Hi RDKitters,
Asking for a friend.
The example below using the given molecule and EmbedMultipleConfs returns
an empty list without throwing anything or producing any warnings. I've got
quite a few smiles that fail in the same manner, but can't see any obvious
pattern. It might be related to chirality.
Cheers, Richard
from rdkit.Chem import AllChem
from rdkit import Chem, rdBase
print rdBase.rdkitVersion
m = Chem.MolFromSmiles('CN1C(=O)[C@H]2[C@H](C1=O)[C@@]1(C)CC[C@H]2O1')
m = AllChem.AddHs(m)
print Chem.MolToSmiles(m, isomericSmiles=True)
ids = AllChem.EmbedMultipleConfs(m, 5)
print list(ids)
Output:
2016.03.1
[H]C([H])([H])N1C(=O)[C@@]2([H])[C@]([H])(C1=O)[C@]1(C([H])([H])[H])O[C@
]2([H])C([H])([H])C1([H])[H]
[]
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