Code Log


Commit Date  
[0a4061] by Egon Willighagen Egon Willighagen

Open for more bug fixing

Change-Id: I12561f1a4f32ff42b8655f2e7f4cab3f3aad4681

2012-12-20 14:26:21 Tree
[26384a] (cdk-1.4.16) by Egon Willighagen Egon Willighagen

Now also has a task to create a source distrib that includes the unit tests (per user request)

Change-Id: I6e47a18d2084ce5cf83efc731e2b3db95acbb6b5

2012-12-20 14:02:03 Tree
[134b01] by Egon Willighagen Egon Willighagen

Bumped version number for the 1.4.16 release

Change-Id: Ifbb742150d7fe39dbe4fd559443ab3777a172835

2012-12-20 11:58:52 Tree
[3f02b7] by Egon Willighagen Egon Willighagen

Expanded explanation of Sigma Electronegativity Descriptor

Change-Id: Ic37241a6a3d161f873b3d2290c41be7c86ab99c3
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-20 11:56:18 Tree
[4cf0f3] by Egon Willighagen Egon Willighagen

Added missing literature reference, and minimal additional information requested in bug #1285

Change-Id: Id4b46baf50130af657cf1c28cd7ce24b96a240aa
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-20 11:31:21 Tree
[601d0a] by John May John May , pushed by Egon Willighagen Egon Willighagen

Correct unit test name and added missing unit tests and annotations.

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

2012-12-17 06:53:03 Tree
[33c99d] by John May John May , pushed by Egon Willighagen Egon Willighagen

Added unit test and annotation for moment generation (3D Similarity)

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

2012-12-17 06:53:02 Tree
[ff8d37] by John May John May , pushed by Egon Willighagen Egon Willighagen

Added explicit atom typing and aromaticity detection to several failing fingerprinter tests.

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

2012-12-17 06:53:02 Tree
[f37cfa] by John May John May , pushed by Egon Willighagen Egon Willighagen

Changed saturation conditional to also check that a bond is not aromatic.

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

2012-12-17 06:53:02 Tree
[9c4bd5] by Egon Willighagen Egon Willighagen

Throw an error when a non-ring is attempted to be closed

Change-Id: Ib83fa0721b24dec61e3156797b285c9c7e7526ba
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:30:25 Tree
[fc6310] by Egon Willighagen Egon Willighagen

C1C1 is an invalid SMILES; expect an thrown error

Change-Id: Ib965ecbafe67fc82e556ce60210cefee2fc89e2f
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:29:25 Tree
[7627d8] by Egon Willighagen Egon Willighagen

Properly pad the resulting descriptor value list to MAX_PROTON_COUNT, fixing two failing unit tests

Change-Id: Ic679ec53cb222d1cafc092d50e8156656a2bd8d1
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:28:38 Tree
[7a81ea] by Egon Willighagen Egon Willighagen

Small fixes: remove STDOUT use and proper int-based assertEquals() method

Change-Id: I8dfa14c1b50f1aad44ca3db43dc089add51133a4
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:27:45 Tree
[51cf99] by Egon Willighagen Egon Willighagen

Typed the input class and added support for IChemFile.class input

Change-Id: Iabdb1ca4650dc51c424ea7b95fa7d996013de101
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:23:05 Tree
[76ade3] by Egon Willighagen Egon Willighagen

Added a missing dependency on the test data

Change-Id: Ie88b82a64af0d799eadf543ac9104dc5723dc38c

2012-12-13 13:00:09 Tree
[2e6fc9] by Egon Willighagen Egon Willighagen

Added a missing dependency

Change-Id: I65535e895bbff1cfba23ec84da79c9080a3d625d

2012-12-13 12:57:24 Tree
[09868f] by Egon Willighagen Egon Willighagen

Properly implemented Isotope.compare() for data and silent

Change-Id: Iff60038106b126062f2566749c5e719f4672bc7a
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 09:26:36 Tree
[2e62bd] by Egon Willighagen Egon Willighagen

And the Groovy deps for the CDKSourceCodeWriterTest

Change-Id: I79e0a709bd3b641bce219e3c0154b2dd72cdfa20

2012-12-13 09:06:22 Tree
[3f8825] by Egon Willighagen Egon Willighagen

Also updated the Eclipse .classpath

Change-Id: I21e6057736021e342bff62e78a488171c3b4c5a6

2012-12-13 09:04:44 Tree
[fa99bc] by Egon Willighagen Egon Willighagen

Also updated the other two PMD config files for 5.0.1

Change-Id: Ic862e2856a697b1a29856c49c7ccc69c0f66c78b

2012-12-13 08:49:56 Tree
[44572c] by Egon Willighagen Egon Willighagen

Updated PMD to version 5.0.1

Change-Id: Ibb369c1eefdf6e65ad5d32cc99495f82ad9c0908

2012-12-13 07:59:33 Tree
[0d658d] by John May John May , pushed by Egon Willighagen Egon Willighagen

Updated comparator on AtomPlacer. The comparator now uses the built in Integer comparator. To avoid null pointer exceptions the access to the weight value is wrapped in a private method which return the minimum integer value when the weight is not set (i.e. null).

2012-12-12 17:23:17 Tree
[ed399d] by John May John May , pushed by Egon Willighagen Egon Willighagen

Corrected null handling on AtomContainer 2D centre comparison. Previous if either container was null the comparator would incorrectly return '0' indicating they were equal. The method was changed to always provide a minimum Point2d when an atom container is null. This will sort all null containers lower then non-null containers.

Change-Id: I49d919c7d0cf0ea17a65e2a031c1a827bdbbbb50
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-12 15:30:20 Tree
[e5b1bc] by John May John May , pushed by Egon Willighagen Egon Willighagen

Replaced subtraction based comparator. This comparator is unlikely to overflow but the safety of using the equalities ensures the proper behaviour of this comparator.

Change-Id: I4cf311f327e53754e189c5734147a245446495ac
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-12 15:06:45 Tree
[425c79] by John May John May , pushed by Egon Willighagen Egon Willighagen

Replaced subtraction based comparison. When the difference (which is a double) is converted to an integer the result may overflow. This overflow can occur in rare cases but would cause the comparator to be non-transitive.

Change-Id: Ic7deea389f63273202288e6d11cc19af94f08d63
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-12 14:39:23 Tree
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