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**Description**
In the [Virtual Sites vignette](https://github.com/Yoshanuikabundi/2024_workshops/blob/main/vignettes/01-G-vsites.ipynb), I noticed that the positions Interchange produces for monov…
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**Describe the bug**
I have an rdkit molecule object in which I have to set custom `SetAtomMapNum` for all atoms. Whenever I want to parse that rdkit object to an openff-toolkit Molecule object, I ge…
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## Description
### What steps will reproduce the problem?
1) Install Spyder-Terminal into conda virtual environment.
2) Restart Spyder,
3) Go to View...Panes to enable Spyder-Terminal, and …
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**Describe the bug**
I recently encountered almost the same issue in [https://github.com/rapidsai/cudf/issues/8948](https://github.com/rapidsai/cudf/issues/8948) :I have a GPU on my machine and am tr…
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**Description**
[NADP](https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate) (SMILES `"c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C…
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## Description
After uninstalling the conda package, I still get collaboration api messages in the log
## Reproduce
1. conda install jupyter-collaboration
2. launch jupyterlab
3. close jupy…
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**Describe the bug**
Trying to load a PDB of the new blockbuster drug semaglutide, a 31-residue polypeptide with two non-canonical residues, using the experimental `_additional_substructures` argumen…
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### Checklist
- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate
### What happened?
As part of PyTorch release workflow, we build conda release for…
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## Description
Copier command is broken in the extension tutorial.
## Reproduce
Follow the JupyterLab Extension Tutorial, up to and including the copier command.
## Expected behavior
…
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**Describe the bug**
We have omega (but not omega toolkit) and oequacpac license. In this condition, openeye license check is not done correctly.
**To Reproduce**
```python
from openmm.app import …