The Chemistry Development Kit
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last commit on 2012-05-27
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The Chemistry Dev...
egonw pushed 4 commit(s) to refs/heads/cdk-1.4.x in the cdk Git repository of the The Chemistry Development Kit project.
2012-05-27 11:41:54 PDT by egonw
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Comment: ModelBuilder3D bug - N=0 and NC=0 bond length missing
Cannot find Namide-N=O bond length in mmff94 param file.
2012-05-24 08:16:00 PDT by danielszisz
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Comment: ModelBuilder3D bug - bad N atom type in rings with NC=O atom
Bad N atom type assigned to ring N atom : sp3 N atom is assigned instead of planar sp2.
2012-05-24 08:10:28 PDT by danielszisz
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ModelBuilder3D bug - cannot find S-N bond length
The builder cannot find the corresponding S and N bond length in the Cc1ccc(cc1)S(=O)(=O)NC(=O)NN1CC2CCCC2C1 molecule. See the corresponding test.
2012-05-24 03:29:53 PDT by danielszisz
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Comment: ModelBuilder3D bug - bad MMFF94 N atom type handling
Bug seems to be solved by now as patches has been applied. Rerun the test with the updated version.
2012-05-24 03:27:16 PDT by danielszisz
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Comment: ModelBuilder3D bug - incorrect MMFF94 S and N atom types
I close this bug as the original bug report is not actually what I wrote. New bug report will be opened for this.
2012-05-24 03:24:31 PDT by danielszisz
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Comment: ModelBuilder3D bug - bad N atom type in rings with NC=O atom
JUnit test added to bug report.
2012-05-24 03:13:05 PDT by danielszisz
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Comment: Atom symbols background is always white
I don't think bond drawing is best clipped with the atom drawing area, but the bond should be shortened. I have a screenshot of a big wedge pointing from an H atom, where it was in fact clipped, like the H biting out a tooth from the wedge. That looks nearly as bad as not clipping.
2012-05-24 03:03:48 PDT by rwst
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Patch for @cdk.bug 3525144 in ModelBuilder3D
This patch solves @cdk.bug #3525144. For reference see the bug report in bug tracker.
2012-05-24 02:24:34 PDT by danielszisz
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Comment: SDG may flip structure, but not change wedges
Note that while the given drawing does not conform to IUPAC stereo drawing recommendations -- the wedge should come from the OH onto the ring -- this bug is also triggered by such a 100 per cent correct conformation. Isn't it possible to clean a structure by converting to SMILES and back?.
2012-05-23 09:08:55 PDT by rwst
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