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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