rdkit.ipynb

Kernel: Python 3 (Anaconda 5)

RDKit in Anaconda 5 Python 3

https://www.rdkit.org/docs/GettingStartedInPython.html

import rdkit
rdkit

<module 'rdkit' from '/ext/anaconda5/lib/python3.6/site-packages/rdkit/__init__.py'>

rdkit.__version__

'2019.03.1'

from rdkit import Chem

m2 = Chem.MolFromSmiles('Clc(c(Cl)c(Cl)c1C(=O)O)c(Cl)c1Cl')
print(Chem.MolToMolBlock(m2))

     RDKit          2D

 14 14  0  0  0  0  0  0  0  0999 V2000
    3.0000    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5000   -2.5981    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000   -2.5981    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500   -1.2990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    1.2990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5000    2.5981    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    2.5981    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 13  7  1  0
M  END