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[terminal-imine.pdb.txt](https://github.com/rdkit/rdkit/files/13278105/terminal-imine.pdb.txt)
Assigning bond orders to the attached PDB with SMILES:` [H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[…
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**Describe the bug**
I have found a number of examples where the choice of which tautomer is canonical depends on stereochemistry elsewhere in the molecule. I think this behavior is a bug or misfeatu…
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it looks like the default wrinkle manager does not work properly?
especially not when a character smiles.
![image](https://github.com/soupday/cc_unity_tools_URP/assets/20005379/85f850d4-5a42-4e4…
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```
Does is possible to add option for manually adding smiles like on MSN that
would be nice.
thanks.
```
Original issue reported on code.google.com by `kos...@gmail.com` on 17 Feb 2011 at 1:12
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**Describe the bug**
A reaction family could not be found for the reaction C3H6-2 + O C3H6O.
**How to reproduce**
```python
from arc.rmgdb import make_rmg_database_object, load_families_only
f…
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As of v2.5.0, OPSIN outputs kekulized SMILES (`benzene` is translated to `C1=CC=CC=C1`). If the information about the ring aromaticity is known to OPSIN, output of aromatic SMILES (`benzene` translate…
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### Bug Description
I'm trying to create a rmgpy.molecule.Molecule() using smiles
```
rmgpy.molecule.Molecule(smiles='O=C=[X]')
```
But it fails from an RDKit error:
```
-----------------…
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During some testing I came across a few smaller things/inconsistencies/bugs in the filtering pipeline.
1. `repair_not_matching_annotation`
- sometimes gave the following warning: ```WARNING:match…
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Some of the annotations found on pubchem, can not be loaded by RDkit.
For example: C[N+](C)(C)CCOS(=O)(=O)[O-] GIves a error of Valence =8 for the Sulfur.
I will dive into this later to check if …
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```{r}
#R
library(rcdk)
library(fingerprint)
NORMAN