wvdtoorn / dmmimesim Goto Github PK

The value for KD_WT in params reflects the Kd of the wildtpye species, not of a single position.

In the case that KD_WT == 1, the Kd's of the single positions are equal to the species Kd and multiplicative processing of all position-wise Kd's (as done in https://github.com/wvandertoorn/dmMIMESim/blob/3ab12d908c8d33167a7dcc34d3b33547b2fbbf71/src/Species.cpp#L223C19-L223C35 ) will return a species Kd of 1.
However, in the case that KD_WT =/= 1, multiplicative processing of all position-wise Kd's will return incorrect species Kd values.

Possible fix:

Assume all position-wise Kd's in the wildtype have the same magnitude. Let's call it KD_WT_pos. Estimate KD_WT_pos through the Nth root of the KD_WT value. With N the sequence length.
Use KD_WT_pos as default value in the FuncitonalSequence creation in FunctionalSequence::drawKdValues