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gen_conformers is a function that will take some xyz file which is deemed to be inadequate and generate some number of conformers as sample geometries. Is this an accurate description?
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With exactly the same command line, .censo2rc, and crest_conformers.xyz files, 2.0.2 works, and 2.1.0 crashes. The following output is given in the latter case:
$ python3.12 -m censo --input "crest_…
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**Describe the bug**
I am generating conformers for the DUDE dataset. For some molecules, the conformer generation process takes a long time and then fails to generate a conformer model.
I have …
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Hi,
I'm trying to use a sdf file with possible conformers as an input file, but I tried all of the initial conformers were optimized separately (even though all of them share SMILES pattern). Is th…
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Hi,
would you be able to provide a script to download model weights? We are running Chai1 on cluster with job nodes having no internet access. Having such a script would really help us!
(Sometim…
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Hello, I am very interested in your work. If I only need the code for the 3D molecular conformation as an encoder for my own work, can I do that? Could you tell me specifically where this part of the …
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**Description:**
The following code to generate conformers using `datamol` works fine with RDKit version `2022.09.5`, but fails with RDKit version `2024.03.1`. This inconsistency might be due to chan…
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Currently MMSchema does not handle multi-conformers (whereas OpenFF toolkit does). What is the best way to handle this disrepancy?
1 - Add another dimension to `Molecule.geometry` ? This would make…
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Dear Developers,
We have a problem, which I have not seen in the report page. It does not occur every time, but eventually like 1 out of 5 runs. If the job is submitted again, it might finish succe…
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Fantastic work!
However, I’m a bit confused about the GNN encoding and 3D feature aspects of your project.
Although GNN encoding is referenced in your article, I couldn’t find the correspondin…