State of Builder3D?
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State of Builder3D?
by Egon Willighagen-5
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Stefan,
didn't you just recently fix the builder3d? I see 10/12 unit tests failing: http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-builder3d.html What exactly did you fix? And possibly any clue why those 10 tests are failing? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Stefan Kuhn-3
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After my commit all tests (all 12) were running. Grrrrr... I will check this.
Stefan On Thursday 10 July 2008 21:56:35 Egon Willighagen wrote: > Stefan, > > didn't you just recently fix the builder3d? > > I see 10/12 unit tests failing: > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/resul >t-builder3d.html > > What exactly did you fix? And possibly any clue why those 10 tests are > failing? > > Egon ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Stefan Kuhn-3
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For me, the status is as follows:
In cdk 1.0.x, all builder3d tests work. I did not do an update for approximately 2 weeks In trunk, 9 of 11 fail. I ported my latest changes, reasons must be different. Some are due to npe when reading files etc. - need to look at this. Egon, where did you get your 10/12 failing from? cdk 1.0? Or trunk? Stefan On Thursday 10 July 2008 21:56:35 Egon Willighagen wrote: > Stefan, > > didn't you just recently fix the builder3d? > > I see 10/12 unit tests failing: > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/resul >t-builder3d.html > > What exactly did you fix? And possibly any clue why those 10 tests are > failing? > > Egon ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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On Fri, Jul 11, 2008 at 10:06 AM, Stefan Kuhn <stefan.kuhn@...> wrote:
> After my commit all tests (all 12) were running. Grrrrr... I will check this. I was wondering later... did you fix it in cdk1.0.x, trunk, or both? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by shk3
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> On Fri, Jul 11, 2008 at 10:06 AM, Stefan Kuhn <stefan.kuhn@...>
> wrote: >> After my commit all tests (all 12) were running. Grrrrr... I will check >> this. > > I was wondering later... did you fix it in cdk1.0.x, trunk, or both? I was working in cdk1.0.x, but also applied the changes to trunk, but it seems there are other problems in trunk. For me,, cdk1.0.x (update from yesterday) works, trunk doesn't. Where did you get your 10 of 12 fail from? Stefan > > Egon > > -- > ---- > http://chem-bla-ics.blogspot.com/ > ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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On Sat, Jul 12, 2008 at 2:04 PM, <shk3@...> wrote:
>> I was wondering later... did you fix it in cdk1.0.x, trunk, or both? > I was working in cdk1.0.x, but also applied the changes to trunk, but it > seems there are other problems in trunk. But it was working in trunk too after you applied those changes? > For me,, cdk1.0.x (update from > yesterday) works, trunk doesn't. Where did you get your 10 of 12 fail > from? CDK Nightly: http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-builder3d.html Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Stefan Kuhn-3
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> On Sat, Jul 12, 2008 at 2:04 PM, <shk3@...> wrote:
>>> I was wondering later... did you fix it in cdk1.0.x, trunk, or both? >> I was working in cdk1.0.x, but also applied the changes to trunk, but it >> seems there are other problems in trunk. > > But it was working in trunk too after you applied those changes? No. > >> For me,, cdk1.0.x (update from >> yesterday) works, trunk doesn't. Where did you get your 10 of 12 fail >> from? > > CDK Nightly: It seems I can't express myself: Is this 1.0.x or trunk nightly? I can't see it - the number of tests (12, in trunk are only 11) point to cdk1.0.x, the classname (without test) to trunk. So which is this? > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-builder3d.html > > Egon > > -- > ---- > http://chem-bla-ics.blogspot.com/ > ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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On Sat, Jul 12, 2008 at 8:23 PM, <stefan.kuhn@...> wrote:
>>> For me,, cdk1.0.x (update from >>> yesterday) works, trunk doesn't. Where did you get your 10 of 12 fail >>> from? >> >> CDK Nightly: > > It seems I can't express myself: Is this 1.0.x or trunk nightly? I can't > see it - the number of tests (12, in trunk are only 11) point to > cdk1.0.x, the classname (without test) to trunk. So which is this? Ah, sorry: trunk: http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-builder3d.html cdk-1.0.x: http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly-1.0.x/test/result-builder3d.html So, typically just: s/nightly/nightly-1.0.x/ Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Stefan Kuhn-3
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> Ah, sorry:
> > trunk: > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-builder3d.html > > cdk-1.0.x: > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly-1.0.x/test/result-builder3d.html Hm, that's odd. I have 12 tests in 1.0 and 11 in trunk with just updated code, nightly has 1 more. The one failing in 1.0 works for me. Trunk has 9 failing for me as well. I will look at these. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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On Sat, Jul 12, 2008 at 8:42 PM, <stefan.kuhn@...> wrote:
> Hm, that's odd. I have 12 tests in 1.0 and 11 in trunk with just updated > code, nightly has 1 more. The one failing in 1.0 works for me. >From the command line with 'ant test-all'? If not, it's a .datafiles problem for creating the test jar... > Trunk has 9 failing for me as well. I will look at these. This very likely has to do with atom typing... I'm online tonite, working on OWL in the CDK... Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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java.lang.Exception: PlaceSubstitutensERROR: Cannot place
substitutents due to:null at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates(ModelBuilder3D.java:240) at org.openscience.cdk.modeling.builder3d.ModelBuilder3dTest.testModelBuilder3D_CF(ModelBuilder3dTest.java:90) .... Caused by: java.lang.NullPointerException at org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D.rescaleBondLength(AtomTetrahedralLigandPlacer3D.java:146) at org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands(AtomTetrahedralLigandPlacer3D.java:122) at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates(ModelBuilder3D.java:236) ... 23 more which is about this line: double d1 = atom1.getCovalentRadius(); double d2 = atom2.getCovalentRadius(); Rajarshi recently deprecated that method... will adapt the code for the new approach... and, fingers crossed, that might help a bit... Egon ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: State of Builder3D?
by Egon Willighagen-5
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On Sun, Jul 13, 2008 at 2:19 PM, Egon Willighagen
<egon.willighagen@...> wrote: > which is about this line: > > double d1 = atom1.getCovalentRadius(); > double d2 = atom2.getCovalentRadius(); > > Rajarshi recently deprecated that method... Sorry, mix up. That was getVdWRadius() :) The actual situation that the radius is missing is tested, but was not fixed for the double2Double transition. However, can't commit right now due to SVN server problem: $ svn commit -m "Fixed NPE due to double 2 Double transition" src svn: Commit failed (details follow): svn: Can't create directory '/svnroot-fuse/cdk/db/transactions/11571-1.txn': No space left on device The full patch looks like: Index: src/main/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java =================================================================== --- src/main/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java (revision 11566) +++ src/main/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java (working copy) @@ -143,11 +143,10 @@ */ public Point3d rescaleBondLength(IAtom atom1, IAtom atom2, Point3d point2) throws Exception { Point3d point1 = atom1.getPoint3d(); - double d1 = atom1.getCovalentRadius(); - double d2 = atom2.getCovalentRadius(); + Double d1 = atom1.getCovalentRadius(); + Double d2 = atom2.getCovalentRadius(); // in case we have no covalent radii, set to 1.0 - double distance = (d1 < 0.1 || d2 < 0.1) ? 1.0 : - atom1.getCovalentRadius() + atom2.getCovalentRadius(); + double distance = (d1 == null || d2 == null) ? 1.0 : d1 + d2; if (pSet != null) { distance = getDistanceValue(atom1.getAtomTypeName(), atom2.getAtomTypeName()); } That should fix 8 of the 12 failing tests. The other seem to be test files it cannot find... might be only in Eclipse, as they are listed in the test-builder3d.datafiles... Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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