Rintarou,
On Tue, Feb 7, 2017 at 9:25 AM, Suzuki, Rintarou
wrote:
>
> For the second point, atoms 6 and 8 can be inverted by RDKit_2015_03_1.
>
> RDKit_2015_03_1
> -
> >>>
Hi James,
This is definitely a bug. The problem seems to be connected to the way what
the RDKit calls "ring stereochemistry" is handled when there are spiro
linkages.
Here's the github issue: https://github.com/rdkit/rdkit/issues/1294
I'll take a look.
Best,
-greg
On Tue, Feb 7, 2017 at
On Feb 7, 2017, at 22:26, Curt Fischer wrote:
> def same_implicit_valence(mol_1, mol_2, atom_idx=1):
> """Returns True if mol_1 and mol_2 have the same implicit valence for the
> indexed atom"""
> mol_1_implicitH =
I think you've persuaded me that .SetIsotope() is the way to go...
I don't understand how that avoids any problem. How do you specify the
> target atom for that case?
> In any case, won't the InChI normalization affect some of your structures
> (e.g., detaching metals) and make it even harder to
Dear All,
I have hit what I think is a problem with stereochemistry perception/handling
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical
information gets lost when an RDKit molecule is generated.
But I
On Feb 7, 2017, at 19:02, Curt Fischer wrote:
> My ultimate goal is an easy way to create rdkit molecules that have isotopic
> substitutions but which are otherwise exactly the same as non-substituted
> variants. What's the best approach? Is it to directly call
I replied to Andrew's very nice discussion of implicit hydrogens in SMILES
but forgot to include the whole list.
Wow, thank you, that was very useful. I didn't realize those nuances of
> SMILES.
>
> On the rdkit "side", the distinction made in Smiles between implicit and
> explicit hydrogens
Hi Greg,
Thanks for your quick response.
I look forward to more flexible version of the command.
For the second point, atoms 6 and 8 can be inverted by RDKit_2015_03_1.
RDKit_2015_03_1
-
>>>
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