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 = '0.2.8'

Functions

check_dt

check_dt()

Validate that every "dt" in params is numeric and within allowed bounds.

Traverses the nested parameters dictionary and validates that each occurrence of a key named "dt" has a numeric value within the inclusive range [min_dt, max_dt]. If any non-numeric or out-of-range values are found, an error is raised listing all offending paths.

Raises:

Type	Description
DeepOriginException	If any "dt" value is non-numeric or outside the allowed range.

get_jobs

get_jobs(
    *,
    include_metadata: bool = False,
    include_outputs: bool = False
)

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

run

run(
    *,
    ligands: Optional[list[Ligand] | LigandSet] = None,
    ligand: Optional[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] | LigandSet]	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 parameter 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