Code Log


Commit Date  
[714c51] by Egon Willighagen Egon Willighagen

Updated version and confirmed inception year

2010-10-01 12:39:54 Tree
[a0e7df] by Rajarshi  Guha Rajarshi Guha

Updated getVersion method to not print to stdout

2010-09-23 23:51:36 Tree
[239d20] (cdk-1.3.6) by Egon Willighagen Egon Willighagen

Set version for release 1.3.6

2010-09-14 17:16:46 Tree
[b72740] by Egon Willighagen Egon Willighagen

Updated copyright to 2010

2010-09-12 19:05:57 Tree
[1e4ada] by Egon Willighagen Egon Willighagen

Compare values not objects (fixes #3061263)

Signed-off-by: maclean <gilleain.torrance@gmail.com>

2010-09-12 12:19:31 Tree
[87f8bf] by Egon Willighagen Egon Willighagen

Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object

Signed-off-by: maclean <gilleain.torrance@gmail.com>

2010-09-12 12:19:22 Tree
[ae21ee] by Mark Rynbeek Mark Rynbeek , pushed by Egon Willighagen Egon Willighagen

Smiles parser setting to preserve aromaticity as provided in the Smiles String itself.

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

2010-09-07 15:03:50 Tree
[91c58d] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added two further unit tests: one to see if the descriptor properly 'ignores' hydrogens; a second to reproduce the numbers in the original Wiener paper from 1947

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

2010-09-07 13:44:05 Tree
[ac82b1] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Renabled test which was (accidentally?) outcommented when switching to JUnit4 in commit 06a1a3dd

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

2010-09-07 13:44:02 Tree
[0c5187] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Added a reference to the original Wiener paper

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

2010-09-07 13:43:59 Tree
[e73a29] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

No need to declare throws for other Exception's if the superclass is already declared thrown itself (also, no need to define java.lang explicitly)

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

2010-09-07 13:43:56 Tree
[629287] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Minor cleanup: corrected copyright statement; simplified JavaDoc by removing empty parameter table

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

2010-09-07 13:43:54 Tree
[8ddbb1] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Replaced inline citation by reference to the main bibliography

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

2010-09-07 13:43:51 Tree
[6a6db0] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms

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

2010-09-07 13:39:05 Tree
[ac211c] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Updated javadocs and added extra unit test

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

2010-09-07 13:32:52 Tree
[bd9fb4] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms

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

2010-09-07 13:32:46 Tree
[18f7d5] by Egon Willighagen Egon Willighagen

Removed output to STDOUT

2010-09-07 12:57:48 Tree
[526362] by Saravanaraj Saravanaraj , pushed by Egon Willighagen Egon Willighagen

Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br

This fix check for the position of the new chain with respect to its
parent. It also checks the position of the parent to see if it is at the begining
of the SMILES string.

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

2010-09-07 12:57:43 Tree
[3bf839] by Saravanaraj Saravanaraj , pushed by Egon Willighagen Egon Willighagen

Unit test for bug #3040273.

This unit test works and shows the error on the SMILES Generator code.

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

2010-09-07 12:57:29 Tree
[e8cec0] by Egon Willighagen Egon Willighagen

Fixed hybridization information: these are sp3 hybridized systems

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

2010-09-07 12:55:15 Tree
[bcb843] by Egon Willighagen Egon Willighagen

More missing elements for SMILES parsing problems reported in bug #3048501

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

2010-09-07 12:54:49 Tree
[bb5ffe] by Egon Willighagen Egon Willighagen

Unit tests for SMILES parsing bugs reported in #3048501

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

2010-09-07 12:54:23 Tree
[3f6056] by Egon Willighagen Egon Willighagen

Upper case the first character to also properly recognize lower cased 'aromatic' two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1

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

2010-09-07 12:53:10 Tree
[d097ac] by Egon Willighagen Egon Willighagen

JavaDoc fixes: correct @cdk.cite use, and small typo

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

2010-09-07 12:53:04 Tree
[3e1aba] by Egon Willighagen Egon Willighagen

Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890)

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

2010-09-07 12:52:59 Tree
Older >