Menu
▾
▴
joelib-help — JOELib-Help
You can subscribe to this list here.
| 2003 |
Jan
|
Feb
(2) |
Mar
(2) |
Apr
(4) |
May
(1) |
Jun
(10) |
Jul
(1) |
Aug
(14) |
Sep
(4) |
Oct
(1) |
Nov
(11) |
Dec
(8) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2004 |
Jan
(5) |
Feb
(14) |
Mar
(21) |
Apr
(7) |
May
(8) |
Jun
(18) |
Jul
(14) |
Aug
(21) |
Sep
(4) |
Oct
(10) |
Nov
(8) |
Dec
(12) |
| 2005 |
Jan
(7) |
Feb
(9) |
Mar
(2) |
Apr
(8) |
May
(11) |
Jun
(2) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
(1) |
| 2006 |
Jan
(1) |
Feb
(1) |
Mar
(1) |
Apr
(1) |
May
|
Jun
|
Jul
(7) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
(1) |
| 2007 |
Jan
(1) |
Feb
(2) |
Mar
|
Apr
(3) |
May
|
Jun
(2) |
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2008 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
|
Feb
(1) |
Mar
(1) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(2) |
Nov
(1) |
Dec
|
| 2016 |
Jan
|
Feb
(2) |
Mar
|
Apr
(1) |
May
(2) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Joerg K. W. <we...@in...> - 2003-11-04 07:53:59
|
Hi all, the SMARTS bug for bridging root atoms (also in inner rings!) and then selecting sometimes two root atoms in the same ring (bug!) is fixed. Changes were added to CVS also. http://sourceforge.net/tracker/index.php?func=detail&aid=823931&group_id=39708&atid=425969 OELib/OpenBabel works here fine, because they use the primitive root atom picking which causes problems in inner rings. This should be fixed. JOELib works with both cases, please see joelib.data.JOEAromaticTyper and 'root atom picking'-method. By the way: the improved PDF writer in CVS writes also descriptor informations and can be used to visualize SMARTS if you have a little programming experience. In my opinion a very usefull tool. Every structure+descriptors starts at a new page. 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: Joerg K. W. <we...@in...> - 2003-10-13 12:18:38
|
Hi, for avoiding duplicate replies the usage of the joelib-help mailing list is helpfull: http://sourceforge.net/mail/?group_id=39708 > I have downloaded JOELibrary src - windows(JOELib-20030826) and trying > to compile (jdk 1.4) using JBuilder7 (i am not using ANT compilation of > JBuilder, coz dont know how to do it). There exists surely an ANT plugin for JBuilder, too ... but i can't remember the name, but i used it before i changed to the free eclipse IDE, which is faster and has better refactoring and software design tools. http://www.eclipse.org/ > With the src i downloaded there were some jar files distributed. so i > have added them to the project. Errors displayed at the first instance > are related to javax.media.. > i couldnt access the javax.media and j3d related classes form the > existing javax lib. > Now my question, is there any separare jar file i need to access for all > the java3d related functionalities and javax functionalities?? if so > just give me some guidance to that?? Of course, the Java3D installer adds normally the required library paths to your library path. If not, do that by hand ... > I never worked before with java3d, just advice me completely about the > known steps to compile the JOELibrary. > Do i require to add some of the files\libraries of CDK development kit?? Only if you want to use the 2D structures layout facility of the CDK. BTW, the new release of today contains a 2D-AWT renderer without requiring Java3D. See for example: http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/documentation/documentation.html Regards, Joerg > Thanks > Subba > India. > -- 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...> - 2003-09-11 07:47:33
|
Hi, fine ... if you would not to use RH you can recompile the shared library by your own. The sources and the makefile for the Java and C++/C part are included. Regards, Joerg Gert Sclep wrote: >>Hi Gert, >> >>are you using IBM's JDK ? >> >>The interface works only under the IBM JDK under Linux ... SUN's JDK >>seems to have an JNI bug. > > > Thanks a lot. > > This seems to work. > > Greetings, > Gert Sclep > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Joelib-help mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-help > -- 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...> - 2003-09-11 00:10:04
|
Hi Gert,
are you using IBM's JDK ?
The interface works only under the IBM JDK under Linux ... SUN's JDK
seems to have an JNI bug.
Regards, Joerg
>>the package path in the LibGhemical JNI interface was corrected.
>>
>>Now the precompiled shared libraries should work correctly !;-)
>>
>>Regards, Joerg
>
>
> I can't seem to get LibGhemical to work properly under Linux. At the
> bottom of the mail I will attach the error message I'm constantly
> receiving. I tried upgrading from RedHat 7.2 to RedHat 9.0, but to no
> avail. Trying to compile the interface-source (in libghemical/src/jni)
> didn't help either.
>
> I'm no hero when it comes to C++ and I'm quite stuck in the further
> investigation of this error, so hints would be most welcome.
>
> -------------------------Error Message-------------------------------
>
> [gert@leffe linux]$ joetest.sh joelib/test/WekaTest LR N L O
> Adding /home/gert/.//dev/src/joelib_test to CLASSPATH.
> ...(snip)...
> 21:10:10 [INFO ] joelib.data.JOEElementTable - Using element
> table: joelib/data/plain/element.txt
> 21:10:10 [INFO ] joelib.io.IOTypeHolder - 14
> input/output types loaded.
> 21:10:10 [INFO ] joelib.data.JOEAtomTyper - Using atom
> type model: joelib/data/plain/atomtype.txt
> 21:10:10 [INFO ] joelib.data.JOEAromaticTyper - Using
> aromaticity model: joelib/data/plain/aromatic.txt
> 21:10:13 [INFO ] joelib.io.SimpleReader - ... 96
> molecules successful loaded in 2806 ms.
> reading file "param_mm/default/atomtypes.txt": found 23 atomtypes.
> reading file "param_mm/default/parameters1.txt": found 86 bs-terms.
> reading file "param_mm/default/parameters2.txt": found 186 ab-terms.
> reading file "param_mm/default/parameters3.txt": found 70 tr-terms.
> reading file "param_mm/default/parameters4.txt": found 3 op-terms.
> reading file "param_mm/default/parameters5.txt": found 24 lj-datasets.
> reading file "param_mm/default/parameters6.txt": found 19 ci-datasets.
>
> An unexpected exception has been detected in native code outside the VM.
> Unexpected Signal : 11 occurred at PC=0x0
> Function=[Unknown.]
> Library=(N/A)
>
> NOTE: We are unable to locate the function name symbol for the error
> just occurred. Please refer to release documentation for possible
> reason and solutions.
>
>
> Current Java thread:
> at joelib.util.ghemical.GhemicalInterface.addAtom(Native Method)
> at
> joelib.util.ghemical.GhemicalInterface.createGhemicalModel(GhemicalInterface.java:317)
> at
> joelib.util.ghemical.GhemicalInterface.doGeometryOptimization(GhemicalInterface.java:371)
> at joelib.test.WekaTest.optimizeMolecules(WekaTest.java:273)
> at joelib.test.WekaTest.main(WekaTest.java:77)
>
> Dynamic libraries:
> 08048000-0804e000 r-xp 00000000 08:02 2633593
> /usr/java/j2sdk1.4.1_02/bin/java
> 0804e000-0804f000 rw-p 00005000 08:02 2633593
> /usr/java/j2sdk1.4.1_02/bin/java
> 40000000-40015000 r-xp 00000000 08:02 2534563 /lib/ld-2.3.2.so
> 40015000-40016000 rw-p 00014000 08:02 2534563 /lib/ld-2.3.2.so
> 40017000-40020000 r-xp 00000000 08:02 2339520
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
> 40020000-40021000 rw-p 00008000 08:02 2339520
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
> 40022000-40023000 r--p 0092f000 08:02 457938
> /usr/lib/locale/locale-archive
> 40023000-4002e000 r-xp 00000000 08:02 2534598
> /lib/libnss_files-2.3.2.so
> 4002e000-4002f000 rw-p 0000a000 08:02 2534598
> /lib/libnss_files-2.3.2.so
> 4002f000-40031000 r--s 00000000 08:02 180933
> /home/gert/dev/src/joelib/lib/cdk-libio.jar
> 40031000-4003b000 r-xp 00000000 08:02 589445
> /lib/tls/libpthread-0.29.so
> 4003b000-4003c000 rw-p 0000a000 08:02 589445
> /lib/tls/libpthread-0.29.so
> 4003e000-40040000 r-xp 00000000 08:02 2534584 /lib/libdl-2.3.2.so
> 40040000-40041000 rw-p 00002000 08:02 2534584 /lib/libdl-2.3.2.so
> 40042000-4035a000 r-xp 00000000 08:02 1521284
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
> 4035a000-4053e000 rw-p 00317000 08:02 1521284
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
> 4054f000-40561000 r-xp 00000000 08:02 2534591 /lib/libnsl-2.3.2.so
> 40561000-40562000 rw-p 00011000 08:02 2534591 /lib/libnsl-2.3.2.so
> 40564000-40585000 r-xp 00000000 08:02 589443 /lib/tls/libm-2.3.2.so
> 40585000-40586000 rw-p 00020000 08:02 589443 /lib/tls/libm-2.3.2.so
> 40586000-40596000 r-xp 00000000 08:02 2339526
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
> 40596000-40598000 rw-p 0000f000 08:02 2339526
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
> 40598000-405b9000 r-xp 00000000 08:02 2339527
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
> 405b9000-405bb000 rw-p 00020000 08:02 2339527
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
> 405bb000-405d0000 r-xp 00000000 08:02 2339529
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
> 405d0000-405d2000 rw-p 00014000 08:02 2339529
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
> 405d2000-41ca1000 r--s 00000000 08:02 2339771
> /usr/java/j2sdk1.4.1_02/jre/lib/rt.jar
> 41ce4000-41cfb000 r--s 00000000 08:02 2339751
> /usr/java/j2sdk1.4.1_02/jre/lib/sunrsasign.jar
> 41cfb000-41d6c000 r--s 00000000 08:02 2339753
> /usr/java/j2sdk1.4.1_02/jre/lib/jsse.jar
> 41d6c000-41d7f000 r--s 00000000 08:02 2339752
> /usr/java/j2sdk1.4.1_02/jre/lib/jce.jar
> 41fa7000-41fd9000 r--p 008e1000 08:02 457938
> /usr/lib/locale/locale-archive
> 41fd9000-41ff6000 r--s 00000000 08:02 1587110
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/sunjce_provider.jar
> 41ff6000-41ff9000 r--s 00000000 08:02 1587111
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/dnsns.jar
> 41ff9000-42000000 r--s 00000000 08:02 180922
> /home/gert/dev/src/joelib/lib/aelfred-1.2.jar
> 42000000-4212e000 r-xp 00000000 08:02 589441 /lib/tls/libc-2.3.2.so
> 4212e000-42131000 rw-p 0012e000 08:02 589441 /lib/tls/libc-2.3.2.so
> 42133000-423ef000 r--s 00000000 08:02 2339769
> /usr/java/j2sdk1.4.1_02/jre/lib/charsets.jar
> 443ef000-443f0000 r--s 00000000 08:02 1832792
> /home/gert/dev/src/joelib/lib/database.jar
> 4c470000-4c670000 r--p 00000000 08:02 457938
> /usr/lib/locale/locale-archive
> 4c870000-4c90f000 r--s 00000000 08:02 1587112
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/localedata.jar
> 4c90f000-4c91d000 r--s 00000000 08:02 1587113
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/ldapsec.jar
> 4c91d000-4c964000 r--s 00000000 08:02 1587618
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/vecmath.jar
> 4c964000-4cbca000 r--s 00000000 08:02 1587619
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dcore.jar
> 4cbca000-4cd13000 r--s 00000000 08:02 1587620
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dutils.jar
> 4cd13000-4ce66000 r--s 00000000 08:02 1587621
> /usr/java/j2sdk1.4.1_02/jre/lib/ext/j3daudio.jar
> 4ce66000-4d31a000 r--s 00000000 08:02 1521290
> /usr/java/j2sdk1.4.1_02/lib/tools.jar
> 4d31a000-4d3ca000 r--s 00000000 08:02 180916
> /home/gert/dev/src/joelib/lib/ant.jar
> 4d3ca000-4d46a000 r--s 00000000 08:02 180924
> /home/gert/dev/src/joelib/lib/optional.jar
> 4d46a000-4d4bc000 r--s 00000000 08:02 180938
> /home/gert/dev/src/joelib/lib/ccl.jar
> 4d4bc000-4d4c1000 r--s 00000000 08:02 180929
> /home/gert/dev/src/joelib/lib/cdk-apps.jar
> 4d4c1000-4d4cb000 r--s 00000000 08:02 180930
> /home/gert/dev/src/joelib/lib/cdk-core.jar
> 4d4cb000-4d50b000 r--s 00000000 08:02 180931
> /home/gert/dev/src/joelib/lib/cdk-extra.jar
> 4d50b000-4d532000 r--s 00000000 08:02 179889
> /home/gert/dev/src/joelib/lib/log4j.jar
> 4d532000-4d550000 r--s 00000000 08:02 180932
> /home/gert/dev/src/joelib/lib/cdk-io.jar
> 4d550000-4d564000 r--s 00000000 08:02 180934
> /home/gert/dev/src/joelib/lib/cdk-render.jar
> 4d564000-4d56f000 r--s 00000000 08:02 180935
> /home/gert/dev/src/joelib/lib/cdk-standard.jar
> 4d56f000-4d59f000 r--s 00000000 08:02 180918
> /home/gert/dev/src/joelib/lib/crimson.jar
> 4d59f000-4d5a8000 r--s 00000000 08:02 180919
> /home/gert/dev/src/joelib/lib/jaxp.jar
> 4d5a8000-4d686000 r--s 00000000 08:02 180939
> /home/gert/dev/src/joelib/lib/jalopy-1.0b10.jar
> 4d686000-4d68a000 r--s 00000000 08:02 180957
> /home/gert/dev/src/joelib/lib/jalopy-ant-0.6.1.jar
> 4d68a000-4d6a0000 r--s 00000000 08:02 180961
> /home/gert/dev/src/joelib/lib/jdom-1.0b8.jar
> 4d6a0000-4d6f6000 r--s 00000000 08:02 180962
> /home/gert/dev/src/joelib/lib/log4j-1.2.6.jar
> 4d6f6000-4d706000 r--s 00000000 08:02 180963
> /home/gert/dev/src/joelib/lib/oro-2.0.6.jar
> 4d706000-4d720000 r--s 00000000 08:02 180958
> /home/gert/dev/src/joelib/lib/javancss.jar
> 4d720000-4d748000 r--s 00000000 08:02 180959
> /home/gert/dev/src/joelib/lib/jaxen-core-1.0-fcs.jar
> 4d748000-4d74f000 r--s 00000000 08:02 180960
> /home/gert/dev/src/joelib/lib/jaxp-1.2.jar
> 4d74f000-4d76f000 r--s 00000000 08:02 180920
> /home/gert/dev/src/joelib/lib/jdom.jar
> 4d76f000-4d786000 r--s 00000000 08:02 180928
> /home/gert/dev/src/joelib/lib/JSX1.0.7.4.jar
> 4d786000-4d79e000 r--s 00000000 08:02 180921
> /home/gert/dev/src/joelib/lib/junit-3.2.jar
> 4d79e000-4d7bd000 r--s 00000000 08:02 180923
> /home/gert/dev/src/joelib/lib/mm.mysql-2.0.14-bin.jar
> 4d7bd000-4d7d6000 r--s 00000000 08:02 180971
> /home/gert/dev/src/joelib/lib/mysql.jar
> 4d7d6000-4d8f6000 r--s 00000000 08:02 180936
> /home/gert/dev/src/joelib/lib/plucker-build-1.2.jar
> 4d8f6000-4d967000 r--s 00000000 08:02 180964
> /home/gert/dev/src/joelib/lib/pmd-1.2.jar
> 4d967000-4d96e000 r--s 00000000 08:02 180965
> /home/gert/dev/src/joelib/lib/sax-2.0.1.jar
> 4d96e000-4d974000 r--s 00000000 08:02 180966
> /home/gert/dev/src/joelib/lib/saxpath-1.0-fcs.jar
> 4d974000-4da3f000 r--s 00000000 08:02 180925
> /home/gert/dev/src/joelib/lib/sgt.jar
> 4da3f000-4ddf8000 r--s 00000000 08:02 180927
> /home/gert/dev/src/joelib/lib/weka.jar
> 4ddf8000-4df80000 r--s 00000000 08:02 180926
> /home/gert/dev/src/joelib/lib/xerces.jar
> 4df80000-4e248000 r-xp 00000000 08:02 2339537
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
> 4e248000-4e25d000 rw-p 002c7000 08:02 2339537
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
> 4e283000-4e2d6000 r-xp 00000000 08:02 2339536
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
> 4e2d6000-4e2d7000 rw-p 00052000 08:02 2339536
> /usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
> 4e2f1000-4e2f8000 r-xp 00000000 08:02 768661
> /usr/X11R6/lib/libXp.so.6.2
> 4e2f8000-4e2f9000 rw-p 00006000 08:02 768661
> /usr/X11R6/lib/libXp.so.6.2
> 4e2f9000-4e347000 r-xp 00000000 08:02 768669
> /usr/X11R6/lib/libXt.so.6.0
> 4e347000-4e34b000 rw-p 0004d000 08:02 768669
> /usr/X11R6/lib/libXt.so.6.0
> 4e34b000-4e358000 r-xp 00000000 08:02 768647
> /usr/X11R6/lib/libXext.so.6.4
> 4e358000-4e359000 rw-p 0000c000 08:02 768647
> /usr/X11R6/lib/libXext.so.6.4
> 4e359000-4e35d000 r-xp 00000000 08:02 768671
> /usr/X11R6/lib/libXtst.so.6.1
> 4e35d000-4e35e000 rw-p 00004000 08:02 768671
> /usr/X11R6/lib/libXtst.so.6.1
> 4e35e000-4e43a000 r-xp 00000000 08:02 768637
> /usr/X11R6/lib/libX11.so.6.2
> 4e43a000-4e43d000 rw-p 000db000 08:02 768637
> /usr/X11R6/lib/libX11.so.6.2
> 4e43d000-4e445000 r-xp 00000000 08:02 768635
> /usr/X11R6/lib/libSM.so.6.0
> 4e445000-4e446000 rw-p 00007000 08:02 768635
> /usr/X11R6/lib/libSM.so.6.0
> 4e446000-4e45a000 r-xp 00000000 08:02 768631
> /usr/X11R6/lib/libICE.so.6.3
> 4e45a000-4e45b000 rw-p 00013000 08:02 768631
> /usr/X11R6/lib/libICE.so.6.3
> 4e45d000-4e66e000 r-xp 00000000 08:02 2013189
> /home/gert/dev/src/joelib/lib/linux/libghemical.so
> 4e66e000-4e85c000 rw-p 00210000 08:02 2013189
> /home/gert/dev/src/joelib/lib/linux/libghemical.so
> 51a93000-51aca000 r-xp 00000000 08:02 344420
> /usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
> 51aca000-51ad3000 rw-p 00037000 08:02 344420
> /usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
> 51ad5000-51adc000 r-xp 00000000 08:02 2536295
> /lib/libgcc_s-3.2.2-20030225.so.1
> 51adc000-51add000 rw-p 00007000 08:02 2536295
> /lib/libgcc_s-3.2.2-20030225.so.1
>
> Local Time = Wed Sep 10 15:10:13 2003
> Elapsed Time = 4
> #
> # The exception above was detected in native code outside the VM
> #
> # Java VM: Java HotSpot(TM) Client VM (1.4.1_02-b06 mixed mode)
> #
> # An error report file has been saved as hs_err_pid1713.log.
> # Please refer to the file for further information.
> #
> /home/gert/.//bin/joetest.sh: line 72: 1713 Aborted (core
> dumped) ${JAVA_HOME}/bin/java -classpath ${CLASSPATH} "$@"
>
> ----------------------End Error Message---------------------------
>
> Thank you,
>
> Gert Sclep
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
>
--
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: Gert S. <Ger...@re...> - 2003-09-10 15:47:18
|
> Hi Gert, > > are you using IBM's JDK ? > > The interface works only under the IBM JDK under Linux ... SUN's JDK > seems to have an JNI bug. Thanks a lot. This seems to work. Greetings, Gert Sclep |
|
From: Gert S. <Ger...@re...> - 2003-09-10 13:19:04
|
> the package path in the LibGhemical JNI interface was corrected.
>
> Now the precompiled shared libraries should work correctly !;-)
>
> Regards, Joerg
I can't seem to get LibGhemical to work properly under Linux. At the
bottom of the mail I will attach the error message I'm constantly
receiving. I tried upgrading from RedHat 7.2 to RedHat 9.0, but to no
avail. Trying to compile the interface-source (in libghemical/src/jni)
didn't help either.
I'm no hero when it comes to C++ and I'm quite stuck in the further
investigation of this error, so hints would be most welcome.
-------------------------Error Message-------------------------------
[gert@leffe linux]$ joetest.sh joelib/test/WekaTest LR N L O
Adding /home/gert/.//dev/src/joelib_test to CLASSPATH.
...(snip)...
21:10:10 [INFO ] joelib.data.JOEElementTable - Using element
table: joelib/data/plain/element.txt
21:10:10 [INFO ] joelib.io.IOTypeHolder - 14
input/output types loaded.
21:10:10 [INFO ] joelib.data.JOEAtomTyper - Using atom
type model: joelib/data/plain/atomtype.txt
21:10:10 [INFO ] joelib.data.JOEAromaticTyper - Using
aromaticity model: joelib/data/plain/aromatic.txt
21:10:13 [INFO ] joelib.io.SimpleReader - ... 96
molecules successful loaded in 2806 ms.
reading file "param_mm/default/atomtypes.txt": found 23 atomtypes.
reading file "param_mm/default/parameters1.txt": found 86 bs-terms.
reading file "param_mm/default/parameters2.txt": found 186 ab-terms.
reading file "param_mm/default/parameters3.txt": found 70 tr-terms.
reading file "param_mm/default/parameters4.txt": found 3 op-terms.
reading file "param_mm/default/parameters5.txt": found 24 lj-datasets.
reading file "param_mm/default/parameters6.txt": found 19 ci-datasets.
An unexpected exception has been detected in native code outside the VM.
Unexpected Signal : 11 occurred at PC=0x0
Function=[Unknown.]
Library=(N/A)
NOTE: We are unable to locate the function name symbol for the error
just occurred. Please refer to release documentation for possible
reason and solutions.
Current Java thread:
at joelib.util.ghemical.GhemicalInterface.addAtom(Native Method)
at
joelib.util.ghemical.GhemicalInterface.createGhemicalModel(GhemicalInterface.java:317)
at
joelib.util.ghemical.GhemicalInterface.doGeometryOptimization(GhemicalInterface.java:371)
at joelib.test.WekaTest.optimizeMolecules(WekaTest.java:273)
at joelib.test.WekaTest.main(WekaTest.java:77)
Dynamic libraries:
08048000-0804e000 r-xp 00000000 08:02 2633593
/usr/java/j2sdk1.4.1_02/bin/java
0804e000-0804f000 rw-p 00005000 08:02 2633593
/usr/java/j2sdk1.4.1_02/bin/java
40000000-40015000 r-xp 00000000 08:02 2534563 /lib/ld-2.3.2.so
40015000-40016000 rw-p 00014000 08:02 2534563 /lib/ld-2.3.2.so
40017000-40020000 r-xp 00000000 08:02 2339520
/usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
40020000-40021000 rw-p 00008000 08:02 2339520
/usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
40022000-40023000 r--p 0092f000 08:02 457938
/usr/lib/locale/locale-archive
40023000-4002e000 r-xp 00000000 08:02 2534598
/lib/libnss_files-2.3.2.so
4002e000-4002f000 rw-p 0000a000 08:02 2534598
/lib/libnss_files-2.3.2.so
4002f000-40031000 r--s 00000000 08:02 180933
/home/gert/dev/src/joelib/lib/cdk-libio.jar
40031000-4003b000 r-xp 00000000 08:02 589445
/lib/tls/libpthread-0.29.so
4003b000-4003c000 rw-p 0000a000 08:02 589445
/lib/tls/libpthread-0.29.so
4003e000-40040000 r-xp 00000000 08:02 2534584 /lib/libdl-2.3.2.so
40040000-40041000 rw-p 00002000 08:02 2534584 /lib/libdl-2.3.2.so
40042000-4035a000 r-xp 00000000 08:02 1521284
/usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
4035a000-4053e000 rw-p 00317000 08:02 1521284
/usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
4054f000-40561000 r-xp 00000000 08:02 2534591 /lib/libnsl-2.3.2.so
40561000-40562000 rw-p 00011000 08:02 2534591 /lib/libnsl-2.3.2.so
40564000-40585000 r-xp 00000000 08:02 589443 /lib/tls/libm-2.3.2.so
40585000-40586000 rw-p 00020000 08:02 589443 /lib/tls/libm-2.3.2.so
40586000-40596000 r-xp 00000000 08:02 2339526
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
40596000-40598000 rw-p 0000f000 08:02 2339526
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
40598000-405b9000 r-xp 00000000 08:02 2339527
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
405b9000-405bb000 rw-p 00020000 08:02 2339527
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
405bb000-405d0000 r-xp 00000000 08:02 2339529
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
405d0000-405d2000 rw-p 00014000 08:02 2339529
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
405d2000-41ca1000 r--s 00000000 08:02 2339771
/usr/java/j2sdk1.4.1_02/jre/lib/rt.jar
41ce4000-41cfb000 r--s 00000000 08:02 2339751
/usr/java/j2sdk1.4.1_02/jre/lib/sunrsasign.jar
41cfb000-41d6c000 r--s 00000000 08:02 2339753
/usr/java/j2sdk1.4.1_02/jre/lib/jsse.jar
41d6c000-41d7f000 r--s 00000000 08:02 2339752
/usr/java/j2sdk1.4.1_02/jre/lib/jce.jar
41fa7000-41fd9000 r--p 008e1000 08:02 457938
/usr/lib/locale/locale-archive
41fd9000-41ff6000 r--s 00000000 08:02 1587110
/usr/java/j2sdk1.4.1_02/jre/lib/ext/sunjce_provider.jar
41ff6000-41ff9000 r--s 00000000 08:02 1587111
/usr/java/j2sdk1.4.1_02/jre/lib/ext/dnsns.jar
41ff9000-42000000 r--s 00000000 08:02 180922
/home/gert/dev/src/joelib/lib/aelfred-1.2.jar
42000000-4212e000 r-xp 00000000 08:02 589441 /lib/tls/libc-2.3.2.so
4212e000-42131000 rw-p 0012e000 08:02 589441 /lib/tls/libc-2.3.2.so
42133000-423ef000 r--s 00000000 08:02 2339769
/usr/java/j2sdk1.4.1_02/jre/lib/charsets.jar
443ef000-443f0000 r--s 00000000 08:02 1832792
/home/gert/dev/src/joelib/lib/database.jar
4c470000-4c670000 r--p 00000000 08:02 457938
/usr/lib/locale/locale-archive
4c870000-4c90f000 r--s 00000000 08:02 1587112
/usr/java/j2sdk1.4.1_02/jre/lib/ext/localedata.jar
4c90f000-4c91d000 r--s 00000000 08:02 1587113
/usr/java/j2sdk1.4.1_02/jre/lib/ext/ldapsec.jar
4c91d000-4c964000 r--s 00000000 08:02 1587618
/usr/java/j2sdk1.4.1_02/jre/lib/ext/vecmath.jar
4c964000-4cbca000 r--s 00000000 08:02 1587619
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dcore.jar
4cbca000-4cd13000 r--s 00000000 08:02 1587620
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dutils.jar
4cd13000-4ce66000 r--s 00000000 08:02 1587621
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3daudio.jar
4ce66000-4d31a000 r--s 00000000 08:02 1521290
/usr/java/j2sdk1.4.1_02/lib/tools.jar
4d31a000-4d3ca000 r--s 00000000 08:02 180916
/home/gert/dev/src/joelib/lib/ant.jar
4d3ca000-4d46a000 r--s 00000000 08:02 180924
/home/gert/dev/src/joelib/lib/optional.jar
4d46a000-4d4bc000 r--s 00000000 08:02 180938
/home/gert/dev/src/joelib/lib/ccl.jar
4d4bc000-4d4c1000 r--s 00000000 08:02 180929
/home/gert/dev/src/joelib/lib/cdk-apps.jar
4d4c1000-4d4cb000 r--s 00000000 08:02 180930
/home/gert/dev/src/joelib/lib/cdk-core.jar
4d4cb000-4d50b000 r--s 00000000 08:02 180931
/home/gert/dev/src/joelib/lib/cdk-extra.jar
4d50b000-4d532000 r--s 00000000 08:02 179889
/home/gert/dev/src/joelib/lib/log4j.jar
4d532000-4d550000 r--s 00000000 08:02 180932
/home/gert/dev/src/joelib/lib/cdk-io.jar
4d550000-4d564000 r--s 00000000 08:02 180934
/home/gert/dev/src/joelib/lib/cdk-render.jar
4d564000-4d56f000 r--s 00000000 08:02 180935
/home/gert/dev/src/joelib/lib/cdk-standard.jar
4d56f000-4d59f000 r--s 00000000 08:02 180918
/home/gert/dev/src/joelib/lib/crimson.jar
4d59f000-4d5a8000 r--s 00000000 08:02 180919
/home/gert/dev/src/joelib/lib/jaxp.jar
4d5a8000-4d686000 r--s 00000000 08:02 180939
/home/gert/dev/src/joelib/lib/jalopy-1.0b10.jar
4d686000-4d68a000 r--s 00000000 08:02 180957
/home/gert/dev/src/joelib/lib/jalopy-ant-0.6.1.jar
4d68a000-4d6a0000 r--s 00000000 08:02 180961
/home/gert/dev/src/joelib/lib/jdom-1.0b8.jar
4d6a0000-4d6f6000 r--s 00000000 08:02 180962
/home/gert/dev/src/joelib/lib/log4j-1.2.6.jar
4d6f6000-4d706000 r--s 00000000 08:02 180963
/home/gert/dev/src/joelib/lib/oro-2.0.6.jar
4d706000-4d720000 r--s 00000000 08:02 180958
/home/gert/dev/src/joelib/lib/javancss.jar
4d720000-4d748000 r--s 00000000 08:02 180959
/home/gert/dev/src/joelib/lib/jaxen-core-1.0-fcs.jar
4d748000-4d74f000 r--s 00000000 08:02 180960
/home/gert/dev/src/joelib/lib/jaxp-1.2.jar
4d74f000-4d76f000 r--s 00000000 08:02 180920
/home/gert/dev/src/joelib/lib/jdom.jar
4d76f000-4d786000 r--s 00000000 08:02 180928
/home/gert/dev/src/joelib/lib/JSX1.0.7.4.jar
4d786000-4d79e000 r--s 00000000 08:02 180921
/home/gert/dev/src/joelib/lib/junit-3.2.jar
4d79e000-4d7bd000 r--s 00000000 08:02 180923
/home/gert/dev/src/joelib/lib/mm.mysql-2.0.14-bin.jar
4d7bd000-4d7d6000 r--s 00000000 08:02 180971
/home/gert/dev/src/joelib/lib/mysql.jar
4d7d6000-4d8f6000 r--s 00000000 08:02 180936
/home/gert/dev/src/joelib/lib/plucker-build-1.2.jar
4d8f6000-4d967000 r--s 00000000 08:02 180964
/home/gert/dev/src/joelib/lib/pmd-1.2.jar
4d967000-4d96e000 r--s 00000000 08:02 180965
/home/gert/dev/src/joelib/lib/sax-2.0.1.jar
4d96e000-4d974000 r--s 00000000 08:02 180966
/home/gert/dev/src/joelib/lib/saxpath-1.0-fcs.jar
4d974000-4da3f000 r--s 00000000 08:02 180925
/home/gert/dev/src/joelib/lib/sgt.jar
4da3f000-4ddf8000 r--s 00000000 08:02 180927
/home/gert/dev/src/joelib/lib/weka.jar
4ddf8000-4df80000 r--s 00000000 08:02 180926
/home/gert/dev/src/joelib/lib/xerces.jar
4df80000-4e248000 r-xp 00000000 08:02 2339537
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
4e248000-4e25d000 rw-p 002c7000 08:02 2339537
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
4e283000-4e2d6000 r-xp 00000000 08:02 2339536
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
4e2d6000-4e2d7000 rw-p 00052000 08:02 2339536
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
4e2f1000-4e2f8000 r-xp 00000000 08:02 768661
/usr/X11R6/lib/libXp.so.6.2
4e2f8000-4e2f9000 rw-p 00006000 08:02 768661
/usr/X11R6/lib/libXp.so.6.2
4e2f9000-4e347000 r-xp 00000000 08:02 768669
/usr/X11R6/lib/libXt.so.6.0
4e347000-4e34b000 rw-p 0004d000 08:02 768669
/usr/X11R6/lib/libXt.so.6.0
4e34b000-4e358000 r-xp 00000000 08:02 768647
/usr/X11R6/lib/libXext.so.6.4
4e358000-4e359000 rw-p 0000c000 08:02 768647
/usr/X11R6/lib/libXext.so.6.4
4e359000-4e35d000 r-xp 00000000 08:02 768671
/usr/X11R6/lib/libXtst.so.6.1
4e35d000-4e35e000 rw-p 00004000 08:02 768671
/usr/X11R6/lib/libXtst.so.6.1
4e35e000-4e43a000 r-xp 00000000 08:02 768637
/usr/X11R6/lib/libX11.so.6.2
4e43a000-4e43d000 rw-p 000db000 08:02 768637
/usr/X11R6/lib/libX11.so.6.2
4e43d000-4e445000 r-xp 00000000 08:02 768635
/usr/X11R6/lib/libSM.so.6.0
4e445000-4e446000 rw-p 00007000 08:02 768635
/usr/X11R6/lib/libSM.so.6.0
4e446000-4e45a000 r-xp 00000000 08:02 768631
/usr/X11R6/lib/libICE.so.6.3
4e45a000-4e45b000 rw-p 00013000 08:02 768631
/usr/X11R6/lib/libICE.so.6.3
4e45d000-4e66e000 r-xp 00000000 08:02 2013189
/home/gert/dev/src/joelib/lib/linux/libghemical.so
4e66e000-4e85c000 rw-p 00210000 08:02 2013189
/home/gert/dev/src/joelib/lib/linux/libghemical.so
51a93000-51aca000 r-xp 00000000 08:02 344420
/usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
51aca000-51ad3000 rw-p 00037000 08:02 344420
/usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
51ad5000-51adc000 r-xp 00000000 08:02 2536295
/lib/libgcc_s-3.2.2-20030225.so.1
51adc000-51add000 rw-p 00007000 08:02 2536295
/lib/libgcc_s-3.2.2-20030225.so.1
Local Time = Wed Sep 10 15:10:13 2003
Elapsed Time = 4
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (1.4.1_02-b06 mixed mode)
#
# An error report file has been saved as hs_err_pid1713.log.
# Please refer to the file for further information.
#
/home/gert/.//bin/joetest.sh: line 72: 1713 Aborted (core
dumped) ${JAVA_HOME}/bin/java -classpath ${CLASSPATH} "$@"
----------------------End Error Message---------------------------
Thank you,
Gert Sclep
|
|
From: Joerg K. W. <we...@in...> - 2003-08-26 16:39:01
|
Hi, thanks ! Sorry, for this distribution bug (in the ant xml-script), both are now available in the new release. http://sourceforge.net/project/showfiles.php?group_id=39708 BTW, when talking about the atom typer ... the aromaticity model bug for complex rings is fixed: http://sourceforge.net/tracker/index.php?func=detail&aid=795313&group_id=39708&atid=425969 The weka library and patch mechanism is now available as optional library. http://sourceforge.net/project/showfiles.php?group_id=39708 Regards, Joerg > I've found that the three files: > LogP.contributions > MR.contributions > PSA.contributions > are missing from the source distribution. > > Furthermore it seems that "atomtyper.html" is missing from the "tutorial" directory (even from CVS!) > > Regards > > Ambrogio > > > ------------------------------------------------------- > This SF.net email is sponsored by: VM Ware > With VMware you can run multiple operating systems on a single machine. > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines > at the same time. Free trial click here:http://www.vmware.com/wl/offer/358/0 > _______________________________________________ > Joelib-help mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-help > -- 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: Oliva A. <Amb...@no...> - 2003-08-26 12:14:10
|
Hi All, I've found that the three files: LogP.contributions MR.contributions PSA.contributions are missing from the source distribution. Furthermore it seems that "atomtyper.html" is missing from the = "tutorial" directory (even from CVS!) Regards Ambrogio |
|
From: Joerg K. W. <we...@in...> - 2003-08-18 08:05:04
|
Hello Gert,
> I suppose you mean by "if this works" that the system shouldn't crash
> anymore.
>
> Well, indeed, it doesn't crash any further. But, now the ViewerFrame is
> shown while the molecules can't be drawn. Shouldn't the execution of
> Viewer.main() better be entirely stopped when a buggy Java3D is detected?
Yes !;-)
The problem is located in one of this 4 lines, but which one !?
GraphicsConfigTemplate3D tmpl = new GraphicsConfigTemplate3D();
GraphicsEnvironment env =
GraphicsEnvironment.getLocalGraphicsEnvironment();
GraphicsDevice device = env.getDefaultScreenDevice();
GraphicsConfiguration config = device.getBestConfiguration(tmpl);
There seems definitely a problem when getting a screen device, but i
can't see why ?
http://www.j3d.org/tutorials/raw_j3d/chapter1/world_window.html
The clean version will be to throw an Exception or throw only one single
error in the constructor before line 72, which is also clearer than
adding to every method a logging error or Exception (my previous mail
was a quick fix !;-)
Additionally i've nothing usefull found in the Java3D mailing lists ...
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: Gert S. <Ger...@re...> - 2003-08-17 22:00:02
|
> If this works i recommend to add these changes to CVS directly to avoid > this problem for other users ! Unfortunately the Java3D API for other > platform is often not really up-to-date ... I suppose you mean by "if this works" that the system shouldn't crash anymore. Well, indeed, it doesn't crash any further. But, now the ViewerFrame is shown while the molecules can't be drawn. Shouldn't the execution of Viewer.main() better be entirely stopped when a buggy Java3D is detected? Greetings, Gert |
|
From: Joerg K. W. <we...@in...> - 2003-08-14 21:48:07
|
Hi,
eventually you could use:
line 72:
if(config!=null)
{
moleculeCanvas = new Canvas3D(config);
mScene = new MolecularScene(moleculeCanvas);
add(moleculeCanvas, BorderLayout.CENTER);
}
and for all other methods you should add
if(mScene!=null)
{
...
}
else
{
logger.error(...)
}
or
if(moleculeCanvas!=null)
{
...
}
else
{
logger.error(...)
}
If this works i recommend to add these changes to CVS directly to avoid
this problem for other users ! Unfortunately the Java3D API for other
platform is often not really up-to-date ...
Regards, Joerg
> ************************************************************************
> *** ERROR: Canvas3D constructed with a null GraphicsConfiguration ***
> This will cause a NullPointerException in a subsequent release
> ************************************************************************
> java.lang.NullPointerException:
> Canvas3D: null GraphicsConfiguration at
> javax.media.j3d.Canvas3D.<init>(Canvas3D.java:1100) at
> javax.media.j3d.Canvas3D.<init>(Canvas3D.java:1065) at
> joelib.gui.molviewer.java3d.graphics3D.JPanel3D.<init>(JPanel3D.java:72) at
> joelib.gui.molviewer.java3d.ViewerFrame.jbInit(ViewerFrame.java:154)
>
>
> I am using "Java 3DTM v.1.2.1_01 API for IRIX" on a SGI Indigo2 (I know
> it's an old beast, but still it should work). The graphics board
> is listed as "IMPACTPC".
>
> In accordance with advice in some newsgroups I tried to change the
> DepthSize of the GraphicsConfigTemplate3D, but to no avail.
>
> Anybody else solved this same problem?
>
> Greetings,
> Gert
>
> PS: on the Linux PC it works smoothly
>
>
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
>
--
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: Gert S. <Ger...@re...> - 2003-08-14 17:08:31
|
When trying to user the molviewer I get following java3D error: ************************************************************************ *** ERROR: Canvas3D constructed with a null GraphicsConfiguration *** This will cause a NullPointerException in a subsequent release ************************************************************************ java.lang.NullPointerException: Canvas3D: null GraphicsConfiguration at javax.media.j3d.Canvas3D.<init>(Canvas3D.java:1100) at javax.media.j3d.Canvas3D.<init>(Canvas3D.java:1065) at joelib.gui.molviewer.java3d.graphics3D.JPanel3D.<init>(JPanel3D.java:72) at joelib.gui.molviewer.java3d.ViewerFrame.jbInit(ViewerFrame.java:154) I am using "Java 3DTM v.1.2.1_01 API for IRIX" on a SGI Indigo2 (I know it's an old beast, but still it should work). The graphics board is listed as "IMPACTPC". In accordance with advice in some newsgroups I tried to change the DepthSize of the GraphicsConfigTemplate3D, but to no avail. Anybody else solved this same problem? Greetings, Gert PS: on the Linux PC it works smoothly |
|
From: Joerg K. W. <we...@in...> - 2003-08-14 09:31:55
|
Hi Gert, > But shouldn't you better add the modified weka.jar to the lib-directory in > that case? Or mention the necessary modifications to weka in the build.xml > file? I think these things can already be freely discussed in the developer mailing list. I hope this will not to much 'developer stuff' for the subscribers of the helping mailing list. On the other side JOELib has (in my opinion) a 70% developer focus, so the division into help-, and developer-mailing list is not really clear. Please write a comment if you want to tell us your thoughts ... > Anyway, my opinion would be to try to subclass the classes of the used > packages in case of a protected modifier or to write new classes in the > same package as the 'stubborn' class in case of a package modifier. In my > eyes this is more elegant, since you leave the other peoples code intact. > How does it look in the eyes of a more skilled coder? I don't care, because that's only one single entry. Because this functionality has it's focus on developers, i think they will be easily able to change 'protected' to 'public' and recompile the sources. If not i can offer a source code patch and/or the ant target for doing such things. Furthermore i do not find the weka design decision for this class not really good. Protected is to restricted for such an important class, that like making atoms protected. Another possibility is to add a simple Mol2Instance class in the weka source package to fullfill the protected case. Adding the weka.jar is definitely possible, but will increment the joelib distribution. And last but not least you can write a wrapper if you like and pick the required functionalites from the InstancesHelper from JOELib. So i think adding somewere a note in the tutorial would be fine, because i've an internal CVS version also. That's my way, when developing 'machine learning' tools and hacking them. > Regards, > Gert 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: Gert S. <Ger...@re...> - 2003-08-14 09:14:02
|
> > But shouldn't you better add the modified weka.jar to the lib-directory in > > that case? Or mention the necessary modifications to weka in the build.xml > > file? > I think these things can already be freely discussed in the developer > mailing list. I hope this will not to much 'developer stuff' for the > subscribers of the helping mailing list. On the other side JOELib has > (in my opinion) a 70% developer focus, so the division into help-, and > developer-mailing list is not really clear. Please write a comment if > you want to tell us your thoughts ... I still think it is a good thing to have this division between help and developer list. The help list would be for problems when using the program or when installing the program. The developer list for problems concerning analysis and design and for problems when compiling the source code. Just as long as developers are not to proud to post something in the help list, there will not be a lot of confusion. |
|
From: Joerg K. W. <we...@in...> - 2003-08-13 10:12:57
|
Hi Gert, > Both the stable version, the developer version and the current cvs version > of weka don't use an Attribute(String,FastVector,int) constructor in the > core.Attribute class, but instead expect a ProtectedProperties object if a > third argument is given in the constructor-call. If i'm reminding this correclty i've just changed this constructor from 'protected' to 'public' ... ... in my Weka version i've changed some more things, but that's not really interesting for you ... > So, I must be missing something here. Do I use a wrong weka library, or do > I overlook something else? Just remind we are using source code, if something does not fit ... we change these things ! 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: Gert S. <Ger...@re...> - 2003-08-13 09:33:31
|
Both the stable version, the developer version and the current cvs version of weka don't use an Attribute(String,FastVector,int) constructor in the core.Attribute class, but instead expect a ProtectedProperties object if a third argument is given in the constructor-call. And yet, this Attribute(String,FastVector,int) constructor is called in the algo.dataming.weka.InstancesHelper class. I tracked down the versions of the Attribute.java file in the weka repository and apparently the current constructor syntax already exists for more than 2 years. So, I must be missing something here. Do I use a wrong weka library, or do I overlook something else? Thanks, Gert Sclep |
|
From: Joerg K. W. <we...@in...> - 2003-08-06 12:55:19
|
Hi all, this is just a reminder, that nearly all classes contains a specific Logger with a debugging functionality. If we take the aromatic typer for example you can switch on this functionality by changing log4j.category.joelib.data.JOEAromaticTyper=INFO in the file joelib/src/log4j.properties to log4j.category.joelib.data.JOEAromaticTyper=DEBUG and recompile the project, which copies the resource files to the joelib/build directory. This will show you the assigned SMARTS pattern with the number of electrons and the typer process, when calling any method which requires this functionality. This can be *VERY* helpfull when trying to resolve, why e.g. some atoms are not recognized as aromatic (see my last bug fix mail !;-) It's recommended to use one one or two molecule for such tasks, or you will have a lot of console filling messages, e.g. for testing a SMILES/SMARTS match i used and you can use: SMILESTest to generate a molecule file SMARTTest for substructure search in the generated file and MoleculeLoadTest for showing the atom properties, e.g. aromaticity flags 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: Joerg K. W. <we...@in...> - 2003-08-06 12:08:54
|
Hi all, Hi Geoff, Hi Hou, i've found a serious bug in the SMARTS matcher. This is caused when picking bridging closure ring atoms (root atoms) by the aromatic typer. This will cause the false negative detection of aromatic atoms in this special ring. E.g. when treating: Oc1c(O)c2cccc3ccc4cccc1c4c23, Pyrene-4,5-diol Atoms 2,3 should be aromatic also ! I've implemented a bug fix, i would recommend to add these things to OpenBabel, also. For JOELib users it's recommended to get the latest version from the CVS or download only the changed JOEAromaticTyper.java under (with one day delay, because of SF server strategy, sorry !) http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/joelib/joelib/src/joelib/data/ Regards, Joerg JOELib Administrator -- 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...> - 2003-08-04 14:17:47
|
Hi all, the tutorial was extended with examples and source code snippets (26 pages). 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: Joerg K. W. <we...@in...> - 2003-08-04 12:56:37
|
Hi all, a new code cleanup release is available: Two important changes, if you've implemented your own descriptors: 1. method 'void testDescriptor()' in the Descriptor interfaces has changed to 'boolean testDescriptor()'. Please change the return value, or your compiler will fail at your own implementations. 2. The initialization for descriptors has changed slightly, but please refer to the API docu, the old constructor for DescInfo is deprecated, but still at work. That's not serious only a design decision, because the previous version caused inhomogenities. 3. The rest is AddOn to facilitate tasks: SimpleReaderWriterPipe AtomDynamicDesc AtomDoubleDesc 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: Joerg K. W. <we...@in...> - 2003-07-21 07:17:23
|
Hi all, a new JOELib release with new features is available ! !!! This is developer release, because there are no standard applications available for using the new features !!! And i will be happy to arrange duties for such applications, but have no time to implement them. Here is the Change Log: ------------------------------------ - interface to the Weka data mining library (http://www.cs.waikato.ac.nz/ml/weka/) - JavaNativeInterface (JNI) to (Lib)Ghemical for calculating Molecular Mechanics (MM) and rotate bonds (http://bioinformatics.org/project/?group_id=41). - fragmentation methods for molecules - generation method for molecules using a scaffold and R-groups - JDBC data base interface - bug fixes: --- corrected ant build file for missing CDK libraries which is also available under: https://sourceforge.net/project/shownotes.php?group_id=39708&release_id=172841 Be aware that the LibGhemical connection works *ONLY* under Cygwin/Windows and Linux/IBM-JRE-1.4 ... this interface is still beta and depends on a bug free JDK/JRE (so Linux SUN-JRE will definitely not work and the Windows version could be much more stable ... in my opinion ... unfortunately the Windows-IBM-JRE is only 1.3 and not 1.4 which will be required here). ... feel free to modify the interface for your requirements ... i'm still interested in a method for calculateing molecular surfaces (using Ghemical) and would be happy about some helping hands 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 |
|
From: Joerg K. W. <we...@in...> - 2003-06-26 09:19:10
|
Hello,
> I can compile but can't run: (KAWA interface)
> I don't know whether it is correct!!
Seems to be o.k.
The line breaks in the mails are really bad when trying to compile the
source code. Please use zipped files for large source code files.
Here is a working version of your code:
ant/build.xml
build/demo.smi
src/joelib/gui/molviewer/java3d/ViewerFrame2.java
lib/cdk-core.jar
lib/cdk-extra.jar
lib/cdk-libio.jar
lib/cdk-render.jar
lib/cdk-standard.jar
What have i changed:
0. Not really much !!!
1. I changed your filename to ViewerFrame2.java
2. added
<target name="ViewerTest" depends="init" >
...
<java classname="joelib.gui.molviewer.java3d.ViewerFrame2"
fork="yes" dir="${build.directory}">
<classpath refid="project.class.path" />
...
</target>
instead of
<target name="ViewerTest" depends="init" >
...
<java classname="joelib.gui.molviewer.java3d.Viewer" fork="yes"
dir="${build.directory}">
<classpath refid="project.class.path" />
...
</target>
3. changed your SMILES code to
demo.smi
C1C=CCCC1 Cyclohexen
because this is the standard entry in joelib.properties
which says:
joelib.io.types.Smiles.lineStructure=SMILES|TITLE
if you don't want a title defined use:
joelib.io.types.Smiles.lineStructure=SMILES
4. Because your are using smiles you will not see really a structure,
because SMILES generates only atom and bond lists without coordinates
so i've added to getJOEMol(...):
if (jmol != null)
{
// create 2D coordinates
if (!jmol.has2D() && !jmol.has3D())
{
CDKTools.generate2D(jmol);
}
if (tmpMol != null)
{
this.removeMolecule(tmpMol);
}
// if the i will publish the Ghemical connection you can use:
// GhemicalTools.createEnergyMinimized3D(jmol);
this.clear();
this.addMolecule(jmol);
}
because you will need the CDK for 2D generation i've added the relevant
CDK jar files.
You can start your example with:
ant compile ViewerTest
Regards, Joerg
--
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
|
|
From: Joerg K. W. <we...@in...> - 2003-06-26 08:44:10
|
Hello, > Then I edited the joelib.properties stripping out all the "jcompchem.". That's perfect !!! I'm sorry for that problems again ... > Then I built all thing (with several messages). I replaced the joelib.jar of the release 20030625 with the new one. > I tried reading the source, but I could not guess the format of the "descNamesURL". o.k. that's definitely a bug: Here is the bug fix and the descSelection scripts to facilitate the process: descSelection.bat descSelection.sh src/joelib.properties src/wsi/ra/tool/ResourceLoader.java Then i used: cygwin>sh descSelection.sh -iSDF d:/workingAt/datasets/algorithmTuning/regression2/moe/LogPS/huuskonen.sdf -oSDF test.sdf d:/workingAt/datasets/algorithmTuning/regression2/moe/LogPS/huuskonen.inputs normal " " Problem description: The resource loader is really important, because it can load resource files from files AND archives, likr .jar/.zip. The problem was, that it has tried to load c:/yourDir as URL which does only work if you use file:/c:/yourDir I've fixed it and it works noe also with: X:/yourdir and /cygdrive/x/yourDir By the way you can change src/log4j.properties for debugging purpose, e.g. change: #WSI log4j.category.wsi.ra.io.BatchScriptReplacer=DEBUG log4j.category.wsi.ra.tool.ResourceLoader=INFO to: #WSI log4j.category.wsi.ra.io.BatchScriptReplacer=DEBUG log4j.category.wsi.ra.tool.ResourceLoader=DEBUG and you will see was the ResourceLoader is doing. I hope this will not necessary again !;-) > Regards, Ambrogio Regards, Joerg > > -----Original Message----- > From: Joerg K. Wegner [mailto:we...@in...] > Sent: Wednesday, June 25, 2003 4:59 PM > To: Oliva Ambrogio; JOELib help > Subject: Re: joelib.test.DescriptorSelection > > > Hello Ambrogio, > > >>I modified the descNameFile as suggested but I keep receiving the same NullPointerException. Maybe I've put the wrong "delimiter" on the command line? > > mmmh, oh sorry ... that's my fault, because i'm using another > joelib.properties file. > > Please add the following lines to the src/joelib.properties file (after > joelib.filter.5.descriptionFile ...): > > joelib.filter.6.name =DescriptorFilter > joelib.filter.6.representation =joelib.process.filter.DescriptorFilter > joelib.filter.6.descriptionFile =docs/process/descriptorFilter > > >>Thanks for the quick reply. > > I'll hope this will work. I'll release a new JOELib version with the bug > fixes this day. > > >>Regards, Ambrogio > > Regards, Joerg > > >>PS. Your PSs are a little bit too technical for my knowledge of java programming. > > P.S.:This is possible !;-) > > >>-----Original Message----- >>From: Joerg K. Wegner [mailto:we...@in...] >>Sent: Wednesday, June 25, 2003 3:46 PM >>To: Oliva Ambrogio; JOELib help >>Subject: Re: joelib.test.DescriptorSelection >> >> >>Dear Dr. Ambrogio, >> >> >> >>>first of all thanks for making available JOELib. >> >>thanks ... >>... i'm crossposting this message also to the JOELib-help mailing list. >>You can join if you want ... >>http://sourceforge.net/mail/?group_id=39708 >> >> >> >> >>>I successfully used the Convert application for adding descriptors to SD files. However I do not need all the descriptors. Then I tried to use DescriptorSelection to "select" the descripors I need. >> >>That's exactly the same way i use it, especially when calculating >>autocorrelation or other more extended descriptors (not public). >> >> >> >>>The problem is that it's not clear to me the syntax, in particular the format of the descriptors list and what the "delimiter" is. >> >>Let's try to resolve that... >> >> >> >>>I tried: >>>C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF -oSDF +d c:\temp\sample.sdf c:\tem >>>p\sample_wd.sdf >> >>All fine ! >> >> >> >>>Then: >>>C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd. >>>sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ; >>>13:34:44 [INFO ] joelib.data.JOEElementTable - Using element table: joelib/data/plain/e >>>lement.txt >>>13:34:44 [INFO ] joelib.io.IOTypeHolder - 12 input/output types loaded. >>>13:34:44 [INFO ] joelib.process.filter.FilterFactory - 5 filter informations loaded. >>>Exception in thread "main" java.lang.NullPointerException >>> at joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java:167) >>> at joelib.test.DescriptorSelection.main(DescriptorSelection.java:301) >>> >>>where c:\temp\Sample_desc.txt is: >>> >>>Number_of_bonds;LogP;Topological_radius >> >>No, this should be simply: >> >>Number_of_bonds >>LogP >>Topological_radius >> >>so you can simply use the JOELib statistic-file and import it under >>Excel and extract the descriptor names you want !;-) >> >> >> >>>Can you help me in getting DescriptorSelection work? >>>Thanks in advance. >> >>Was me a pleasure. >> >> >> >>>By the way I've also have a couple of "bug reports": >>>- In the Tutorial I've noticed that "bor", "chlor", "brom", "iod", "fluor" and "phosphor" are used instead of "boron", "chlorine", "bromine", "iodine", "fluorine" and "phosphorus". >>> >>>- In the .bat files, there are extra semicolons at the end of the "set CLASSPSTH" instructions. >> >>Thanks, i will fix it. >> >> >> >>>Thanks again. >>> >>>Ambrogio >> >> >>Regards, Joerg >> >>P.S.: BTW there exists also a descriptor normalization under >>joelib.process.types.DescVarianceNorm if you plan to normalize your data >>with mean=0, sdtdev=1, which requires a little bit of programming. E.g. >>you can add this process simply to the selection process pipe in >>joelib.test.DescriptorSelection >> >>P.P.S.: All descriptors in >>joelib\data\plain\desc2ignore.txt >>defined in the joelib.properties file as: >>joelib.process.types.DescVarianceNorm.descriptors2ignore=joelib/data/plain/desc2ignore.txt >>will be ignored for normalization. This is extremely usefull if you have >> an nominal classification problem or the sdf-file contains also some >>id's, ... >> > > -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
|
From: Oliva A. <Amb...@no...> - 2003-06-26 07:28:04
|
Hallo,
I just tried the new release and it doesn't work yet.
I got:
C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% =
joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd.
sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ;
08:22:51 [INFO ] joelib.data.JOEElementTable - Using =
element table: joelib/data/plain/e
lement.txt
08:22:51 [INFO ] joelib.io.IOTypeHolder - 13 =
input/output types loaded.
08:22:51 [INFO ] joelib.process.filter.FilterFactory - 6 filter =
informations loaded.
08:22:51 [INFO ] joelib.process.ProcessFactory - 5 process =
informations loaded.
joelib.process.JOEProcessException: =
jcompchem.joelib.process.types.DescSelectionWriter not found.
at =
joelib.process.ProcessFactory.getProcess(ProcessFactory.java:133)
at =
joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java=
:173)
at =
joelib.test.DescriptorSelection.main(DescriptorSelection.java:301)
Then I edited the joelib.properties stripping out all the "jcompchem.".
Then I built all thing (with several messages). I replaced the =
joelib.jar of the release 20030625 with the new one.
Now:
C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% =
joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd.
sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ;
08:59:15 [INFO ] joelib.data.JOEElementTable - Using =
element table: joelib/data/plain/e
lement.txt
08:59:15 [INFO ] joelib.io.IOTypeHolder - 13 =
input/output types loaded.
08:59:15 [INFO ] joelib.process.filter.FilterFactory - 6 filter =
informations loaded.
08:59:15 [INFO ] joelib.process.ProcessFactory - 5 process =
informations loaded.
08:59:15 [ERROR] joelib.test.DescriptorSelection - Can't load =
c:\temp\Sample_desc.txt
=20
I tried reading the source, but I could not guess the format of the =
"descNamesURL".
Regards, Ambrogio
-----Original Message-----
From: Joerg K. Wegner [mailto:we...@in...]
Sent: Wednesday, June 25, 2003 4:59 PM
To: Oliva Ambrogio; JOELib help
Subject: Re: joelib.test.DescriptorSelection
Hello Ambrogio,
> I modified the descNameFile as suggested but I keep receiving the same =
NullPointerException. Maybe I've put the wrong "delimiter" on the =
command line?
mmmh, oh sorry ... that's my fault, because i'm using another=20
joelib.properties file.
Please add the following lines to the src/joelib.properties file (after=20
joelib.filter.5.descriptionFile ...):
joelib.filter.6.name =3DDescriptorFilter
joelib.filter.6.representation =
=3Djoelib.process.filter.DescriptorFilter
joelib.filter.6.descriptionFile =3Ddocs/process/descriptorFilter
> Thanks for the quick reply.
I'll hope this will work. I'll release a new JOELib version with the bug =
fixes this day.
> Regards, Ambrogio
Regards, Joerg
> PS. Your PSs are a little bit too technical for my knowledge of java =
programming.
P.S.:This is possible !;-)
>=20
> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]
> Sent: Wednesday, June 25, 2003 3:46 PM
> To: Oliva Ambrogio; JOELib help
> Subject: Re: joelib.test.DescriptorSelection
>=20
>=20
> Dear Dr. Ambrogio,
>=20
>=20
>>first of all thanks for making available JOELib.
>=20
> thanks ...
> ... i'm crossposting this message also to the JOELib-help mailing =
list.
> You can join if you want ...
> http://sourceforge.net/mail/?group_id=3D39708
>=20
>=20
>=20
>>I successfully used the Convert application for adding descriptors to =
SD files. However I do not need all the descriptors. Then I tried to use =
DescriptorSelection to "select" the descripors I need.
>=20
> That's exactly the same way i use it, especially when calculating=20
> autocorrelation or other more extended descriptors (not public).
>=20
>=20
>>The problem is that it's not clear to me the syntax, in particular the =
format of the descriptors list and what the "delimiter" is.
>=20
> Let's try to resolve that...
>=20
>=20
>>I tried:=20
>>C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF =
-oSDF +d c:\temp\sample.sdf c:\tem
>>p\sample_wd.sdf
>=20
> All fine !
>=20
>=20
>>Then:
>>C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% =
joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd.
>>sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ;
>>13:34:44 [INFO ] joelib.data.JOEElementTable - Using =
element table: joelib/data/plain/e
>>lement.txt
>>13:34:44 [INFO ] joelib.io.IOTypeHolder - 12 =
input/output types loaded.
>>13:34:44 [INFO ] joelib.process.filter.FilterFactory - 5 filter =
informations loaded.
>>Exception in thread "main" java.lang.NullPointerException
>> at =
joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java=
:167)
>> at =
joelib.test.DescriptorSelection.main(DescriptorSelection.java:301)
>>
>>where c:\temp\Sample_desc.txt is:
>>
>>Number_of_bonds;LogP;Topological_radius
>=20
> No, this should be simply:
>=20
> Number_of_bonds
> LogP
> Topological_radius
>=20
> so you can simply use the JOELib statistic-file and import it under=20
> Excel and extract the descriptor names you want !;-)
>=20
>=20
>>Can you help me in getting DescriptorSelection work?
>>Thanks in advance.
>=20
> Was me a pleasure.
>=20
>=20
>>By the way I've also have a couple of "bug reports":
>>- In the Tutorial I've noticed that "bor", "chlor", "brom", "iod", =
"fluor" and "phosphor" are used instead of "boron", "chlorine", =
"bromine", "iodine", "fluorine" and "phosphorus".
>>
>>- In the .bat files, there are extra semicolons at the end of the "set =
CLASSPSTH" instructions.
>=20
> Thanks, i will fix it.
>=20
>=20
>>Thanks again.
>>
>>Ambrogio
>=20
>=20
> Regards, Joerg
>=20
> P.S.: BTW there exists also a descriptor normalization under
> joelib.process.types.DescVarianceNorm if you plan to normalize your =
data=20
> with mean=3D0, sdtdev=3D1, which requires a little bit of programming. =
E.g.=20
> you can add this process simply to the selection process pipe in
> joelib.test.DescriptorSelection
>=20
> P.P.S.: All descriptors in
> joelib\data\plain\desc2ignore.txt
> defined in the joelib.properties file as:
> =
joelib.process.types.DescVarianceNorm.descriptors2ignore=3Djoelib/data/pl=
ain/desc2ignore.txt
> will be ignored for normalization. This is extremely usefull if you =
have=20
> an nominal classification problem or the sdf-file contains also some =
> id's, ...
>
--=20
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, =
Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
|
|
From: Joerg K. W. <we...@in...> - 2003-06-25 14:55:53
|
Hello Ambrogio, > I modified the descNameFile as suggested but I keep receiving the same NullPointerException. Maybe I've put the wrong "delimiter" on the command line? mmmh, oh sorry ... that's my fault, because i'm using another joelib.properties file. Please add the following lines to the src/joelib.properties file (after joelib.filter.5.descriptionFile ...): joelib.filter.6.name =DescriptorFilter joelib.filter.6.representation =joelib.process.filter.DescriptorFilter joelib.filter.6.descriptionFile =docs/process/descriptorFilter > Thanks for the quick reply. I'll hope this will work. I'll release a new JOELib version with the bug fixes this day. > Regards, Ambrogio Regards, Joerg > PS. Your PSs are a little bit too technical for my knowledge of java programming. P.S.:This is possible !;-) > > -----Original Message----- > From: Joerg K. Wegner [mailto:we...@in...] > Sent: Wednesday, June 25, 2003 3:46 PM > To: Oliva Ambrogio; JOELib help > Subject: Re: joelib.test.DescriptorSelection > > > Dear Dr. Ambrogio, > > >>first of all thanks for making available JOELib. > > thanks ... > ... i'm crossposting this message also to the JOELib-help mailing list. > You can join if you want ... > http://sourceforge.net/mail/?group_id=39708 > > > >>I successfully used the Convert application for adding descriptors to SD files. However I do not need all the descriptors. Then I tried to use DescriptorSelection to "select" the descripors I need. > > That's exactly the same way i use it, especially when calculating > autocorrelation or other more extended descriptors (not public). > > >>The problem is that it's not clear to me the syntax, in particular the format of the descriptors list and what the "delimiter" is. > > Let's try to resolve that... > > >>I tried: >>C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF -oSDF +d c:\temp\sample.sdf c:\tem >>p\sample_wd.sdf > > All fine ! > > >>Then: >>C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd. >>sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ; >>13:34:44 [INFO ] joelib.data.JOEElementTable - Using element table: joelib/data/plain/e >>lement.txt >>13:34:44 [INFO ] joelib.io.IOTypeHolder - 12 input/output types loaded. >>13:34:44 [INFO ] joelib.process.filter.FilterFactory - 5 filter informations loaded. >>Exception in thread "main" java.lang.NullPointerException >> at joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java:167) >> at joelib.test.DescriptorSelection.main(DescriptorSelection.java:301) >> >>where c:\temp\Sample_desc.txt is: >> >>Number_of_bonds;LogP;Topological_radius > > No, this should be simply: > > Number_of_bonds > LogP > Topological_radius > > so you can simply use the JOELib statistic-file and import it under > Excel and extract the descriptor names you want !;-) > > >>Can you help me in getting DescriptorSelection work? >>Thanks in advance. > > Was me a pleasure. > > >>By the way I've also have a couple of "bug reports": >>- In the Tutorial I've noticed that "bor", "chlor", "brom", "iod", "fluor" and "phosphor" are used instead of "boron", "chlorine", "bromine", "iodine", "fluorine" and "phosphorus". >> >>- In the .bat files, there are extra semicolons at the end of the "set CLASSPSTH" instructions. > > Thanks, i will fix it. > > >>Thanks again. >> >>Ambrogio > > > Regards, Joerg > > P.S.: BTW there exists also a descriptor normalization under > joelib.process.types.DescVarianceNorm if you plan to normalize your data > with mean=0, sdtdev=1, which requires a little bit of programming. E.g. > you can add this process simply to the selection process pipe in > joelib.test.DescriptorSelection > > P.P.S.: All descriptors in > joelib\data\plain\desc2ignore.txt > defined in the joelib.properties file as: > joelib.process.types.DescVarianceNorm.descriptors2ignore=joelib/data/plain/desc2ignore.txt > will be ignored for normalization. This is extremely usefull if you have > an nominal classification problem or the sdf-file contains also some > id's, ... > -- Dipl. Chem. Joerg K. Wegner Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de |
10 messages has been excluded from this view by a project administrator.
