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.ResultsCols(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

PATH = 'Path'

NAME = 'Name'

PRED_RES_TIME = 'Pred.Res.Time(s)'

P_VALUE = 'P-value'

SIM_TIME = 'Sim.Time(ns)'

SIMS = '#Sims'

UNBOUND_SIMS = '#Unbound.Sims'

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)

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)

Parameters

• chkpt_file – Multisim checkpoint filenames from the master stage

• asl_receptor – Atom selection language for the receptor

• asl_ligand – Atom selection language for the ligand

• mtd_reports – Generate PNG reports with detail mtd subjob analysis

• residence_time_cutoff – A cutoff value to determine if the ligand is too slow to unbind

Variables

• path_cv_idcs – List of indices for all path CVs used to bias metadynamics unbinding simulations.

• subjob_to_unbinding_path_map – Dictionary linking the subjob names to their unbinding path structures.

property exec_dir

run()

Run the cleanup workflow.

write_unbinding_paths_summary()

If unbinding paths are found, write summary structure showing sampled paths

and their associated path CVs.

print_results()

Print formatted results to the log file.

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)