| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
| H A D | equilibrium_probs.c | 1453 expMLclosing = pf_params->expMLclosing;
1513 *expMLclosing
1533 prmt *= expMLclosing;
1728 expMLclosing = pf_params->expMLclosing;
3021 expMLclosing = pf_params->expMLclosing;
3317 expMLclosing = pf_params->expMLclosing;
3657 expMLclosing = pf_params->expMLclosing;
3841 expMLclosing *
3852 expMLclosing *
3875 expMLclosing *
[all …]
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| H A D | boltzmann_sampling.c | 1257 kTn, closingPair, expMLclosing; in backtrack() local
1311 expMLclosing = pf_params->expMLclosing; in backtrack()
1322 expMLclosing = pow(pf_params->expMLclosing, (double)n_seq); in backtrack()
1517 closingPair = expMLclosing * in backtrack()
1656 qb_ij, expMLclosing; in pbacktrack_circ() local
1670 expMLclosing = pf_params->expMLclosing; in pbacktrack_circ()
1697 expMLclosing = pf_params->expMLclosing; in pbacktrack_circ()
1707 expMLclosing = pow(pf_params->expMLclosing, (double)n_seq); in pbacktrack_circ()
1842 expMLclosing * in pbacktrack_circ()
1861 expMLclosing; in pbacktrack_circ()
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| H A D | part_func.c | 533 qbt1, qot, expMLclosing, n_seq; in postprocess_circular() local
552 expMLclosing = pf_params->expMLclosing; in postprocess_circular()
725 qbt1 *= expMLclosing; in postprocess_circular()
748 qbt1 *= pow(expMLclosing, fc->n_seq); in postprocess_circular()
765 qbt1 *= expMLclosing; in postprocess_circular()
786 qbt1 *= pow(expMLclosing, fc->n_seq); in postprocess_circular()
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| H A D | LPfold.c | 1031 *scale, *expMLbase, expMLclosing, temp, prm_MLb, prmt1, prmt, *tmp, in compute_probs() local
1055 expMLclosing = pf_params->expMLclosing; in compute_probs()
1221 prmt *= expMLclosing; in compute_probs()
1228 expMLclosing * in compute_probs()
1513 FLT_OR_DBL expMLclosing, *expMLbase, **q, **qm, **qm2, *scale, **pR, **QI5, in compute_pU() local
1531 expMLclosing = pf_params->expMLclosing; in compute_pU()
1621 expMLclosing; in compute_pU()
1739 expMLclosing * in compute_pU()
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| H A D | 2Dpfold.c | 572 … temp2 = pf_params->expMLclosing * exp_E_MLstem(tt, S1[j - 1], S1[i + 1], pf_params) * scale[2]; in pf2D_linear()
1732 …_rem += Q_M_rem[my_iindx[1] - k] * matrices->Q_M2[k + 1][cnt1][cnt2 / 2] * pf_params->expMLclosing; in pf2D_circ()
1736 …trices->Q_cM_rem += Q_M_rem[my_iindx[1] - k] * matrices->Q_M2_rem[k + 1] * pf_params->expMLclosing; in pf2D_circ()
1747 …_rem += Q_M[my_iindx[1] - k][cnt1][cnt2 / 2] * matrices->Q_M2_rem[k + 1] * pf_params->expMLclosing; in pf2D_circ()
1763 …my_iindx[1] - k][cnt1][cnt2 / 2] * matrices->Q_M2[k + 1][cnt3][cnt4 / 2] * pf_params->expMLclosing; in pf2D_circ()
1774 …my_iindx[1] - k][cnt1][cnt2 / 2] * matrices->Q_M2[k + 1][cnt3][cnt4 / 2] * pf_params->expMLclosing; in pf2D_circ()
2955 * pf_params->expMLclosing; in backtrack_qcM()
2967 * pf_params->expMLclosing; in backtrack_qcM()
2986 * pf_params->expMLclosing; in backtrack_qcM()
3021 * pf_params->expMLclosing; in backtrack_qcM()
[all …]
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| H A D | part_func_up.c | 384 temp = prpr[po] * exp_E_MLstem(tt, S1[o - 1], S1[p + 1], Pf) * scale[2] * Pf->expMLclosing; in pf_unstru()
496 temp = prpr[po] * exp_E_MLstem(tt, S1[p - 1], S1[o + 1], Pf) * Pf->expMLclosing * scale[2]; in pf_unstru()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/loops/ |
| H A D | multibranch_pf.c | 247 FLT_OR_DBL qbt1, temp, qqqmmm, *qm, **qm_local, *scale, expMLclosing, *qqm1; in exp_E_mb_loop_fast() local
275 expMLclosing = pf_params->expMLclosing; in exp_E_mb_loop_fast()
284 qqqmmm = pow(expMLclosing, (double)n_seq) * in exp_E_mb_loop_fast()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/params/ |
| H A D | basic.h | 126 double expMLclosing; member
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| H A D | params.c | 585 pf->expMLclosing = RESCALE_BF(ML_closing37, ML_closingdH, TT, kT); in get_scaled_exp_params()
765 pf->expMLclosing = RESCALE_BF(ML_closing37, ML_closingdH, TT, kTn); in get_exp_params_ali()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/ |
| H A D | params.i | 86 const double expMLclosing; member
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| /dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/ |
| H A D | params_2basic_8h_source.tex | 100 \DoxyCodeLine{00126 \textcolor{keywordtype}{double} expMLclosing;}
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/ |
| H A D | RNA.py | 1652 expMLclosing = property(_RNA.exp_param_expMLclosing_get) variable in exp_param
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| H A D | RNA_wrap.cpp | 42187 result = (double)(double) ((arg1)->expMLclosing); in _wrap_exp_param_expMLclosing_get()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/ |
| H A D | RNA.py | 1652 expMLclosing = property(_RNA.exp_param_expMLclosing_get) variable in exp_param
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| H A D | RNA_wrap.cpp | 42325 result = (double)(double) ((arg1)->expMLclosing); in _wrap_exp_param_expMLclosing_get()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/ |
| H A D | RNA_wrap.cpp | 22171 result = (double)(double) ((arg1)->expMLclosing); in XS()
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