Code Log


Commit Date  
2011-05-28 11:29:55 Tree
[bdb4e0] by Onkar Shinde Onkar Shinde , pushed by Egon Willighagen Egon Willighagen

Copy data files into the right folder of the puredist

2011-05-27 15:03:34 Tree
[7947f0] by Egon Willighagen Egon Willighagen

Added a test to demonstrate the ClassPathException in bug #3305581

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-22 17:18:21 Tree
[7a795a] by Egon Willighagen Egon Willighagen

Test if the descriptor results are the same for two implementations (unfortunately, the nonotify IMolecule extends the data IMolecule, so it does not catch bug #3305581)

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-22 17:18:00 Tree
[2945d4] by Egon Willighagen Egon Willighagen

Factored out a method to test whether to descriptor calculations give the same results

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-22 17:17:08 Tree
[9b99f1] by Egon Willighagen Egon Willighagen

Parameterized method to create water to allow alternative implementations

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-22 17:16:38 Tree
[aee368] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Updated code to avoid dependency on specific implementation of molecule object. Now use IAtomContainer

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2011-05-22 05:13:14 Tree
[2f7402] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Added detection of a Te atom type, found in ChEMBL

Signed-off-by: jonalv <jonathan.alvarsson@gmail.com>
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-21 22:42:09 Tree
[1b9afc] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Added unit tests^Cor Te.3 atom type detection

Signed-off-by: jonalv <jonathan.alvarsson@gmail.com>

2011-05-21 22:42:02 Tree
[449c77] (cdk-1.2.9) by Egon Willighagen Egon Willighagen

Release 1.2.9 version bump

2011-05-21 14:27:52 Tree
[95ad78] by Egon Willighagen Egon Willighagen

Added Onkar Shinde, a Debian developer who recently patched the build system

2011-05-21 13:02:35 Tree
[d619db] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Fixed detection of P.ate atom types with one implicit hydrogen

2011-05-21 12:39:43 Tree
[ea248f] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Added unit tests for bug #3141611

* with explicit hydrogens it looks fine (CDKAtomTypeMatcherTest)
* without it has trouble (errors.sdf, CDKAtomTypeMatcherFilesTest)

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-21 12:39:13 Tree
[989b15] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Fixed detection of PH3 with implicit hydrogens

2011-05-21 12:32:48 Tree
[32f9aa] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Added a unit test for a failing sulphur AT detection + fix: 3 coordinate sulphur without double bonds has one implicit hydrogen and is S.anyl

Signed-off-by: jonalv <jonathan.alvarsson@gmail.com>
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-05-21 12:27:29 Tree
[82d76f] by Onkar Shinde Onkar Shinde , pushed by Egon Willighagen Egon Willighagen

Use wildcards (*) in jar file references. This fixes the problem while packaging the library for Debian as jar versions in Debian may not match with upstream.

2011-05-18 16:52:28 Tree
[4e2e66] by maclean maclean , pushed by Egon Willighagen Egon Willighagen

Use IAtomContainer instead of AtomContainer in AtomContainerSet

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2011-03-30 09:20:48 Tree
2011-03-28 10:32:04 Tree
[3ab7c2] by Jules Kerssemakers Jules Kerssemakers , pushed by Egon Willighagen Egon Willighagen

fixed pdb_atomtypes.xml errors mentioned in https://sourceforge.net/mailarchive/message.php?msg_id=27206678, including the nigly vdwRadius for GLN.CD

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2011-03-25 11:32:36 Tree
[5b51e1] by Jules Kerssemakers Jules Kerssemakers , pushed by Egon Willighagen Egon Willighagen

whitespace-only: alignment of TYR-section

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2011-03-25 11:32:28 Tree
[f72be8] by Egon Willighagen Egon Willighagen

Added two new authors

2011-03-13 07:31:06 Tree
[9f54af] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Fixed a concurrency error, caused by the use of a static field which was not supposed to be static, as the classes are instantiated just to allow customization

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-03-12 14:13:10 Tree
[3ea918] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Fixed the use of the proper Convertor

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-03-12 14:13:00 Tree
[c368c3] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Added the Co(3+) atom type (fixes #3093644)

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-03-12 14:08:30 Tree
[851c1a] by Julio Peironcely Julio Peironcely , pushed by Rajarshi  Guha Rajarshi Guha

Added the unit test phosphine for bug #3190151

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2011-03-12 14:07:34 Tree
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