Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Noel O'Boyle <no228@ca...>]

Your image is exactly what I get also. This is the problem.

It should be closer to the image attached, which is exactly the same
image shown in the JCP applet on the page. There should not be any
numbers at the vertices of the benzene ring (presumably these are for
debugging SMILES or something?). When I first saw the result on this
page (a few months ago), I was disappointed when I compared it to the
commercial online structure generators.

(Image created by saving the mdl file created by the Jmol applet on the
chemistry-development-kit page for benzene, and running Rajarshi's
2DBatchGen on the result)

Regards,
 Noel

On Wed, 2006-02-08 at 13:53 +0100, Christoph Steinbeck wrote:
> Noel O'Boyle wrote:
> > If http://www.chemistry-development-kit.org is to showcase the CDK
> > effectively, the 2D drawer should be updated to show the sort of
> > diagrams that Rajarshi's code is able to create. At the moment, the 2D
> > diagrams on the website are not a good advertisement for the CDK. (For
> > example, try importing benzene from the structure editor)
> 
> Well, Rajarshi's code is no different from this code, since it both uses my 
> Structure Diagram Generator.
> No matter what I do (draw benzene and import it, insert c1ccccc1 in the smiles 
> import) I get the display shown below.
> 
> Can you describe what you did and what you get. Detailed bug reports and a 
> pictorial (if possible) depiction of the outcome help a lot.
> 
> > Also, is there some problem with the SMILES reader (or with me)? When I
> > try my standard test smile of "CCCC", it says "No valid smiles".
> 
> I can confirm this. It must be fixed.
> 
> Cheers,
> 
> Chris
> 

[Cdk-devel] Comment on chemistry-development-kit.org

[Noel O'Boyle <no228@ca...>]

If http://www.chemistry-development-kit.org is to showcase the CDK
effectively, the 2D drawer should be updated to show the sort of
diagrams that Rajarshi's code is able to create. At the moment, the 2D
diagrams on the website are not a good advertisement for the CDK. (For
example, try importing benzene from the structure editor)

Also, is there some problem with the SMILES reader (or with me)? When I
try my standard test smile of "CCCC", it says "No valid smiles".

Regards,
 Noel

Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Stefan Kuhn <stefan.kuhn@un...>]

Hi Noel,
thanks for you comments and my humble excuses. I will have a look at this.
One problem: If or when I update the cdk on cdk.org, the 3d generation wi=
ll=20
mostly fail due to this still existing bug with modelbuilder3d.
Stefan

Am Tuesday 07 February 2006 16:54 schrieb Noel O'Boyle:
> If http://www.chemistry-development-kit.org is to showcase the CDK
> effectively, the 2D drawer should be updated to show the sort of
> diagrams that Rajarshi's code is able to create. At the moment, the 2D
> diagrams on the website are not a good advertisement for the CDK. (For
> example, try importing benzene from the structure editor)
>
> Also, is there some problem with the SMILES reader (or with me)? When I
> try my standard test smile of "CCCC", it says "No valid smiles".
>
> Regards,
>  Noel
>
>
>
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--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Christoph Steinbeck <c.steinbeck@un...>]

Noel O'Boyle wrote:
> If http://www.chemistry-development-kit.org is to showcase the CDK
> effectively, the 2D drawer should be updated to show the sort of
> diagrams that Rajarshi's code is able to create. At the moment, the 2D
> diagrams on the website are not a good advertisement for the CDK. (For
> example, try importing benzene from the structure editor)

Well, Rajarshi's code is no different from this code, since it both uses =
my=20
Structure Diagram Generator.
No matter what I do (draw benzene and import it, insert c1ccccc1 in the s=
miles=20
import) I get the display shown below.

Can you describe what you did and what you get. Detailed bug reports and =
a=20
pictorial (if possible) depiction of the outcome help a lot.

> Also, is there some problem with the SMILES reader (or with me)? When I
> try my standard test smile of "CCCC", it says "No valid smiles".

I can confirm this. It must be fixed.

Cheers,

Chris

--=20
Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck@...)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d=
e)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Noel O'Boyle <no228@ca...>]

Your image is exactly what I get also. This is the problem.

It should be closer to the image attached, which is exactly the same
image shown in the JCP applet on the page. There should not be any
numbers at the vertices of the benzene ring (presumably these are for
debugging SMILES or something?). When I first saw the result on this
page (a few months ago), I was disappointed when I compared it to the
commercial online structure generators.

(Image created by saving the mdl file created by the Jmol applet on the
chemistry-development-kit page for benzene, and running Rajarshi's
2DBatchGen on the result)

Regards,
 Noel

On Wed, 2006-02-08 at 13:53 +0100, Christoph Steinbeck wrote:
> Noel O'Boyle wrote:
> > If http://www.chemistry-development-kit.org is to showcase the CDK
> > effectively, the 2D drawer should be updated to show the sort of
> > diagrams that Rajarshi's code is able to create. At the moment, the 2D
> > diagrams on the website are not a good advertisement for the CDK. (For
> > example, try importing benzene from the structure editor)
> 
> Well, Rajarshi's code is no different from this code, since it both uses my 
> Structure Diagram Generator.
> No matter what I do (draw benzene and import it, insert c1ccccc1 in the smiles 
> import) I get the display shown below.
> 
> Can you describe what you did and what you get. Detailed bug reports and a 
> pictorial (if possible) depiction of the outcome help a lot.
> 
> > Also, is there some problem with the SMILES reader (or with me)? When I
> > try my standard test smile of "CCCC", it says "No valid smiles".
> 
> I can confirm this. It must be fixed.
> 
> Cheers,
> 
> Chris
> 

Re: [Cdk-devel] Comment on chemistry-development-kit.org

[<tenebrelux@gm...>]

hi,

> Your image is exactly what I get also. This is the problem.
I think that is more an aesthetic problem. When one calculates atom
properties (e.g. QSAR) than this numbering is quite helpful (currently not
displayed in the showcase). I think it resembles the code from NmrShiftDB
where one has to assign shifts to atoms. For my chemist view this picture is
ok (because of the mentioned reasons before, I find this better than the
commercial ones) , but of course when you want to show this in presentations
than it might look a little odd. I dont know if this is possible, but the
solution would be a numbering on/off. 


best regards 
Christian



> It should be closer to the image attached, which is exactly the same
> image shown in the JCP applet on the page. There should not be any
> numbers at the vertices of the benzene ring (presumably these are for
> debugging SMILES or something?). When I first saw the result on this
> page (a few months ago), I was disappointed when I compared it to the
> commercial online structure generators.
> 
> (Image created by saving the mdl file created by the Jmol applet on the
> chemistry-development-kit page for benzene, and running Rajarshi's
> 2DBatchGen on the result)
> 
> Regards,
>  Noel
> 
> On Wed, 2006-02-08 at 13:53 +0100, Christoph Steinbeck wrote:
> > Noel O'Boyle wrote:
> > > If http://www.chemistry-development-kit.org is to showcase the CDK
> > > effectively, the 2D drawer should be updated to show the sort of
> > > diagrams that Rajarshi's code is able to create. At the moment, the 2D
> > > diagrams on the website are not a good advertisement for the CDK. (For
> > > example, try importing benzene from the structure editor)
> > 
> > Well, Rajarshi's code is no different from this code, since it both uses
> my 
> > Structure Diagram Generator.
> > No matter what I do (draw benzene and import it, insert c1ccccc1 in the
> smiles 
> > import) I get the display shown below.
> > 
> > Can you describe what you did and what you get. Detailed bug reports and
> a 
> > pictorial (if possible) depiction of the outcome help a lot.
> > 
> > > Also, is there some problem with the SMILES reader (or with me)? When
> I
> > > try my standard test smile of "CCCC", it says "No valid smiles".
> > 
> > I can confirm this. It must be fixed.
> > 
> > Cheers,
> > 
> > Chris
> > 
> 

-- 
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Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Stefan Kuhn <stefan.kuhn@un...>]

Am Wednesday 08 February 2006 14:42 schrieb tenebrelux@...:
> hi,
>
> > Your image is exactly what I get also. This is the problem.
>
> I think that is more an aesthetic problem. When one calculates atom
> properties (e.g. QSAR) than this numbering is quite helpful (currently =
not
> displayed in the showcase). I think it resembles the code from NmrShift=
DB
> where one has to assign shifts to atoms. For my chemist view this pictu=
re
> is ok (because of the mentioned reasons before, I find this better than=
 the
> commercial ones) , but of course when you want to show this in
> presentations than it might look a little odd. I dont know if this is
> possible, but the solution would be a numbering on/off.
This is what I will do. The numbering is needed when doing the qsar=20
predicitons, but might look odd in other situations.
Stefan
>
>
> best regards
> Christian
>
> > It should be closer to the image attached, which is exactly the same
> > image shown in the JCP applet on the page. There should not be any
> > numbers at the vertices of the benzene ring (presumably these are for
> > debugging SMILES or something?). When I first saw the result on this
> > page (a few months ago), I was disappointed when I compared it to the
> > commercial online structure generators.
> >
> > (Image created by saving the mdl file created by the Jmol applet on t=
he
> > chemistry-development-kit page for benzene, and running Rajarshi's
> > 2DBatchGen on the result)
> >
> > Regards,
> >  Noel
> >
> > On Wed, 2006-02-08 at 13:53 +0100, Christoph Steinbeck wrote:
> > > Noel O'Boyle wrote:
> > > > If http://www.chemistry-development-kit.org is to showcase the CD=
K
> > > > effectively, the 2D drawer should be updated to show the sort of
> > > > diagrams that Rajarshi's code is able to create. At the moment, t=
he
> > > > 2D diagrams on the website are not a good advertisement for the C=
DK.
> > > > (For example, try importing benzene from the structure editor)
> > >
> > > Well, Rajarshi's code is no different from this code, since it both
> > > uses
> >
> > my
> >
> > > Structure Diagram Generator.
> > > No matter what I do (draw benzene and import it, insert c1ccccc1 in=
 the
> >
> > smiles
> >
> > > import) I get the display shown below.
> > >
> > > Can you describe what you did and what you get. Detailed bug report=
s
> > > and
> >
> > a
> >
> > > pictorial (if possible) depiction of the outcome help a lot.
> > >
> > > > Also, is there some problem with the SMILES reader (or with me)? =
When
> >
> > I
> >
> > > > try my standard test smile of "CCCC", it says "No valid smiles".
> > >
> > > I can confirm this. It must be fixed.
> > >
> > > Cheers,
> > >
> > > Chris

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

Re: [Cdk-devel] Comment on chemistry-development-kit.org

[Stefan Kuhn <stefan.kuhn@un...>]

Hi all,
I changed cdk.org to
1) accept smiles
2) not to show atom numbers by default
3) to load the current structure in jcp
4) to use latest cdk
Stefan
--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu