Yes, this is due to the fact that SWIG doesn't expose nested classes. I've
fixed this for python so this should hopefully also be possible for java.
On Thu, Dec 5, 2013 at 10:15 PM, Yoel wrote:
> Thanks Noel
>
> On 5 December 2013 16:12, Noel O'Boyle wrote:
> > ...and in relation to this, I've
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 2013 19:15, Yoel wrote:
>> Thank Noel,
>>
>>
...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 2013 19:15, Yoel wrote:
> Thank Noel,
>
> I found the docs pretty clear. My problem isn’t with open babel
> directly
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
The ability to determine CIP rules is a nice feature to have but not really
necessary for most cheminformatics applications. If someone donates this
code it would certainly be considered a valuable addition. I rewrote most
of the sterochemistry code for OB a few years ago and never got around to
im
Ana this is great! Thanks so much for letting us take peek!
I'll take a closer look later.
Best wishes
Yoel
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---
Hi all,
Interesting discussion. I have been facing this problem recently and I did
not know that RDKit could do it.
I developed an algorithm to classify stereocenters as R/S and double bonds
as E/Z using CIP rules and the information provided by openbabel. There is
only one CIP rule that for
On 2013-12-03 22:28, Geoffrey Hutchison wrote:
> Craig's point is not that CIP is impossible, but rather from a
practical implementation side, it's easier to use other local stereo
designations. I might be wrong, but the codes that I can think of with
CIP implementations are all commercial, and as
On Wed, Dec 4, 2013 at 5:27 AM, Yoel wrote:
> Thanks Noel,
>
> Sure I agree and thanks for answering the original question. For
> Dimitri and I that are looking for assigning R and S your original
> answer was also the correct one since this winding property bears no
> relation to R/S because the
Thanks Noel,
Sure I agree and thanks for answering the original question. For
Dimitri and I that are looking for assigning R and S your original
answer was also the correct one since this winding property bears no
relation to R/S because there are no guarantees that atom 1 is the
smallest in prior
Let me just answer the original question as this is getting somewhat
out of hand. :-)
Open Babel stores tetrahedral stereochemistry in a Config object. A
typical Config object associated with a tetrahedral center may have
the following fields and values:
winding: "Clockwise"
center: 2
from: 1
refs
It does to me in the sense that I am think of assigning R and S - not
other labels - in a correct manner according to the CIP rules. Why do
I want to do that and not @/@@? Well because that how we do it. @/@@
it is useful for database search etc but we don’t use it in the
classroom or in the semina
Hi Yoel,
On Tue, Dec 3, 2013 at 7:44 PM, Yoel wrote:
> Hum! I’m pretty confident with what I know but the issue here is that
> you answer isn’t contributing to clarifying the question. The question
> is how to we determine the chirality of a centre regardless of how you
> may choose to represent
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 we usually ta
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
> inevitable will come down to applying the CIP rules. Do you disagree with
> that?
No, I disagree. Yes, there are implementations of the CIP rules in code.
Generally these are used when generating IUPAC names, and that's about it.
If I take a structure to a colleague to synthesize, I only need
Hum! I’m pretty confident with what I know but the issue here is that
you answer isn’t contributing to clarifying the question. The question
is how to we determine the chirality of a centre regardless of how you
may choose to represent it at a later point. And this problem
inevitable will come down
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 pretty sure I understand chirality. If I
> understood your article I see that explains how chirality is
> represented in smile notations but I sti
On 12/03/2013 03:11 PM, Yoel wrote:
> Craig,
>
> Thanks a lot for this. I do not know the smile notation in details
> however as a chemist I’m pretty sure I understand chirality. If I
> understood your article I see that explains how chirality is
> represented in smile notations but I still don’t
Craig,
Thanks a lot for this. I do not know the smile notation in details
however as a chemist I’m pretty sure I understand chirality. If I
understood your article I see that explains how chirality is
represented in smile notations but I still don’t see how do you know
what chirality to represent
On Tue, Dec 3, 2013 at 11:43 AM, Dimitri Maziuk wrote:
> On 12/03/2013 01:28 PM, Yoel wrote:
> > 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 assi
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
On 12/03/2013 01:28 PM, Yoel wrote:
> 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 th
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
On 12/03/2013 12:54 PM, Noel O'Boyle wrote:
> We don't support generation of R and S labels. However, we do store
> the stereochemistry. It's all stored in that config object. Clockwise
> and Anticlockwise are with respect to the stereo refs in the config.
> It should be clear enough from the docs
We don't support generation of R and S labels. However, we do store
the stereochemistry. It's all stored in that config object. Clockwise
and Anticlockwise are with respect to the stereo refs in the config.
It should be clear enough from the docs (googling "openbabel
stereochemistry"): http://openb
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.
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On 12/03/2013 12:19 PM, Yoel wrote:
> 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 p
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
On 2013-11-19 03:09, Noel O'Boyle wrote:
> We neither have R/S perception nor E/Z.
OK, thanks.
Dima
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We neither have R/S perception nor E/Z.
- Noel
On 19 November 2013 00:17, Dimitri Maziuk wrote:
> Someone familiar with OB's stereo perception (Geoff?)
>
> -- is there a way to get 'R' and 'S' labels from one of the *Stereo classes?
>
> Also, is there a way to find E and Z labels for a bond? --
Someone familiar with OB's stereo perception (Geoff?)
-- is there a way to get 'R' and 'S' labels from one of the *Stereo classes?
Also, is there a way to find E and Z labels for a bond? -- I could use
those, too.
TIA
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www
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