Disallow all pairs which can only occur as lonely pairs (i.e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases.
Switch the energy model for dangling end contributions (0, 1, 2, 3)
If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm pf_fold() these checks are neglected. If dangles is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-axial stacking.
If dangles = 3 co-axial stacking is explicitly included for adjacent helices in mutli-loops. The option affects only mfe folding and energy evaluation (fold() and energy_of_structure()), as well as suboptimal folding (subopt()) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.
Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2
If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A pairs B, C pairs D, etc. using either GC (1) or AU parameters (2); default is 0, you probably don't want to change it.
Lists additional base pairs that will be allowed to form in addition to GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking energy of 0.
Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence.
To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -1 stands for single molecule folding. The cut_point variable is also used by PS_rna_plot() and PS_dot_plot() to mark the chain break in postscript plots.
A scaling factor used by pf_fold() to avoid overflows.
Should be set to approximately , where is an estimate for the ensemble free energy, for example the minimum free energy. You must call update_pf_params() after changing this parameter.
If pf_scale is -1 (the default) , an estimate will be provided automatically when computing partition functions, e.g. pf_fold() The automatic estimate is usually insufficient for sequences more than a few hundred bases long.