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Parameters

​
n_mutations
int
default:"1"
Number of mutations to perform in each step.
​
mutation_bias
Dict[str, float]
default:"mutation_bias_no_cystein"
Bias for the substitution. The keys are the amino acids, the values are the probabilities.
​
move_probabilities
dict[str, float]
Probabilities for the different moves. The keys are ‘substitution’, ‘addition’, and ‘removal’, and the values are the probabilities of performing the corresponding move. These should be normalized to sum to 1.
​
exclude_self
bool
default:"True"

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Methods

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remove_random_residue

Parameters
​
chain
Chain
required
​
system
System
required

​
add_random_residue

Parameters
​
chain
Chain
required
​
system
System
required

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one_step

Parameters
​
system
System
required

​
Example

import bagel as bg

residues = [bg.Residue(name='A', chain_ID='A', index=i, mutable=True) for i in range(6)]
state = bg.State(name='state_A', chains=[bg.Chain(residues)], energy_terms=[])
system = bg.System(states=[state])

mutator = bg.mutation.GrandCanonical(
    move_probabilities={'substitution': 0.5, 'addition': 0.25, 'removal': 0.25}
)
mutated_system, mutation_record = mutator.one_step(system)