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**Is your feature request related to a problem? Please describe.**
Limited option for the drawing of non-determined _relative_ stereochemistry
**Describe the solution you'd like**
In addition to …
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**Describe the bug**
Generating a conformer for this SMILES fails in both OE/RD, but it seems like all stereocenters are specified:
```
from openforcefield.topology.molecule import Molecule
mol =…
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Looking at the python script it looks like the modeller.addHydrogens method simply places new hydrogens ~0.1 nm away from the parent atom and then does a energy minimization. Is it not possible for th…
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Hi,
I bumped into the following issue while processing this sulfoxide compound ("O=S(c1ccc(Nc2nc(OCC3CCCCC3)c4c([nH]cn4)n2)cc1)C"). Dissecting the code looks like it builds fragments around all ro…
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**Description:**
[reported by Jean-Marc Nuzillard]
This is one of those "crowded" stereochemistry cases:
```
In [23]: print(Chem.CanonSmiles('F/C1=C/C/C=C(/O)CCCCCCC/C=C/1') ) …
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Copy-paste from email received; @meier-rene are you able to follow-up? Thx!
Comparing data from different databases, I found some discrépancies between your data. For the mentioned entry of your da…
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ChemDraw names certain meso cyclic compounds with lowercase r/s, rather than using cis/trans, like in the issue title. For example, the name provided by ChemDraw in the attached figure.
ds = client.get_collection('OptimizationDataset', 'OpenFF Full Optimization Benchmark 1'…
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Thread here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02934.html
```
In [2]: mol1 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@@]3(OCc2cc(C#N)ccc23)CCCN(C)C")
In [3]: mol2 = Chem.Mo…