deeporigin.drug_discovery.Pocket

A class representing a binding pocket in a protein structure.

Attributes

block_content class-attribute instance-attribute

block_content: str = ''

block_type class-attribute instance-attribute

block_type: str = ''

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
)

structure class-attribute instance-attribute

structure: Optional[ndarray] = None

Functions

from_block classmethod

from_block(
    block_content: str,
    block_type: str = "pdb",
    **kwargs: Any
) -> Pocket

Create a Pocket instance from block content.

Parameters:

Name	Type	Description	Default
block_content	str	The content of the pocket structure.	required
block_type	str	The format of the block content (default: "pdb").	'pdb'
**kwargs	Any	Additional arguments to pass to the Pocket constructor.	{}

Returns:

Name	Type	Description
Pocket	Pocket	A new Pocket instance.

from_file classmethod

from_file(file_path: str, **kwargs: Any) -> Pocket

Create a Pocket instance from a file.

Parameters:

Name	Type	Description	Default
file_path	str	Path to the pocket structure file.	required
**kwargs	Any	Additional arguments to pass to the Pocket constructor.	{}

Returns:

Name	Type	Description
Pocket	Pocket	A new Pocket instance.

from_name classmethod

from_name(name: str, **kwargs: Any) -> Pocket

Create a Pocket instance by searching for a file with the given name in the pockets directory.

Parameters:

Name	Type	Description	Default
name	str	Name of the pocket to search for.	required
**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_structure classmethod

from_structure(
    structure: ndarray,
    name: Optional[str] = None,
    **kwargs: Any
) -> Pocket

Create a Pocket instance directly from a structure array.

Parameters:

Name	Type	Description	Default
structure	ndarray	The structure array.	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.

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

Generates and ensures the existence of a directory for pockets.

Returns:

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

load_structure

load_structure(structure_file_path: str | Path) -> None

Load a PDB structure from a file path into the structure attribute.

Parameters:

Name	Type	Description	Default
structure_file_path	str | Path	Path to the PDB file.	required

load_structure_from_block

load_structure_from_block(
    block_content: str, block_type: str
)

Load a pocket structure from block content.

Parameters: - block_content (str): String containing the pocket data. - block_type (str): Format of the block content ('pdb').

Returns: - AtomArray: Loaded structure.

Raises: - ValueError: If the block type is unsupported.

pocket_props

pocket_props()

get the properties of the pocket

show

show()

show the pocket in a jupyter notebook

update_coordinates

update_coordinates(coords: ndarray)

update coordinates of the pocket structure

write_to_file

write_to_file(output_path: str, output_format: str = 'pdb')

Write the current state of the structure to a PDB file.

Parameters: - file_path (str): Path where the pocket structure will be written.