Hi all,
No error on rdkit 2022.09.04 boost 1_78 (Ubuntu 20.04).
However I am able to reproduce the error on 2022.03.2, here it is:
****
Invariant Violation
no eligible neighbors for chiral center
Violation occurred on line 238 in file
/project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: nbrScores.size()
****
---------------------------------------------------------------------------RuntimeError
Traceback (most recent call
last)<ipython-input-2-b7212a330f82> in <module> 3 for m1 in
Chem.SDMolSupplier("full.sdf", removeHs=False): 4
m2=Chem.RemoveHs(m1)----> 5 print (Chem.MolToMolBlock(m2))
RuntimeError: Invariant Violation
no eligible neighbors for chiral center
Violation occurred on line 238 in file
Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: nbrScores.size()
RDKIT: 2022.03.2
BOOST: 1_75
In fact, just rendering m2 in the jupyter notebook using display() causes a
crash
RuntimeError: Invariant Violation
no eligible neighbors for chiral center
Violation occurred on line 238 in file
Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: nbrScores.size()
RDKIT: 2022.03.2
BOOST: 1_75
This seems to be related to sulfoxide stereochemistry assignment, see this
issue https://github.com/rdkit/rdkit/issues/2227
In any case, it seems like it is fixed in up-to-date rdkit.
However, it looks like there is still a subtle stereochemistry related
issue: if i convert m2 to SMILES I get:
C[C@@H]1[C@@H](C)[C@H](C=C[At])[S@](=O)[C@@H]1*[SH]*=O
I.e. the second sulfur (bolded) is not assigned stereochemistry, but the
first one is. Both are asymmetric.
best wishes
wim
On Wed, Feb 22, 2023 at 4:20 PM Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Ling,
>
> I can't reproduce this problem on windows using the most recent version of
> the RDKit.
> Which version of the RDKit are you using and how did you install it?
>
> Please also share exactly what you see for an error message.
>
> -greg
>
>
> On Tue, Feb 21, 2023 at 7:03 AM Ling Chan <lingtrek...@gmail.com> wrote:
>
>> Dear colleagues,
>>
>> Don't know if this is a bug, or if my input molecule is not good. I
>> suspect that it is the former.
>>
>> If you run the following on the file "full.sdf", it will crash at the
>> MolToMolBlock line.
>>
>> for m1 in Chem.SDMolSupplier(inputsdf, removeHs=False):
>> m2=Chem.RemoveHs(m1)
>> print (Chem.MolToMolBlock(m2))
>>
>> You can confirm that the problem is due to the stereo definition of the
>> double bond, since if you edit the bond line " 4 5 2 3" to " 4 5 2 0" it
>> will not crash.
>>
>> I tried to simplify the situation by boiling the molecule down to
>> "simple.sdf". Unfortunately it does not crash any more.
>>
>> Thanks.
>>
>> Ling
>>
>>
>>
>> _______________________________________________
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>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
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