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.

clear()

Cleans the state of this object for a new execution.

execute(db: schrodinger.application.desmond.arkdb.ArkDb)

Executes this task. This should only be called after all premises of this task are met. The premises of the subtasks are ignored until the subtask is executed. Subclasses should implement an execute, either as an instance method, or as an instance’s public callable attribute. After execution, all results desired to be put into the database should be saved as the results attribute.

The first argument of execute should always be for the database.

property options

property premises

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.

clear()

Cleans the state of this object for a new execution.

execute(db: schrodinger.application.desmond.arkdb.ArkDb)

Executes this task. This should only be called after all premises of this task are met. The premises of the subtasks are ignored until the subtask is executed. Subclasses should implement an execute, either as an instance method, or as an instance’s public callable attribute. After execution, all results desired to be put into the database should be saved as the results attribute.

The first argument of execute should always be for the database.

property options

property premises

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.

clear()

Cleans the state of this object for a new execution.

execute(db: schrodinger.application.desmond.arkdb.ArkDb)

Executes this task. This should only be called after all premises of this task are met. The premises of the subtasks are ignored until the subtask is executed. Subclasses should implement an execute, either as an instance method, or as an instance’s public callable attribute. After execution, all results desired to be put into the database should be saved as the results attribute.

The first argument of execute should always be for the database.

property options

property premises

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