Hi guys,
Does clustering change conformer ID? See code below:
from rdkit import Chem
from rdkit.Chem import AllChem, TorsionFingerprints
from rdkit.ML.Cluster import Butina
mh = Chem.AddHs(Chem.MolFromSmiles('OCCCN'))
AllChem.EmbedMultipleConfs(mh, numConfs=5, maxAttempts=1000,
pruneRmsThresh=1.0, numThreads=0, randomSeed=-1)
print([conf.GetId() for conf in mh.GetConformers()])
mh.RemoveConformer(0)
mh.RemoveConformer(1)
print([conf.GetId() for conf in mh.GetConformers()])
m = Chem.RemoveHs(mh)
mat_a = AllChem.GetConformerRMSMatrix(m, prealigned=False)
mat_b = TorsionFingerprints.GetTFDMatrix(m)
num = m.GetNumConformers()
clusters_a = Butina.ClusterData(mat_a, num, distThresh=2.0,
isDistData=True, reordering=False)
clusters_b = Butina.ClusterData(mat_b, num, distThresh=2.0,
isDistData=True, reordering=False)
print(clusters_a)
print(clusters_b)
print([conf.GetId() for conf in mh.GetConformers()])
Here is the result:
[0, 1, 2, 3, 4]
[2, 3, 4]
((2, 0, 1),)
((2, 0, 1),)
[2, 3, 4]
You see it does not actually change the id in mh, but the result in the
tuple from clustering is actually index. Is this a bug? This could be
misleading when you try to grab conformer ids from the clustering result.
Thank you!
Best,
Leon
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