Nabble - The Chemistry Development Kit

[ cdk-Patches-2740730 ] SSSRFinder fix

2009-12-23T04:44:49Z

Patches item #2740730, was opened at 2009-04-07 15:34
Message generated for change (Comment added) made by egonw
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2740730&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: Accepted
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Egon Willighagen (egonw)
Summary: SSSRFinder fix

Initial Comment:

Some issues with SSSRFinder have come to light, Ulrich Bauer has been contacted and is having a look.

I've created a new patch to make the following fixes:
- correct implementation of methods findEssentialRings(), findRelevantRings() and findSSSR() in SSSRFinder
- avoiding duplicate ringsets in output result (occurs with bucky balls sometimes, example handed over to Ulrich)

Initially: no files/patch attached, but see e-mail below for more info

_____________________________

------- Original Message --------
Subject: Re: SSSR (CDK)
Date: Mon, 6 Apr 2009 15:28:12 +0200
From: Ulrich Bauer <bauer@...>
To: Mark Rijnbeek <markr@...>

>> Hi Mark,
>>
>> this error seems to have crept in at revisions 5704 and 12004. Now
>> cycleBasis().cycles() is returned instead of
>> cycleBasis().relevantCycles().keySet(); similarly for the essential
>> cycles. Maybe you can fix this, I do not have my repository set up
>> and working yet.
>>
>> Best regards, Ulrich
>>
>

> I noticed the difference for the methods, one returns a Map, the
> other a Collection.
> So the change would be as below ?
>
> public IRingSet findEssentialRings() {
> if (atomContainer==null) {
> return null;
> }
> IRingSet ringSet =
> toRingSet(atomContainer,cycleBasis().essentialCycles());
> return ringSet;
> }
>
> public IRingSet findRelevantRings() {
> if (atomContainer==null) {
> return null;
> }
> IRingSet ringSet = toRingSet(atomContainer,
> cycleBasis().relevantCycles().keySet());
> return ringSet; }
>
>
> I'll ask for a patch on cdk-devel.
>

Yes, that change looks correct. Thanks for the info about git.
The Map returned by cycleBasis().relevantCycles() provides additional
information about the relevant cycles; since we are only interested in
the cycles themselves, the keySet() of this map is needed.

Ulrich
-----------------------------

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

>Comment By: Egon Willighagen (egonw)
Date: 2009-12-23 13:44

Message:
Applied to master.

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

Comment By: Mark Rijnbeek (mark_rynbeek)
Date: 2009-10-26 18:05

Message:
>>>The patch has a few shortcomings...
Which are?

>>but most importantly, it lack unit tests...
Done, new attachment

>>For the rest, I'd like to see it use parameterized types: List<Foo>
instead of just List, etc.
I tried for example
List<Edge> edges = edgesOf(vertex);
.. but then get IDE warnings (unsound conversion), and that's because in
org._3pq
public java.util.List edgesOf(java.lang.Object p1) is not parameterized.
So I won't make changes there.

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

Comment By: Egon Willighagen (egonw)
Date: 2009-09-18 22:53

Message:
The patch has a few shortcomings... but most importantly, it lack unit
tests...

For the rest, I'd like to see it use parameterized types: List<Foo>
instead of just List, etc.

BTW, anyone can fix such shortcomings...

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

Comment By: Mark Rijnbeek (mark_rynbeek)
Date: 2009-07-27 17:59

Message:
Patch received from Ulrich Bauer, see attachment - git patch

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

Comment By: Mark Rijnbeek (mark_rynbeek)
Date: 2009-06-10 10:28

Message:

More fixes should be included in this patch than just the one mentioned in
the report. But Egon (7th april) suggested "Please file that quick fix
anyway, so that we have that as back up when the other fix takes more
time..."
Therefore the empty patch; now waiting for fixes from Ulrich (none so far
) to be combined into one patch to fix bugs in the SSSRFinder.

I can make a small patch just fixing what is listed in the report text.
But I am actually not sure that those suggested lines work. I gave a bucky
ball to the SSSRFinder with these new code lines, but got a whole new error
thrown.

If Ulrich doesn't have time for a fix of the SSSRFinder then someone else
will have to do it. I'll check with Chris if we should do it here at the
EBI. It's not trivial, the bigger patch would need to fix the current
duplicate ring sets that can occur in the output of SSSRFinder when
processing a bucky ball.

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

Comment By: Rajarshi Guha (rajarshi)
Date: 2009-06-10 04:11

Message:
I see the changes in the text of the report and they look OK - but it would
be useful to have a patch and associated unit tests (if relevant) that I
could apply to a branch

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

Comment By: Stefan Kuhn (shk3)
Date: 2009-06-09 17:26

Message:
I can't really see what's the patch here.

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

You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2740730&group_id=20024

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: [Cdk-commits] SF.net SVN: cdk:[15222] jchempaint/trunk/src/main/org/openscience/ jchempaint/renderer

2009-12-22T07:37:44Z

On Tue, Dec 22, 2009 at 4:33 PM, Mark Rijnbeek <markr@...> wrote:
> okay, done; restored the existing class.

Great! I'll review it for inclusion in CDK master. New classes are
much easier to add.

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: [Cdk-commits] SF.net SVN: cdk:[15222] jchempaint/trunk/src/main/org/openscience/ jchempaint/renderer

2009-12-22T07:33:23Z

hi Egon,

okay, done; restored the existing class.

> Hi Mark,
>
> I suggest to make a separate class for this, instead of changing an
> existing color scheme.
>
> Egon
>
> On Tue, Dec 22, 2009 at 3:36 PM, <mark_rynbeek@...> wrote:
>> Log Message:
>> -----------
>> Element colurs according to RasMol/Chime.
>> https://sourceforge.net/apps/trac/jchempaint/ticket/41
>>
>> Modified Paths:
>> --------------
>> jchempaint/trunk/src/main/org/openscience/jchempaint/renderer/RendererModel.java
>> jchempaint/trunk/src/main/org/openscience/jchempaint/renderer/color/CDK2DAtomColors.java
>
> Egon
>

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: [Cdk-commits] SF.net SVN: cdk:[15222] jchempaint/trunk/src/main/org/openscience/ jchempaint/renderer

2009-12-22T06:57:52Z

Hi Mark,

I suggest to make a separate class for this, instead of changing an
existing color scheme.

Egon

On Tue, Dec 22, 2009 at 3:36 PM, <mark_rynbeek@...> wrote:
> Log Message:
> -----------
> Element colurs according to RasMol/Chime.
> https://sourceforge.net/apps/trac/jchempaint/ticket/41
>
> Modified Paths:
> --------------
> jchempaint/trunk/src/main/org/openscience/jchempaint/renderer/RendererModel.java
> jchempaint/trunk/src/main/org/openscience/jchempaint/renderer/color/CDK2DAtomColors.java

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: JavaDoc for 1.2.3 broken

2009-12-22T00:38:26Z

On Mon, Dec 21, 2009 at 8:30 PM, Andrew Dalke <dalke@...> wrote:
> I've now written my first CDK program, and my third Java program ever. ;)

Cool!

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: JavaDoc for 1.2.3 broken

2009-12-21T11:30:39Z

Thanks for updating the link.

I've now written my first CDK program, and my third Java program ever. ;)

Andrew
dalke@...

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: JavaDoc for 1.2.3 broken

2009-12-21T00:41:41Z

Hi Andrew,

On Mon, Dec 21, 2009 at 3:53 AM, Andrew Dalke <dalke@...> wrote:
> The page at
> http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Documentation
> links to
> JavaDoc for 1.2.3
> at
> http://pele.farmbio.uu.se/nightly-1.2.3/cdk-javadoc-1.2.3/index.html
> which does not work. Neither does changing that to 1.2.4 or 1.2.4.1

Fixed.

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: JavaDoc for 1.2.3 broken

2009-12-20T19:24:03Z

Looks like a bug in the nightly build (?) The correct link to the Javadocs is

http://pele.farmbio.uu.se/nightly-1.2.3/cdk-javadoc-1.2.4/index.html

On Sun, Dec 20, 2009 at 9:53 PM, Andrew Dalke <dalke@...> wrote:

Hi all!

The page at
http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Documentation
links to
JavaDoc for 1.2.3
at
http://pele.farmbio.uu.se/nightly-1.2.3/cdk-javadoc-1.2.3/index.html
which does not work. Neither does changing that to 1.2.4 or 1.2.4.1

Andrew
dalke@...

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

--
Rajarshi Guha
NIH Chemical Genomics Center

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

JavaDoc for 1.2.3 broken

2009-12-20T18:53:23Z

Hi all!

The page at
http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Documentation
links to
JavaDoc for 1.2.3
at
http://pele.farmbio.uu.se/nightly-1.2.3/cdk-javadoc-1.2.3/index.html
which does not work. Neither does changing that to 1.2.4 or 1.2.4.1

Andrew
dalke@...

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Setting aromaticity flag with SMILESWriter

2009-12-20T11:30:39Z

On Sun, Dec 20, 2009 at 6:07 PM, Noel O'Boyle <baoilleach@...> wrote:
> Re CDK 1.2.3...
>
> I have been using the SMILESWriter in cinfony to write out SMILES
> strings, but a user reported that benzene was being written out as
> C1CCCCC1. If instead I use the SmilesGenerator, then I can
> setUseAromaticityFlag and there is no problem.
>
> Is it possible to setUseAromaticityFlag with the SMILESWriter, or
> should I simply avoid using this class and use the Generator instead?

I guess this should be added to the writer too... I'll consider this a
feature request... it's easy to implement, so ping me in about a week,
if there is not commit yet...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-user mailing list
Cdk-user@...
https://lists.sourceforge.net/lists/listinfo/cdk-user

From forum: cdk-user

Setting aromaticity flag with SMILESWriter

2009-12-20T09:07:04Z

Re CDK 1.2.3...

I have been using the SMILESWriter in cinfony to write out SMILES
strings, but a user reported that benzene was being written out as
C1CCCCC1. If instead I use the SmilesGenerator, then I can
setUseAromaticityFlag and there is no problem.

Is it possible to setUseAromaticityFlag with the SMILESWriter, or
should I simply avoid using this class and use the Generator instead?

- Noel

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-user mailing list
Cdk-user@...
https://lists.sourceforge.net/lists/listinfo/cdk-user

From forum: cdk-user

Re: Depricated methods

2009-12-19T06:45:28Z

On Sat, Dec 19, 2009 at 4:55 AM, Syed Asad Rahman <s9asad@...> wrote:

Hi,
While compiling the cdk code I found these warnings in abundance for example

org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated
[javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar);
[javac] ^

For the warnings of this type I think it might be useful to remove the model.R package from master. IMO, a statistics interface is not really core cheminformatics. Does anybody actually use classes in this pacakge?

[javac] /DebugAdductFormula.java:76: warning: [deprecation] setCharge(java.lang.Integer) in org.openscience.cdk.formula.AdductFormula has been deprecated
[javac] public void setCharge(Integer charge) {

lastly

DebugAminoAcid.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated
[javac] public double getBondOrderSum(IAtom atom) {

Yes, these should probably get cleaned up in master

From forum: cdk-devel

Depricated methods

2009-12-19T01:55:44Z

Hi,
While compiling the cdk code I found these warnings in abundance for example

org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated
[javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar);
[javac] ^

secondly

[javac] /DebugAdductFormula.java:76: warning: [deprecation] setCharge(java.lang.Integer) in org.openscience.cdk.formula.AdductFormula has been deprecated
[javac] public void setCharge(Integer charge) {

lastly

DebugAminoAcid.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated
[javac] public double getBondOrderSum(IAtom atom) {

Dr. Syed Asad Rahman
Research Scientist
s9asad@...

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-16T08:43:07Z

On Wed, Dec 16, 2009 at 11:18 AM, Stefan Kuhn <stefan.kuhn@...> wrote:

Hm, I just looked at the Chi* stuff and I can't really see which of them
counts Carbons (which is what the CarbonConnectivityOrderZeroDescriptor did,
as you said). Do you know which one actually replaces it?

ChiPathDescriptor. Within that, see order0()

(OK, on looking at that, I see that it considers all non-H atoms, not just carbon atoms)

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-16T08:18:59Z

Hm, I just looked at the Chi* stuff and I can't really see which of them
counts Carbons (which is what the CarbonConnectivityOrderZeroDescriptor did,
as you said). Do you know which one actually replaces it?
Sorry for bothering you
Stefan

On Tuesday 15 December 2009 13:46:03 Rajarshi Guha wrote:

> IIRC it was dropped since one of the Chi descriptors did the same thing
>
> On Dec 15, 2009, at 6:08 AM, Stefan Kuhn wrote:
> > There used to be a CarbonConnectivityOrderZeroDescriptor - does
> > anybody know
> > what this is now or if it has been removed or whatever?
> > Stefan
> > --
> > Stefan Kuhn B. Sc. M. A.
> > Software Engineer in the Chemoinformatics and Metabolism Team
> > European Bioinformatics Institute (EBI)
> > Wellcome Trust Genome Campus
> > Hinxton, Cambridge CB10 1SD UK
> > Phone +44 1223 49 2657
> > Fax +44 (0)1223 494 468
> >
> > -------------------------------------------------------------------------
> >----- Return on Information:
> > Google Enterprise Search pays you back
> > Get the facts.
> > http://p.sf.net/sfu/google-dev2dev
> > _______________________________________________
> > Cdk-devel mailing list
> > Cdk-devel@...
> > https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
> ----------------------------------------------------
> Rajarshi Guha | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> Entropy requires no maintenance.
> -- Markoff Chaney
>
>
>
> ---------------------------------------------------------------------------
>--- Return on Information:
> Google Enterprise Search pays you back
> Get the facts.
> http://p.sf.net/sfu/google-dev2dev
> _______________________________________________
> Cdk-devel mailing list
> Cdk-devel@...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel

--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-16T06:22:54Z

A separate file is fine as well - formatting might be tricky in the properties
file.

On Wednesday 16 December 2009 09:43:41 Egon Willighagen wrote:
> On Wed, Dec 16, 2009 at 10:38 AM, Stefan Kuhn <stefan.kuhn@...> wrote:
> > On Wednesday 16 December 2009 07:14:07 Egon Willighagen wrote:
> >> On Tue, Dec 15, 2009 at 1:13 PM, Stefan Kuhn <stefan.kuhn@...>
wrote:

> >> > Sounds good. We should also have freetext section, which will be
> >> > included in the license file, since many licenses require you to
> >> > include a particular statement or whatever, so we need to be flexible.
> >>
> >> Can I suggest a .comments file? Then we don't have to worry about
> >> messing with the machine readable structure of the .meta file...
> >
> > Can't we include that machine readable? If possible, extra files should
> > be avoided.
>
> Yes, but then we have to start worry much more about the file format
> and take into account multiline content, likely with empty lines,
> etc... but not impossible:
>
> http://en.wikipedia.org/wiki/.properties
>
> It restricts you in the exact 'free' text, and you'd have to end each
> line with a '\', making copy pasting taking more effort ...
>
> That's why I prefer a separate file...
>
> Egon

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-16T06:03:37Z

On Wed, Dec 16, 2009 at 2:43 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
> I didn't really check the original algorithm - all it does is is
> basically count the number of carbons. I don't think there is an
> algorithm for that :)

Ah, OK. The 'zero order' connectivity is just *no* connectivity? Did
not realize that, and was too lazy to look up the full specs of the
Chi descriptors...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-16T05:43:13Z

On Dec 16, 2009, at 2:15 AM, Egon Willighagen wrote:

> On Tue, Dec 15, 2009 at 2:46 PM, Rajarshi Guha <rajarshi.guha@...
> > wrote:
>> IIRC it was dropped since one of the Chi descriptors did the same
>> thing
>
> So, it was replaced? Is it using the same algorithm too?

I didn't really check the original algorithm - all it does is is
basically count the number of carbons. I don't think there is an
algorithm for that :)

----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
All science is either physics or stamp collecting.
-- Ernest Rutherford

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-16T01:43:41Z

On Wed, Dec 16, 2009 at 10:38 AM, Stefan Kuhn <stefan.kuhn@...> wrote:

> On Wednesday 16 December 2009 07:14:07 Egon Willighagen wrote:
>> On Tue, Dec 15, 2009 at 1:13 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
>> > Sounds good. We should also have freetext section, which will be included
>> > in the license file, since many licenses require you to include a
>> > particular statement or whatever, so we need to be flexible.
>>
>> Can I suggest a .comments file? Then we don't have to worry about
>> messing with the machine readable structure of the .meta file...
>
> Can't we include that machine readable? If possible, extra files should be
> avoided.

Yes, but then we have to start worry much more about the file format
and take into account multiline content, likely with empty lines,
etc... but not impossible:

http://en.wikipedia.org/wiki/.properties

It restricts you in the exact 'free' text, and you'd have to end each
line with a '\', making copy pasting taking more effort ...

That's why I prefer a separate file...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-16T01:38:45Z

On Wednesday 16 December 2009 07:14:07 Egon Willighagen wrote:
> On Tue, Dec 15, 2009 at 1:13 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
> > Sounds good. We should also have freetext section, which will be included
> > in the license file, since many licenses require you to include a
> > particular statement or whatever, so we need to be flexible.
>
> Can I suggest a .comments file? Then we don't have to worry about
> messing with the machine readable structure of the .meta file...
>
> Egon

Can't we include that machine readable? If possible, extra files should be
avoided.
Stefan

--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-15T23:15:09Z

On Tue, Dec 15, 2009 at 2:46 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
> IIRC it was dropped since one of the Chi descriptors did the same thing

So, it was replaced? Is it using the same algorithm too?

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T23:14:07Z

On Tue, Dec 15, 2009 at 1:13 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
> Sounds good. We should also have freetext section, which will be included in
> the license file, since many licenses require you to include a particular
> statement or whatever, so we need to be flexible.

Can I suggest a .comments file? Then we don't have to worry about
messing with the machine readable structure of the .meta file...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: CarbonConnectivityOrderZeroDescriptor

2009-12-15T05:46:03Z

IIRC it was dropped since one of the Chi descriptors did the same thing

On Dec 15, 2009, at 6:08 AM, Stefan Kuhn wrote:

> There used to be a CarbonConnectivityOrderZeroDescriptor - does
> anybody know
> what this is now or if it has been removed or whatever?
> Stefan
> --
> Stefan Kuhn B. Sc. M. A.
> Software Engineer in the Chemoinformatics and Metabolism Team
> European Bioinformatics Institute (EBI)
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD UK
> Phone +44 1223 49 2657
> Fax +44 (0)1223 494 468
>
> ------------------------------------------------------------------------------
> Return on Information:
> Google Enterprise Search pays you back
> Get the facts.
> http://p.sf.net/sfu/google-dev2dev
> _______________________________________________
> Cdk-devel mailing list
> Cdk-devel@...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel

----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
Entropy requires no maintenance.
-- Markoff Chaney

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T05:26:02Z

On Tue, Dec 15, 2009 at 2:24 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
> Could we also have a copyright notice section in the file? Many licences
> require inclusion of some copyright notice and so it might be useful to keep
> it separate.

Ah, yes. Indeed, that should be included too.

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T05:24:22Z

Could we also have a copyright notice section in the file? Many licences
require inclusion of some copyright notice and so it might be useful to keep
it separate.
Stefan

On Tuesday 15 December 2009 12:03:20 Egon Willighagen wrote:
> Stefan,
>
> On Thu, Dec 10, 2009 at 8:21 PM, Egon Willighagen
>
> <egon.willighagen@...> wrote:
> > On Thu, Dec 10, 2009 at 6:44 PM, Stefan Kuhn <stefan.kuhn@...>
wrote:

> >> To overcome this I suggest we do a document in the distribution where
> >> for each library we do whatever the license asks.
>
> I was thinking to have a foo.jar.meta file for each foo.jar we have.
> The file content would like like, with additional sections if the jar
> contains third party stuff, like:
>
> [jniinchi-0.5.jar]
> Library=JNI-InChI
> Version=0.5
> License=GNU Lesser General Public License, unspecified version
> Download=http://jni-inchi.sourceforge.net/license.html
> # SourceCode=
>
> [jniinchi-0.5.jar/inchi.c] # file name or so
> Library=InChI C sofware
> Version=1.0
> Licence=GNU Lesser General Public License, unspecified version.
> Download=http://www.iupac.org/inchi/
> # SourceCode=
>
> We can create the LICENSE file automatically from these .meta data files...
>
> Egon

--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T04:13:15Z

Sounds good. We should also have freetext section, which will be included in
the license file, since many licenses require you to include a particular
statement or whatever, so we need to be flexible.
Stefan

On Tuesday 15 December 2009 12:03:20 Egon Willighagen wrote:
> Stefan,
>
> On Thu, Dec 10, 2009 at 8:21 PM, Egon Willighagen
>
> <egon.willighagen@...> wrote:
> > On Thu, Dec 10, 2009 at 6:44 PM, Stefan Kuhn <stefan.kuhn@...>
wrote:

--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T04:05:18Z

On Tue, Dec 15, 2009 at 1:00 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
>> We need to carefully double check what the license of a project now
>> says, and the version we actually use... they are not always in
>> sync... in that respect, we should include the library version numbers
>> (if we can dig them up, and recursively) in the metadata too...
>
> Yes, I tried to consider this, but when no version number is given it is
> difficult.

Indeed. I tried to systematically add some useful info in the commit
message, but not all have.

> This is especially tricky with the apache xml libs, which changed
> apache project while being developed. I do my best to get accurate
> information, but I cannot guarantee anything, obviously.

Indeed, which is why I asked about how you had done it so far...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T04:03:20Z

Stefan,

On Thu, Dec 10, 2009 at 8:21 PM, Egon Willighagen
<egon.willighagen@...> wrote:
> On Thu, Dec 10, 2009 at 6:44 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
>> To overcome this I suggest we do a document in the distribution where for each
>> library we do whatever the license asks.

I was thinking to have a foo.jar.meta file for each foo.jar we have.
The file content would like like, with additional sections if the jar
contains third party stuff, like:

[jniinchi-0.5.jar]
Library=JNI-InChI
Version=0.5
License=GNU Lesser General Public License, unspecified version
Download=http://jni-inchi.sourceforge.net/license.html
# SourceCode=

[jniinchi-0.5.jar/inchi.c] # file name or so
Library=InChI C sofware
Version=1.0
Licence=GNU Lesser General Public License, unspecified version.
Download=http://www.iupac.org/inchi/
# SourceCode=

We can create the LICENSE file automatically from these .meta data files...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T04:00:51Z

> We need to carefully double check what the license of a project now
> says, and the version we actually use... they are not always in
> sync... in that respect, we should include the library version numbers
> (if we can dig them up, and recursively) in the metadata too...
Yes, I tried to consider this, but when no version number is given it is
difficult. This is especially tricky with the apache xml libs, which changed
apache project while being developed. I do my best to get accurate
information, but I cannot guarantee anything, obviously.
Stefan
>
> Egon

--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T03:56:10Z

On Tue, Dec 15, 2009 at 12:44 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
>> I have a half-finished patch to create module pages... license info
>> for the jars would be very welcome there.
>> If I set up a machine readable system, will you follow it?
> Of course, given it is possible to collaborate on this.

I'll set up machine readable format (will be very simple, likely just
Java Properties file like) and the stuff to use it shortly. For now,
please continue your efforts; I'm busy finishing course material for
our PharmBio course due Jan 5th...

>> To reduce work duplication, how did you check licenses and copyrights?
>
> I looked it up on the websites given in LICENSE file.

We need to carefully double check what the license of a project now
says, and the version we actually use... they are not always in
sync... in that respect, we should include the library version numbers
(if we can dig them up, and recursively) in the metadata too...

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T03:47:00Z

On 15/12/2009 10:00, Egon Willighagen wrote:
> I have a half-finished patch to create module pages... license info
> for the jars would be very welcome there.
> If I set up a machine readable system, will you follow it?

Of course we will.

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

Video meliora proboque deteriora sequor.
... Ovid, Metamorphoses VII, 20/21

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Re: Licensing issues

2009-12-15T03:44:47Z

> I have a half-finished patch to create module pages... license info
> for the jars would be very welcome there.
> If I set up a machine readable system, will you follow it?
Of course, given it is possible to collaborate on this.
> To reduce work duplication, how did you check licenses and copyrights?
I looked it up on the websites given in LICENSE file.
Stefan
--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

CarbonConnectivityOrderZeroDescriptor

2009-12-15T03:08:58Z

There used to be a CarbonConnectivityOrderZeroDescriptor - does anybody know
what this is now or if it has been removed or whatever?
Stefan
--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel

Fwd: [Cdk-devel] Coordination bonds

2009-12-15T02:35:07Z

Hi all,

Stefan asked last week about coordination bonds (see below)... these
have been long missing in the CDK, though there is certainly room for
them: the IBond extends IElectronContainer, which is flexible in the
number of atoms and the number of electrons involved...

There was discussion on LonePairs involved in dative bonds... but I
like to ask the user community to define important use cases the
support for coordination/dative bonds should support...

Please let us know what you would like to see supported, so that we
can work out a proposal with a wide scope.

Thanx,

Egon

---------- Forwarded message ----------
From: Stefan Kuhn <stefan.kuhn@...>
Date: Mon, Dec 7, 2009 at 5:02 PM
Subject: [Cdk-devel] Coordination bonds
To: "Developers forum for discussion about the Chemistry Development
Kit (CDK)" <cdk-devel@...>

Hi all,

do we have support for coordination bonds in CDK? If not, how could these be
introduced? As a property on bonds? From my short wikipedia reading I get the
impression it is very similar to "normal" bonds, so it might be appropriate
to have them as such with a property. Any thoughts?

Thanks,

Stefan
--
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468
---------- Forwarded message ----------

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-user mailing list
Cdk-user@...
https://lists.sourceforge.net/lists/listinfo/cdk-user

From forum: cdk-user

Re: Licensing issues

2009-12-15T02:00:47Z

On Tue, Dec 15, 2009 at 10:55 AM, Stefan Kuhn <stefan.kuhn@...> wrote:
> On Monday 14 December 2009 18:10:08 Egon Willighagen wrote:
>> On Mon, Dec 14, 2009 at 7:02 PM, Stefan Kuhn <stefan.kuhn@...> wrote:
>> > Please find attached a file to replace the license file in cdk/jar. I
>> > will add required sources, license texts etc., but I think the file
>> > should go in asap, since the old one was fairly outdated.
>>
>> You did not opt for a machine readable way?
>
> No.

I have a half-finished patch to create module pages... license info
for the jars would be very welcome there.
If I set up a machine readable system, will you follow it?

>> > - vecmath being GPL (not LGPL)
>>
>> We use a public domain version, and have the source code in SVN
>> (vecmath project).
>
> Hm, checking that out I cannot find any licensing information. The URL given
> in the readme is not existing (if I correctly interpret the Japanese text I
> get). Do you have any information about the status of that code?

Don't see the PD claim either, but this is what the source code says:

/*
2 Copyright (C) 1997,1998,1999
3 Kenji Hiranabe, Eiwa System Management, Inc.
4
5 This program is free software.
6 Implemented by Kenji Hiranabe(hiranabe@...),
7 conforming to the Java(TM) 3D API specification by Sun Microsystems.
8
9 Permission to use, copy, modify, distribute and sell this software
10 and its documentation for any purpose is hereby granted without fee,
11 provided that the above copyright notice appear in all copies and
12 that both that copyright notice and this permission notice appear
13 in supporting documentation. Kenji Hiranabe and Eiwa System
Management,Inc.
14 makes no representations about the suitability of this software for any
15 purpose. It is provided "AS IS" with NO WARRANTY.
16 */

>> > Ok, I will continue with this, also for the develjar files.
>>
>> Did you examine the content of the jars? At least the cmlxom.jar has
>> additional different-licensed files in the jars...
>
> Not yet. Everybody is invited to join in with the effort.

To reduce work duplication, how did you check licenses and copyrights?

Egon

--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Cdk-devel mailing list
Cdk-devel@...
https://lists.sourceforge.net/lists/listinfo/cdk-devel

From forum: cdk-devel