Nabble - The Chemistry Development Kit

Re: [Cdk-devel] Please help moving the Wiki one last time

2008-10-13T02:21:17Z

On Mon, Oct 13, 2008 at 10:44 AM, Egon Willighagen
<egon.willighagen@...> wrote:
> On Thu, Oct 9, 2008 at 5:26 PM, Christoph Steinbeck <steinbeck@...> wrote:
>> Please help moving the old pages.
>
> Any ideas on how to coordinate this?

I have noted that the the wiki
http://www.steinbeck-molecular.de/cdk/index.php/Documentation only
contains a bit of the wiki contain we have...

We should also integrate the info from this wiki:

Egon

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From forum: cdk-user

Re: Please help moving the Wiki one last time

2008-10-13T02:21:17Z

On Mon, Oct 13, 2008 at 10:44 AM, Egon Willighagen
<egon.willighagen@...> wrote:
> On Thu, Oct 9, 2008 at 5:26 PM, Christoph Steinbeck <steinbeck@...> wrote:
>> Please help moving the old pages.
>
> Any ideas on how to coordinate this?

I have noted that the the wiki
http://www.steinbeck-molecular.de/cdk/index.php/Documentation only
contains a bit of the wiki contain we have...

We should also integrate the info from this wiki:

Egon

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From forum: cdk-devel

Re: [Cdk-devel] Please help moving the Wiki one last time

2008-10-13T01:44:46Z

On Thu, Oct 9, 2008 at 5:26 PM, Christoph Steinbeck <steinbeck@...> wrote:
> Please help moving the old pages.

Any ideas on how to coordinate this?

Egon

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From forum: cdk-user

Re: Please help moving the Wiki one last time

2008-10-13T01:44:46Z

On Thu, Oct 9, 2008 at 5:26 PM, Christoph Steinbeck <steinbeck@...> wrote:
> Please help moving the old pages.

Any ideas on how to coordinate this?

Egon

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From forum: cdk-devel

JUnit test failed - 2008-10-13

2008-10-13T00:23:24Z

compile-module:
[echo] Compiling classes for CDK's test-smarts module from src/test...
[echo] Datafiles defined: ${module.datafiles.present}
[echo] Extra files defined: ${module.extrafiles.present}
[echo] CDK dependencies defined: true
[echo] Library dependencies defined: true
[echo] Developer Library dependencies defined: true
[echo] Autogenerated files specified: ${module.autogenerated.present}
[javac] Compiling 9 source files to /home/rguha/src/java/cdk-1.2.x/cdk/build/test-smarts
[javac] /home/rguha/src/java/cdk-1.2.x/cdk/build/src/test-smarts/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java:33: package org.openscience.cdk.nonotify does not exist
[javac] import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
[javac] ^
[javac] /home/rguha/src/java/cdk-1.2.x/cdk/build/src/test-smarts/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java:189: cannot find symbol
[javac] symbol : variable NoNotificationChemObjectBuilder
[javac] location: class org.openscience.cdk.smiles.smarts.SMARTSQueryToolTest
[javac] NoNotificationChemObjectBuilder.getInstance().newMolecule();
[javac] ^
[javac] Note: /home/rguha/src/java/cdk-1.2.x/cdk/build/src/test-smarts/org/openscience/cdk/modulesuites/MsmartsTests.java uses unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 2 errors

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From forum: cdk-devel

Re: Benchmarks for CDK fp's - enrichment curves

2008-10-12T23:57:03Z

Rajarshi Guha wrote:
> I had thought of writing an article - but a blog post was less effort :)

I think that blog posts are generally less effort and maybe a good way
to document things.
We might indeed even think about converting CDKNews into a feed of
CDK-related, tutorial-like blog posts.

Cheers,

Chris

--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

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

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From forum: cdk-devel

Re: Benchmarks for CDK fp's - enrichment curves

2008-10-12T10:47:54Z

On Oct 12, 2008, at 11:44 AM, Christoph Steinbeck wrote:

> Excellent work - thanks a lot.
> We somehow need a way to automatically convert these recent blog items
> on CDK performance to CDK News articles. Or collect them elsewhere.

I had thought of writing an article - but a blog post was less effort :)

Maybe an RSS feed of CDK related articles could be created?

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From forum: cdk-devel

Re: Benchmarks for CDK fp's - enrichment curves

2008-10-12T08:44:29Z

Excellent work - thanks a lot.
We somehow need a way to automatically convert these recent blog items
on CDK performance to CDK News articles. Or collect them elsewhere.

Cheers,

Chris

Rajarshi Guha wrote:

> I did a quick analysis of the CDK fp's compared to some structural
> keys and it turns out the results aren't too bad!
>
> http://rguha.wordpress.com/2008/10/11/do-the-cdk-fingerprints-work/
>
> -------------------------------------------------------------------
> Rajarshi Guha <rguha@...>
> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
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> Bus error -- driver executed.
>
>
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--
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European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

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

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From forum: cdk-devel

Benchmarks for CDK fp's - enrichment curves

2008-10-10T22:49:29Z

I did a quick analysis of the CDK fp's compared to some structural
keys and it turns out the results aren't too bad!

http://rguha.wordpress.com/2008/10/11/do-the-cdk-fingerprints-work/

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Bus error -- driver executed.

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From forum: cdk-devel

Re: isotopic masses

2008-10-10T06:09:58Z

On Oct 10, 2008, at 3:59 AM, Miguel Rojas Cherto wrote:

> Hi,
>
>> Firstly, what is getExactMass resturning? It doesn't look like an
>> isotopic mass? Shouldn't the first line ~ 14.0? How does one get the
>> exact mass for a given atom?
>
> Well I think at the moment CDK only can create a IAtom from a String
> symbol or from a IElement object. That means that the atoms will be
> created systematic from its element (wich doesn't contain information
> about the neutrons characteristic of the isotope)
>
> For this reason I would propose that the IAtom is not only created
> from
> IElement but from a IIsotope too. That may be could help for this
> conflict.

Why not make the isotopic information a property of the atom, rather
than some sort of parent/sibling?

Also, does the SDF reader handle isotopic information?
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All seems condemned in the long run to approximate a state akin to
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-- James Martin

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From forum: cdk-user

Re: isotopic masses

2008-10-10T00:59:24Z

Hi,

> Firstly, what is getExactMass resturning? It doesn't look like an
> isotopic mass? Shouldn't the first line ~ 14.0? How does one get the
> exact mass for a given atom?

Well I think at the moment CDK only can create a IAtom from a String
symbol or from a IElement object. That means that the atoms will be
created systematic from its element (wich doesn't contain information
about the neutrons characteristic of the isotope)

For this reason I would propose that the IAtom is not only created from
IElement but from a IIsotope too. That may be could help for this
conflict.

Best regards,
Miquel

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From forum: cdk-user

isotopic masses

2008-10-09T14:44:45Z

Hi, I was a little hasty as usual, but found a method to configure
the isotopic information in a molecule. However it seems to be wrong:

public class isotopes {

public static void main(String[] args) throws CDKException,
IOException {
String s1 = "[14C]CC";
String s2 = "CCC";

IsotopeFactory ifac = IsotopeFactory.getInstance
(DefaultChemObjectBuilder.getInstance());

SmilesParser sp = new SmilesParser
(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol1 = sp.parseSmiles(s1);
IAtomContainer mol2 = sp.parseSmiles(s2);

ifac.configureAtoms(mol1);
ifac.configureAtoms(mol2);

for (IAtom atom : mol1.atoms()) {
System.out.println("atom.getExactMass() = " +
atom.getExactMass());
}

System.out.println("");

for (IAtom atom : mol1.atoms()) {
System.out.println("atom.getExactMass() = " +
atom.getExactMass());
}
}
}

The result of this code is

atom.getExactMass() = 12.0
atom.getExactMass() = 12.0
atom.getExactMass() = 12.0

atom.getExactMass() = 12.0
atom.getExactMass() = 12.0
atom.getExactMass() = 12.0

Firstly, what is getExactMass resturning? It doesn't look like an
isotopic mass? Shouldn't the first line ~ 14.0? How does one get the
exact mass for a given atom?

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After an instrument has been assembled, extra components will be found
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From forum: cdk-user

using isotopic masses

2008-10-09T14:37:19Z

Hi, if I have a SMILES string like [14C]CC I'd like to parse it and
get the exact masses of the atoms. However doing atom.getExactMass()
returns NULL and I think I need to configure the isotopic masses.

Does anybody have a code snippet showing how I can do that?

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From forum: cdk-user

Please help moving the Wiki one last time

2008-10-09T08:26:09Z

Dear all,

you may have heard that SourceForge made the surprising move to offer
MediaWiki as a hosted app and an alternative to their own wiki impl.

Since we like to have everything in one place, we would like to move the
wiki on last time and be set for ever :-)

I requested Mediawiki space for CDK and we've got it:

http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Main_Page

Please help moving the old pages.

People like Angel have already put in
effort to fill the wiki on steinbeck-molecular and I feel bad to ask
them to move again, but, again, I hope that will be the last time.
See the page on
http://www.steinbeck-molecular.de/cdk/index.php/JChemPaint

In addition, we need to move things from the "regular" sf wiki at
http://cdk.wiki.sourceforge.net/
to the new wiki at
http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Main_Page

Thanks a lot for your understanding.

Chris

--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

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

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From forum: cdk-user

Please help moving the Wiki one last time

2008-10-09T08:26:09Z

Dear all,

you may have heard that SourceForge made the surprising move to offer
MediaWiki as a hosted app and an alternative to their own wiki impl.

Since we like to have everything in one place, we would like to move the
wiki on last time and be set for ever :-)

I requested Mediawiki space for CDK and we've got it:

http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Main_Page

Please help moving the old pages.

People like Angel have already put in
effort to fill the wiki on steinbeck-molecular and I feel bad to ask
them to move again, but, again, I hope that will be the last time.
See the page on
http://www.steinbeck-molecular.de/cdk/index.php/JChemPaint

In addition, we need to move things from the "regular" sf wiki at
http://cdk.wiki.sourceforge.net/
to the new wiki at
http://apps.sourceforge.net/mediawiki/cdk/index.php?title=Main_Page

Thanks a lot for your understanding.

Chris

--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

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

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From forum: cdk-devel

Re: CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T05:37:51Z

On Oct 9, 2008, at 7:33 AM, Egon Willighagen wrote:

>>
>> Or do I need to reverse engineer their URL's?
>
> Yes, this is basically too what the Mylyn connector is doing too...
> but with only very minimal functionality... :(

Hmm, a quick test with Firebug seems to indicate that a lot of data
is passed via hidden fields, since they don't show up in the POST
request. Side effect of AJAX?

Anyway, looks like it won't happen soon :(

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From forum: cdk-devel

Re: CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T04:33:46Z

On Thu, Oct 9, 2008 at 1:23 PM, Rajarshi Guha <rguha@...> wrote:
>> BTW, wouldn't it be great if Nightly would automatically file a bug
>> report??
>
> Does SF provide a way (REST, CGI, etc) to file bug reports?

Not that I am aware of...

> Or do I need to reverse engineer their URL's?

Yes, this is basically too what the Mylyn connector is doing too...
but with only very minimal functionality... :(

Egon

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From forum: cdk-devel

Re: CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T04:23:35Z

On Oct 9, 2008, at 4:50 AM, Egon Willighagen wrote:

> On Thu, Oct 9, 2008 at 10:50 AM, Egon Willighagen
> <egon.willighagen@...> wrote:
>> Sorry, that was a Java 1.6 method:
>
> BTW, wouldn't it be great if Nightly would automatically file a bug
> report??

Does SF provide a way (REST, CGI, etc) to file bug reports? Or do I
need to reverse engineer their URL's?

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From forum: cdk-devel

Unit testing the io module

2008-10-09T02:21:09Z

Hi all,

triggered by a recent patch by Jonathan in the ReaderFactory and a
clean up I made yesterday, I ran into a problem with variants of how a
IChemObjectReader can be constructed... for 4-ish readers that is.
Also with a long list of missing unit tests in mind [0], I set off to
add missing unit tests... many of these common to all reader, so I've
extended the unit test class pattern for IO testing:

SomeReaderTest
extends SimpleChemObjectTest (new)
extends ChemObjectReaderTest (new)
extends ChemObjectIOReaderTest

Matching the interfaces for readers in the CDK: each Test class tests
the functionality of that interface.

This adds about 400 tests, breaking the 8000 unit tests for the whole
of the CDK. I'll be adding more missing unit tests during the day.

Egon

0.Nightly reported: "io 1068 1 2 99.72 709 methods in 152 class"

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From forum: cdk-devel

Re: CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T01:50:54Z

On Thu, Oct 9, 2008 at 10:50 AM, Egon Willighagen
<egon.willighagen@...> wrote:
> Sorry, that was a Java 1.6 method:

BTW, wouldn't it be great if Nightly would automatically file a bug report??

Egon

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From forum: cdk-devel

Re: CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T01:50:04Z

Sorry, that was a Java 1.6 method:

On Thu, Oct 9, 2008 at 9:02 AM, nightly. py <rguha@...> wrote:
> [javac] symbol : constructor IOException(java.lang.String,org.openscience.cdk.exception.CDKException)
> [javac] location: class java.io.IOException
> [javac] throw new IOException("Exception while setting the InputStream: " + e1.getMessage(), e1);
> [javac] ^

http://java.sun.com/javase/6/docs/api/java/io/IOException.html#IOException(java.lang.String,
java.lang.Throwable)

Egon

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From forum: cdk-devel

Re: CDK on Mono and .Net

2008-10-09T01:14:42Z

On Thu, Oct 9, 2008 at 8:14 AM, Matt Sprague <mesprague@...> wrote:
> I've just posted tutorial on my blog explaining how to use the CDK on
> Mono and the .Net framework with C# and IronPython. Anyone who is
> interested can check it out at sharperscience.blogspot.com.

I'm not a C#/Mono user, but it's great to see having access from that
language to the CDK too!

Egon

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From forum: cdk-devel

CDK Nightly Trunk Build Failed - 2008-10-09

2008-10-09T00:02:01Z

compile-module:
[echo] Compiling classes for CDK's io module from src/main...
[echo] Datafiles defined: true
[echo] Extra files defined: ${module.extrafiles.present}
[echo] CDK dependencies defined: true
[echo] Library dependencies defined: true
[echo] Developer Library dependencies defined: ${module.devellibdepends.present}
[echo] Autogenerated files specified: ${module.autogenerated.present}
[mkdir] Created dir: /home/rguha/src/java/cdk-1.2.x/cdk/build/src/io
[mkdir] Created dir: /home/rguha/src/java/cdk-1.2.x/cdk/build/io
[copy] Copying 167 files to /home/rguha/src/java/cdk-1.2.x/cdk/build/src/io
[javac] Compiling 167 source files to /home/rguha/src/java/cdk-1.2.x/cdk/build/io
[javac] /home/rguha/src/java/cdk-1.2.x/cdk/build/src/io/org/openscience/cdk/io/ReaderFactory.java:261: cannot find symbol
[javac] symbol : constructor IOException(java.lang.String,org.openscience.cdk.exception.CDKException)
[javac] location: class java.io.IOException
[javac] throw new IOException("Exception while setting the InputStream: " + e1.getMessage(), e1);
[javac] ^
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 1 error

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From forum: cdk-devel

CDK on Mono and .Net

2008-10-08T23:14:59Z

I've just posted tutorial on my blog explaining how to use the CDK on
Mono and the .Net framework with C# and IronPython. Anyone who is
interested can check it out at sharperscience.blogspot.com.

-Matt Sprague

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From forum: cdk-devel

Re: PDBReader and PDBWriter

2008-10-08T05:23:59Z

Hi Raphael,

I still need to check your patches in detail, but...

On Wed, Oct 1, 2008 at 2:50 PM, Raphael A. Bauer
<raphael.a.bauer@...> wrote:
> => I added a method called setLazyMode(boolean) that manually switches
> on the protein mode and
> solves this thing.
> - I also added a method setParseHetAtoms(boolean) that omits parsing
> of hetero atoms for "performance" reasons.

These two should be handled as IOSettings... see this CDK News 1.2 for
some information on it.

Egon

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From forum: cdk-devel

[ cdk-Feature Requests-2117572 ] Detect Chiral Centers using 3D coordinates

2008-10-06T13:14:09Z

Feature Requests item #2117572, was opened at 2008-09-18 11:25
Message generated for change (Comment added) made by shk3
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Sebastian Rohrer (srohrer)
Assigned to: Nobody/Anonymous (nobody)
Summary: Detect Chiral Centers using 3D coordinates

Initial Comment:
Here is a SD-File of compounds with Chiral Centers that are not detected by
org.openscience.cdk.geometry.BondTools.isStereo.

The compounds originate from PubChem, explicit Hs were added and 3D-structures generated with CORINA.

Thanks for having a look at it.

Sebastian

----------------------------------------------------------------------

>Comment By: Stefan Kuhn (shk3)
Date: 2008-10-06 22:14

Message:
Well, depends on what you want to do, I suppose. Detecting where a
potential chiral centre is, is probably possible (at least for tetrahedral
chiralities) without the coordinates. The current method (which is not well
named, as I realize) doesn't just detect this, but it detects fully
specified chiral centres, i. e. such, where the positions of the atoms are
fully given. This is the case in the example only using 3D coordinates,
obviously.

----------------------------------------------------------------------

Comment By: Nobody/Anonymous (nobody)
Date: 2008-10-06 21:09

Message:
I could be wrong, but I don't think that coordinates are necessary for
detection of these chiral centers. I'll look into this and see if it can be
fixed with a minimum of hassle.

-Matt

----------------------------------------------------------------------

Comment By: Stefan Kuhn (shk3)
Date: 2008-10-06 18:04

Message:
The method only works on molecules containing wedge bonds. It does not take
3d coordinates into account. I put this into the javadoc comment. I make
this a bug request, but do not expect it to be done soon (3d handling is
weak in cdk overall, so the method would not be of much use _given the
current cdk - e. g. smiles generation also works on 2d/wedges as well, to
make this 3d more methods would need to be adopted etc.)

----------------------------------------------------------------------

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From forum: cdk-devel

[ cdk-Feature Requests-2117572 ] Detect Chiral Centers using 3D coordinates

2008-10-06T12:09:29Z

Feature Requests item #2117572, was opened at 2008-09-18 09:25
Message generated for change (Comment added) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Sebastian Rohrer (srohrer)
Assigned to: Nobody/Anonymous (nobody)
Summary: Detect Chiral Centers using 3D coordinates

Initial Comment:
Here is a SD-File of compounds with Chiral Centers that are not detected by
org.openscience.cdk.geometry.BondTools.isStereo.

The compounds originate from PubChem, explicit Hs were added and 3D-structures generated with CORINA.

Thanks for having a look at it.

Sebastian

----------------------------------------------------------------------

Comment By: Nobody/Anonymous (nobody)
Date: 2008-10-06 19:09

Message:
I could be wrong, but I don't think that coordinates are necessary for
detection of these chiral centers. I'll look into this and see if it can be
fixed with a minimum of hassle.

-Matt

----------------------------------------------------------------------

Comment By: Stefan Kuhn (shk3)
Date: 2008-10-06 16:04

Message:
The method only works on molecules containing wedge bonds. It does not take
3d coordinates into account. I put this into the javadoc comment. I make
this a bug request, but do not expect it to be done soon (3d handling is
weak in cdk overall, so the method would not be of much use _given the
current cdk - e. g. smiles generation also works on 2d/wedges as well, to
make this 3d more methods would need to be adopted etc.)

----------------------------------------------------------------------

You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

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From forum: cdk-devel

[ cdk-Feature Requests-1941417 ] JChemPaint background color

2008-10-06T09:04:59Z

Feature Requests item #1941417, was opened at 2008-04-13 18:46
Message generated for change (Settings changed) made by shk3
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=1941417&group_id=20024

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not just the latest update.
Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: Angel Herraez (aherraez)
Assigned to: Stefan Kuhn (shk3)
Summary: JChemPaint background color

Initial Comment:
It would be nice that
<param name="background" value="12632256">
would accept hexadecimal values for color, say:
<param name="background" value="#C0C0C0">

(Easier to code, particularly inside HTML, JS, CSS)

----------------------------------------------------------------------

Comment By: Stefan Kuhn (shk3)
Date: 2008-09-15 18:11

Message:
implemented in 1.0.x branch

----------------------------------------------------------------------

You can respond by visiting:
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From forum: cdk-devel

[ cdk-Feature Requests-2117572 ] Detect Chiral Centers using 3D coordinates

2008-10-06T09:04:31Z

Feature Requests item #2117572, was opened at 2008-09-18 11:25
Message generated for change (Comment added) made by shk3
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Sebastian Rohrer (srohrer)
>Assigned to: Nobody/Anonymous (nobody)
>Summary: Detect Chiral Centers using 3D coordinates

Initial Comment:
Here is a SD-File of compounds with Chiral Centers that are not detected by
org.openscience.cdk.geometry.BondTools.isStereo.

The compounds originate from PubChem, explicit Hs were added and 3D-structures generated with CORINA.

Thanks for having a look at it.

Sebastian

----------------------------------------------------------------------

>Comment By: Stefan Kuhn (shk3)
Date: 2008-10-06 18:04

Message:
The method only works on molecules containing wedge bonds. It does not take
3d coordinates into account. I put this into the javadoc comment. I make
this a bug request, but do not expect it to be done soon (3d handling is
weak in cdk overall, so the method would not be of much use _given the
current cdk - e. g. smiles generation also works on 2d/wedges as well, to
make this 3d more methods would need to be adopted etc.)

----------------------------------------------------------------------

You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T08:59:16Z

Egon Willighagen wrote:

On Mon, Oct 6, 2008 at 4:48 PM, Nina Jeliazkova nina@... wrote:

I would also be interested in finding a solution to the MOE SMARTS
extensions. Does MOE documentation come only with their products?

With the supporting info the implementation is pretty quick and
straightforward (here is mine from Friday evening :)
https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.java


At least I got first post :)

Are your PkaNode use the SMARTSQueryTool too? How did you deal with

https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKANode.java

the difficult SMARTS?

Actually it uses Smarts implementation written by my colleague. But nevertheless, difficult smiles are not dealt yet - too much to expect from a quick implementation. I hope it will be possible to rewrite the smarts, given MOE documentation.

Regards,
Nina

Egon

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From forum: cdk-devel

Re: [Cdk-commits] SF.net SVN: cdk:[12559] cdk/branches/cdk-1.0.x

2008-10-06T08:10:42Z

On Mon, Oct 6, 2008 at 5:06 PM, <shk3@...> wrote:
> Revision: 12559
> http://cdk.svn.sourceforge.net/cdk/?rev=12559&view=rev
> Author: shk3
> Date: 2008-10-06 15:06:39 +0000 (Mon, 06 Oct 2008)
>
> Log Message:
> -----------
> mol files are now scaled to angstrom (roughly)

Not really, I hope... That does not really fit my laptop screen... :)

Egon

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From forum: cdk-devel

Re: help in MoleculeListViewer class

2008-10-06T08:09:45Z

Weirdly enough, this code works for me on windows. What operating
system are you using?

gilleain torrance

On Mon, Oct 6, 2008 at 4:04 PM, Rajarshi Guha <rguha@...> wrote:

> You could take a look at
>
> http://cheminfo.informatics.indiana.edu/~rguha/code/java/#depict
>
> On Oct 6, 2008, at 6:47 AM, Bipin Bihari wrote:
>
>> Dear sir,
>> I needed the coordinate of a molecule and wanted to display on
>> MoleculeListViewer, there were no error and I got the Panel for
>> MoleculeListviewer but there were no structure of molecule, it was
>> blank.
>> The program is give below and the same is attached.
>> I am using jdk1.6.
>> Please guide me what correctios are needed?
>>
>> package org.openscience.cdk.myPackage;
>>
>> import org.openscience.cdk.smiles.SmilesParser;
>> import org.openscience.cdk.interfaces.IMolecule;
>> import org.openscience.cdk.Molecule;
>> import org.openscience.cdk.layout.StructureDiagramGenerator;
>> import org.openscience.cdk.applications.swing.MoleculeListViewer;
>> import org.openscience.cdk.applications.swing.MoleculeViewer2D;
>> import org.openscience.cdk.exception.CDKException;
>>
>> public class MyMoleculeViewer
>> {
>> public MyMoleculeViewer()
>> {
>> SmilesParser smileParser = new SmilesParser();
>> MoleculeListViewer moleculeListViewer = new
>> MoleculeListViewer();
>> String smiles = new String("c1ccccc1");
>> try
>> {
>> IMolecule molecule = smileParser.parseSmiles
>> (smiles);
>> StructureDiagramGenerator
>> structureDiagramGenerator = new
>> StructureDiagramGenerator();
>> MoleculeViewer2D moleculeViewer2D = new
>> MoleculeViewer2D();
>> structureDiagramGenerator.setMolecule
>> ((Molecule)molecule.clone());
>>
>> structureDiagramGenerator.generateCoordinates();
>> moleculeViewer2D.setAtomContainer
>> (structureDiagramGenerator.getMolecule());
>> moleculeListViewer.addStructure
>> (moleculeViewer2D,
>> "Structure");
>> }
>> catch(Exception e)
>> {
>> e.printStackTrace();
>> }
>> }
>>
>> public static void main(String args[])
>> {
>> new MyMoleculeViewer();
>> }
>> }
>>
>> thanks
>> bipin
>> ---------------------------------------------------
>> Bipin Bihari,
>> Student(PGDB),
>> Institute of Bioinformatics and Applied Biotechmology(IBAB),
>> G-05, Tech Park Mall, ITPB, White field road,
>> Bangalore, Karnatka-560066,
>> India.
>> ---------------------------------------------------
>> <MyMoleculeViewer.java>-----------------------------------------------
>> --------------------------
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>
> -------------------------------------------------------------------
> Rajarshi Guha <rguha@...>
> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
> -------------------------------------------------------------------
> All life evolves by the differential survival of replicating entities.
> -- Dawkins
>
>
>
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From forum: cdk-devel

Re: help in MoleculeListViewer class

2008-10-06T08:04:13Z

You could take a look at

http://cheminfo.informatics.indiana.edu/~rguha/code/java/#depict

On Oct 6, 2008, at 6:47 AM, Bipin Bihari wrote:

> Dear sir,
> I needed the coordinate of a molecule and wanted to display on
> MoleculeListViewer, there were no error and I got the Panel for
> MoleculeListviewer but there were no structure of molecule, it was
> blank.
> The program is give below and the same is attached.
> I am using jdk1.6.
> Please guide me what correctios are needed?
>
> package org.openscience.cdk.myPackage;
>
> import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.Molecule;
> import org.openscience.cdk.layout.StructureDiagramGenerator;
> import org.openscience.cdk.applications.swing.MoleculeListViewer;
> import org.openscience.cdk.applications.swing.MoleculeViewer2D;
> import org.openscience.cdk.exception.CDKException;
>
> public class MyMoleculeViewer
> {
> public MyMoleculeViewer()
> {
> SmilesParser smileParser = new SmilesParser();
> MoleculeListViewer moleculeListViewer = new
> MoleculeListViewer();
> String smiles = new String("c1ccccc1");
> try
> {
> IMolecule molecule = smileParser.parseSmiles
> (smiles);
> StructureDiagramGenerator
> structureDiagramGenerator = new
> StructureDiagramGenerator();
> MoleculeViewer2D moleculeViewer2D = new
> MoleculeViewer2D();
> structureDiagramGenerator.setMolecule
> ((Molecule)molecule.clone());
>
> structureDiagramGenerator.generateCoordinates();
> moleculeViewer2D.setAtomContainer
> (structureDiagramGenerator.getMolecule());
> moleculeListViewer.addStructure
> (moleculeViewer2D,
> "Structure");
> }
> catch(Exception e)
> {
> e.printStackTrace();
> }
> }
>
> public static void main(String args[])
> {
> new MyMoleculeViewer();
> }
> }
>
> thanks
> bipin
> ---------------------------------------------------
> Bipin Bihari,
> Student(PGDB),
> Institute of Bioinformatics and Applied Biotechmology(IBAB),
> G-05, Tech Park Mall, ITPB, White field road,
> Bangalore, Karnatka-560066,
> India.
> ---------------------------------------------------
> <MyMoleculeViewer.java>-----------------------------------------------
> --------------------------
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-------------------------------------------------------------------
Rajarshi Guha <rguha@...>
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-------------------------------------------------------------------
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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T08:01:17Z

On Mon, Oct 6, 2008 at 4:02 PM, Rajarshi Guha <rguha@...> wrote:

>
> On Oct 6, 2008, at 9:44 AM, Egon Willighagen wrote:
>
>> On Mon, Oct 6, 2008 at 3:41 PM, Rajarshi Guha <rguha@...> wrote:
>>>
>>> On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote:
>>>
>>>> I identified at least the following constructs not supported:
>>>>
>>>> 1. [#G6] (or [#G7] etc)
>>>
>>> Shouldn't be difficult I expect
>
> Personally, I'd go for rewriting the above as an OR.
>
> Also if G6 indicates Group 6 of the periodic table then the elements are Cr,
> Mo, W so I'm not sure how it matches C, S etc

Maybe Group VI of the main group elements?

[1] describes [#G7!F] as "halogens (other than fluorine)"...

Egon

1.http://www.chemcomp.com/journal/sdtools.htm

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From forum: cdk-devel