perses.samplers.ProtonationStateSampler¶
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class
perses.samplers.ProtonationStateSampler(complex_sampler, solvent_sampler, log_state_penalties, storage=None, verbose=False)[source]¶ Protonation state sampler with given fixed target probabilities for ligand in solvent.
Parameters: - samplers : list of SAMSSampler
The SAMS samplers whose relative partition functions go into the design objective computation.
- sampler_exponents : dict of SAMSSampler
samplers.keys() are the samplers, and samplers[key]
- log_target_probabilities : dict of hashable object
log_target_probabilities[key] is the computed log objective function (target probability) for chemical state key
- verbose : bool
If True, verbose output is printed.
Attributes: - state_keys
Methods
run([niterations])Run the protonation state sampler for the specified number of iterations. update()Run one iteration of the sampler. update_samplers()Update all samplers. update_target_probabilities()Update all target probabilities. -
__init__(complex_sampler, solvent_sampler, log_state_penalties, storage=None, verbose=False)[source]¶ Initialize a protonation state sampler with fixed target probabilities for ligand in solvent.
Parameters: - complex_sampler : ExpandedEnsembleSampler
Ligand in complex sampler
- solvent_sampler : SAMSSampler
Ligand in solution sampler
- log_state_penalties : dict
log_state_penalties[smiles] is the log state free energy (in kT) for ligand state ‘smiles’
- storage : NetCDFStorage, optional, default=None
If specified, will use the storage layer to write trajectory data.
- verbose : bool, optional, default=False
If true, will print verbose output
Methods
__init__(complex_sampler, solvent_sampler, …)Initialize a protonation state sampler with fixed target probabilities for ligand in solvent. run([niterations])Run the protonation state sampler for the specified number of iterations. update()Run one iteration of the sampler. update_samplers()Update all samplers. update_target_probabilities()Update all target probabilities. Attributes
state_keys
