Substitution Probability Models
Minimal API for developing substitution likelihood probability models for species mutation.
Probability models for species substitution.
Implements base class SubstitutionModel
,
which can be extended to allow for development of new
lambda tables. An example of such an extension,
RadiusModel
, is also implemented.
Todo
Allow for parallelism in lambda table calculations by implementing a sub_probs abstractmethod that
SubstitutionModel.gen_lambda()
uses, if available.
- class smact.structure_prediction.probability_models.RadiusModel[source]
Bases:
SubstitutionModel
Substitution probability model based on Shannon radii.
- sub_prob(s1, s2)[source]
Calculate the probability of substituting species s1 for s2.
Based on the difference in Shannon radii, the probability is assumed to be:
\[p = 1 - k \Delta r^2.\]- Parameters
s1 – The species being substituted.
s2 – The species substituting.
- Returns
The probability of substitution.
- class smact.structure_prediction.probability_models.SubstitutionModel[source]
Bases:
ABC
Abstract base class for substitution models.