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This issue is inspired by a hotfix I quickly wrote to solve a strange openbabel import error, but I thought it was worth a wider discussion because of a few more issues that are worth addressing.
C…
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Warning messages upon Somn SMILES input validation for molecules containing stereochemistry (dashes etc.) or heavy atoms (more than 150 atoms etc.)
1. Stereochemistry
See the following Slack link fo…
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### Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
### Issue
Hello everyone,
I've installed openbabel via conda but when I tried reading file with pyb…
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# Context
I need to convert thousands of SMILES into SDF file using pybel via python scripts (several code lines below).
```
for ind, row in df.iterrows():
df.loc[ind, 'ROMol'] = pybel.reads…
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Hi Piyawat,
I did a global search over GitHub to see what people were doing who mentioned BEL. I saw some of your notebooks for converting Text2BEL, and think that's very interesting. I just wanted…
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next, I found incompatibilities running import SqlAlchemy and Pybel
how to fix
pip3 uninstall purge sqlalchemy
python3 -m pip install SQLAlchemy==1.3.0
python3 -m pip install seaborn
python…
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I am trying to run PyBox (https://github.com/loftytopping/PyBox) and when I try to run umansysprop I keep getting the error _AttributeError: module 'pybel' has no attribute 'Smarts'_. This is trigger…
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**Is your feature request related to a problem? Please describe.**
Our code uses on Openbabel for 3D and 2D processing of crystal molecular structures. For effective unit testing, we need a way to d…
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Charlie Hoyt seems to still maintain PyBEL; not sure how many people use it, but since it is fairly low effort, we could include a PyBel-BioCypher adapter. https://github.com/cthoyt
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- [ ] Add default namespaces to terminology service
- [ ] Add equivalents for the following GO terms that Charlie listed to the DEFAULT namespaces for pmod
- [ ] Add a entity types for the DEFAULT nam…