Hi guys,
I am new to RDKit, and have a question about adding and removing Hs.
As recommended in the documentation, hydrogen atoms should be added for
generating conformers, optimization, etc.
However, for clustering, should the Hs be removed first, before generating
the conformer RMS matrix? For instance:
from rdkit import Chem
from rdkit.Chem import AllChem, TorsionFingerprints
suppl = Chem.SDMolSupplier('molecule.sdf')
for mol in suppl:
mh = Chem.AddHs(mol)
cids = AllChem.EmbedMultipleConfs(mh, numConfs=5, maxAttempts=1000,
pruneRmsThresh=0.5, numThreads=0,
randomSeed=1)
m = Chem.RemoveHs(mh)
# RMS matrix
rmsmat = AllChem.GetConformerRMSMatrix(m, prealigned=False)
# TFD matrix
tfdmat = TorsionFingerprints.GetTFDMatrix(m)
print(rmsmat)
print(tfdmat)
Note I remove the Hs before getting RMS and TFD matrices. Both resulting
matrices are different if I do not remove Hs. The RMS without Hs, in
general, tend to be smaller than the RMS with Hs. This will in turn affect
the subsequent clustering result.
Could you guys give me some suggestions? Thank you!
Best,
Leon
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
