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Thanks Noel
On 5 December 2013 16:12, Noel O'Boyle wrote:
> ...and in relation to this, I've just checked and I'm afraid that
> access to the stereo object is missing in the Java bindings. I will
> add it to my TODO list.
>
> - Noel
>
> On 3 December 20
is it right that you don't support R and S? I'm new to openbabel like two
days old only but I have already seen that
"facade.GetTetrahedralStereo(atom.GetId())" will return OBTetrahedralConfig
(java) wich contain a Config structure/object with a winding property that
has two possible values: clockw
Ana this is great! Thanks so much for letting us take peek!
I'll take a closer look later.
Best wishes
Yoel
--
View this message in context:
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Sent from the General discussion mailing list archive at Nabbl
lockwise"
> center: 2
> from: 1
> refs: 3 4 5
>
> This means that looking from atom 1 towards 2, the atoms 3, 4, 5
> should be arranged clockwise. I hope you agree that this perfectly
> specifies the stereochemistry at atom 2.
>
> - Noel
>
>
> On 4 December 2013
seminars, in no place at all!
Clearly I made a mistake in trying to help Dimitri with the chemistry.
Good luck!
On 4 December 2013 00:00, Craig James wrote:
> Hi Yoel,
>
> On Tue, Dec 3, 2013 at 7:44 PM, Yoel wrote:
>>
>> Hum! I’m pretty confident with what I know but the issu
I meant I didn’t* see anyone that couldn’t do it
On 3 December 2013 23:36, Yoel wrote:
> Indeed it is hard but I have to STRONGLY disagree that we chemists
> assign R and S configuration in any other way that by applying the CIP
> rules… and for those molecules that are more complex w
Indeed it is hard but I have to STRONGLY disagree that we chemists
assign R and S configuration in any other way that by applying the CIP
rules… and for those molecules that are more complex we usually take
more time. Neither during my PhD years or my postgrad years I saw any
organic chemist that c
down to applying the CIP rules. Do you disagree
with that?
On 3 December 2013 22:34, Craig James wrote:
> On Tue, Dec 3, 2013 at 1:11 PM, Yoel wrote:
>>
>> Craig,
>>
>> Thanks a lot for this. I do not know the smile notation in details
>> however as a chemist I’m p
I’m going to
want to understand more about smile representation.
Cheers
Yoel
On 3 December 2013 15:51, Craig James-2 [via Open Babel]
wrote:
>
>
>
> On Tue, Dec 3, 2013 at 11:43 AM, Dimitri Maziuk <[hidden email]> wrote:
>>
>> On 12/03/2013 01:28 PM, Yoel wrote:
>&g
I find you one of the most interesting paper I know regarding this topic
http://pubs.acs.org/doi/abs/10.1021/ci990090v
The principle author P. Matos has several other papers on implementing CIP
algorithms
I have never tackle this problem myself but she is quite convinced that the
CIP are a most
It shouldn't be any different to CIP since those are the rules I was talking
about however I was being super short! There very interesting research
papers on the topic that I came across quite sometime ago. I am sure that
with time I could get one for you.
However, the local connectivity should be
Dimitri,
In this case you do know which way you are looking. For brevity let's
consider a tetrahedral carbon atom with four different substituents... the
first thing you do is to assign them priorities based on there atomic
numbers then you place the smallest priority backward... this gives you t
Thank Noel,
I found the docs pretty clear. My problem isn’t with open babel
directly but with understanding how to, for example, use standard out
to write my object using the java bindings…
the lit example:
converting this "std::cout <<
facade.GetTetrahedralStereo(atom->GetId()) << std::endl;"
t
I still haven't been able to print the winding property but obviously if it
turns out that the algorithm can't properly find the clockwise and
anticlockwise values then it is not useful unless ALA is the an exceptional
error.
--
View this message in context:
http://forums.openbabel.org/stereo-c
Is it right that you don't support R and S? I'm new to openbabel like two
days old only but I have already seen that
"facade.GetTetrahedralStereo(atom.GetId())" will return OBTetrahedralConfig
(java) wich contain a Config structure/object with a winding property that
has two possible values: clockw
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