BatchProtein API

docksuitex.batch_docking.batch_protein.BatchProtein

Handles batch protein preparation with parallel processing.

__init__

__init__(
    inputs: Union[List[Union[str, Path]], str, Path],
    fix_pdb: bool = True,
    remove_heterogens: bool = True,
    remove_water: bool = True,
    add_hydrogens: bool = True,
    ph: float = 7.4,
    add_charges: bool = True,
    preserve_charge_types: Optional[list[str]] = None,
)

Initialize the batch processor and preparation parameters.

Parameters:

Name	Type	Description	Default
inputs	Union[List[Union[str, Path]], str, Path]	List or directory of single-model PDB files.	required
fix_pdb	bool	Fix missing residues/atoms. Defaults to True.	True
remove_heterogens	bool	Remove ligands/heterogens. Defaults to True.	True
remove_water	bool	Remove water molecules. Defaults to True.	True
add_hydrogens	bool	Add hydrogens using PDBFixer. Defaults to True.	True
ph	float	Custom pH for adding missing hydrogens via PDBFixer. Defaults to 7.4.	7.4
add_charges	bool	Assign Gasteiger charges. Defaults to True.	True
preserve_charge_types	Optional[list[str]]	Atom types to preserve charges for. Defaults to None.	None

prepare_all

prepare_all(
    save_to: Union[str, Path],
    cpu: int = (os.cpu_count() or 2) - 1,
) -> List[Dict[str, Union[str, Path, bool]]]

Prepare all proteins in batch and save PDBQT files to the specified folder.

Parameters:

Name	Type	Description	Default
save_to	str | Path	Directory to save all prepared PDBQT files.	required
cpu	int	Total number of CPU cores to use. Defaults to os.cpu_count() - 1. Each worker uses 1 CPU.	(cpu_count() or 2) - 1

Returns:

Type	Description
List[Dict[str, Union[str, Path, bool]]]	list[dict]: Result dictionary for each protein file.