API Documentation for Drawer

class mdonatello.drawer.FunctionalGroupHighlighter(molecule: Mol, checkboxes: Dict[str, Checkbox])

Bases: object

A class responsible for highlighting of the functional groups in a molecule.

Parameters:

moleculeRDKit.Chem.Mol

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

checkboxesdict

A dictionary of checkbox widgets indicating which functional groups to highlight. Keys are functional group names (e.g., “Alcohol”), and values are the corresponding checkbox widgets.

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 highlight colors.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determine the atom and bond indices to highlight based on the selected functional groups.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

class mdonatello.drawer.MoleculeDrawer(molecule: Mol, pharmacophore_checkboxes: Dict[str, Checkbox], functional_groups_checkboxes: Dict[str, Checkbox], rotatable_bonds_checkbox: Checkbox, partial_charges_checkbox: Checkbox, partial_charges_heatmap_checkbox: Checkbox, stereocenters_checkbox: Checkbox, murcko_scaffold_checkbox: Checkbox, factory: MolChemicalFeatureFactory)

Bases: object

A class for drawing a molecule with various highlighted features.

Parameters:

moleculeRDKit.Chem.Mol

An RDKit molecule object representing the molecule to be drawn.

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.

functional_groups_checkboxesdict

A dictionary of checkbox widgets indicating which functional groups to highlight. Keys are functional group names (e.g., “Alcohol”), and values are the corresponding checkbox widgets.

rotatable_bonds_checkboxCheckbox

A checkbox widget indicating whether to highlight rotatable bonds of the molecule.

partial_charges_checkboxCheckbox

A checkbox widget indicating whether to display partial charges of the molecule.

partial_charges_heatmap_checkboxCheckbox

A checkbox widget indicating whether to use a heatmap for partial charges of the molecule.

stereocenters_checkboxCheckbox

A checkbox widget indicating whether to highlight the stereocenters of the molecule.

murcko_scaffold_checkboxCheckbox

A checkbox widget indicating whether to highlight the Murcko scaffold of the molecule.

factoryChemicalFeatures.MolChemicalFeatureFactory

A factory object used to generate pharmacophore features for the molecule.

Returns:

svgstr

An SVG string representing the drawn molecule with highlighted features.

draw_molecule(show_atom_indices: bool, width: int, height: int) → str

Draws the molecule with the highlighted features.

Parameters:

show_atom_indicesbool

Whether to show atom indices on the drawn molecule.

widthint

Width of the drawing canvas.

heightint

Height of the drawing canvas.

Returns:

svgstr

An SVG string representing the drawn molecule with highlighted features.

class mdonatello.drawer.MurckoScaffoldHighlighter(molecule: Mol, checkbox: Dict[str, Checkbox])

Bases: object

A class responsible for highlighting of the Murcko scaffold in a molecule.

Parameters:

moleculeRDKit.Chem.rdchem.Mol

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

checkboxCheckbox

A checkbox widget indicating whether to highlight the Murcko scaffold of the 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 highlight colors.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determines the atom and bond indices to highlight them based on the presence of Murcko scaffolds.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

class mdonatello.drawer.PartialChargeHighlighter(molecule: Mol, checkbox: Dict[str, Checkbox])

Bases: object

A class responsible for highlighting of partial charges in a molecule.

Parameters:

moleculeRDKit.Chem.rdchem.Mol

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

checkboxCheckbox

A checkbox widget indicating whether to highlight the partial charges of the 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 highlight colors.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determines the atom and bond indices to highlight them based on the partial charges.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

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

Bases: object

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.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determines the atom and bond indices to highlight them based on the selected pharmacophore features.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

class mdonatello.drawer.RotatableBondsHighlighter(molecule: Mol, checkbox: Dict[str, Checkbox])

Bases: object

A class responsible for highlighting of rotatable bonds in a molecule.

Parameters:

moleculeRDKit.Chem.rdchem.Mol

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

checkboxCheckbox

A checkbox widget indicating whether to highlight rotatable bonds.

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 highlight colors.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determines the atom and bond indices to highlight them based on the presence of rotatable bonds.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

class mdonatello.drawer.StereocenterHighlighter(molecule: Mol, checkbox: Dict[str, Checkbox])

Bases: object

A class responsible for highlighting of stereocenters in a molecule.

Parameters:

moleculeRDKit.Chem.rdchem.Mol

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

checkboxCheckbox

A checkbox widget indicating whether to highlight the stereocenters of the 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 highlight colors.

determine_highlights() → Tuple[Dict[str, List[int]], Dict[int, str]]

Determine the atom and bond indices to highlight based on their stereocenter configuration.

Returns:

highlightsdict

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

highlight_colorsdict

A dictionary mapping atom indices and bond indices to their respective highlight colors.

PharmacophoreHighlighter(molecule, ...)	A class responsible for highlighting of pharmacophore features in a molecule.
FunctionalGroupHighlighter(molecule, checkboxes)	A class responsible for highlighting of the functional groups in a molecule.
RotatableBondsHighlighter(molecule, checkbox)	A class responsible for highlighting of rotatable bonds in a molecule.
PartialChargeHighlighter(molecule, checkbox)	A class responsible for highlighting of partial charges in a molecule.
StereocenterHighlighter(molecule, checkbox)	A class responsible for highlighting of stereocenters in a molecule.
MurckoScaffoldHighlighter(molecule, checkbox)	A class responsible for highlighting of the Murcko scaffold in a molecule.
MoleculeDrawer(molecule, ...)	A class for drawing a molecule with various highlighted features.