deeporigin.drug_discovery.complex

Module to support Drug Discovery workflows using Deep Origin

Classes

Complex dataclass

class to represent a set of a protein and 1 or many ligands

Attributes

ligands property writable

ligands: list[Ligand]

Get the current ligands

protein instance-attribute

protein: Protein = protein

Functions

from_dir classmethod

from_dir(
    directory: str,
    *,
    _platform_clients: Optional[PlatformClients] = None
) -> Complex

Initialize a Complex from a directory containing protein and ligand files.

Parameters:

Name	Type	Description	Default
directory	str	Directory containing ligand and protein files.	required

The directory should contain: - Exactly one PDB file for the protein - One or more SDF files for the ligands. Each SDF file can contain one or more molecules.

Returns:

Name	Type	Description
Complex	Complex	A new Complex instance initialized from the files in the directory.

Raises:

Type	Description
ValueError	If no PDB file is found or if multiple PDB files are found.

prepare

prepare(
    ligand: Ligand,
    *,
    padding: float = 1.0,
    keep_waters: bool = False,
    is_lig_protonated: bool = True,
    is_protein_protonated: bool = True
) -> None

run system preparation on the protein and one ligand from the Complex

Parameters:

Name	Type	Description	Default
ligand	Ligand	The ligand to prepare.	required
padding	float	Padding to add around the system. Defaults to 1.0.	1.0
keep_waters	bool	Whether to keep water molecules. Defaults to False.	False
is_lig_protonated	bool	Whether the ligand is already protonated. Defaults to True.	True
is_protein_protonated	bool	Whether the protein is already protonated. Defaults to True.	True

show_ligands

show_ligands(
    *, view: str = "2d", limit: Optional[int] = None
)

Display ligands in the complex object.

Parameters:

Name	Type	Description	Default
view	str	Visualization type, either "2d" (default) or "3d". - "2d": Shows ligands in a table with 2D structure renderings - "3d": Shows 3D molecular structures using SDF files	'2d'
limit	Optional[int]	Optional; maximum number of ligands to display. If None, all ligands will be shown.	None