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If you search in LOTUS for Valencene, you get two hits:
[Q105219112](https://lotus.naturalproducts.net/compound/lotus_id/LTS0031707) and
[Q289496](https://lotus.naturalproducts.net/compound/lotus_id…
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**Is your feature request related to a problem? Please describe.**
The "warning" `(not error because allow_undefined_stereo=True)` is not actually a warning emitted by the `warnings` module, but …
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**Steps to reproduce:**
1. Convert SMILES `O=C(O)[C@@]([H])(N)C ` string to Mol by executing convert or layout endpoint
2. Convert resulted Mol string to SMILES (convert endpoint)
**Actual result…
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string smiles="C1=CC=C2(C=C1)CCC(c1ccccc1)CC2";
indigo.setOption("ignore-stereochemistry-errors", true);
IndigoObject indigoObject = indigo.loadMolecule(smiles);
bingo.insert(indigoObject, id) > 0;…
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**Configuration:**
RDKit Version: 2019.03.3
Ubuntu 18.04
Python version: 3.6.9
**Description:**
I have problem in identifying the cis/trans isomers. See decalin example below.
**Code Example…
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``` python
In [2]: mol = Chem.MolFromSmiles("C1C[C@@H](CC)CC[C@@H](CC)1")
In [3]: print Chem.MolToSmiles(mol, isomericSmiles=True)
CC[C@@H]1CC[C@@H](CC)CC1
```
Reported by Toby Wright
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**Is your feature request related to a problem? Please describe.**
It with be useful if the toolkit tracked (or added a method to find) which atoms / bonds in a molecule have undefined stereochemis…
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**Describe the bug**
Previously, we had run into issues where the `openforcefield` toolkit using the OpenEye toolkit backend perceives trivalent nitrogens as stereocenters, causing issues for loading…
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Such as when a benzene is ortho or meta substituted, the new group built in might be in the wrong direction in the active site which may not be sampled.
It would be good to check the _direction_ of…
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**Is your feature request related to a problem? Please describe.**
Currently, there is no way to read _only_ the molecules with fully-specified stereochemistry from a multi-molecule SDF file. `Molecu…