conditions (rarely in the millions :-))
So, if I deal with something like implementing RDKit, things are
probably always quite close to scenario 1, hence my suggestion to
disregard stereochemistry on these type of N atoms (you need a lot of
information from scenario 2 to even decide whether there is
f the page..
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>
> On Thu, Aug 20, 2015 at 10:30 AM, Greg Landrum
> wrote:
>>
>> This isn't a simple one, so it may take a bit to get to an answer that's
>> comprehensible.
>>
>> There are two things going on here in the RDKit:
>> 1) Ring stereochemistry
>
get to an answer that's
> comprehensible.
>
> There are two things going on here in the RDKit:
> 1) Ring stereochemistry
> 2) stereochemistry about nitrogen centers
>
> Let's start with the second, because it's easier: RDKit does not generally
> "believe in&
o it may take a bit to get to an answer that's
> comprehensible.
>
> There are two things going on here in the RDKit:
> 1) Ring stereochemistry
> 2) stereochemistry about nitrogen centers
>
> Let's start with the second, because it's easier: RDKit does not generally
This isn't a simple one, so it may take a bit to get to an answer that's
comprehensible.
There are two things going on here in the RDKit:
1) Ring stereochemistry
2) stereochemistry about nitrogen centers
Let's start with the second, because it's easier: RDKit does not g
h due to
inversion I can understand) and interpreting it as having only two chiral
centers (which is correct).
What is confusing me, is that when I supply RDKit with the canonical smiles
string from Indigo (which has the conformer "encoded" in it), and then ask
for the isomeric canonical
e para position to the nitrogen
>>
>> For the record just tested and ChemAxon/CDK/OpenBabel do the same.
>>
>> John
>>
>> Regards,
>> John W May
>> john.wilkinson...@gmail.com
>>
>>> On 19 August 2015 at 09:00, Rob Smith wrote:
>>>
hat?
Thanks,
-greg
On Wed, Aug 19, 2015 at 3:00 PM, Rob Smith wrote:
> Dear RDKit community,
>
> I'm trying to use RDKit to read in Corina generated stereoisomers (from a
> Mol file), assign chiral tags and stereochemistry to the structure and
> output the canonical smiles
to use RDKit to read in Corina generated stereoisomers (from a
>> Mol file), assign chiral tags and stereochemistry to the structure and
>> output the canonical smiles string for each isomer of a given molecule (in
>> Python), when I do this, half the canonical smiles strings are
n I read in the output from Corina into an Indigo instance, then use
> the canonical smiles from Indigo to create an RDKit molecule, canonical
> smiles strings generated from the molecule objects are all unique.
>
> I may be missing an option to enable RDKit to 'visualise' the ch
Dear RDKit community,
I'm trying to use RDKit to read in Corina generated stereoisomers (from a
Mol file), assign chiral tags and stereochemistry to the structure and
output the canonical smiles string for each isomer of a given molecule (in
Python), when I do this, half the canonical s
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