[Rdkit-discuss] An ultimate way to compute 3D coordinates?

[Michał N. <mm...@gm...>]

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