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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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RDKit has an API for this so should be reasonably straightforward
https://www.rdkit.org/docs/source/rdkit.Chem.inchi.html
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This new cell will nicely demonstrate some of the rich functionality that can be achieved, and is based on things that a close to working.
The basic purpose is a cell that read a set of 2D molecules …
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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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# RDKit blog - Understanding conformer generation failures
Getting more information when the conformer generation doesn’t work
[https://greglandrum.github.io/rdkit-blog/posts/2023-05-17-understandin…
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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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# Optimizing conformer generation parameters | RDKit blog
Improving the speed of the RDKit’s conformer generator
[https://greglandrum.github.io/rdkit-blog/3d/conformers/optimization/2022/09/29/optim…
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Dear professors: When I used the function fprints_from_smiles in e3fp, it cost much time to find the conformers if there were none. For example, I wanted to get the fingerprint of A, it cost 10 minute…
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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…
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Hi,
I was wondering if there is a way to drop unwanted molecules after the toxicity prediction. Just to filter before to perfomr the conformer generation or the optimization. Might reduce the time …