Hi,
I've found this (http://code.google.com/p/rdkit/wiki/Generating3DCoordinates)
wiki page suggesting how to compute 3D coordinates:
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('c1ccccc1C(=O)O')
AllChem.EmbedMolecule(m)
# the molecule now has a crude conformation, clean it up:
AllChem.UFFOptimizeMolecule(m)
On the other hand, "Getting started document" describes this differently:
AllChem.EmbedMolecule(m2)AllChem.UFFOptimizeMolecule(m2)
In the meantime, someone suggested that I should call:
Chem.AddHs(m)
Before calculating 3D properties.
So what is an ultimate way of doing this? Lets assume I already have
rdkit molecule:
m = Chem.MolFromSmiles('Cc1ccccc1')
or:
m = Chem.MolFromMolFile('data/input.mol')
what should I do with 'm' to compute 3D coordinates?
Also, once we have MMFF implemented in rdkit, is there any benefit of
using UFF (apart from maybe backwards compatibility, as this is a new
feature)?
Is UFF significantly faster then MMFF?
Kind regards,
Michał Nowotka
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