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deeporigin.drug_discovery.abfe

This module encapsulates methods to run ABFE and show ABFE results on Deep Origin.

The ABFE object instantiated here is contained in the Complex class is meant to be used within that class.

Attributes

LOCAL_BASE module-attribute

LOCAL_BASE = home() / '.deeporigin'

Classes

ABFE

Bases: WorkflowStep

class to handle ABFE-related tasks within the Complex class.

Objects instantiated here are meant to be used within the Complex class.

Attributes

tool_version class-attribute instance-attribute
tool_version = '0.2.7'

Functions

get_jobs
get_jobs()

get jobs for this workflow step

get_results
get_results() -> DataFrame | None

get ABFE results and return in a dataframe.

This method returns a dataframe showing the results of ABFE runs associated with this simulation session. The ligand file name and ΔG are shown, together with user-supplied properties

parse_progress classmethod
parse_progress(job: Job) -> dict

parse progress from a ABFE job

run_end_to_end
run_end_to_end(
    *,
    ligands: Optional[list[Ligand]] = None,
    re_run: bool = False,
    _output_dir_path: Optional[str] = None
) -> list[Job] | None

Method to run an end-to-end ABFE run.

Parameters:

Name Type Description Default
ligands Optional[list[Ligand]]

List of ligand to run. Defaults to None. When None, all ligands in the object will be run. To view a list of valid ligands, use the .show_ligands() method

None
set_test_run
set_test_run(value: int = 1)

set test_run paramemter in abfe parameters

show_jobs
show_jobs()

show jobs for this workflow step

show_results
show_results()

Show ABFE results in a dataframe.

This method returns a dataframe showing the results of ABFE runs associated with this simulation session. The ligand file name, 2-D structure, and ΔG are shown.

show_trajectory
show_trajectory(
    *,
    ligand: Ligand,
    step: Literal["md", "binding"],
    window: int = 1
)

Show the system trajectory FEP run.

Parameters:

Name Type Description Default
ligand Ligand

The ligand to show the trajectory for.

required
step Literal['md', 'abfe']

The step to show the trajectory for.

required
window int

The window number to show the trajectory for. Defaults to 1.

1