deeporigin.drug_discovery.Pocket

A simplified class representing a binding pocket in a protein structure.

This class focuses on coordinate-based operations and removes the complexity of maintaining full biotite structure objects. It provides essential methods for pocket analysis, visualization, and coordinate manipulation.

Attributes

color class-attribute instance-attribute

color: str = 'red'

coordinates class-attribute instance-attribute

coordinates: Optional[ndarray] = None

file_path class-attribute instance-attribute

file_path: Optional[Path] = None

index class-attribute instance-attribute

index: Optional[int] = 0

name class-attribute instance-attribute

name: Optional[str] = None

pdb_id class-attribute instance-attribute

pdb_id: Optional[str] = None

props class-attribute instance-attribute

props: Optional[Dict[str, Any]] = field(
    default_factory=dict
)

Functions

from_ligand classmethod

from_ligand(
    ligand: Ligand, name: Optional[str] = None
) -> Pocket

Create a Pocket instance from a Ligand instance.

from_pdb_file classmethod

from_pdb_file(
    pdb_file_path: str | Path,
    name: Optional[str] = None,
    **kwargs: Any
) -> Pocket

Create a Pocket instance from a PDB file.

Parameters:

Name	Type	Description	Default
pdb_file_path	str | Path	Path to the PDB file.	required
name	Optional[str]	Name for the pocket.	None
**kwargs	Any	Additional arguments to pass to the Pocket constructor.	{}

Returns:

Name	Type	Description
Pocket	Pocket	A new Pocket instance.

from_pocket_finder_results classmethod

from_pocket_finder_results(
    pocket_finder_results_dir: str | Path,
) -> List[Pocket]

Create a list of Pocket objects from pocket finder results directory.

Parameters:

Name	Type	Description	Default
pocket_finder_results_dir	str | Path	Directory containing pocket finder results with PDB files for each pocket and a CSV properties file.	required

Returns:

Type	Description
List[Pocket]	List of Pocket objects with properties from the CSV file.

from_residue_number classmethod

from_residue_number(
    protein,
    residue_number: int,
    chain_id: str | None = None,
    cutoff: float = 5.0,
) -> Pocket

Creates a pocket centered on a given residue (by number)

Parameters:

Name	Type	Description	Default
protein	Protein	A DeepOrigin Protein Object	required
residue_number	int	Residue number of the target residue	required
chain_id	str	Chain ID that the residue is in	None
cutoff	float	Minimum distance cutoff (Angstroms) from target residue to be included in pocket	5.0

Returns:

Type	Description
Pocket	A Pocket object matching the above design.

get_center

get_center() -> ndarray

Get the center of the pocket based on its coordinates.

Returns:

Type	Description
ndarray	np.ndarray: A numpy array containing the center of the pocket.

get_directory staticmethod

get_directory() -> str

Get the pockets directory path.

Returns:

Name	Type	Description
str	str	The path to the pockets directory.

show

show()

show the pocket in a jupyter notebook

to_pdb_file

to_pdb_file(output_path: str)

Write coordinates to a PDB file.

update_coordinates

update_coordinates(coords: ndarray)

update coordinates of the pocket