop()
605 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in E_internal_loop()
695 if ((noGUclosure) && (type2 == 3 || type2 == 4)) in E_internal_loop()
|
| H A D | multibranch.c | 223 if (md->noGUclosure && ((tt == 3) || (tt == 4))) in ml_pair_d0()
314 if (md->noGUclosure && ((tt == 3) || (tt == 4))) in ml_pair_d2()
380 if (md->noGUclosure && ((tt == 3) || (tt == 4))) in ml_pair5()
446 if (md->noGUclosure && ((tt == 3) || (tt == 4))) in ml_pair3()
513 if (md->noGUclosure && ((tt == 3) || (tt == 4))) in ml_pair53()
556 int decomp, en, e, *fC, dangle_model, tt, noGUclosure; in E_mb_loop_fake() local
569 noGUclosure = md->noGUclosure; in E_mb_loop_fake()
580 if (noGUclosure && ((tt == 3) || (tt == 4))) in E_mb_loop_fake()
|
| H A D | internal.h | 583 int noGUclosure = P->model_details.noGUclosure; in exp_E_IntLoop() local
585 if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4))) in exp_E_IntLoop()
|
| H A D | internal_bt.c | 310 no_close = (((type == 3) || (type == 4)) && md->noGUclosure); in BT_int_loop()
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/ |
| H A D | model_details.i | 25 int noGUclosure; member
66 const int noGUclosure = vrna_md_defaults_noGUclosure_get(),
92 md->noGUclosure = noGUclosure;
150 out << ", noGUclosure: " << $self->noGUclosure ; in __str__()
212 extern int noGUclosure;
|
| H A D | model_details.dox | 33 | no_closingGU | this is an alias of @em noGUclosure | |
34 | noGUclosure | vrna_md_defaults_noGUclosure_get() | vrna_md_defaults_noGUclosure() |
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
| H A D | model.c | 229 if (md->noGUclosure) in vrna_md_option_string()
318 defaults.noGUclosure = VRNA_MODEL_DEFAULT_NO_GU_CLOSURE; in vrna_md_defaults_reset()
352 vrna_md_defaults_noGUclosure(md_p->noGUclosure); in vrna_md_defaults_reset()
385 no_closingGU = defaults.noGUclosure; in vrna_md_defaults_reset()
533 defaults.noGUclosure = flag ? 1 : 0; in vrna_md_defaults_noGUclosure()
535 no_closingGU = defaults.noGUclosure; in vrna_md_defaults_noGUclosure()
543 return defaults.noGUclosure; in vrna_md_defaults_noGUclosure_get()
976 md->noGUclosure = no_closingGU; in set_model_details()
|
| H A D | cofold.c | 204 int dangle_model, noGUclosure, noLP, hc_decompose, turn; in fill_arrays() local
216 noGUclosure = P->model_details.noGUclosure; in fill_arrays()
269 no_close = (((type == 3) || (type == 4)) && noGUclosure); in fill_arrays()
408 int noGUclosure = P->model_details.noGUclosure; in backtrack_co() local
544 no_close = (((type == 3) || (type == 4)) && noGUclosure); in backtrack_co()
|
| H A D | model.h | 211 …int noGUclosure; /**< @brief Do not allow loops to be closed by GU pair… member
|
| H A D | mfe_window.c | 876 dangle_model, noLP, noGUclosure, **c, dangle3, ml, cij, in backtrack() local
889 noGUclosure = md->noGUclosure; in backtrack()
1006 no_close = (((type == 3) || (type == 4)) && noGUclosure); in backtrack()
|
| H A D | subopt.c | 1970 int rt, *indx, *rtype, noGUclosure, noLP, with_gquad, dangle_model, turn; in repeat() local
1987 noGUclosure = md->noGUclosure; in repeat()
2009 no_close = (((type == 3) || (type == 4)) && noGUclosure); in repeat()
2081 if (noGUclosure) in repeat()
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/ |
| H A D | globals-md.i | 87 %typemap(varin) int noGUclosure {
91 %typemap(varout) int noGUclosure {
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/ |
| H A D | globals-md.i | 87 %typemap(varin) int noGUclosure {
91 %typemap(varout) int noGUclosure {
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/ |
| H A D | globals-md.i | 86 %typemap(varin) int noGUclosure {
90 %typemap(varout) int noGUclosure {
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
| H A D | RNApvmin.c | 161 md.noGUclosure = 1; in main()
|
| H A D | gengetopt_helper.h | 179 ggo_get_noGUclosure(ggostruct, md.noGUclosure); \
|
| H A D | RNAPKplex.c | 110 md.noGUclosure = no_closingGU = 1; in main()
|
| H A D | RNApdist.c | 313 md->noGUclosure = no_closingGU = 1; in command_line()
|
| H A D | RNALfold.c | 158 md.noGUclosure = no_closingGU = 1; in main()
|
| H A D | RNA2Dfold.c | 134 md.noGUclosure = no_closingGU = 1; in main()
|
| H A D | RNAplfold.c | 222 md.noGUclosure = no_closingGU = 1; in main()
|
| /dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/ |
| H A D | internal_8h_source.tex | 459 …noGUclosure = P-\/>\mbox{\hyperlink{group__energy__parameters_ac18055127bccc27c1223f1d2f3b01b53}{m…
461 \DoxyCodeLine{00585 \textcolor{keywordflow}{if} ((noGUclosure) \&\& ((type2 == 3) || (type2 == 4)…
|