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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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Perhaps worth discussing: should packmol only write out 1 conformer for the components in a box? Relevant function: https://github.com/openforcefield/openff-interchange/blob/8d2cee156c8a6763fde0e19388…
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The C++ function `generateDepictionMatching2DStructure` calls `compute2DCoords` with `clearConfs` set to true, and `generateDepictionMatching3DStructure` likewise calls `compute2DCoordsMimicDistMat` w…
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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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**Describe the bug**
When running auto3d to generate 3D structures with multiple GPUs (e.g., using --gpu_idx 0,1), I encounter an OSError related to an invalid file, arated.sdf. This error does not o…
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1) Configuration:
RDKit Version: '2019.03.4.0'
Operating system: Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-58-generic x86_64)
Python version (if relevant): Python 3.7.3
Are you using conda? Yes
If yo…
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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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**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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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…