Standardization

Here are some examples of how to standardize molecules.

First set our iPython notebook to display molecule images and log messages:



In [1]:

    
from rdkit.Chem.Draw import IPythonConsole
import logging
logger = logging.getLogger('molvs')
logger.setLevel(logging.INFO)









    



/Users/matt/.virtualenvs/molvs/lib/python2.7/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.
  "`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning)

Standardizing a SMILES string

The standardize_smiles function provides a quick and easy way to get the standardized version of a given SMILES string:



In [2]:

    
from molvs import standardize_smiles
standardize_smiles('C[n+]1c([N-](C))cccc1')









    



INFO:molvs.normalize:Rule applied: Recombine 1,3-separated charges






    Out[2]:





'CN=c1ccccn1C'

While this is convenient for one-off cases, it's inefficient when dealing with multiple molecules and doesn't allow any customization of the standardization process.

The Standardizer class

The Standardizer class provides flexibility to specify custom standardization stages and efficiently standardize multiple molecules.



In [3]:

    
from rdkit import Chem
import molvs
from molvs import Standardizer



In [4]:

    
mol = Chem.MolFromSmiles('[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1')
mol









    Out[4]:



In [5]:

    
s = Standardizer()
smol = s.standardize(mol)
smol









    



INFO:molvs.metal:Removed covalent bond between Na and O
INFO:molvs.normalize:Rule applied: Sulfone to S(=O)(=O)






    Out[5]:



In [6]:

    
Chem.MolToSmiles(smol)









    Out[6]:





'O=C([O-])c1ccc(C[S](=O)=O)cc1.[Na+]'

The Standardizer class takes a number of initialization parameters to customize its behaviour:



In [7]:

    
from molvs.normalize import Normalization
norms = (
    Normalization('Nitro to N+(O-)=O', '[*:1][N,P,As,Sb:2](=[O,S,Se,Te:3])=[O,S,Se,Te:4]>>[*:1][*+1:2]([*-1:3])=[*:4]'),
    Normalization('Pyridine oxide to n+O-', '[n:1]=[O:2]>>[n+:1][O-:2]'),
)

my_s = Standardizer(normalizations=norms)
smol = my_s.standardize(mol)
smol









    



INFO:molvs.metal:Removed covalent bond between Na and O






    Out[7]:

Notice that the sulfone group wasn't normalized in this case, because when initializing the Standardizer we only specified two Normalizations.

The default list of normalizations is molvs.normalize.NORMALIZATIONS.

It is possible to resuse a Standardizer instance on many molecules once it has been initialized with some parameters:



In [8]:

    
my_s.standardize(Chem.MolFromSmiles('C1=C(C=C(C(=C1)O)C(=O)[O-])[S](O)(=O)=O.[Na+]'))









    



INFO:molvs.charge:Moved proton from –SO3H to -CO2H






    Out[8]:



In [9]:

    
my_s.standardize(Chem.MolFromSmiles('[Ag]OC(=O)O[Ag]'))









    



INFO:molvs.metal:Removed covalent bond between Ag and O
INFO:molvs.metal:Removed covalent bond between Ag and O






    Out[9]:



In [ ]: