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From: Daniel L. <dan...@gm...> - 2004-08-19 09:46:19
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xpost to joelib-devel mailing list E.L. Willighagen wrote: > On Thursday 19 August 2004 09:06, E.L. Willighagen wrote: > > On Wednesday 18 August 2004 19:39, Daniel Leidert wrote: > > > * The follwing methods must be changed: > > > * * > > > * * getX2D() --> getX2d() > > > * * getY2D() --> getY2d() > > > * * > > > * * That's all. > > > > That's a bug... we still need to set up som build deamons, that build with > > certain JVM's and configurations (with/-out Java3d, JOELib)... > > Huh? I thought I understood what was happening here... but... > > Daniel, where do those changes need to be made? In <joelib-source-20040729>/src/joelib/util/cdk/CDKTools.java (line 83+84). This seems to be a bug in JOElib, not in the CDK-source (IMHO). Yesterday, there was no time, to post the problem to the JOElib-developers mailing list. The compiler stops with an error, when you try to compile joelib.jar with the cdk-*.jars (target: compile.cdk.parts, see joebuild.xml - the second joelib-build-run in Makefile). He complains about the methods getX2D() and getY2D(). So I think, the above changes have to be made, to build joelib.jar with compiled-in cdk-parts (it is working then, but it seems not to be necessary to compile joelib.jar with cdk-*.jar for building cdk-libio.jar -> maybe, this can be an own package: libcdk-java-joelib, which will contain joelib.jar with compiled-in cdk-parts). BTW: I wanted to ask you, if we can remove several directories from cvs/cdk/packages/debian/? In the next days/weeks, I will try to make a cdk-package for the Shell-wrappers (and maybe one doc-package if possible). So it should be possible, to delete libcdk/ and libcdkextra/ and maybe cdk/ and cdk-doc/. Regards, Daniel -- |
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From: E.L. W. <eg...@us...> - 2004-08-19 11:21:26
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 19 August 2004 11:47, Daniel Leidert wrote: > E.L. Willighagen wrote: > > On Thursday 19 August 2004 09:06, E.L. Willighagen wrote: > > > On Wednesday 18 August 2004 19:39, Daniel Leidert wrote: > > > > * The follwing methods must be changed: > > > > * * > > > > * * getX2D() --> getX2d() > > > > * * getY2D() --> getY2d() > > > > * * > > > > * * That's all. > > > > > > That's a bug... we still need to set up som build deamons, that build > > > with certain JVM's and configurations (with/-out Java3d, JOELib)... > > > > Huh? I thought I understood what was happening here... but... > > > > Daniel, where do those changes need to be made? > > In <joelib-source-20040729>/src/joelib/util/cdk/CDKTools.java (line > 83+84). This seems to be a bug in JOElib, not in the CDK-source (IMHO). > Yesterday, there was no time, to post the problem to the > JOElib-developers mailing list. Ah, ic...=20 > The compiler stops with an error, when you try to compile joelib.jar > with the cdk-*.jars (target: compile.cdk.parts, see joebuild.xml - the > second joelib-build-run in Makefile). He complains about the methods > getX2D() and getY2D(). So I think, the above changes have to be made, to > build joelib.jar with compiled-in cdk-parts (it is working then, but it > seems not to be necessary to compile joelib.jar with cdk-*.jar for > building cdk-libio.jar -> maybe, this can be an own package: > libcdk-java-joelib which will contain joelib.jar with compiled-in=20 > cdk-parts). Or a libjoelib-java package for joelib, and a libcdklibio-java for the=20 cdk-libio.jar? JOELib compiles also with Ant, so it should be fairly easy to start with th= e=20 debian files for CDK or JChemPaint... > BTW: I wanted to ask you, if we can remove several directories from > cvs/cdk/packages/debian/? In the next days/weeks, I will try to make a > cdk-package for the Shell-wrappers (and maybe one doc-package if > possible).=20 Cool. Then I can learn how to do that... As said, I've tried that for CDK, = but=20 did not have enough deb building experience... > So it should be possible, to delete libcdk/ and libcdkextra/=20 > and maybe cdk/ and cdk-doc/. Yes, go ahead. Was thinking about that too, but busy with non-CDK stuff dur= ing=20 the day (well, except for email :) Egon =2D --=20 eg...@us... =2D --------------------------------------- CDK: http://cdk.sf.net/ JChemPaint: http://jchempaint.sf.net/ Jmol: http://www.jmol.org/ =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBJI0kd9R8I9Yza6YRAozyAKCQnMawLYeHPZ56b2uWdNJsjRh35wCgsY/a lqn8cpSaGukt0VBb2azhpr8=3D =3DYbgh =2D----END PGP SIGNATURE----- |
=2D----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
On Thursday 19 August 2004 13:21, E.L. Willighagen wrote:
> On Thursday 19 August 2004 11:47, Daniel Leidert wrote:
> > E.L. Willighagen wrote:
> > > On Thursday 19 August 2004 09:06, E.L. Willighagen wrote:
> > > > On Wednesday 18 August 2004 19:39, Daniel Leidert wrote:
> > > > > * The follwing methods must be changed:
> > > > > * *
> > > > > * * getX2D() --> getX2d()
> > > > > * * getY2D() --> getY2d()
> > > > > * *
> > > > > * * That's all.
> > > >
> > > > That's a bug... we still need to set up som build deamons, that bui=
ld
> > > > with certain JVM's and configurations (with/-out Java3d, JOELib)...
> > >
> > > Daniel, where do those changes need to be made?
> >
> > In <joelib-source-20040729>/src/joelib/util/cdk/CDKTools.java (line
> > 83+84). This seems to be a bug in JOElib,=20
CDK changed the D to d recently... not really a bug, more of a version=20
incompatibility :)
> > not in the CDK-source (IMHO).=20
> > Yesterday, there was no time, to post the problem to the
> > JOElib-developers mailing list.
>
> Ah, ic...
Joerg, the patch is:
=2D --- src/joelib/util/cdk/CDKTools.java 2004-08-19 13:22:57.623944000 +=
0200
+++ src/joelib/util/cdk/CDKTools.java.fixed 2004-08-19 13:26:18.5988090=
00=20
+0200
@@ -80,8 +80,8 @@
for (int i =3D 0; i < cdkAtoms.length; i++)
{
=2D - mol.getAtom(i + 1).setVector(cdkAtoms[i].getX2D(),
=2D - cdkAtoms[i].getY2D(), 0.0);
+ mol.getAtom(i + 1).setVector(cdkAtoms[i].getX2d(),
+ cdkAtoms[i].getY2d(), 0.0);
}
// remove all 3D coordinates in all atoms
Egon
=2D --=20
eg...@us...
=2D ---------------------------------------
CDK: http://cdk.sf.net/
JChemPaint: http://jchempaint.sf.net/
Jmol: http://www.jmol.org/
=2D----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (SunOS)
iD8DBQFBJI8Xd9R8I9Yza6YRAj9zAJ975tCjFbnt8zArYxrKi4XHReMyigCdFFFC
qehKS9BPOcMUSml9pkbM/yI=3D
=3D7Jd+
=2D----END PGP SIGNATURE-----
|
Hi all, thanks guys. That's not a big effort. This will be checked in and part of the monthly new release. Kind regards, Joerg > xpost to joelib-devel mailing list > > E.L. Willighagen wrote: > >>On Thursday 19 August 2004 09:06, E.L. Willighagen wrote: >> >>>On Wednesday 18 August 2004 19:39, Daniel Leidert wrote: >>> >>>>* The follwing methods must be changed: >>>> * * >>>> * * getX2D() --> getX2d() >>>> * * getY2D() --> getY2d() >>>> * * >>>> * * That's all. >>> >>>That's a bug... we still need to set up som build deamons, that build with >>>certain JVM's and configurations (with/-out Java3d, JOELib)... >> >>Huh? I thought I understood what was happening here... but... >> >>Daniel, where do those changes need to be made? > > > In <joelib-source-20040729>/src/joelib/util/cdk/CDKTools.java (line > 83+84). This seems to be a bug in JOElib, not in the CDK-source (IMHO). > Yesterday, there was no time, to post the problem to the > JOElib-developers mailing list. > > The compiler stops with an error, when you try to compile joelib.jar > with the cdk-*.jars (target: compile.cdk.parts, see joebuild.xml - the > second joelib-build-run in Makefile). He complains about the methods > getX2D() and getY2D(). So I think, the above changes have to be made, to > build joelib.jar with compiled-in cdk-parts (it is working then, but it > seems not to be necessary to compile joelib.jar with cdk-*.jar for > building cdk-libio.jar -> maybe, this can be an own package: > libcdk-java-joelib, which will contain joelib.jar with compiled-in > cdk-parts). > > BTW: I wanted to ask you, if we can remove several directories from > cvs/cdk/packages/debian/? In the next days/weeks, I will try to make a > cdk-package for the Shell-wrappers (and maybe one doc-package if > possible). So it should be possible, to delete libcdk/ and libcdkextra/ > and maybe cdk/ and cdk-doc/. > > Regards, Daniel -- 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) |
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