Please ignore the "conda update" question in my previous email. Problem solved. Thank you!
> 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? I forgot to set the channel to conda-forge. After I set this, the update was successful. Ling Chan <lingtrek...@gmail.com> 於 2023年2月22日週三 下午4:13寫道： > 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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