New function of rdkit

To design new small molecule, we often consider about shape of molecule.
Molecular conformation analysis is difficult but important task.
Because small molecule is too flexible.
Gregory. A. Landrum( developer of rdkit ) reported new function of conformation generation in J. Chem. Inf. Model.

The author developed two functions called Experimental Torsion Distance Geometry (ETDG) and Experimental Torsion Distance Geometry(with Knowledge) ETKDG .
Experimental means, the algorithm generate torsion angle distribution using Cambridge Structural Database (CSD).
And “Knowledge” means i.e. flat aromatic rings and liner triple bond is preferred.
It feels good, because I often use rdkit conformation generator (EmbedMolecule etc.) and the generator make skewed molecules.

And it’s worth to remember that if user want to use the function, it can only add the optional parameters.

from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles( "C1(=C(C=CC(=C1[C@H](OC2=C(N=CC(=C2)C3=C[N](N=C3)C4CCNCC4)N)C)Cl)F)Cl" )
hmol = Chem.AddHs( mol )
#gen 3d set option to use ETKDG
AllChem.EmbedMolecule( mol, useExpTorsionAnglePrefs=True , useBasicKnowledge=True )

Reference discussed more details of the function.
Nice stuff. ;-)

Today is an anniversary.

I got account of wordpress today’s 4 year ago.



Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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