I don't know about the "ultimate way": but this works for me (to generate n
conformers):
writer = Chem.SDWriter('some_file.sdf')
# add Hydrogens
molH = Chem.AddHs(mol)
# create n conformers for molecule
confIds = AllChem.EmbedMultipleConfs(molH, n)
# E optimize
for confId in confIds:
AllChem.UFFOptimizeMolecule(molH, confId=confId)
# write to output file
writer.write(molH, confId=confId)
You should replace the EmbedMultipleConfs with EmbedMolecule if you are
only interested in generating only one conformer. UFFOptimizeMolecule(...)
returns an integer, which if 0 tells you the optimization has converged (or
1 otherwise).
UFF is significantly faster, and I do not think the results are worse of
than the ones generated for MMFF. At least for the small molecules I was
looking at, but I am sure there are exceptions to this. Paolo has done a
lot of excellent work on the forcefields, and I think the amide and
carbonyl planarity issues for UFF have now been fixed.
-
Jean-Paul Ebejer
Early Stage Researcher
On 5 April 2014 13:35, Michał Nowotka <mmm...@gmail.com> wrote:
> 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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