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## Environment Information
Open Babel version: Open Babel 3.1.1 -- Dec 12 2023 -- 11:30:06
Operating system and version:
## Expected Behavior
obrms should output the RMSD for all conformation…
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Thank you for providing the latest code updates! I've been exploring the force_matching.ipynb notebook, and I noticed that the loss value obtained during the training seems quite large, reaching aroun…
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- keep only final xyz
- parse out the other fields
- reparse
example scripts:
- loading the entire database
- Akshat will only need the dipole and polarizability only at the dft lev…
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Should `Molecule` support multiple conformations, or leave this to a collection model?
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From the tutorial I have been using the following code block to view the alignment of my prbMol to my refMol.
`p = py3Dmol.view(width=400,height=400)
dt = {}
for i in range(len(prbMols)):
dt[…
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I have some "flexible" molecules obtained from crystal structures or DFT calculations, and I want to use aISS to generate aggregate structures for them. When directly using the default aISS process, I…
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A goal for version 2 is to improve the accuracy of trained models by generating additional data. This can be done in a few ways.
The simplest approach is to train a model, select maybe the 1000 mo…
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We should add a new version of Fig. 8 showing the equivalent of Fig,. 8 for another kinase (maybe for DDR1?).
Reviewer comment:
> - The example shown here is not very convincing, because the two con…
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I think we can find a published list of some proteins with large conformational changes and spin off simulations of these and run through the analysis. Correlations between angles with large direction…
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```
What steps will reproduce the problem?
1.I try to generate conformations by Confab using: confab HH0.sdf HH0_confab.sdf
but any conformation is generated, I have some ligands with that problem. I…