Drawing molecules in iPython Notebook



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from __future__ import print_function
import oddt



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print(oddt.__version__)









    



0.4.1-15-gf7f6653

1. Download molecule from PDBbind



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%%bash
wget -q -N www.pdbbind.org.cn/v2007/10gs/10gs_ligand.mol2

2. Variables controling images

There are two main variables for controling the drawing, namely image_size and image_backend located in a oddt.toolkit namespace. There are two backends available PNG (default) and SVG.



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print('Default size: ', oddt.toolkit.image_size)
print('Default backend: ', oddt.toolkit.image_backend)









    



Default size:  (200, 200)
Default backend:  png

3. OpenBabel Drawing

OpenBabel is the default toolkit, although just for assurance will asign is as the toolkit of choice.



In [5]:

    
oddt.toolkit = oddt.toolkits.ob
mol = next(oddt.toolkit.readfile('mol2', '10gs_ligand.mol2'))
mol.removeh()

3.1 OB PNG (default)



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mol









    Out[6]:

3.2 OB SVG



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oddt.toolkit.image_backend = 'svg'
mol









    Out[7]:

4. RDKit molecules are drawn in the same way



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oddt.toolkit = oddt.toolkits.rdk
mol = next(oddt.toolkit.readfile('mol2', '10gs_ligand.mol2'))
mol.removeh()

4.1 RDKit PNG



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oddt.toolkit.image_backend = 'png'
mol









    Out[9]:

4.2 RDKit SVG



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oddt.toolkit.image_backend = 'svg'
mol









    Out[10]:



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5. Changing a size of a molecule

A size can be arbitrally set to an int or two element tuple/list. It is a global setting appplied in all subsequent images.



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oddt.toolkit.image_backend = 'png'
oddt.toolkit.image_size = 100



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mol









    Out[12]:



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oddt.toolkit.image_size = (600, 400)



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mol









    Out[14]:



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