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deeporigin.drug_discovery.Complex

Deprecated

Complex is deprecated. For new code, use the workflow-specific APIs Docking, ABFE, RBFE, PocketFinder, and SystemPrep instead.

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 = 1.0,
    retain_waters: bool = False,
    add_H_atoms: bool = False,
    protonate_protein: bool = False,
    quote: bool = False
) -> FunctionResult

Run system preparation on the protein and one or more ligands.

Parameters:

Name Type Description Default
ligand Optional[Ligand]

The ligand to prepare. If None, prepares all ligands in the Complex.

 None
padding float

Padding to add around the system.

 1.0
retain_waters bool

Whether to keep water molecules.

 False
add_H_atoms bool

Whether to add hydrogen atoms to the ligand.

 False
protonate_protein bool

Whether to protonate the protein.

 False
quote bool

If True, request a cost estimate without executing.

 False

Returns:

Type Description
FunctionResult

FunctionResult with a prepared_systems attribute containing
FunctionResult

a list of prepared Protein objects (empty when quote=True).