schrodinger.application.desmond.kinetics.mtd_cleanup module¶
Unbinding Kinetics Cleanup workflow for infrequent MtD subjobs. Generate reports and copy one subjob cms/xtc that best matches the predicted tau.
- class schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp(chkpt_file: str, asl_receptor: str, asl_ligand: str, mtd_reports: bool, residence_time_cutoff: float = 1000000000000.0, frac_unbound_thresholds: Optional[List[float]] = None, p_value_thresholds: Optional[List[float]] = None)¶
Bases:
object
Class for cleaning up unbinding kinetics mtd subjobs.
- TODO: Return the traj for the subjob closes to the predicted value
(DESMOND-12822)
- __init__(chkpt_file: str, asl_receptor: str, asl_ligand: str, mtd_reports: bool, residence_time_cutoff: float = 1000000000000.0, frac_unbound_thresholds: Optional[List[float]] = None, p_value_thresholds: Optional[List[float]] = None)¶
- property exec_dir¶
- run()¶
Run the cleanup workflow.
- write_unbinding_paths_summary(results_df: pandas.core.frame.DataFrame)¶
- If unbinding paths are found, write summary structure showing sampled paths
and their associated path CVs.
- write_unbinding_statistics(results_df: pandas.core.frame.DataFrame)¶
This function writes an ‘result’ file ($JOBNAME.dat) which is a fixed-width table with jobname and simulation resuls.
- calculate_unbinding_statistics() pandas.core.frame.DataFrame ¶
- read_archive_data()¶
Extract files from tgz archives
- schrodinger.application.desmond.kinetics.mtd_cleanup.parse_cmd(cmdline: List[str]) argparse.Namespace ¶
- schrodinger.application.desmond.kinetics.mtd_cleanup.main(cmdline=None)¶