Protein API

docksuitex.protein.Protein

Protein structure preparation for molecular docking.

This module provides automated protein preparation using PDBFixer for fixing structures and AutoDockTools (MGLTools) for PDBQT generation.

The preparation workflow

1. Optionally fixing missing residues/atoms and nonstandard residues (using PDBFixer).
2. Optionally removing heterogens (using PDBFixer) and removing water molecules (using AutoDockTools).
3. Optionally adding pH-aware hydrogens (using PDBFixer) and Gasteiger charges (using AutoDockTools).
4. Removing non-polar hydrogens and converting to PDBQT format (using AutoDockTools).

Supported Input Formats

PDB (Single Model only).

Note

If you have files in other formats (CIF, MOL2, etc.) or multi-model files (NMR ensembles), use the Format Converter utility to prepare a single-model PDB file before using this module.

Intermediate files (fixed PDB) are saved in an intermediate_proteins/ subfolder within the output directory.

__init__

__init__(
    input: Union[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 a Protein object with a given file path and preparation parameters.

Parameters:

Name	Type	Description	Default
input	str | Path	Path to the single-model PDB file.	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 at the specified pH. Defaults to True.	True
ph	float	Custom pH for adding missing hydrogens. Defaults to 7.4.	7.4
add_charges	bool	Assign Gasteiger charges. Defaults to True.	True
preserve_charge_types	list[str]	Atom types (e.g.,["Zn", "Fe"]) whose charges are preserved; others get Gasteiger charges; ignored if add_charges=False. Defaults to None.	None

Raises:

Type	Description
FileNotFoundError	If the provided file does not exist.
ValueError	If the file extension is not a supported format.

prepare

prepare(save_to: Union[str, Path] = '.') -> Path

Handle protein preparation for docking using PDBFixer, Open Babel, and AutoDockTools (ADT).

Saves the prepared PDBQT file to the specified location.

Parameters:

Name	Type	Description	Default
save_to	str | Path	Destination path for the PDBQT file. - If a directory: file will be saved with original name. - If a file path: saved with the given name. Defaults to current directory.	'.'

Returns:

Name	Type	Description
Path	Path	Path to the saved PDBQT file.

Raises:

Type	Description
RuntimeError	If Open Babel or AutoDockTools commands fail.

view_molecule

view_molecule() -> nv.NGLWidget

Visualize the protein structure in a Jupyter notebook.

Uses NGLView to render either the prepared PDBQT file or the original input file in an interactive 3D viewer.

Returns:

Type	Description
NGLWidget	nglview.NGLWidget: Interactive 3D molecular viewer widget.

Raises:

Type	Description
FileNotFoundError	If neither prepared nor input file exists.
ImportError	If nglview is not installed.

Note

This method requires a Jupyter Notebook/Lab environment and the nglview package.