Hello,
I have this sdf:
example
SciTegic06111912192D
2 0 0 0 0 0 999 V2000
2.4541 -4.8083 0.0000 Cd 0 1
3.9125 -4.8083 0.0000 Sb 0 7
M CHG 2 1 3 2 -3
M END
$$$$
When I use this code:
from rdkit import Chem
sdfile = Chem.SDMolSupplier('example.sdf')
print(sdfile[0])
smistring = Chem.MolToSmiles(sdfile[0])
print(smistring)
molecule = Chem.MolFromSmiles(smistring)
print(molecule)
The result is:
<rdkit.Chem.rdchem.Mol object at 0x7f5c93689030>
[Cd+3].[SbH6-3]
[12:53:33] Explicit valence for atom # 1 Sb, 9, is greater than permitted
None
My question is how can I save the molecule as a smiles string, in a way that it
will be read as a molecule also in the future.
Benny
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