the sdf doesnt parse so well for me when pasted from the mail(and seems to
contain an unusual conformation) but have you tried to turn
includeNeighbors=True in this line:
numHs = a.GetTotalNumHs(includeNeighbors=True)
in case this fixes your issue, discussion why this flag is needed can be
found
Dear list,
This code:
---
#!/usr/bin/env python3
import argparse, sys
from rdkit import Chem
def debug_mol(m):
for a in m.GetAtoms():
i = a.GetIdx()
anum = a.GetAtomicNum()
numHs = a.GetTotalNumHs()
print('%d %d %d' % (i, anum, numHs))
if __name__ ==
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