flexs.landscapes.additive_aav_packaging¶

Defines the AdditiveAAVPackaging landscape and problem registry.

class flexs.landscapes.additive_aav_packaging.AdditiveAAVPackaging(phenotype='heart', minimum_fitness_multiplier=1, start=0, end=735, noise=0)[source]¶

Bases: flexs.landscape.Landscape

An Additive landscape based on data from AAV2 packaging fitness measurements.

By additive landscape, we mean that each residue at each position is given a fitness and the fitness of the sequence is the sum of these individual fitnesses. This means that the fitness contribution per residue is independent of the identities of the other residues. This makes for a very simple landscape.

wild_type[source]¶

AAV2 wild_type substring between positions start and end.

Type: str

compute_max_possible()[source]¶: Compute max possible fitness of any sequence (used for normalization).

flexs.landscapes.additive_aav_packaging.registry()[source]¶

Return a dictionary of problems of the form: ```{

“problem name”: {
“params”: …

}```

where flexs.landscapes.AdditiveAAVPackaging(**problem[“params”]) instantiates the additive AAV packaging landscape for the given set of parameters.

Returns: Problems in the registry.
Return type: dict