Hello Greg,
Indeed it was the RDKit version. I was using 2021.03.4. Sorry about the
false alarm! The error message was as below. When I use 2022.09.4, there
was no problem.
HOWEVER, I would also need some advice. When I was in my original rdkit
environment, I did a "conda update rdkit". It downloaded many packages,
installed many, removed some. But at the end of the exercise, I still ended
up with what I initially had, namely RDKit 2021.03.4. I had to install
rdkit again from scratch to get the new version. What am I doing wrongly?
Thanks again!
Ling
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
****
Invariant Violation
no eligible neighbors for chiral center
Violation occurred on line 209 in file
/home/conda/feedstock_root/build_artifacts/rdkit_1626029732763/work/Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: nbrScores.size()
****
Traceback (most recent call last):
File "/home/c/Documents/Notes/rdkIllustrate/MolToMolBlock/p1.py", line 9,
in <module>
MolBlock2(sys.argv[1])
File "/home/c/Documents/Notes/rdkIllustrate/MolToMolBlock/p1.py", line 7,
in MolBlock2
print (Chem.MolToMolBlock(m2))
RuntimeError: Invariant Violation
no eligible neighbors for chiral center
Violation occurred on line 209 in file
Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: nbrScores.size()
RDKIT: 2021.03.4
BOOST: 1_74
Greg Landrum <greg.land...@gmail.com> 於 2023年2月22日週三 上午7:14寫道：
> 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
>>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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