View#

Visualizing a molecular system.

Molecular visualization engines allow us to inspect and interact with molecular systems directly in Jupyter notebooks. MolSysMT provides the function molsysmt.basic.view() with MolSysViewer as the default interactive 3D visualization engine, while also supporting third-party viewers such as NGLView.

Hint

Visit the section Viewers for an overview of supported visualization backends.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.basic.view().

Basic usage#

Let’s explore how molsysmt.basic.view() visualizes a molecular system (181L) using MolSysViewer as the default visualization engine:

import molsysmt as msm

msm.view('181L')

Tip

All methods defined in the molsysmt.basic module can also be invoked from the main level of the library. Hence, molsysmt.view() is the same function as molsysmt.basic.view().

As with many other MolSysMT functions, molsysmt.basic.view() operates on any supported molecular system form and accepts arguments such as selection or structure_indices:

msm.view('181L', selection='molecule_name=="BENZENE"')

Let’s now see another example using a different molecular system form, and applying a spatial selection constraint:

molsys = msm.convert('181L', selection='molecule_type=="protein" or molecule_name=="BENZENE"', to_form='openmm.Modeller')

msm.view(molsys, selection='all within 7.0 angstroms of molecule_type=="small molecule"')

Working with NGLView#

In addition to MolSysViewer, MolSysMT also supports NGLView as a third-party visualization backend. Specifying viewer='NGLView' returns an nglview.NGLWidget object, which is recognized by MolSysMT as a valid molecular system form:

view = msm.view('181L', viewer='NGLView')

To display the interactive NGLView widget in the notebook, evaluate the view object:

view

As such, nglview.NGLWidget is recognized as a valid form in MolSysMT and can be passed directly to any function that operates on molecular systems:

msm.get_form(view)

'nglview.NGLWidget'

msm.info(view)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_ions	n_small_molecules	n_proteins	n_structures
nglview.NGLWidget	1441	302	141	6	141	5	136	2	2	1	1

msm.get(view, box=True)

Magnitude	[[[6.089999999999999 0.0 0.0] [-3.044999999999998 5.274094709047231 0.0] [5.939536975864663e-16 1.0287579815631596e-15 9.7]]]
Units	nanometer

msm.get_form(msm.convert(view, to_form='openmm.Modeller'))

'openmm.Modeller'

msm.structure.get_distances(view, selection='atom_index==0', selection_2='atom_index==20')

Magnitude	[[[0.9586227516599015]]]
Units	nanometer

Tip

There are more examples on how MolSysMT works with nglview.NGLWidget objects in the third-party NGLView guide.