Dear all,

please consider the following code:

IAtomContainer mol = new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles("C[C@@H](O)CC[C@H](C)/C=C(/C)C(=O)O");
SmilesGenerator smiGen = new SmilesGenerator(SmiFlavor.Stereo);
System.out.println(smiGen.create(mol));
mol.removeAtom(0);
System.out.println(smiGen.create(mol));

Input structure:

The Output:

C[C@@H](O)CC[C@H](C)/C=C(/C)\C(=O)O
[CH](O)CC[C@H](C)C=C(C)C(=O)O

Before removal:

After removal of one atom (sorry for the orientation flip):

This shows that even tough an atom that has nothing to do with the double bond stereochemistry "further down the line" is removed here, said stereo configuration is lost.

I think the problem is in this method:

At the end, a double bond stereochemistry object is marked as invalidated when it has no overlap with the removed bond/atom.

What do you think about this?

I tried fixing it by simply removing these lines:

} else {
    invalidated.add(se);
}

... but that caused a test to fail (SmilesGeneratorTest.deletingBondUpdatesCisTrans2().