rdtools.view.conf#

Module for viewing conformers of RDKit molecules.

rdtools.view.conf.conformer_animation(mol: Mol, conf_ids: list[int] | None = None, **kwargs: Any) → view#

Create an animation viewer for viewing the RDKit Molecules.

This viewer accepts additional keyword arguments for viewer specs, following the same way base_viewer is implemented.

Parameters:

  • mol (Chem.Mol) – An RDKitMol object with embedded conformers.

  • conf_ids (Optional[list[int]]) – A list of IDs of the conformers to view. If None (default), all conformers will be shown.

  • **kwargs (Any) – Additional keyword arguments to be passed to the viewer.

Returns:

py3Dmol.view – The viewer.

rdtools.view.conf.conformer_viewer(mol: Mol, conf_ids: list[int] | None = None, highlight_ids: list[int] | None = None, conf_opacity: float = 0.5, **kwargs: Any) → view#

Create a viewer for viewing multiple overlaid conformers.

This viewer accepts additional keyword arguments following the same way base_viewer is implemented. It is recommended aligning the conformers before viewing the structures for a better visualization.

Parameters:

  • mol (Chem.Mol) – An Mol object with embedded conformers.

  • conf_ids (Optional[list[int]], optional) – A list of conformer ids (as int) to be overlaid and viewed. If not provided, all embedded conformers will be used.

  • highlight_ids (Optional[list[int]], optional) – It is possible to highlight some of the conformers while greying out other conformers by providing the conformer IDs you want to highlight. Default to None.

  • conf_opacity (float, optional) – Set the opacity of the non-highlighted conformers and is only used with the highlighting feature. the value should be a float between 0.0 to 1.0. The default value is 0.5. Values below 0.3 may be hard to see.

  • **kwargs (Any) – Additional keyword arguments to be passed to the viewer.

Returns:

py3Dmol.view – The conformer viewer.