gufe.visualization.mapping_visualization

Functions

draw_mapping(mol1_to_mol2, mol1, mol2[, d2d])

Method to visualise the atom map correspondence between two rdkit molecules given an input mapping.

draw_one_molecule_mapping(mol1_to_mol2, ...)

Draw the mapping visualization for a single molecular of a mapping

draw_unhighlighted_molecule(mol[, d2d])

Draw a molecule without any mapping information.
gufe.visualization.mapping_visualization.draw_mapping(mol1_to_mol2: dict[int, int], mol1: rdkit.Chem.Mol, mol2: rdkit.Chem.Mol, d2d=None)

Method to visualise the atom map correspondence between two rdkit molecules given an input mapping.

Legend:

  • Red highlighted atoms: unique atoms, i.e. atoms which are not mapped.

  • Blue highlighted atoms: element changes, i.e. atoms which are mapped but change elements.

  • Red highlighted bonds: any bond which involves at least one unique atom or one element change.

Parameters:

  • mol1_to_mol2 (dict of int:int) – Atom mapping between input molecules.

  • mol1 (RDKit.Mol) – RDKit representation of molecule 1

  • mol2 (RDKit.Mol) – RDKit representation of molecule 2

  • d2d (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D) – Optional MolDraw2D backend to use for visualisation.

gufe.visualization.mapping_visualization.draw_one_molecule_mapping(mol1_to_mol2, mol1, mol2, d2d=None)

Draw the mapping visualization for a single molecular of a mapping

This will always draw molA. To draw molB, switch order/invert molA_to_molB mapping.

See draw_mapping() for details on the meaning of different colors.

Parameters:

  • mol1_to_mol2 (dict of int:int) – Atom mapping between input molecules.

  • mol1 (RDKit.Mol) – RDKit representation of molecule 1

  • mol2 (RDKit.Mol) – RDKit representation of molecule 2

  • d2d (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D) – Optional MolDraw2D backend to use for visualisation.

gufe.visualization.mapping_visualization.draw_unhighlighted_molecule(mol, d2d=None)

Draw a molecule without any mapping information.

This uses the same mechanisms as the mapping visualizations, and so can be useful in cases where you want the same visual style both for a plain molecule and a molecule with the mapping highlighted.

Parameters: