mdonatello.drawer.PharmacophoreHighlighter

class mdonatello.drawer.PharmacophoreHighlighter(molecule: Mol, pharmacophore_checkboxes: Dict[str, Checkbox], factory: MolChemicalFeatureFactory)

A class responsible for highlighting of pharmacophore features in a molecule.

Parameters:

moleculeRDKit.Chem.Mol

An RDKit molecule object representing the molecule that should be highlighted.

pharmacophore_checkboxesdict

A dictionary of checkbox widgets indicating which pharmacophore features to highlight. Keys are pharmacophore feature names (e.g., “Aromatic”), and values are the corresponding checkbox widgets.

factoryRDKit.Chem.ChemicalFeatures.MolChemicalFeatureFactory

A factory object used to generate pharmacophore features available in RDKit for the given molecule.

Returns:

highlightsdict

A dictionary with keys “atoms” and “bonds”, each containing lists of atom indices and bond indices that should be highlighted, respectively.

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective colors that should be used for highlighting.

__init__(molecule: Mol, pharmacophore_checkboxes: Dict[str, Checkbox], factory: MolChemicalFeatureFactory)

Initialize the PharmacophoreHighlighter with a molecule, pharmacophore checkboxes, and an RDKit feature factory.

Methods

__init__(molecule, pharmacophore_checkboxes, ...)	Initialize the PharmacophoreHighlighter with a molecule, pharmacophore checkboxes, and an RDKit feature factory.
determine_highlights()	Determines the atom and bond indices to highlight them based on the selected pharmacophore features.