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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 = '0.2.7'

Functions

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

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
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.