Hi Paolo,
Thanks for helping me! Appreciate it.
Best,
Leon
On Tue, Nov 19, 2019 at 5:01 PM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Hi Leon,
>
> you are right, that's a documentation bug: The confId parameter is
> actually ignored, as you have already found out.
>
> Thanks for reporting this, cheers
> p.
>
> On 19/11/2019 20:56, topgunhaides . wrote:
>
> Hi guys,
>
> Does the "confID" argument actually work for "MMFFOptimizeMoleculeConfs"?
> Try the following code:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> mh = Chem.AddHs(Chem.MolFromSmiles('OCCCN'))
> cids = AllChem.EmbedMultipleConfs(mh, numConfs=3, maxAttempts=1000,
> pruneRmsThresh=0.5, numThreads=0,
> randomSeed=-1)
>
> # try to optimize one conformer at a time in the loop:
> for cid in cids:
> mmffopt_1 = AllChem.MMFFOptimizeMoleculeConfs(mh, confId=cid,
> maxIters=1000,
> mmffVariant='MMFF94s',
> numThreads=0)
> print(mmffopt_1)
>
> # just optimize one specific conformer (ID = 0):
> mmffopt_2 = AllChem.MMFFOptimizeMoleculeConfs(mh, confId=0, maxIters=1000,
> mmffVariant='MMFF94s',
> numThreads=0)
> print(mmffopt_2)
>
> # Or optimize all conformers:
> mmffopt_3 = AllChem.MMFFOptimizeMoleculeConfs(mh, confId=-1, maxIters=1000,
> mmffVariant='MMFF94s',
> numThreads=0)
> print(mmffopt_3)
>
>
> In the document for MMFFOptimizeMoleculeConfs: "confId : indicates which
> conformer to optimize". However, in all three cases, it still optimize
> all conformers and give me the "whole" thing:
>
> [(0, 1.0966514172064503), (0, -1.5120724826923375), (0,
> 0.6847373779429624)]
> [(0, 1.0966514171119535), (0, -1.512072483200475), (0, 0.6847373779078172)]
> [(0, 1.0966514168939838), (0, -1.5120724834832924), (0,
> 0.6847373779001575)]
> [(0, 1.0966514168498929), (0, -1.512072483655178), (0, 0.6847371291858746)]
> [(0, 1.096651416829605), (0, -1.5120724837465005), (0, 0.6847371291858746)]
>
> Thank you.
>
> Best,
> Leon
>
>
>
>
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