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I am using Manjaro I3 (Arch) and compile rdkit from source as described here https://www.rdkit.org/docs/Install.html
I also installed boost as was described (version boost_1_67_0).
i installed rdkit…
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Hi,
We have a process currently where we read in a reaction SMILES, generate a RXN block / file and read it back into RDKit, and want to export it back as reaction SMILES.
The issue is: if the r…
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When using rdkit.Chem.rdmolops.FindAtomEnvironmentOfRadiusN with small molecules like LiF or LiCl, this function returns ValueError for atom index 0.
Found it while reimplementing [MAP4 fingerprint](…
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**Describe the bug**
There are a number of cases from https://github.com/rdkit/rdkit/issues/6242 where RDKit does not flag an expected valence violation:
```
"[C+5]",
"[C+](C)(C)(C)C",
"[C](C)(C)…
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@rachelnwalker @cdvonbargen
Following conversations we had during the 2023 RDKit UGM, here's a report of a case where the RDKit generates a layout with many clashes, while CoordGen does a better job…
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Hi!
When setting up VSFlow in a new environment using both the environment.yml and later again with the manual set-up, I ran into this issue:
ImportError: cannot import name 'Standardizer' from …
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- RDKit Version: 2020.03.2.0
- Operating system: windows 10
- Python version (if relevant): 3.7.7
- Are you using conda? yes
- If you are using conda, which channel did you install the rdkit from…
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**Describe the bug**
A valid MDL RXN file drawn in BIOVIA Draw with bond query features such as "single or aromatic" or "double or aromatic" seems to not survive a few roundtrips to SMARTS and back, …
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**Describe the bug**
I applied the rdMolStandardize.NormalizeInPlace method to an odd but valid 5-membered heterocycle and got a non-kekulizable molecule.
**To Reproduce**
```
from rdkit import …
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**Describe the bug**
Tautomer enumeration appears to not always go to completion when `RemoveSp3Stereo` is disabled.
_[Edit: or maybe when there's any stereochemistry at all that's not being ignore…