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

[Michal K. <mic...@gm...>]

Michal: from my experience, MMFF in rdkit is slower than UFF (ca. 2x
for my test cases) but converges faster, so in certain cases the
overall execution time (embedding+optimization) won't be much shorter
for UFF. It really depends on what molecules you work on. AFAIK
rdkit's 3d coord generation algorithm was designed for small- to
medium-sized "druglike" molecules, so you may expect it to fail in
areas very far from this territory. For example, it does not work well
for long conjugated oligomers - sometimes it produces molecular knots
instead of straight strands, and is quite slow for large systems.
That's why I switched to CORINA, btw.
Best wishes,
Michal Krompiec


On 5 April 2014 18:05, JP <jea...@in...> wrote:
> 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 <mm...@gm...> 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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