Code Log


Commit Date  
2010-07-29 06:17:43 Tree
[6ef1fb] by Egon Willighagen Egon Willighagen

Updated the DebugBond unit test too now: new DebugBond() has zero atoms

2010-07-28 08:12:04 Tree
[ce9b1b] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Backport patch, to make the patches compile with cdk-1.2.x

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

2010-07-27 23:33:51 Tree
[6cf95d] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior.

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

2010-07-27 23:33:49 Tree
[23d968] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Also fix the new NNBond() == 0 atoms for the nonotify module

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

2010-07-27 23:33:46 Tree
[916ab9] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom, int) to increase the atom count if a null entry is filled with a non-null IAtom.

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

2010-07-27 23:33:43 Tree
[4ac711] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Updated test to assume new Bond() creates a bond with zero atoms

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

2010-07-27 23:33:40 Tree
[c5d4cd] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Exceptions when clone atomless ISingleElectron and ILonePair too

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

2010-07-22 12:59:44 Tree
[d71c31] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms

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

2010-07-22 12:59:36 Tree
[890d0f] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010

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

2010-07-22 12:58:19 Tree
[bb431e] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added the N.oxide atom type, for structures like (CH3)N=O

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

2010-07-22 12:57:19 Tree
[3133a1] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Fixed reading of SD properties: keep the first line too

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

2010-07-21 23:06:22 Tree
[14003d] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added missing dependency

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

2010-07-21 23:05:32 Tree
[c888e4] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Fixed unit test: surely there is no atom with symbol 0... how long has this been failing??

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

2010-07-21 23:03:59 Tree
[a454ab] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added a test class to aromaticity of three compounds: the last incorrectly fails

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

2010-07-18 13:21:30 Tree
[335711] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Also except N.amide as part of an aromatic ring

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

2010-07-18 13:17:21 Tree
[0bd5b4] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added a test class to repeat atom type perception and test consistency

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

2010-07-18 12:35:48 Tree
[cd8323] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up

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

2010-07-18 02:28:42 Tree
[483c85] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then

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

2010-07-18 02:24:19 Tree
[1f8bb2] by maclean maclean , pushed by Egon Willighagen Egon Willighagen

Improved javadoc generation using a link tag, so that references to java library classes are resolved properly

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

2010-06-17 17:34:57 Tree
[1523f6] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Removed use of the proprietary DocCheck utility

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

2010-06-11 01:35:53 Tree
[e8b13b] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Use the new tests in more situations

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

2010-05-23 15:19:20 Tree
[406930] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Introducing PMD test for CDK specific issues:

* "Molecule mol = ..." -> "IMolecule mol = ..."
* "ac instanceof Molecule" -> "ac instanceof IMolecule"

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

2010-05-23 14:01:36 Tree
[d6b6c6] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Added copyright and license header

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

2010-05-23 11:30:08 Tree
[ad2bd3] by Egon Willighagen Egon Willighagen , pushed by Rajarshi  Guha Rajarshi Guha

Replaced outdated URL with entry in WikiPedia (fixes #3002741)

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

2010-05-20 22:51:43 Tree
Older >