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Parameters

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mutation_bias
Dict[str, float]
default:"lambda: mutation_bias_no_cystein()"
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n_mutations
int
default:"1"
​
exclude_self
bool
default:"True"

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Methods

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one_step

Abstract method for performing a single mutation step. Parameters
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system
System
required
The system to be mutated
Returns
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return
System
The mutated system (new copy) MutationRecord Record of all mutations performed in this step

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choose_chain

Choose one of the chains in the whole System that needs to be mutated. This is done by selecting a chain Parameters
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system
System
required

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mutate_random_residue

Mutate a random residue on a chain. Parameters
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chain
Chain
required
The chain to mutate.
Returns
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return
Mutation
The mutation performed. This includes the chain_id, the move_type, the residue_index, the old_amino_acid, and the new_amino_acid.

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replay

Replay a mutation record on a system, reusing existing mutation logic. Parameters
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system
System
required
The system to apply mutations to
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mutation_record
MutationRecord
required
Record of mutations to replay
Returns
​
return
System
System with mutations applied

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Example

import bagel as bg

class AlwaysSubstitute(bg.mutation.MutationProtocol):
    def one_step(self, system: bg.System) -> tuple[bg.System, bg.mutation.MutationRecord]:
        mutated = system.__copy__()
        chain = self.choose_chain(mutated)
        mutation = self.mutate_random_residue(chain)
        return mutated, bg.mutation.MutationRecord(mutations=[mutation])