schrodinger.application.desmond.starter.generator.fep_residue_scanning module¶
Copyright Schrodinger, LLC. All rights reserved.
- 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