RNAlib-2.2.0c
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The data structure that contains the complete model details used throughout the calculations. More...
Data Fields | |
double | temperature |
The temperature used to scale the thermodynamic parameters. | |
double | betaScale |
A scaling factor for the thermodynamic temperature of the Boltzmann factors. | |
int | dangles |
Specifies the dangle model used in any energy evaluation (0,1,2 or 3) More... | |
int | special_hp |
Include special hairpin contributions for tri, tetra and hexaloops. | |
int | noLP |
Only consider canonical structures, i.e. no 'lonely' base pairs. | |
int | noGU |
Do not allow GU pairs. | |
int | noGUclosure |
Do not allow loops to be closed by GU pair. | |
int | logML |
Use logarithmic scaling for multi loops. | |
int | circ |
Assume RNA to be circular instead of linear. | |
int | gquad |
Include G-quadruplexes in structure prediction. | |
int | canonicalBPonly |
remove non-canonical bp's from constraint structures | |
int | uniq_ML |
Flag to ensure unique multibranch loop decomposition during folding. | |
int | energy_set |
Specifies the energy set that defines set of compatible base pairs. | |
int | backtrack |
Specifies whether or not secondary structures should be backtraced. | |
char | backtrack_type |
Specifies in which matrix to backtrack. | |
int | compute_bpp |
Specifies whether or not backward recursions for base pair probability (bpp) computation will be performed. | |
char | nonstandards [33] |
contains allowed non standard bases | |
int | max_bp_span |
maximum allowed base pair span | |
int | min_loop_size |
Minimum size of hairpin loops. More... | |
int | oldAliEn |
Use old alifold energy model. | |
int | ribo |
Use ribosum scoring table in alifold energy model. | |
double | cv_fact |
Covariance scaling factor for consensus structure prediction. | |
double | sfact |
Scaling factor for partition function scaling. | |
The data structure that contains the complete model details used throughout the calculations.
int model_detailsT::dangles |
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
int model_detailsT::min_loop_size |
Minimum size of hairpin loops.