Dear All,
I think this question is in some way related to the following closed issue:
https://github.com/rdkit/rdkit/pull/3015
I am working with 2020.09.1, but see the following error when calling
EnumerateStereoisomers():
RuntimeError: Pre-condition Violation
Stereo atoms should be specified before specifying
CIS/TRANS bond stereochemistry
Violation occurred on line 288 in file Code/GraphMol/Bond.h
Failed Expression: what <= STEREOE ||
getStereoAtoms().size() == 2
RDKIT: 2020.09.1
BOOST: 1_72
I may be wrong, but I think my issue has something to do with incoming
STEREOANY bonds *terminating* at double bonds.
Here is an example (not very pretty, I know!):
[cid:[email protected]]
The intention for the wavy bonds is (probably) to say that nothing is known
about the configuration at the 3 stereocentres.
But the intention for the double bonds is that they are as drawn (the hydrazone
is trans, and the alkene is cis).
Here is the corresponding molblock:
Mrv1921 12222012592D
10 11 0 0 0 0 999 V2000
15.6513 1.4711 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.0635 0.7558 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.8890 0.7546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3010 0.0394 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
17.3788 -0.6754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.0262 -1.1519 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
18.7209 -1.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.6301 -0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.3831 -1.5741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.8753 -0.3874 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
4 3 1 4 0 0 0
4 5 1 0 0 0 0
6 5 1 4 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
6 9 1 0 0 0 0
10 9 1 4 0 0 0
10 4 1 0 0 0 0
10 8 1 0 0 0 0
M END
And we can see 3 atoms are set with atom parity = 3 (either or unmarked;
ignored when read).
And 3 single bonds are set with bond stereo = 4 (either).
Both double bonds are set with bond stereo = 0 (use coords to determine cis or
trans).
If I read this into RDKit, however, I see one of the double bonds (the
hydrazone one) is interpreted as STEREOANY and not STEREONONE as the molblock
intended:
mol = Chem.MolFromMolBlock(test_mb_20)
for bond in mol.GetBonds():
if bond.GetBondType() == Chem.BondType.DOUBLE:
print(bond.GetStereo())
STEREOANY
STEREONONE
And if I make a call to EnumerateStereoisomers() I see the above error.
Is there a step (or understanding) I am missing?
Kind regards
James
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