Coming back to an old one that was mostly answered already:
On Thu, Jan 12, 2017 at 3:11 AM, Curt Fischer
wrote:
>
> I recently wanted to use RDKit to model the famous copper-catalyzed
> cycloaddition of alkynes and azides.
>
> I eventually got things working, kind of, but had two questions. Fi
Oof, thanks for the pointer MIchal. I'm sorry I didn't read the docs
carefully enough! ~CF
On Thu, Jan 12, 2017 at 9:32 AM, Michal Krompiec
wrote:
> You need to sanitize the products, just run Chem.SanitizeMol on each
> molecule. See http://www.rdkit.org/docs/GettingStartedInPython.html#
> chem
You need to sanitize the products, just run Chem.SanitizeMol on each
molecule. See
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions :
"the molecules that are produced by the chemical reaction processing code
are not sanitized".
Best,
Michal
On 12 January 2017 at 17:22, Cur
What makes you think the molecules are nonsensical? They look OK to me.
Converting to SMILES before doing any UpdatePropertyCache() stuff
*products_tuples = copper_click.RunReactants((diyne, azide))products =
list(chain(*products_tuples))print [Chem.MolToSmiles(prod) for prod in
products]*
The outputs of reaction are a bit confusing.
Reactions can have multiple product templates so the output of RunReactants is
a list of list of molecules.
For products in result:
For molecule in products:
Molecule.UpdatePropertyCache()
However, it looks like your reaction is generating non
5 matches
Mail list logo
