perses.rjmc.topology_proposal.PeptideLibraryEngine

class perses.rjmc.topology_proposal.PeptideLibraryEngine(system_generator, library, chain_id, proposal_metadata=None, verbose=False, always_change=True)

system_generator : SystemGenerator library : list of strings

each string is a 1-letter-code list of amino acid sequence

chain_id : str

id of the chain to mutate (using the first chain with the id, if there are multiple)

proposal_metadata : dict – OPTIONAL

Contains information necessary to initialize proposal engine

Attributes:

chemical_state_list

Methods

compute_state_key(topology)	Compute the corresponding state key of a given topology, according to this proposal engine’s scheme.
propose(current_system, current_topology[, …])

__init__(system_generator, library, chain_id, proposal_metadata=None, verbose=False, always_change=True)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(system_generator, library, chain_id)	Initialize self.
compute_state_key(topology)	Compute the corresponding state key of a given topology, according to this proposal engine’s scheme.
propose(current_system, current_topology[, …])

Attributes

chemical_state_list

compute_state_key(topology)

Compute the corresponding state key of a given topology, according to this proposal engine’s scheme.

Parameters:

topology : app.Topology

the topology in question

Returns:

chemical_state_key : str

The chemical_state_key

propose(current_system, current_topology, current_metadata=None)