Rdkit: RemoveHs not properly updating double bond stereoatoms

[shayakhmetov]

rdkit.__version__ = '2017.09.2'
running the code below causes Segmentation Fault

from rdkit import Chem
from rdkit.Chem import AllChem
smiles='CCCCCCCCCCCCCCCC(=O)O[C@@H]1CC(C)=C(/C=C/C(C)=C/C=C/C(C)=C/C=C\\C=C(C)\\C=C\\C=C(C)\\C=C\\C2=C(C)C[C@@H](OC(=O)CCCCCCCCCCCCCCC)CC2(C)C)C(C)(C)C1'
mol = Chem.MolFromSmiles(smiles)
mol = AllChem.AddHs(mol)
mol = AllChem.RemoveHs(mol) # Without RemoveHs there is no segmentation fault
AllChem.EmbedMolecule(mol) # the same for AllChem.EmbedMultipleConfs

[greglandrum]

Confirmed. I can reproduce this. Thanks for reporting it!

[greglandrum]

Here's a smaller reproducible that also shows that the problem is connected to double bond stereochemistry:

In [1]: from rdkit.Chem import AllChem

In [2]: from rdkit import Chem

In [3]: m = Chem.RemoveHs(Chem.AddHs(Chem.MolFromSmiles('CC=CC')))

In [4]: AllChem.EmbedMolecule(m)
Out[4]: 0

In [5]: m = Chem.RemoveHs(Chem.AddHs(Chem.MolFromSmiles('C/C=C/C')))

In [6]: AllChem.EmbedMolecule(m)
Segmentation fault (core dumped)
(base) glandrum@otter:~$