`deeporigin.drug_discovery.Complex`¶

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

Attributes¶

ligands `class-attribute` `instance-attribute` ¶

ligands: LigandSet = field(default_factory=LigandSet)

protein `instance-attribute` ¶

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,
    use_cache: 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`

deeporigin.drug_discovery.Complex¶