Hi Axel,
The format like "c11” is implicitly defining the bonds between atoms and
the output of the “canonical” SMILES has redundant ring labels (1 and 2) ,
which I think confused the parser and caused the problem.
I have no idea whether it is a bug or whether it is true reason.
But try
Dear Hongbin,
kekulizing the Smiles does indeed work in this case, that's a good tip.
Thanks a lot.
KR Axel
On 03.09.19 11:26, Hongbin Yang wrote:
Hi Axel,
The format like "c11” is implicitly defining the bonds between
atoms and the output of the “canonical” SMILES has redundant ring
Dear all,
I'm trying to generate .rxn files or one single .rdf file from a csv file
where I have a bunch of reactions smiles stored.
I know how to instantiate a rxn object but I no idea how to safe this to
several .rxn files or a RDF file.
I already asked this question last Friday but
Hi,
I know that the RDKit makes no guarantees abount being able to
round-trip (Smiles -> Mol -> Smiles -> Mol) every molecule, but I would
like to know if there are any recommendations on how to handle such cases.
In my current case the problem seems to lie in different aromatic models
for a
Dear colleagues, I've been reading the documentation and a series of online
posts about RDKit and the use of the ETKDG algorithm to effictiently find
conformers for organic structures. RDKit's own page showd that:
>>> m = Chem.MolFromSmiles('C1CCC1OC')
>>> m2=Chem.AddHs(m)
>>> # run ETKDG 10
Hi Markus,
You can generate the RXN file output from the rxn object via
ReactionToRxnBlock, like this Python code:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> rxn = AllChem.ReactionFromSmarts('CC(=O)O.OCC>>CC(=O)OCC')
>>> AllChem.ReactionToRxnBlock(rxn)
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