Add contacts#

Adding contact distance cylinders and representations to NGLView widgets.

The function molsysmt.third_party.nglview.add_contacts() identifies and draws 3D cylinders between interacting atom pairs that satisfy a spatial distance threshold.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects: molsysmt.third_party.nglview.add_contacts().

Basic usage#

Let’s demonstrate how to use this function on an interactive NGLView view:

import molsysmt as msm

molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'], to_form='molsysmt.MolSys')
view = msm.convert(molsys, to_form='nglview.NGLWidget')
msm.third_party.nglview.add_contacts(view, atom_pairs=[[10, 50], [20, 80], [30, 100]], color='#3498DB', radius='0.3 angstroms')

Evaluating the view object displays the interactive visualization:

view