Hi, list.
I use the code below to generate conformers.
The thing is that If I generate conformers, they are without hydrogens, and
when I add hydrogens, they are all in the center of the ring overlapping.
What am I doing wrong?
Thanks.
Petro.
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolAlign
from rdkit.Chem import rdShapeHelpers
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import PyMol
from rdkit.Chem import Draw
params = Chem.rdDistGeom.srETKDGv3()
params.randomSeed = 0xf00d
params.clearConfs = True
m = Chem.MolFromSmiles(''C1CCCCCCC1'')
m2=Chem.AddHs(m)
cids = AllChem.EmbedMultipleConfs(m2, numConfs=10, params=params)
rmslist = []
AllChem.AlignMolConformers(m2, RMSlist=rmslist)
print(rmslist)
res = []
for i in range(5):
mb = Chem.MolToMolBlock(m2, confId=i)
mb_h = Chem.AddHs(Chem.MolFromMolBlock(mb))
res.append(mb_h)
--
______________________________
Petro Khoroshyy
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