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Parameters

​
states
list[State]
required
​
name
str | None
default:"None"
​
total_energy
float | None
default:"None"

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Methods

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get_total_energy

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dump_config

Saves information about how each energy term was configured in a csv file named “config.csv”. Columns include ‘state_name’, ‘energy_name’, and ‘weight’. Parameters
​
path
pl.Path
required
The directory in which the config.csv file will be created.

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add_chain

Add a chain to the state. Parameters
​
sequence
str
required
amino acid sequence of the chain
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mutability
list[int]
required
list of 0s and 1s indicating if the residue is mutable or not
​
chain_ID
str
required
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state_index
list[int]
required
index of the state in the system

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Example

import bagel as bg

state = bg.State(name='state_A', chains=[], energy_terms=[])
system = bg.System(states=[state], name='example_system')
system.add_chain(sequence='AAAA', mutability=[1, 1, 0, 0], chain_ID='A', state_index=[0])