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Currently, we collect the torsion QM data using the CLI interface to torsiondrive and we run each grid point optimisation in series which can be quite slow even for simple small molecules. Here I want…
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**Describe the bug**
This is odd, hopefully it's not because I've misunderstood how the charge assignment works. I seem to be getting different charges from `create_openmm_system` depending on how …
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**Describe the bug**
In some cases, switching between multiple conformers using nglview mixes up the bonding of the molecule.
**To Reproduce**
```
from openforcefield.topology import Molecule
f…
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These are the lines I have issue with:
https://github.com/deepchem/deepchem/blob/ac98cf0f128273599f27dee3a8f562f2b1c5d6e0/deepchem/feat/graph_features.py#L573-L580
My problem is this:
When I try …
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**Problem**
`store.get_qm_conformer_by_qcarchive_id()` returns a `Quantity` object, whereas `store.get_mm_conformer_by_qcarchive_id()` returns a `np.array`. This makes it hard to compare them as the …
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I just ran
`python examples/predict_structure.py`
Then, I see
```
Traceback (most recent call last):
File "/people/kimd999/bin/Miniconda3-py311_24.5.0-0-Linux-x86_64/lib/python3.11/site-packa…
kimdn updated
1 month ago
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plot molecules on the scatter plots to see if the flexibility might be the issue for the deviations
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Hi
I wanted to try the framework and assess its efficacy for hit enrichment.
What I did is follows:
1) choose HDAC6 as target and download the structure PDB id: 5EEN
2) generate pharmacophor…
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For files containing a lot of molecules (e.g. `data/molecules/MiniDrugBank.sdf`) this should help cutting the time necessary to run the toolkit.
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**Describe the bug**
Previously, we had run into issues where the `openforcefield` toolkit using the OpenEye toolkit backend perceives trivalent nitrogens as stereocenters, causing issues for loading…