View#

Showing a molecular system

Molecular visualization libraries such as NGLView allow us to visualize and interact with molecular systems directly in Jupyter notebooks. MolSysMT provides the function molsysmt.basic.view() to simplify this integration in your workflow.

Tip

Visit the section User guide > Introduction > Viewers to know about the supported viewers by this function.

Added in version 1.0.0.

How this function works#

API documentation

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

Let’s explore how molsysmt.basic.view() can be used to visualize a complete system and apply different rendering options:

import molsysmt as msm

msm.view('181L', standard=True, with_water_as='licorice', viewer='NGLView')

Tip

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

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

msm.view('181L', selection='molecule_name=="BENZENE"', standard=True, viewer='NGLView')

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

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

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

Working with NGLView#

At this moment MolSysMT works only with a single molecular visualization library: NGLView. In fact, an nglview.NGLWidget python object is recognized by MolSysMT as the form of a molecular system.

view = msm.view('181L')

msm.get_form(view)

'nglview.NGLWidget'

As such, nglview.NGLWidget is recognized as a valid form in MolSysMT, and can be passed to any function that operates on molecular systems. Let’s see some examples:

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	1	141	5	136	2	2	1	1

msm.get(view, box=True)

Magnitude	[[[6.089999999999999 0.0 0.0] [-3.0449999999999995 5.274094699999999 0.0] [0.0 0.0 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	[[[0.9586227516599012]]]
Units	nanometer

Tip

There are more examples on how MolSysMT can work with nglview.NGLWidget objects in the section User guide > Showcase > Working with NGLView.

Additionally, MolSysMT includes a module with auxiliary functions to work with NGLView in the section User guide > Tools > Thirds > NGLView.