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From: Yoan M. L. <yoa...@re...> - 2011-07-04 15:03:52
|
Hello, I need to download to new version of the jchempaint. Can you help me to find, I need the version what be comptible with con cdk-1.34 Where can I finded?? Thanks -------------------------------------------- Lic. Yoan Martínez López Facultad de Informática Universidad de Camagüey |
From: Egon W. <ego...@gm...> - 2009-08-24 11:46:01
|
Hi all, last week Wednesday Arvid and I discussed JChemPaint and the Bioclipse usage, after we both got back from holidays... I have added the notes as PDF, and will summarize the points here as they are somewhat cryptic: * JCP branch updates (task: EW) There are many patched lined up for the JChemPaint-Primary branch, both from UU as from EBI. These need to be integrated into the main branch on the Pele machine. * wiki about two SWT widgets (task: AB) Wikipage in the Bioclipse and/or JChemPaint wiki about the SWT widgets wrapping the renderer with and without controller(s) * propose factoring out SWT widget (CDK/SWT only) Put these widgets into separate plugins only depending on org.openscience.cdk and eclipse SWT plugins and not one Bioclipse plugins, so that others (e.g. KNIME) can reuse them too * IAtomContainer widgets Currently, Bioclipse only has widgets wrapping the Renderer, but with the arrival of the AtomContainerRenderer these should be wrapped too. * review/port Stefan's patches Combines with the first point. This involves the stereo bonds in the PDF. * look at transparency feedback To the UU team, feedback on selections of the various kinds is of high importance. The current feedback mechanism is not enough and the blue selection indication generally not satisfactory. Proper transparency and highlighting using larger spheres in the background is much requested for, but a common interface underlying SWT and Swing is currently missing. This is a priority for Bioclipse 2.2. * create IEdit Arvid's refactoring of the chemical edits in the ControllerHub into IEdit-based edit classes is unfinished. This has very high priority. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2009-04-08 11:48:17
|
cc: Chris, Rajarshi Hi all, CDK 1.2.0 has been released, Bioclipse 2.0.0 is close to being released, and JChemPaint 3.0(?) has progressed very much too. Our aim was (and should still be) to develop jchempaint-primary as patch to CDK 1.2 so that it can be release in a later 1.2.x release. Since jchempaint-primary was branched from cdk-1.2.x the latter has undergone quite a lot of patching and bug fixes. At the same time, jchempaint-primary has seen patches to code outside the render and control modules. Additionally, the component of the new MVC code in those two modules is not yet complete, and lacks proper modularization of the controller part. This makes it currently impossible to make a small applet. Also, here and there the design needs clean up otherwise. For example, I very much like to see Undo/Redo optional, but that should automatically follow from the modularization of the controller component. In retrospect, very much more code sneaked into the current code base than I originally anticipated, and the end goal has been partly a moving target. I think it is now time to have a good look at the current design, clean up the controller module, and to clean up the jchempaint-primary patch to be a proper patch on cdk-1.2.x again, and I would like to start a discussion on how we want to do that. Because a patch will have to be approved by two independent reviewers, we will want a small set of independent patches, which reviewers can easily oversee. I envision small and very specialized patches for changes to code outside the render and control module; in many cases these patches will have to be accompanied with unit testing etc, and be extremely clean if they apply to the 'stable' modules. New functionality in render and controler, can go in as larger patches, but modular enough that it is clear to the reviewer what the patch is doing. A patch "New JChemPaint" will not do; instead, we need patches which go like: "Renderer modules for IMolecule", "Renderer modules for IReaction and friends", etc. In particular, the interfaces must be separate isolated patches, so that the API can be peer-reviewer separately and independent from any implementing code. Let me stress that the reviewer will be mostly done by Rajarshi, and him alone, being the only independent senior CDK developer with time. And I want to have it such that he can work through the set of patches step by step, and having the highest probabilty that he has a clue what is happening. Therefore, before actually getting into git details, I would like to start this, by setting up a list of patches we want to define. When that is done, we can copy/paste code from the current jchempaint-primary into the appropriate patches. The git details involved here is that we will no longer have a master jchempaint-primary branch, but a set of patches which, if sequentially applied, result in the current jchempaint-primary branch, but then based on the active cdk-1.2.x branch. Are we all up to this job? Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2009-03-05 11:02:15
|
Hi all, there are now two places where isotope information is set, I think. The below patch introduced one: On Thu, Mar 5, 2009 at 11:57 AM, <gog...@us...> wrote: > Log Message: > ----------- > Moved configuring of atom to ControlerHub.setSymbol, and made CycleSymolModule call it fixes bug #544 <snip> > @@ -490,6 +491,14 @@ > > public void setSymbol(IAtom atom, String symbol) { > atom.setSymbol(symbol); > + // configure the atom, so that the atomic number matches the symbol > + try { > + IsotopeFactory.getInstance( > + atom.getBuilder()).configure(atom); > + } catch (Exception exception) { > + exception.printStackTrace(); > + } > + > structurePropertiesChanged(); > } This code should not be here... setSymbol() should only set the symbol. It's a core edit feature, and we do not want the IsotopeFacory in there, as it makes it impossible to make the 50kB applet. I am not sure why this code is added... can someone explain what the goal of setting the isotope information is? Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2008-11-27 07:53:13
|
Gilleain, pleae review the patch I commited: http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/jchempaint-primary/src/main/org/openscience/cdk/controller/IChemModelRelay.java?r1=13321&r2=13325 It basically replaces addRing(int size) with addRing(int size, Point2d), and adds addPhenyl(Point2d)... Adding the Point2d parameter, ensure that we can add a ring at any place, unconnected, independent if it is the first thing added to the drawing area, or at any later stage. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2007-09-02 08:17:34
|
Hi All, Niels and I are having a JChemPaint hack-a-thon today, to integrate Niels' new rendering engine into the JChemPaint framework. The wiki page can be found here: http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=jcp_hack_20070902 and we coordinate things from IRC: irc.freenode.net, #cdk It will last until around 16:00 CEST (14:00 GMT, I think). Getting things properly integrated into SWT environments, is part of the agenda of today; so Bioclipse developers are most welcome! Egon -- ego...@gm... Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Ben A. <ben...@st...> - 2007-06-25 09:27:38
|
Hello there I would greatly appreciate a small amount of your time to assist with my doctoral research at The University of Newcastle. The research concerns open source licensing and we're seeking developers working on Java projects. The research is supervised, ethics-approved, anonymous and results will be freely available. Participation will also provide a custom licensing report for your project. To learn more, please visit: http://licensing-research.newcastle.edu.au Thanks for reading this email, and I hope you'll consider participating. Best regards Ben Alex (My apologies for being off-topic; this list will not be emailed again) |
From: Stefan K. <ste...@un...> - 2006-10-17 18:33:44
|
I think the first thing we need to clarify is what is wrong with jcp as i= t is=20 now. Some people suggest more or less a rewrite, so it seems there is a m= ajor=20 problem. What is this? Functionality? Speed? Size of jars? Usability? BTW, I am not sure if it is such a great idea to do a jme clone. The conc= ep=20 behind jcp - the wrapper around cdk classes, which can be used for other=20 things as well, and to distibute this as standalone, applet, eclipse plug= in=20 is rather cool and I think it has its merits. Stefan Am Sunday 15 October 2006 17:51 schrieb rich apodaca: > --- Egon Willighagen <e.w...@sc...> > > wrote: > > Hi Peter/Stefan/Rajarshi/Rich/others, > > > > I know I am boring everyone with this, but what JCP > > really needs is a better > > Renderer2D, as the current one is no longer > > extendible. > > Maybe it would be worth disucssing at a more basic > level what JChemPaint should be all about. Who is the > target user? What are they trying to do? What do they > really need? What are they wasting a lot of time/money > on? What will make them say "wow"? What are their > frustrations and how can we eliminate them? > > If anything, I'd say that JChemPaint's biggest > liability is not technical. Rather, it's the basic > concept. JCP is a swiss-army-knife, but users want a > machete. A user trying to enter structures on the Web > for querying a database has very different needs from > a user who needs publication-quality graphics pasted > into Word as a live object for writing his/her > dissertation. > > JME (still the gold standard after all of these > years!) succeeds because it squarely targets the user > of a Web database. Exclusively. Deliberately. It's a > strong, sharp machete. You can't use it for opening > bottles or clipping your nails, but it clears a path > through the jungle in nothing flat. > > Why couldn't we do the same? The Web is where the real > opportunities are to make a difference. It's also > where commercial vendors don't dominate. > > > Now, Rich wrote a Java2D based renderer but not > > based on the CDK, and seems > > not to have the time to do that. Rajarshi took this > > code [1] and adapted it > > for the CDK and I asked him to upload that, so that > > we can replace the old > > (pre-Java2D) version with this one. It lacks a lot > > of the functionality from > > the current one, but is a good place to start the > > rewrite. > > I'm not quite sure what your're referring to here, > Egon. Structure-CDK is a port of Structure for use > with CDK: > > http://depth-first.com/articles/2006/08/28/drawing-2-d-structures-with-= stru >cture-cdk > > It's _only_ dependency is on CDK and so is clearly > "based on the CDK". It draws an > org.openscience.cdk.interfaces.IAtomContainer, > provided coordinates have been assigned. I'm happy for > this code to either be used as-is or in any modified > form. > > But again, if the aim is to rewrite JChemPaint (not > sure if it is, though), maybe we could start by > forgetting about JCP in it's current form and > discussing the key problem(s) the new JCP is going to > solve? > > I know this can be done. The key is to focus on making > a subset of all possible users really happy. Then > expand from there. > > > Rajarshi, you have not uploaded this yet, right? > > Stefan and me could take this > > code and write a Controller2D etc around it. > > > > This new code will be much easier to read, much > > easier to maintain, *and* very > > importantly, much easier to extend and customize to > > user needs. > > > > Please also check out this wiki page (feel free to > > add stuff): > > http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=3Drenderer2dredesign > > > Egon > > > > PS. I would very much like to move this list to the > > CDK project too. So, > > cdk...@li.... Comments? > > > > 1.email correspondence > > > > -- > > e.w...@sc... > > Cologne University Bioinformatics Center (CUBIC) > > Blog: http://chem-bla-ics.blogspot.com/ > > GPG: 1024D/D6336BA6 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > -----------------------------------------------------------------------= -- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server v.1.0.1 based on Apach= e > Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > _______________________________________________ > Jchempaint-devel mailing list > Jch...@li... > https://lists.sourceforge.net/lists/listinfo/jchempaint-devel --=20 Stefan Kuhn B. Sc. 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 |
From: Stefan K. <ste...@un...> - 2006-10-17 13:46:40
|
Hi all, well, that's really just a starting point. We need to work on it. Another question: Any objections against me doing a jcp release (2.4) fro= m teh=20 current code? Stefan Am Thursday 12 October 2006 17:29 schrieb Rajarshi Guha: > On Thu, 2006-10-12 at 09:18 +0200, Egon Willighagen wrote: > > Hi Peter/Stefan/Rajarshi/Rich/others, > > > > I know I am boring everyone with this, but what JCP really needs is a > > better Renderer2D, as the current one is no longer extendible. > > Agreed > > > Now, Rich wrote a Java2D based renderer but not based on the CDK, and > > seems not to have the time to do that. Rajarshi took this code [1] an= d > > adapted it for the CDK and I asked him to upload that, so that we can > > replace the old (pre-Java2D) version with this one. It lacks a lot of= the > > functionality from the current one, but is a good place to start the > > rewrite. > > > > Rajarshi, you have not uploaded this yet, right? Stefan and me could = take > > this code and write a Controller2D etc around it. > > No I haven't uploaded yet. However to be honest it's very little code > and all I did was to see how I could draw some different bond types > (wedges) using the Java2D API. > > Obviously these methods can be replicated for the other types of object= s > - I think the main issue was in how the methods would determine the > region in which they were drawing (in a manner similar to Rich's code) > > I've attached the source to this mail > > > PS. I would very much like to move this list to the CDK project too. = So, > > cdk...@li.... Comments? > > Good idea > > ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > ...but there was no one in it....... > - RG --=20 Stefan Kuhn B. Sc. 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 |
From: peter murray-r. <pm...@ca...> - 2006-10-16 21:24:35
|
At 16:29 12/10/2006, Rajarshi Guha wrote: >On Thu, 2006-10-12 at 09:18 +0200, Egon Willighagen wrote: > > Hi Peter/Stefan/Rajarshi/Rich/others, > > > > I know I am boring everyone with this, but what JCP really needs > is a better > > Renderer2D, as the current one is no longer extendible. > I agree with Rich's comments - we have to agree on what we are doing. It may, or may not, need a CDK backend - that doesn't necessarily matter in the UI design. Personally I would suggest we take a good existing metaphor and reverse engineer it while allowing the flexibility to add functionality later. If JCP-lite looked and felt like JME, could act as an applet and also a standalone, and be interfaced into apps (which JME cannot), then we would be able to distribute it and promote it. What I think this requires is: - some idea of user requirements - a comparison of existing systems - a strong-minded guru. I don't know whether JCP as it stands just needs some tweaks or whether it needs complete refactoring. Whatever the analysis we need to be rave and do it properly and quickly. It can't be that hard. P. Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 |
From: rich a. <che...@ya...> - 2006-10-15 15:51:49
|
--- Egon Willighagen <e.w...@sc...> wrote: > > Hi Peter/Stefan/Rajarshi/Rich/others, > > I know I am boring everyone with this, but what JCP > really needs is a better > Renderer2D, as the current one is no longer > extendible. Maybe it would be worth disucssing at a more basic level what JChemPaint should be all about. Who is the target user? What are they trying to do? What do they really need? What are they wasting a lot of time/money on? What will make them say "wow"? What are their frustrations and how can we eliminate them? If anything, I'd say that JChemPaint's biggest liability is not technical. Rather, it's the basic concept. JCP is a swiss-army-knife, but users want a machete. A user trying to enter structures on the Web for querying a database has very different needs from a user who needs publication-quality graphics pasted into Word as a live object for writing his/her dissertation. JME (still the gold standard after all of these years!) succeeds because it squarely targets the user of a Web database. Exclusively. Deliberately. It's a strong, sharp machete. You can't use it for opening bottles or clipping your nails, but it clears a path through the jungle in nothing flat. Why couldn't we do the same? The Web is where the real opportunities are to make a difference. It's also where commercial vendors don't dominate. > Now, Rich wrote a Java2D based renderer but not > based on the CDK, and seems > not to have the time to do that. Rajarshi took this > code [1] and adapted it > for the CDK and I asked him to upload that, so that > we can replace the old > (pre-Java2D) version with this one. It lacks a lot > of the functionality from > the current one, but is a good place to start the > rewrite. I'm not quite sure what your're referring to here, Egon. Structure-CDK is a port of Structure for use with CDK: http://depth-first.com/articles/2006/08/28/drawing-2-d-structures-with-structure-cdk It's _only_ dependency is on CDK and so is clearly "based on the CDK". It draws an org.openscience.cdk.interfaces.IAtomContainer, provided coordinates have been assigned. I'm happy for this code to either be used as-is or in any modified form. But again, if the aim is to rewrite JChemPaint (not sure if it is, though), maybe we could start by forgetting about JCP in it's current form and discussing the key problem(s) the new JCP is going to solve? I know this can be done. The key is to focus on making a subset of all possible users really happy. Then expand from there. > Rajarshi, you have not uploaded this yet, right? > Stefan and me could take this > code and write a Controller2D etc around it. > > This new code will be much easier to read, much > easier to maintain, *and* very > importantly, much easier to extend and customize to > user needs. > > Please also check out this wiki page (feel free to > add stuff): > > http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=renderer2dredesign > > Egon > > PS. I would very much like to move this list to the > CDK project too. So, > cdk...@li.... Comments? > > 1.email correspondence > > -- > e.w...@sc... > Cologne University Bioinformatics Center (CUBIC) > Blog: http://chem-bla-ics.blogspot.com/ > GPG: 1024D/D6336BA6 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: Rajarshi G. <rg...@in...> - 2006-10-12 15:29:14
|
On Thu, 2006-10-12 at 09:18 +0200, Egon Willighagen wrote: > Hi Peter/Stefan/Rajarshi/Rich/others, > > I know I am boring everyone with this, but what JCP really needs is a better > Renderer2D, as the current one is no longer extendible. Agreed > Now, Rich wrote a Java2D based renderer but not based on the CDK, and seems > not to have the time to do that. Rajarshi took this code [1] and adapted it > for the CDK and I asked him to upload that, so that we can replace the old > (pre-Java2D) version with this one. It lacks a lot of the functionality from > the current one, but is a good place to start the rewrite. > > Rajarshi, you have not uploaded this yet, right? Stefan and me could take this > code and write a Controller2D etc around it. No I haven't uploaded yet. However to be honest it's very little code and all I did was to see how I could draw some different bond types (wedges) using the Java2D API. Obviously these methods can be replicated for the other types of objects - I think the main issue was in how the methods would determine the region in which they were drawing (in a manner similar to Rich's code) I've attached the source to this mail > PS. I would very much like to move this list to the CDK project too. So, > cdk...@li.... Comments? Good idea ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- ...but there was no one in it....... - RG |
From: peter murray-r. <pm...@ca...> - 2006-10-12 12:32:09
|
At 08:18 12/10/2006, Egon Willighagen wrote: >Hi Peter/Stefan/Rajarshi/Rich/others, > >I know I am boring everyone with this, but what JCP really needs is a better >Renderer2D, as the current one is no longer extendible. Thanks - what are the main implications of this? >Now, Rich wrote a Java2D based renderer but not based on the CDK, and seems >not to have the time to do that. Rajarshi took this code [1] and adapted it >for the CDK and I asked him to upload that, so that we can replace the old >(pre-Java2D) version with this one. It lacks a lot of the functionality from >the current one, but is a good place to start the rewrite. > >Rajarshi, you have not uploaded this yet, right? Stefan and me could >take this >code and write a Controller2D etc around it. > >This new code will be much easier to read, much easier to maintain, >*and* very >importantly, much easier to extend and customize to user needs. > >Please also check out this wiki page (feel free to add stuff): > >http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=renderer2dredesign > >Egon > >PS. I would very much like to move this list to the CDK project too. So, >cdk...@li.... Comments? Seems fine to me. I will ask one of my colleagues to test out JCP vs other tools. May be a few days. P. >1.email correspondence > >-- >e.w...@sc... >Cologne University Bioinformatics Center (CUBIC) >Blog: http://chem-bla-ics.blogspot.com/ >GPG: 1024D/D6336BA6 > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jchempaint-devel mailing list >Jch...@li... >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 |
From: Egon W. <e.w...@sc...> - 2006-10-12 07:22:26
|
Hi Peter/Stefan/Rajarshi/Rich/others, I know I am boring everyone with this, but what JCP really needs is a better Renderer2D, as the current one is no longer extendible. Now, Rich wrote a Java2D based renderer but not based on the CDK, and seems not to have the time to do that. Rajarshi took this code [1] and adapted it for the CDK and I asked him to upload that, so that we can replace the old (pre-Java2D) version with this one. It lacks a lot of the functionality from the current one, but is a good place to start the rewrite. Rajarshi, you have not uploaded this yet, right? Stefan and me could take this code and write a Controller2D etc around it. This new code will be much easier to read, much easier to maintain, *and* very importantly, much easier to extend and customize to user needs. Please also check out this wiki page (feel free to add stuff): http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=renderer2dredesign Egon PS. I would very much like to move this list to the CDK project too. So, cdk...@li.... Comments? 1.email correspondence -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: peter murray-r. <pm...@ca...> - 2006-10-11 23:56:23
|
At 16:34 11/10/2006, Stefan Kuhn wrote: >Well, I did some work on jcp over the last year or so. What I would like to >see is some more feedback. If somebody thinks jcp has serious problems, I >would like to know this. UI? Speed? Functionality? Stability? We (Tobias,= me, >some other people) felt jcp is pretty good when we did the 2.2 release. >We would continue development, but we would need some feedback. >Stefan OK - didn't mean to criticize strongly. I'll=20 suggest one or two organic chemists here have a go and feed back. P. >Am Wednesday 11 October 2006 17:48 schrieb peter murray-rust: > > At 08:03 24/09/2006, Egon Willighagen wrote: > > >On Wednesday 20 September 2006 11:03, peter murray-rust wrote: > > > > At 06:27 20/09/2006, Egon Willighagen wrote: > > > > I agree. I'm not volunteering personally. I think we need a new guru > > > > - maybe people have been reluctant to volunteer up to now. > > > > > >I agree: leading JChemPaint in the next months/year *is* a golden > > >OpenSource-fame opportunity. And leading !=3D doing everything just by > > >yourself. > > > > When Egon and I met at CompLife we agreed that this is now critical. > > There must be a critical mass of people in which there is one brave > > soul who could concentrate on JChempaint - it's one of the critical > > areas. You would have to be able to navigate Java code and understand > > (mainly organic) chemistry. You would get a lot of help from the > > community - energy and concentration are among the most important= virtues! > > > > P. > > > > >Egon > > > > > >-- > > >e.w...@sc... > > >Cologne University Bioinformatics Center (CUBIC) > > >Blog: http://chem-bla-ics.blogspot.com/ > > >GPG: 1024D/D6336BA6 > > > > >= >------------------------------------------------------------------------- > > >Take Surveys. Earn Cash. Influence the Future of IT > > >Join SourceForge.net's Techsay panel and you'll get the chance to share > > > your opinions on IT & business topics through brief surveys -- and= earn > > > cash > > >= http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DDE= VDEV > > > _______________________________________________ > > >Jchempaint-devel mailing list > > >Jch...@li... > > >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel > > > > Peter Murray-Rust > > Unilever Centre for Molecular Sciences Informatics > > University of Cambridge, > > Lensfield Road, Cambridge CB2 1EW, UK > > +44-1223-763069 > > > > _______________________________________________ > > Blue-obelisk mailing list > > Blu...@ha... > > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk > >-- >Stefan Kuhn B. Sc. 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 > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job= easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D1= 21642 >_______________________________________________ >Jchempaint-devel mailing list >Jch...@li... >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069=20 |
From: Stefan K. <ste...@un...> - 2006-10-11 15:56:42
|
Well, I did some work on jcp over the last year or so. What I would like = to=20 see is some more feedback. If somebody thinks jcp has serious problems, I= =20 would like to know this. UI? Speed? Functionality? Stability? We (Tobias,= me,=20 some other people) felt jcp is pretty good when we did the 2.2 release. We would continue development, but we would need some feedback. Stefan Am Wednesday 11 October 2006 17:48 schrieb peter murray-rust: > At 08:03 24/09/2006, Egon Willighagen wrote: > >On Wednesday 20 September 2006 11:03, peter murray-rust wrote: > > > At 06:27 20/09/2006, Egon Willighagen wrote: > > > I agree. I'm not volunteering personally. I think we need a new gur= u > > > - maybe people have been reluctant to volunteer up to now. > > > >I agree: leading JChemPaint in the next months/year *is* a golden > >OpenSource-fame opportunity. And leading !=3D doing everything just by > >yourself. > > When Egon and I met at CompLife we agreed that this is now critical. > There must be a critical mass of people in which there is one brave > soul who could concentrate on JChempaint - it's one of the critical > areas. You would have to be able to navigate Java code and understand > (mainly organic) chemistry. You would get a lot of help from the > community - energy and concentration are among the most important virtu= es! > > P. > > >Egon > > > >-- > >e.w...@sc... > >Cologne University Bioinformatics Center (CUBIC) > >Blog: http://chem-bla-ics.blogspot.com/ > >GPG: 1024D/D6336BA6 > > > >----------------------------------------------------------------------= --- > >Take Surveys. Earn Cash. Influence the Future of IT > >Join SourceForge.net's Techsay panel and you'll get the chance to shar= e > > your opinions on IT & business topics through brief surveys -- and ea= rn > > cash > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CI= D=3DDEVDEV > > _______________________________________________ > >Jchempaint-devel mailing list > >Jch...@li... > >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel > > Peter Murray-Rust > Unilever Centre for Molecular Sciences Informatics > University of Cambridge, > Lensfield Road, Cambridge CB2 1EW, UK > +44-1223-763069 > > _______________________________________________ > Blue-obelisk mailing list > Blu...@ha... > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk --=20 Stefan Kuhn B. Sc. 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 |
From: peter murray-r. <pm...@ca...> - 2006-10-11 15:48:33
|
At 08:03 24/09/2006, Egon Willighagen wrote: >On Wednesday 20 September 2006 11:03, peter murray-rust wrote: > > At 06:27 20/09/2006, Egon Willighagen wrote: > > I agree. I'm not volunteering personally. I think we need a new guru > > - maybe people have been reluctant to volunteer up to now. > >I agree: leading JChemPaint in the next months/year *is* a golden >OpenSource-fame opportunity. And leading != doing everything just by >yourself. When Egon and I met at CompLife we agreed that this is now critical. There must be a critical mass of people in which there is one brave soul who could concentrate on JChempaint - it's one of the critical areas. You would have to be able to navigate Java code and understand (mainly organic) chemistry. You would get a lot of help from the community - energy and concentration are among the most important virtues! P. >Egon > >-- >e.w...@sc... >Cologne University Bioinformatics Center (CUBIC) >Blog: http://chem-bla-ics.blogspot.com/ >GPG: 1024D/D6336BA6 > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jchempaint-devel mailing list >Jch...@li... >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 |
From: Egon W. <e.w...@sc...> - 2006-09-24 07:06:22
|
On Wednesday 20 September 2006 11:03, peter murray-rust wrote: > At 06:27 20/09/2006, Egon Willighagen wrote: > I agree. I'm not volunteering personally. I think we need a new guru > - maybe people have been reluctant to volunteer up to now. I agree: leading JChemPaint in the next months/year *is* a golden OpenSource-fame opportunity. And leading != doing everything just by yourself. Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Stefan K. <ste...@un...> - 2006-09-20 16:04:58
|
> Yes. I put JChemPaint near the top of our priorities. For example I > would like to see it as our default structure entry tool and also > popularize it as an authoring tool for manuscripts. But it's not > robust enough for this. I would like to point out that JCP, to our knowledge, is robust. It works= on=20 e. g. www.nmrshiftdb.org and this is an externally used website. If you find actual problems and bugs, please report them. Stefan --=20 Stefan Kuhn B. Sc. 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 |
From: peter murray-r. <pm...@ca...> - 2006-09-20 09:03:53
|
At 06:27 20/09/2006, Egon Willighagen wrote: >(please reply to cdk...@li...) > >Hi all, > >there seems to be more and more interest in JChemPaint on the mailing lists >and bug/feature request lists. However, development of JChemPaint as a >separate program (in contrast to a Bioclipse component) a bit low at the >moment. The last years JChemPaint was mostly worked on by Stefan and me, but >we needed to put our priorities elsewhere. > >Maybe we should focus on JChemPaint a bit more again, Yes. I put JChemPaint near the top of our priorities. For example I would like to see it as our default structure entry tool and also popularize it as an authoring tool for manuscripts. But it's not robust enough for this. >and some suggested ideas >are: >- make a Bioclipse based JChemPaint application (branded JChemPaint) >- 'fix' the Renderer2D to use Java2D throughout (will fix many things) > >But with Stefan and my schedule this is not feasible. We need help from >others, especially on the 'fix the Renderer2D' thingy. Is there a critical >development community? If you like to help revamp JChemPaint please reply. I agree. I'm not volunteering personally. I think we need a new guru - maybe people have been reluctant to volunteer up to now. P. >BTW, maybe we can setup a cdk-jchempaint mailing list and shutdown the old >jchempaint.sf.net project completely? Just for interest what is the rationale for this? P. >Egon > >-- >e.w...@sc... >Cologne University Bioinformatics Center (CUBIC) >Blog: http://chem-bla-ics.blogspot.com/ >GPG: 1024D/D6336BA6 > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jchempaint-devel mailing list >Jch...@li... >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 |
From: Egon W. <e.w...@sc...> - 2006-09-20 05:30:55
|
(please reply to cdk...@li...) Hi all, there seems to be more and more interest in JChemPaint on the mailing lists and bug/feature request lists. However, development of JChemPaint as a separate program (in contrast to a Bioclipse component) a bit low at the moment. The last years JChemPaint was mostly worked on by Stefan and me, but we needed to put our priorities elsewhere. Maybe we should focus on JChemPaint a bit more again, and some suggested ideas are: - make a Bioclipse based JChemPaint application (branded JChemPaint) - 'fix' the Renderer2D to use Java2D throughout (will fix many things) But with Stefan and my schedule this is not feasible. We need help from others, especially on the 'fix the Renderer2D' thingy. Is there a critical development community? If you like to help revamp JChemPaint please reply. BTW, maybe we can setup a cdk-jchempaint mailing list and shutdown the old jchempaint.sf.net project completely? Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Stefan K. <ste...@un...> - 2006-03-13 22:15:54
|
Am Monday 13 March 2006 20:45 schrieb Christoph Steinbeck: > Stefan Kuhn wrote: > > Hi all, > > on sf, there is now a binary release of the jcp applet. This should b= e a > > major milestone. > > Indeed! > Thanks a lot to Stefan and everyone involved. > We should probably announce this on a wider basis. > It might be nice to have a static HTML page (read: not the c-d-k.org pa= ge), http://almost.cubic.uni-koeln.de/jcp-applet/ > which demonstrates the use of the applet and some of the API, like > highlighting atoms and so on. > > Cheers, > > Christoph --=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 |
From: Christoph S. <c.s...@un...> - 2006-03-13 19:45:47
|
Stefan Kuhn wrote: > Hi all, > on sf, there is now a binary release of the jcp applet. This should be = a major=20 > milestone. Indeed! Thanks a lot to Stefan and everyone involved. We should probably announce this on a wider basis. It might be nice to have a static HTML page (read: not the c-d-k.org page= ),=20 which demonstrates the use of the applet and some of the API, like highli= ghting=20 atoms and so on. Cheers, Christoph --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=C3=BClpicher 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.. |
From: Christoph S. <c.s...@un...> - 2006-03-12 14:18:00
|
Dear all, sorry for cross-posting so heavily. Peter Murray-Rust informed me about the follwing, which, I think, is real= ly=20 excellent news for CDK and JChemPaint: The European Chemicals Bureau http://ecb.jrc.it/ which runs REACH=20 http://ecb.jrc.it/REACH/ has commissioned an in silico toxicology predict= ion=20 suite toxTree. This is based on the CDK toolkit, is built on CML, and is=20 released as OpenSource under the GPL - see http://ecb.jrc.it/DOCUMENTS/QSAR/TOXTREE/toxTree_user_manual.pdf Cheers, Chris --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) 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.. |
From: peter murray-r. <pm...@ca...> - 2006-03-06 07:34:42
|
At 14:34 05/03/2006, Christoph Steinbeck wrote: >Dear all, > >I'm interested in rendering curly arrows in=20 >JChemPaint/Renderer2D, ideally in an automatic fashion. >Obviously, drawing the arrows such that they do=20 >not overlap with other parts of the reaction/molecule(s) is the biggest= issue. >Generally, splines should be the concept to look=20 >for, when it comes to calculating the graph. > >Just wanted to know if anyone on the list can contribute some wisdom. I don't think there are simple answers, mainly a=20 set of heuristics. These would include: - atom a1 to/from a1-b1 bond - bond a1-a2 to bond a2-a3 These are fairly similar to drawing valence angle=20 info - mainly need to avoid overlap. Other=20 movements are probably too difficult to=20 systematize. It highlights that JCP needs a=20 generic overlap routine for atoms, bonds and=20 ancillary information including labels, charges, electrons, and now arrows. P. >Cheers, > >Chris > > >-- >Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) >Head of the Research Group for Molecular Informatics >Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) >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.. > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live= webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmdk&kid0944&bid$1720&dat1642 >_______________________________________________ >Jchempaint-devel mailing list >Jch...@li... >https://lists.sourceforge.net/lists/listinfo/jchempaint-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069=20 |