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Currently, it is difficult to handle errors when parsing various representations of a chemical structure (such as SMILES, Molfile, etc.) via RDKit Python API. On success, the MolFrom... methods return…
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Hi,
I am trying to repeat this tutorial: https://github.com/MobleyLab/drug-computing/blob/f38a4148e9e70238c88fc8110d95b34688f02838/uci-pharmsci/lectures/SMIRNOFF_simulations/mixture_simulations.ipynb…
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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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ghci> let b = readSmiles "c1ccccc1C(=O)O"
ghci> case b of Right val -> writeSmiles val
"c"
ghci>
It seems that the internal representation of SMILES string lacks proper handling of cyclic struc…
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### Virtual library cleaning: Removing Boc-, Fmoc-, and tbutyl ester- protecting groups from molecule libraries.
The Python script [deprotect.py](https://github.com/user-attachments/files/1750667…
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This repo has been fantastic for me to use within my Rust projects, thanks for all the effort put into this.
Have some questions regarding contributing:
- What are the processes for contributing…
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**Is your feature request related to a problem? Please describe.**
We've integrated part of the openff-toolkit into a closed-source project and so we need to distribute the AmberTools binaries separa…
stgeo updated
2 months ago
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I have an issue when applying a chemical reaction to a given substrate with rings results in unintended ring splitting. Here is an example:
![broken_rings](https://cloud.githubusercontent.com/asse…
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There is an issue with loading aromatic SMILES or kekulized molecules from RDKit where bonds involved in aromatic rings are converted to single bonds.
Discovered by @joshkamm, @andrewtarzia and my…
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**Describe the bug**
The toolkit molecule `to_qcschema` exports to a schema that represents a QCArchive molecule, however the corresponding `from_qcschema` actually wants an Entry object, which has t…