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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)

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,
    *,
    _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: Optional[Ligand] = None,
    *,
    padding: float = 1.0,
    keep_waters: bool = False,
    is_lig_protonated: bool = True,
    is_protein_protonated: bool = True,
    use_cache: bool = True,
    show_prepared_system: 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.

 None
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