To import chemview you can write and execute the following code in a cell:
In [ ]:
from chemview import MolecularViewer
To display a benzene molecule we need at least two pieces of information:
For the scope of this tutorial, the information were extracted from here. You can use a chemical package (like mdtraj or chemlab) to read the coordinates of your molecules.
We define the coordinates as a numpy array, the atomic types as a list of strings and the bonds as a list of start, end tuples.
In [ ]:
import numpy as np
coordinates = np.array([[0.00, 0.13, 0.00], [0.12, 0.07, 0.00], [0.12,-0.07, 0.00],
[0.00,-0.14, 0.00], [-0.12,-0.07, 0.00],[-0.12, 0.07, 0.00],
[ 0.00, 0.24, 0.00], [ 0.21, 0.12, 0.00], [ 0.21,-0.12, 0.00],
[ 0.00,-0.24, 0.00], [-0.21,-0.12, 0.00],[-0.21, 0.12, 0.00]])
atomic_types = ['C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H']
bonds = [(0, 6), (1, 7), (2, 8), (3, 9), (4, 10), (5, 11),
(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 0)]
We can pass those to the class MolecularViewer and call the method lines to render the molecule as a wireframe:
In [ ]:
mv = MolecularViewer(coordinates, topology={'atom_types': atomic_types,
'bonds': bonds})
mv.ball_and_sticks()
mv
You can rotate (left click), pan(right click) and zoom (wheel) to visualize your molecules.