BioSimSpace.Align.viewMapping

BioSimSpace.Align.viewMapping(molecule0, molecule1, mapping=None, property_map0={}, property_map1={}, style=None, orientation='horizontal', pixels=900)

Visualise the mapping between molecule0 and molecule1. This draws a 3D depiction of both molecules with the mapped atoms highlighted in green. Labels specify the indices of the atoms, along with the indices of the atoms to which they map in the other molecule.

Parameters

  • molecule0 (Molecule) – The first molecule.

  • molecule1 (Molecule) – The second molecule.

  • mapping (dict) – A dictionary mapping atoms in molecule0 to those in molecule1.

  • property_map0 (dict) – A dictionary that maps “properties” in molecule0 to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

  • property_map1 (dict) – A dictionary that maps “properties” in molecule1 to their user defined values.

  • style (dict) – Drawing style. See https://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html for some examples.

  • orientation (str) – Whether to display the two molecules in a “horizontal” or “vertical” arrangement.

  • pixels (int) – The size of the largest view dimension in pixel, i.e. either the “horizontal” or “vertical” size.

Returns

view – A view of the two molecules with the mapped atoms highlighted and labelled.

Return type

py3Dmol.view