schrodinger.application.desmond.process_fep_traj module

class schrodinger.application.desmond.process_fep_traj.GenRepStructureForFep(name: str)

Bases: schrodinger.application.desmond.task.Task

Task to generate representative structures for both FEP lambda states. Please refer to the docstrings of _GetRepFrameIndex and _GenRepStructureForFepLambda as for some detail about the generation of the representative structure.

Results: - key = “Keywords[i].ResultLambda0.RepMaeFname” - val = Name of the representative structure file: ‘rep_lambda0.mae’ - key = “Keywords[i].ResultLambda1.RepMaeFname” - val = Name of the representative structure file: ‘rep_lambda1.mae’

__init__(name: str)

Parameters

name – An arbitrary name. Useful for error logging.

class schrodinger.application.desmond.process_fep_traj.GenRepStructureForAbsoluteFep(name: str)

Bases: schrodinger.application.desmond.task.Task

Task to generate representative structures for the fully interacting state of Absolute Binding FEP. Please refer to the docstrings of _GetRepFrameIndex and _GenRepStructureForFepLambda as for some detail about the generation of the representative structure.

Results: - key = “Keywords[i].ResultLambda0.RepMaeFname” - val = Name of the representative structure file: ‘rep_lambda0.mae’

__init__(name: str)

Parameters

name – An arbitrary name. Useful for error logging.

class schrodinger.application.desmond.process_fep_traj.GenRepStructureForSublimationFep(name: str)

Bases: schrodinger.application.desmond.task.Task

Task to generate representative structures for the fully interacting state of Solubility FEP. Please refer to the docstrings of _GetRepFrameIndex and _GenRepStructureForFepLambda as for some detail about the generation of the representative structure.

Results: - key = “Keywords[i].ResultLambda1.RepMaeFname” - val = Name of the representative structure file: ‘rep_lambda1.mae’

__init__(name: str)

Parameters

name – An arbitrary name. Useful for error logging.

schrodinger.application.desmond.process_fep_traj.postprocess_traj(arkdb_fname: str, ref_ct_fname: str = None)