schrodinger.application.desmond.starter.generator.fep_residue_scanning module¶

class schrodinger.application.desmond.starter.generator.fep_residue_scanning.JobPreparedFiles(main_msj_fname: str, md_msj_fname: str)¶

Bases: object

main_msj_fname: str¶

md_msj_fname: str¶

__init__(main_msj_fname: str, md_msj_fname: str) → None¶

schrodinger.application.desmond.starter.generator.fep_residue_scanning.get_phs_from_replica_info(num_total_replicas: int, replica_interval: float) → list[float]¶

Calculate the pH values for the lambda dynamics based on the number of replicas and the sampling interval of the relative population. Note that the pH = 7 replica is always included: it’s the only unbiased replica and useful to check the simulation trajectory information.

Parameters

total_replicas – The total number of replicas to simulate.
replica_interval – The sampling interval of the relative population (to run simulations at) between the wild type and the mutant in the logarithm 10 base scale. e.g. a value of 1.0 indicates a 10-fold change in relative population.

schrodinger.application.desmond.starter.generator.fep_residue_scanning.generate(args: schrodinger.application.desmond.starter.ui.fep_residue_scanning.Args) → List[str]¶

Generate the files and command line to run multisim for the FEP residue scanning (via Lambda Dynamics) workflow.

Parameters: args – Object with input arguments.
Returns: Command line to launch multisim