Greg Landrum
Greg Landrum
Confirmed. This is a bug Here's an example of the same thing starting from SMILES: ``` In [12]: Chem.MolToSmiles(Chem.MolFromSmiles('[H]/N=S(=O)(N)/C')) Out[12]: '[H]N=S(C)(N)=O' ``` Or, simplified: ``` In [14]: Chem.MolToSmiles(Chem.MolFromSmiles('[H]/N=C(C)/C')) Out[14]: '[H]N=C(C)C'...
This isn't really adding exact atom types, right? It's still going to ignore things like charge or isotope, so we get this: ``` In [10]: m2 = Chem.MolFromSmiles('CC[13CH3]') In [11]:...
If you want help here, you need to provide the exact input that you provided.
> As far as I understand, this randomly generated coordinates are Ok as an initial conformation given that the topology / connectivity is correct and there is an MD simulation...
Hi @LiuCMU , unless you can provide the exact input you used, we cannot help you here
@ptosco : I think the idea of having the MMFF aromaticity model available like the other models makes sense. What's your take?
> Added one simple test to `GraphMol/molopstest.cpp`, from where I found other SetAromaticity-related tests. Please let me know what kind of test you want me to add to `GraphMol/catch_molops.cpp`, and...
Thanks @JLVarjo
You don't provide enough sample code for us to know exactly what you did, and I can't reproduce this with something simple: ``` In [1]: from rdkit import Chem In...
Hi @yurivict. There's something strange going on here. Did 2024.03.5 work in exactly the same configuration (same compiler, cmake flags, etc?)