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Hello, thank you for sharing your work.
I have a **question** regarding the decoding process. I'm curious about how to decode more than one molecule from a specific latent space, especially those …
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- [ ] add informative tooltips explaining how different elements work
- [ ] highlight substructure matching inverted MCS. Possibly with reactions
- [x] fix typo in generation tab
- [ ] Fragment tab…
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I have tried to extract the scores from the scores.model_idx_0.npz in the outputs files, but I find there is no pLDDT option in the scores:
scores = np.load("scores.model_idx_0.npz")
print(scores…
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Create a series of function that will generate new molecules by combinations of good molecules.
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**Describe the bug**
I try to generate conformers using the method EmbedMultipleConfs from a 3D sdf file prepared with Chem3D. Molecule A is a macrocycle embedding two aromatic rings. For a reason i …
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Dear author,
Thanks for sharing your wonderful code! Recently when I try to reproduce the ligand generation mentioned in paper for SARS-CoV-2 main protease, I encountered error `OverflowError: can'…
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### Bug Description
`update_charge` from `rmgpy/molecule/molecule.py` does not recognize cutting labels when more than 1 processes are used for reaction generation with `react` from `rmgpy/rmg/react.…
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**Describe the bug**
For organic molecules with -NO2 groups, conformer generation and UFF optimization will produce one conformer with O-N-O angle being 0 degree (and two O almost overlapping). And t…
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Dear OpenFF-Bespokefit Team,
First and foremost I would like to say thank you for the great work you did with BespokeFit!
I would like to ask for you help regarding a bug/problem I am facing testi…
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**Is your feature request related to a problem? Please describe.**
The ordering of a molecule can affect which conformers are generated for it using OE (and probably also RDKit). This can then lead…