Contents

Chemistry — Visualising Chemical Structures

Various tools exist for visualising various chemical structures using static images as well as interactive 3d representations.

2D visualisations

A wide range of packages are available for depicting two dimensional representations of chemical structures defined in conventional ways.

For example ?SMILES

rdkit

The rdkit package, an open source toolkit for cheminformatics, provides a wide range of tools for working with chemical representations.

#%pip install rdkit-pypi
#import rdkit

from rdkit import Chem

m = Chem.MolFromSmiles("C1=NC2=C(N1)C(=NC=N2)N")
m
../_images/visualising-compounds_4_0.png 
m = Chem.AddHs(m)
m
../_images/visualising-compounds_5_0.png 
from rdkit.Chem import Draw

def smilesH(m):
    return Chem.AddHs(Chem.MolFromSmiles(m))

bromomethane = smilesH('CBr')
bromoethane = smilesH('CCBr')
_2_bromopropane =  smilesH('CC(Br)C')
_2_bromo_2_methylpropane = smilesH('CC(Br)(C)C')

my_molecules = [bromomethane, 
                bromoethane,
                _2_bromopropane,
                _2_bromo_2_methylpropane,
               ]

Draw.MolsToGridImage(my_molecules, useSVG=True)
../_images/visualising-compounds_6_0.svg
from rdkit.Chem import RemoveHs

RemoveHs(_2_bromo_2_methylpropane)
../_images/visualising-compounds_7_0.png 
#Highlight a substructure
m.GetSubstructMatch(Chem.MolFromSmiles('C(N)'))
m
../_images/visualising-compounds_8_0.png 
#Following is needed to render molecule structure views in Jupyter notebook
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdChemReactions

IPythonConsole.ipython_useSVG=True  

rdChemReactions.ReactionFromSmarts("C=CCBr>>C=CCI");

openbabel and pybel

openbabel, an open source chemistry toolbox, provides a wide range of tools for searching for and converting between various chemistry related representations.

A key part of the openbabel Python API is the pybel package which supports chemical structure parsing, format conversion, and display.

from openbabel import pybel

mol = pybel.readstring( "smi","C1=NC2=C(N1)C(=NC=N2)N" )

#Add hydrogens
mol.addh()

#By default, we preview a small SVG output graphic
mol
../_images/visualising-compounds_12_0.svg
#  Better preview
from IPython.display import SVG

SVG(mol.write("svg"))
../_images/visualising-compounds_13_0.svg
mol.write("smi")

'c1nc2c([nH]1)c(ncn2)N\t\n'

from IPython.display import display

def smilesSVG(smi, addH=False, bw=False):
    ''' Render molecule structure from SMILES string as SVG. '''
    
    mol = pybel.readstring( "smi",smi )
    if addH: mol.addh()
    conv = pybel.ob.OBConversion()
    conv.SetOutFormat("svg")
    #Optonally, set black and white output
    #The openbabel SVG export formatter has an -xu option which we can pass
    #Via: https://github.com/openbabel/openbabel/issues/1879#issuecomment-411830813
    if bw:
        conv.SetOptions('u', conv.OUTOPTIONS)
    display(SVG(conv.WriteString(mol.OBMol)))
    #display(SVG(mol.write("svg")))

smilesSVG( "C1=NC2=C(N1)C(=NC=N2)N" )
../_images/visualising-compounds_16_0.svg
smilesSVG( "C1=NC2=C(N1)C(=NC=N2)N", addH= True )
../_images/visualising-compounds_17_0.svg
smilesSVG( "C1=NC2=C(N1)C(=NC=N2)N", addH=False, bw=True );
../_images/visualising-compounds_18_0.svg

3D visualisations — py3dmol demo

We can embed interactive 3D widget visualisations of molecules into a page using the py3dmol widget:

import py3Dmol

# Lookup a molecule using its CID (PubChem Compound Identification) code
p=py3Dmol.view(query='cid:702')

# Set the render style
p.setStyle({'stick': {'radius': .1}, 'sphere': {'scale': 0.25}})
p.show()

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Various lookup codes: https://pubchem.ncbi.nlm.nih.gov/search/help_search.html

SMILES/SMARTS Input SMILES – Simplified Molecular Input Line Entry System,

Protein Data Bank (PDB)

p = py3Dmol.view(query='pdb:1ycr')
p.setStyle({'stick': {'radius': .1}, 'sphere': {'scale': 0.25}})

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

<py3Dmol.view at 0x11b734790>

p.setStyle({'cartoon':{'color':'spectrum'}});

nglview

import nglview as nv

view = nv.show_structure_file(nv.datafiles.PDB)
view

# Useful to pop out in Jupyter notebook context?
view.clear_representations()
view.add_licorice('not hydrogen', color='blue')

view.clear_representations()
view.add_cartoon()
view.add_surface(opacity=0.3)

# Force render here but the original is also updated?
view.render_image()

view.download_image("test.png")

# Downloads to download dir
# To specify a download path requires a workaround of working in a separate thread:
# https://github.com/nglviewer/nglview/blob/master/docs/FAQ.md#how-to-make-nglview-view-object-write-png-file
#from IPython.display import Image
#Image(PATH_TO_IMAGE)