From: Joerg K. W. <we...@in...> - 2004-02-24 14:25:22
Attachments:
GetNativeDescriptor.java
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Hi Egon, i've switched to the CDK mailing list :-) 1. O.k. here is an first guess what it can look like. 2. Please give me some short hints for the included comments and some short example code to tell Jmol that there is a plugin available. Some primitive example code without functionality but working under Jmol would be helpfull, so i can test things on my own. E.g. panel with one JLabel and one calculate JButton When pressing the molecule title of the actual molecule is printed to the console. 3. Please fix (if not already done) the javacc dependencies and the *.jj resource files. For my actual version i've simply deleted all iupac stuff. Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
From: E.L. W. <eg...@sc...> - 2004-02-24 14:33:33
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Tuesday 24 February 2004 15:17, Joerg K. Wegner wrote: > i've switched to the CDK mailing list :-) > > 1. O.k. here is an first guess what it can look like. > > 2. Please give me some short hints for the included comments and some > short example code to tell Jmol that there is a plugin available. See cdk.sf.net/plugins.html... Basically, it comes down to copying the jar into $HOME/.jmol/plugins > Some primitive example code without functionality but working under Jmol > would be helpfull, so i can test things on my own. E.g. panel with one > JLabel and one calculate JButton See cdk-plugins module in CDK cvs... DirBrowser and COTViewer are both very= =20 short... > When pressing the molecule title of the actual molecule is printed to > the console. I am planning to write a more comprehensive explanation, but plan to get th= at=20 into the planned 'CDK News' newsletter... > 3. Please fix (if not already done) the javacc dependencies and the *.jj > resource files. For my actual version i've simply deleted all iupac stuff. What's wrong with it? If you don't have javacc (ant < 1.6) then it should n= ot=20 compile it... Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAO164d9R8I9Yza6YRAlUwAJ9RSve74CSlZYfjmDwje3x1kfCUSgCghIAL vJv4sn6RMFPYmITTa6W1dC8=3D =3DRV/C =2D----END PGP SIGNATURE----- |
From: Joerg K. W. <we...@in...> - 2004-02-24 14:48:53
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Hi, > See cdk.sf.net/plugins.html... > Basically, it comes down to copying the jar into > $HOME/.jmol/plugins O.k. > I am planning to write a more comprehensive explanation, but plan to get that > into the planned 'CDK News' newsletter... Fine. >>3. Please fix (if not already done) the javacc dependencies and the *.jj >>resource files. For my actual version i've simply deleted all iupac stuff. > What's wrong with it? If you don't have javacc (ant < 1.6) then it should not > compile it... :-( I'm using Ant 1.6. Regards, Joerg > > Egon > > - -- > eg...@sc... > PhD on Molecular Representation in Chemometrics > Nijmegen University > http://www.cac.sci.kun.nl/people/egonw/ > GPG: 1024D/D6336BA6 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.7 (SunOS) > > iD8DBQFAO164d9R8I9Yza6YRAlUwAJ9RSve74CSlZYfjmDwje3x1kfCUSgCghIAL > vJv4sn6RMFPYmITTa6W1dC8= > =RV/C > -----END PGP SIGNATURE----- > > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with > a free DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id56&alloc_id438&op=click > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
From: E.L. W. <eg...@sc...> - 2004-02-24 14:59:46
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Tuesday 24 February 2004 15:40, Joerg K. Wegner wrote: > >>3. Please fix (if not already done) the javacc dependencies and the *.jj > >>resource files. For my actual version i've simply deleted all iupac > >> stuff. > > > > What's wrong with it? If you don't have javacc (ant < 1.6) then it shou= ld > > not compile it... > > > :-( I'm using Ant 1.6. What is the error you get (Ant output, with ant -verbose)...? Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAO2Tad9R8I9Yza6YRAkDrAJ9VWiZ+lZ6zokxwowGiUl73pL8DFwCfUAC7 brkVltzWlHa/eeep0Q851TI=3D =3D4j2f =2D----END PGP SIGNATURE----- |
From: Joerg K. W. <we...@in...> - 2004-02-24 15:35:56
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mmmhhh, missing NomParser.jj ??? And cvs -z3 -d:pserver:ano...@cv...:/cvsroot/cdk co cdk/src/org/openscience/cdk/iupac/parser causes cvs [checkout aborted]: recv() from server cvs.sourceforge.net: EOF so there is eventually a CVS problem at the moment (for me!?). BUILD FAILED D:\workingAt\cdk\build.xml:336: Invalid target: D:\workingAt\cdk\src\org\openscience\cdk\iupac\parser\NomParser.jj at org.apache.tools.ant.taskdefs.optional.javacc.JavaCC.execute(JavaCC.java:292) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:269) at org.apache.tools.ant.Task.perform(Task.java:364) at org.apache.tools.ant.Target.execute(Target.java:301) at org.apache.tools.ant.Target.performTasks(Target.java:328) at org.apache.tools.ant.Project.executeTarget(Project.java:1215) at org.apache.tools.ant.Project.executeTargets(Project.java:1063) at org.apache.tools.ant.Main.runBuild(Main.java:632) at org.apache.tools.ant.Main.startAnt(Main.java:183) at org.apache.tools.ant.Main.start(Main.java:147) at org.apache.tools.ant.Main.main(Main.java:230) > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On Tuesday 24 February 2004 15:40, Joerg K. Wegner wrote: > >>>>3. Please fix (if not already done) the javacc dependencies and the *.jj >>>>resource files. For my actual version i've simply deleted all iupac >>>>stuff. >>> >>>What's wrong with it? If you don't have javacc (ant < 1.6) then it should >>>not compile it... >>> >> >>:-( I'm using Ant 1.6. > > > What is the error you get (Ant output, with ant -verbose)...? > > Egon > > - -- > eg...@sc... > PhD on Molecular Representation in Chemometrics > Nijmegen University > http://www.cac.sci.kun.nl/people/egonw/ > GPG: 1024D/D6336BA6 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.7 (SunOS) > > iD8DBQFAO2Tad9R8I9Yza6YRAkDrAJ9VWiZ+lZ6zokxwowGiUl73pL8DFwCfUAC7 > brkVltzWlHa/eeep0Q851TI= > =4j2f > -----END PGP SIGNATURE----- > > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with > a free DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id56&alloc_id438&op=click > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. E. Hemingway |
From: Joerg K. W. <we...@in...> - 2004-02-24 17:28:52
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Hi, o.k. primitive joelib4cdk jar for testing the plugin facility: http://www-ra.informatik.uni-tuebingen.de/mitarb/wegner/tmp/ Should i add pluginManager.loadPlugins("joelib.cdk.plugin.GetNativeDescriptor"); to Jmol ? Why does Jmol not recognize this plugin ? Regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
From: Egon W. <eg...@sc...> - 2004-02-24 20:39:37
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On Tuesday 24 February 2004 18:20, Joerg K. Wegner wrote: > o.k. primitive joelib4cdk jar for testing the plugin facility: > http://www-ra.informatik.uni-tuebingen.de/mitarb/wegner/tmp/ OK, downloaded it, and tested it. > Should i add > pluginManager.loadPlugins("joelib.cdk.plugin.GetNativeDescriptor"); > to Jmol ? No, that is not necessary if one puts the jar in $HOME/.jmol/plugins > Why does Jmol not recognize this plugin ? The problem was that your class's name did not end in Plugin.class... Tricky, should have informed you about that... If named like: GetNativeDescriptorPlugin.java then it works fine. Egon |
From: Joerg K. W. <we...@in...> - 2004-02-25 07:16:04
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Hi Egon, > No, that is not necessary if one puts the jar in $HOME/.jmol/plugins I've copied: cdk-apps.jar cdk-core.jar cdk-extra.jar cdk-io.jar cdk-libio.jar cdk-render.jar cdk-standard.jar joelib.jar joelib4cdk.jar log4j.jar to C:\Dokumente und Einstellungen\wegnerj\.jmol\plugins and renamed the class to: GetNativeDescriptorPlugin then i start: sh jmol.sh Nothing happened: Please send me your successfull tested parts and describe your settings ! Question: I assume JChemPaint works with this mechanism also ! Correct ? Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
From: E.L. W. <eg...@sc...> - 2004-02-25 08:32:10
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 25 February 2004 08:07, Joerg K. Wegner wrote: > Hi Egon, > > > No, that is not necessary if one puts the jar in $HOME/.jmol/plugins > I've copied: > cdk-apps.jar > cdk-core.jar > cdk-extra.jar > cdk-io.jar > cdk-libio.jar > cdk-render.jar > cdk-standard.jar > joelib.jar > joelib4cdk.jar > log4j.jar > to > C:\Dokumente und Einstellungen\wegnerj\.jmol\plugins > > and renamed the class to: > GetNativeDescriptorPlugin Can you run it like: java -Dcdk.debugging=3Dtrue -jar jmol.jar And send me the cdk.log that is then created? > then i start: > sh jmol.sh > > Nothing happened: Please send me your successfull tested parts and > describe your settings ! I renamed the plugin class, and then the plugin was loaded... it did not sh= ow=20 much in the panel, and not sure what it should show, but that's all... Does it read a config file? My experience with additional libraries is not that big, but have a look at= =20 the WWMM plugin in CDK cvs too... that one uses other libs too, and check h= ow=20 they do it... > Question: I assume JChemPaint works with this mechanism also ! Correct ? Yes, but the plugin dir is then $HOME/.jchempaint/plugins Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAPFtqd9R8I9Yza6YRAqgKAJ9y9BdrkR2jIGejQSTpxtP1rVmOOgCgtxou 7ovlhlNLvuwP3x9+4CldHM0=3D =3DwXSd =2D----END PGP SIGNATURE----- |
From: Joerg K. W. <we...@in...> - 2004-02-25 08:48:05
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Hi, /cygdrive/d/workingAt/jmol/Jmol> java -Dcdk.debugging=true -jar jmol.jar org.openscience.cdk.tools.AtomTypeFactory INFO: Reading config file from jmol_atomtypes.txt org.openscience.cdk.tools.AtomTypeFactory DEBUG: configFile must be a stream org.openscience.cdk.tools.AtomTypeFactory ERROR: There was a problem getting a stream for jmol_atomtypes.txt org.openscience.cdk.tools.AtomTypeFactory DEBUG: Returning list of size: 224 using Simple Model Adapter Jmol Version 10pre5 Java Sun Microsystems Inc. 1.4.2_03 Windows 2000 org.openscience.cdk.applications.plugin.CDKPluginManager INFO: User dict dir: .jmol\plugins org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: exists: false org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: isDirectory: false org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Setting prop dir in plugin... org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: User plugin dir: .\jmol\dirbrowser.props org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: exists: false Regards, Joerg > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On Wednesday 25 February 2004 08:07, Joerg K. Wegner wrote: > >>Hi Egon, >> >> >>>No, that is not necessary if one puts the jar in $HOME/.jmol/plugins >> >>I've copied: >>cdk-apps.jar >>cdk-core.jar >>cdk-extra.jar >>cdk-io.jar >>cdk-libio.jar >>cdk-render.jar >>cdk-standard.jar >>joelib.jar >>joelib4cdk.jar >>log4j.jar >>to >>C:\Dokumente und Einstellungen\wegnerj\.jmol\plugins >> >>and renamed the class to: >>GetNativeDescriptorPlugin > > > Can you run it like: > > java -Dcdk.debugging=true -jar jmol.jar > > And send me the cdk.log that is then created? > > >>then i start: >>sh jmol.sh >> >>Nothing happened: Please send me your successfull tested parts and >>describe your settings ! > > > I renamed the plugin class, and then the plugin was loaded... it did not show > much in the panel, and not sure what it should show, but that's all... > > Does it read a config file? > > My experience with additional libraries is not that big, but have a look at > the WWMM plugin in CDK cvs too... that one uses other libs too, and check how > they do it... > > >>Question: I assume JChemPaint works with this mechanism also ! Correct ? > > > Yes, but the plugin dir is then $HOME/.jchempaint/plugins > > Egon > > - -- > eg...@sc... > PhD on Molecular Representation in Chemometrics > Nijmegen University > http://www.cac.sci.kun.nl/people/egonw/ > GPG: 1024D/D6336BA6 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.7 (SunOS) > > iD8DBQFAPFtqd9R8I9Yza6YRAqgKAJ9y9BdrkR2jIGejQSTpxtP1rVmOOgCgtxou > 7ovlhlNLvuwP3x9+4CldHM0= > =wXSd > -----END PGP SIGNATURE----- > > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with > a free DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id56&alloc_id438&op=click > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
From: E.L. W. <eg...@sc...> - 2004-02-25 08:55:40
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 25 February 2004 09:39, Joerg K. Wegner wrote: > /cygdrive/d/workingAt/jmol/Jmol> java -Dcdk.debugging=3Dtrue -jar jmol.jar > org.openscience.cdk.tools.AtomTypeFactory INFO: Reading config file from > jmol_atomtypes.txt > org.openscience.cdk.tools.AtomTypeFactory DEBUG: configFile must be a > stream org.openscience.cdk.tools.AtomTypeFactory ERROR: There was a probl= em > getting a stream for jmol_atomtypes.txt > org.openscience.cdk.tools.AtomTypeFactory DEBUG: Returning list of size: > 224 using Simple Model Adapter > Jmol Version 10pre5 > Java Sun Microsystems Inc. 1.4.2_03 Windows 2000 > org.openscience.cdk.applications.plugin.CDKPluginManager INFO: User dict > dir: .jmol\plugins > org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: > exists: false > org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: > isDirectory: false > org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Setting > prop dir in plugin... > org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: User plugin > dir: .\jmol\dirbrowser.props > org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: > exists: false Is that all?? Nothing about your plugin?? Anyway, I see this: CDKPluginManager INFO: User dict dir: .jmol\plugins Which seems to indicate that user.home is not added...=20 And that you are using Jmol v10... I tried it with 9 yesterday... I'll try later today... can you send me the= =20 link again where I can download the zip? Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAPGDtd9R8I9Yza6YRArUbAJ98aA9nqP2zUz83ropAZENW8qat9gCeOrhP RvRV8AeQ2alcendHEK/FECs=3D =3DRwTe =2D----END PGP SIGNATURE----- |
From: Joerg K. W. <we...@in...> - 2004-02-25 08:58:32
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Ah o.k., not user but actual path, i've copied this stuff to Jmol/.jmol/plugins BUT it does not work ... but now i can debug on my own ... Java Sun Microsystems Inc. 1.4.2_03 Windows 2000 org.openscience.cdk.applications.plugin.CDKPluginManager INFO: User dict dir: .jmol\plugins org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: exists: true org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: isDirectory: true org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-apps.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-core.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-extra.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-io.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-libio.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-render.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: cdk-standard.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: joelib.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible plugin found: joelib4cdk.jar org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Setting prop dir in plugin... org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: User plugin dir: .\jmol\dirbrowser.props org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: exists: false |
From: E.L. W. <eg...@sc...> - 2004-02-25 09:01:54
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 25 February 2004 09:49, Joerg K. Wegner wrote: > Ah o.k., not user but actual path, i've copied this stuff to > Jmol/.jmol/plugins :) > BUT it does not work ... but now i can debug on my own ... > > org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible > plugin found: joelib4cdk.jar Ok, here it should have said: found plugin blaPlugin.java too... Sure that this is the jar with the name change? Can you download Jmol from: http://www.woc.sci.kun.nl/devel/egonw/jcp/=20 ? And look at the output from that jmol.jar? thanx. > org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Setting > prop dir in plugin... > org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: User plugin > dir: .\jmol\dirbrowser.props > org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: exists: false Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAPGJhd9R8I9Yza6YRAhbZAKCegZzxYCwah8/Ny61RdAfvXzpgQQCgqjQq 9b+XFQ8i1R4YKeahD+gTl44=3D =3DHZrP =2D----END PGP SIGNATURE----- |
From: Joerg K. W. <we...@in...> - 2004-02-25 09:56:44
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Hi Egon, i've managed it and are now going for the rest of the week in pending mode. [java] 10:44:03 [INFO ] org.openscience.cdk.applications.plugin.CDKPluginManager - Plugin class found: joelib.cdk.plugi [java] 10:44:03 [INFO ] org.openscience.cdk.applications.plugin.CDKPluginManager - loaded. [java] 10:44:03 [INFO ] joelib.data.JOEElementTable - Using element table: joelib/data/plain/element.txt [java] 10:44:03 [INFO ] joelib.io.IOTypeHolder - 19 input/output types loaded. [java] -ISIS- 3D [java] 0 0 0 0 0 0 0 0 0 0 1 V2000 [java] M END [java] $$$$ Problems: - starting with jmol.sh will not add required joelib.jar, log4j.jar, ... dependencies - ant also, but works with. I was astonished that now my real windows preference 'user path' is used ! <path id="project.class.path"> <fileset dir="${lib.dir}"> <include name="*.jar" /> <exclude name="jmolappletcdk.jar"/> </fileset> <fileset dir=""> <include name="Jmol.jar" /> </fileset> </path> ... <target name="run" id="run" depends="main"> <java classname="org.openscience.jmol.app.Jmol" fork="yes" dir="."> <jvmarg value="-Dcdk.debugging=true"/> <classpath refid="project.class.path" /> </java> </target> -General: The dependencies should not be automatically loaded by the plugin manager, not by the user Regards, Joerg > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On Wednesday 25 February 2004 09:49, Joerg K. Wegner wrote: > >>Ah o.k., not user but actual path, i've copied this stuff to >>Jmol/.jmol/plugins > > > :) > > >>BUT it does not work ... but now i can debug on my own ... >> >>org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Possible >>plugin found: joelib4cdk.jar > > > Ok, here it should have said: found plugin blaPlugin.java too... > > Sure that this is the jar with the name change? > > Can you download Jmol from: > > http://www.woc.sci.kun.nl/devel/egonw/jcp/ > > ? And look at the output from that jmol.jar? thanx. > > >>org.openscience.cdk.applications.plugin.CDKPluginManager DEBUG: Setting >>prop dir in plugin... >>org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: User plugin >>dir: .\jmol\dirbrowser.props >>org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin DEBUG: exists: false > > > Egon > > - -- > eg...@sc... > PhD on Molecular Representation in Chemometrics > Nijmegen University > http://www.cac.sci.kun.nl/people/egonw/ > GPG: 1024D/D6336BA6 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.7 (SunOS) > > iD8DBQFAPGJhd9R8I9Yza6YRAhbZAKCegZzxYCwah8/Ny61RdAfvXzpgQQCgqjQq > 9b+XFQ8i1R4YKeahD+gTl44= > =HZrP > -----END PGP SIGNATURE----- > > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with > a free DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id56&alloc_id438&op=click > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |