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.
Classes¶
Bases: WorkflowStep
class to handle ABFE-related tasks within the Complex class.
Objects instantiated here are meant to be used within the Complex class.
Functions¶
download_data_dir(ligand_id: str) -> str
Download the data directory for a given ligand ID.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ligand_id
|
str
|
The ID of the ligand to download the data directory for. |
required |
Returns:
| Name | Type | Description |
|---|---|---|
str |
str
|
The path to the data directory. |
get_results() -> DataFrame
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_end_to_end(*, ligand_ids: Optional[list[str]] = None)
Method to run an end-to-end ABFE run.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ligand_ids
|
Optional[str]
|
List of ligand IDs to run. Defaults to None. When None, all ligands in the object will be run. To view a list of valid ligand IDs, use the |
None
|
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(
*,
ligand_id: str,
step: Literal["md", "binding"],
window: int = 1
)
Show the system trajectory FEP run.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
ligand_id
|
str
|
The ID of 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
|