Comments (3)
jhjensen2
commented on August 28, 2024
I can't reproduce this using the conda version (2019.03.2) on Linux, and I'd rather not introduce a new dependency unless really needed.
Can you send more details such as version number, OS? Are all molecules giving you trouble?
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TermeHansen
commented on August 28, 2024
Ahh yes I can see now that I debug a bit further down, that it is something internally on my environment. If I just import rdkit I have no problems, but when I also import some of my own scripts first I get the segmentation fault. So for sure not related to xyz2mol, and a specific bug for rdkit and my setup. I will investigate and post at rdkit development...
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jhjensen2
commented on August 28, 2024
OK, great. Closing this issue
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Related Issues (20)
- Purpose of 1.3 multiplier in checking covalent bonds HOT 2
- Stranger case when convert xyz file to mol HOT 5
- missing support for boron atoms HOT 1
- Problem with assignment of charges HOT 4
- 'charge_OK' referenced before assignment HOT 1
- Exceptionally long runtime for a few organic structures from materials project HOT 7
- Failure for Ruthenium complexes HOT 2
- `--sdf` argument HOT 1
- Release on conda HOT 25
- Valence greater than 4 HOT 1
- typo? HOT 2
- NameError: name 'defaultdict' is not defined HOT 5
- Parsing nciatlas geometries HOT 1
- Add UserWarning for incorrect charge?
- atomic valence of O atom inconsistent with RDkit HOT 2
- Convert xyz file with several structures in it (different molecules or same molecule, conformers) HOT 2
- how does this relate to rdkit.Chem.rdmolfiles.MolFromXYZBlock and rdkit.Chem.rdmolfiles.MolFromXYZFile ? HOT 1
- Propyl radical gives empty list of molecules HOT 4
- sdf file is empty while converting from xyz file HOT 12
- Comparison with OpenBabel?
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