deeporigin.drug_discovery.Complex

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

Attributes

abfe instance-attribute

abfe = ABFE(parent=self)

client class-attribute instance-attribute

client: Optional[DeepOriginClient] = client

docking instance-attribute

docking = Docking(parent=self)

ligands property writable

ligands: LigandSet

protein instance-attribute

protein: Protein = protein

rbfe instance-attribute

rbfe = RBFE(parent=self)

Functions

from_dir classmethod

from_dir(
    directory: str,
    *,
    client: Optional[DeepOriginClient] = 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: Optional[Ligand] = None,
    *,
    padding: float = 2.0,
    retain_waters: bool = False,
    add_H_atoms: bool = False,
    protonate_protein: bool = False,
    use_cache: bool = True
) -> Protein | list[Protein]

run system preparation on the protein and one or more ligands from the Complex

Parameters:

Name	Type	Description	Default
ligand	Ligand	The ligand to prepare. If None, prepares all ligands in the Complex.	None
padding	float	Padding to add around the system.	2.0
retain_waters	bool	Whether to keep water molecules.	False
add_H_atoms	bool	Whether the ligand is already protonated.	False
protonate_protein	bool	Whether to protonate the protein.	False
use_cache	bool	Whether to use the cache.	True

Returns:

Name	Type	Description
Protein	Protein | list[Protein]	If a single ligand is provided, returns the prepared Protein object.
	Protein | list[Protein]	list[Protein]: If ligand is None, returns a list of prepared Protein objects, one for each ligand.