deeporigin.drug_discovery.rbfe

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

The RBFE 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

RBFE

Bases: WorkflowStep

class to handle RBFE-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

get_jobs

get_jobs() -> None

Get the jobs for jobs corresponding to this network and save to self.jobs

get_results

get_results() -> DataFrame | None

get RBFE results and return in a dataframe.

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

run_ligand_pair

run_ligand_pair(
    *,
    ligand1: Ligand,
    ligand2: Ligand,
    re_run: bool = False,
    _output_dir_path: Optional[str] = None,
    return_job: bool = True
) -> Job | None | str

Method to run an end-to-end RBFE run.

Parameters:

Name	Type	Description	Default
ligand1	Ligand	First ligand to run.	required
ligand2	Ligand	Second ligand to run.	required
re_run	bool	Whether to re-run the job if it already exists.	False
_output_dir_path	Optional[str]	Path to the output directory.	None

run_network

run_network(*, re_run: bool = False) -> Job

Run RBFE for the ligand pairs in the network in the ligand set in the Complex.

Parameters:

Name	Type	Description	Default
re_run	bool	If True, re-run jobs even if results already exist. Defaults to False.	False

Returns:

Name	Type	Description
Job	Job	The Job object representing the network run.

set_test_run

set_test_run(value: int = 1)

set test_run parameter in RBFE parameters

show_results

show_results()

Show RBFE results in a dataframe.

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