molviewer package
Submodules
molviewer.molecules module
Molviewer Molecule classes.
A molecule is either a Macromolecule with information retrieved from the www.rcsb.org database, or a ChemicalMolecule with information retrieved from the www.ebi.ac.uk/chembl database.
- class molviewer.molecules.ChemicalMolecule(chemblid)
Bases:
MoleculeA small chemical molecule from the ChemBL database (searchable at www.ebi.ac.uk/chembl)
- chemblid: str
- conformer: Mol
- mol_data: QuerySet
- save(file_path)
Save the ChemicalMolecule 3D structure using the .sdf file format.
- Parameters
file_path (
Union[str,Path]) – The path to be used when saving the file.- Raise
FileNotFoundError or OSError if the specified file path does not exist
- Return type
Path- Returns
The path to the saved file.
- class molviewer.molecules.Macromolecule(pdbid)
Bases:
MoleculeA macromolecule obtained from the WorldWide Protein Data Bank ( searchable at www.rcsb.org).
- PDB_FILE_URL: ClassVar[str] = 'https://files.rcsb.org/download/'
- pdbid: str
- save(file_path)
Save the Macromolecule using the .pdb file format.
- Parameters
file_path (
Union[str,Path]) – The path to be used when saving the file.- Return type
Path- Returns
The path to the saved file
- Raise
FileNotFoundError or OSError if the specified file path does not exist.
- class molviewer.molecules.Molecule
Bases:
objectThe base class for molecules.
- show(existing_viewer=None)
Display the molecule’s 3D structure inside a nglview.NGLWidget viewer in a Jupyter notebook. If no viewer currently exists, a new one is created and the 3D molecular structure is displayed. If a viewer does currently exist then the 3D molecule structure is added to the existing viewer.
- Parameters
existing_viewer (
Optional[NGLWidget]) – a 3D molecule model viewer, defaults to None.- Return type
NGLWidget- Returns
An nglview.NGLWidget viewer.
- structure: Optional[Structure] = None