luna.mol.depiction module

class PharmacophoreDepiction(feature_extractor=None, colors=<luna.util.ColorPallete object>, format='png', fig_size=(800, 800), font_size=0.5, circle_dist=0.2, circle_radius=0.3, use_bw_atom_palette=True)[source]

Bases: object

Draw molecules and depict pharmacophoric properties as colored circles.

Parameters

  • feature_extractor (FeatureExtractor) – Perceive pharmacophoric properties from molecules.

  • colors (ColorPallete) – Color scheme for pharmacophoric properties perceived by feature_extractor. The default value is ATOM_TYPES_COLOR.

  • format ({‘png’, ‘svg’}) – The output file format. The default value is ‘png’.

  • figsize (tuple of (float, float)) – Width and height in inches. The default value is (800, 800).

  • font_size (float) – The font size. The units are, roughly, pixels. The default value is 0.5.

  • circle_dist (float) – Distance between circles (pharmacophoric properties). The default value is 0.2.

  • circle_radius – Circles’ radius size of pharmacophoric properties. The default value is 0.3.

  • use_bw_atom_palette (bool) – Use a black & white palette for atoms and bonds.

Examples

First, let’s read a molecule (glutamine).

>>> from luna.wrappers.base import MolWrapper
>>> mol = MolWrapper.from_smiles("N[C@@H](CCC(N)=O)C(O)=O")

Now, create a feature factory and instantiate a new FeatureExtractor object.

>>> from luna.util.default_values import ATOM_PROP_FILE
>>> from rdkit.Chem import ChemicalFeatures
>>> from luna.mol.features import FeatureExtractor
>>> feature_factory = ChemicalFeatures.BuildFeatureFactory(ATOM_PROP_FILE)
>>> feature_extractor = FeatureExtractor(feature_factory)

Instantiate a new PharmacophoreDepiction object with the desired configuration. For example, you can provide a color scheme for pharmacophoric properties, the image size, and its format.

>>> from luna.util.default_values import ATOM_TYPES_COLOR
>>> from luna.mol.depiction import PharmacophoreDepiction
pd = PharmacophoreDepiction(feature_extractor=feature_extractor, colors=ATOM_TYPES_COLOR,
                            fig_size=(500, 500), format="svg")

Finally, you can draw the molecule with annotated pharmacophoric properties.

>>> pd.plot_fig(mol, "output.svg")
plot_fig(mol_obj, output=None, atm_types=None, legend=None)[source]

Draw the molecule mol_obj and depict its pharmacophoric properties.

Parameters

  • mol_obj (MolWrapper, rdkit.Chem.rdchem.Mol, or openbabel.pybel.Molecule) – The molecule.

  • output (str) – The output file where the molecule will be drawn. If None, returns a drawing object (MolDraw2DCairo or MolDraw2DSVG).

  • atm_types (dict or None) – A pre-annotated dictionary for mapping atoms and pharmacophoric properties. If None, try to perceive properties with feature_extractor.

  • legend (str) – A title for the figure.

Returns

drawer

Return type

None or a drawing object (MolDraw2DCairo or MolDraw2DSVG)