Code Log


Commit Date  
[29d6fb] 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 15:35:56 Tree
[be20be] 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 15:35:51 Tree
[ab1dc1] 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 15:35:45 Tree
[acbe8b] 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 15:35:40 Tree
[46b51a] 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 15:35:34 Tree
[74ba3a] by Egon Willighagen Egon Willighagen

s/implmentorsOf/implementorsOf/

Change-Id: I5aaf8329ec9a52f06ded5912af05a5630e255898
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

2012-12-13 15:10:32 Tree
[b31470] by John May John May , pushed by Egon Willighagen Egon Willighagen

Corrected typo in DynamicFactory javadoc and made the interfaces static

2012-12-13 15:10:00 Tree
[4c0bcd] by John May John May , pushed by Egon Willighagen Egon Willighagen

updated DefaultChemObject to use the new DynamicFactory

2012-12-13 15:10:00 Tree
[613d21] by John May John May , pushed by Egon Willighagen Egon Willighagen

Corrected bad practice in ConstructorKey.equals

2012-12-13 15:10:00 Tree
[5b97d0] by John May John May , pushed by Egon Willighagen Egon Willighagen

Included missing javadoc for DynamicFactory and SilentChemObjectBuilder

2012-12-13 15:10:00 Tree
[d14839] by John May John May , pushed by Egon Willighagen Egon Willighagen

Implemented SilentChemObjectBuilder using the new DynamicFactory

2012-12-13 15:09:59 Tree
[61b736] by Egon Willighagen Egon Willighagen

Added mockito to the Eclipse .classpath

Change-Id: Ifda0976c8c5e5cc7244cbc2016e0155dda4cca87

2012-12-13 15:09:59 Tree
[f9ede2] by John May John May , pushed by Egon Willighagen Egon Willighagen

Implemented a dynamic factory so we can replace the decision tree in the ChemObjectBuilders. The dynamic factory uses reflection to inspect an implementations constructor. The factory also allows simple registration of an implementation with a given interface. As the factory uses a symbol table the factory can provide near constant time access (might have some hash collisions) for all class types. This implementation is advantageous to a decision tree (existing ChemObejctBuilders) as it is easier to register new classes and there is a negligible performance improvement. The factory also allows explict definition of object creation and post instantation modification (see. the javadoc).

2012-12-13 15:09:59 Tree
[a87dd7] by John May John May , pushed by Egon Willighagen Egon Willighagen

Including the Mockito library in devellib. The library allows us to mock objects and create stub implementations in unit tests. The library is particularly useful in core where there is no access to data,silent or datadebug domain objects.

2012-12-13 15:09:59 Tree
[971aa3] by Egon Willighagen Egon Willighagen

Added a missing dependency on the test data

Change-Id: Ie88b82a64af0d799eadf543ac9104dc5723dc38c

2012-12-13 14:20:27 Tree
[0a937a] by Egon Willighagen Egon Willighagen

Added a missing dependency

Change-Id: I65535e895bbff1cfba23ec84da79c9080a3d625d

2012-12-13 14:20:20 Tree
[3f8bcc] by Stephan Beisken Stephan Beisken , pushed by Egon Willighagen Egon Willighagen

Updated of patch: "Added correct radical perception to the SDF writer / reader (tests included)."

Change-Id: I06115684fa4f42bf944a3bd24bc736c6a72daa01
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-13 12:21:11 Tree
[101541] by Stephan Beisken Stephan Beisken , pushed by Egon Willighagen Egon Willighagen

Added correct radical perception to the SDF writer / reader (tests included).

Change-Id: Ia767c27529fd590cdf123cf33a1861cd2e3504b8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-13 12:20:49 Tree
[88a3b1] 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 10:16:03 Tree
[0e20e8] by Egon Willighagen Egon Willighagen

And the Groovy deps for the CDKSourceCodeWriterTest

Change-Id: I79e0a709bd3b641bce219e3c0154b2dd72cdfa20

2012-12-13 10:15:56 Tree
[c9a9be] by Egon Willighagen Egon Willighagen

Also updated the Eclipse .classpath

Change-Id: I21e6057736021e342bff62e78a488171c3b4c5a6

Conflicts:
.classpath

2012-12-13 10:15:44 Tree
[c7493d] by Egon Willighagen Egon Willighagen

Also updated the other two PMD config files for 5.0.1

Change-Id: Ic862e2856a697b1a29856c49c7ccc69c0f66c78b

Conflicts:
pmd-migrating.xml
pmd-unused.xml

2012-12-13 10:14:53 Tree
[412d7e] by Egon Willighagen Egon Willighagen

Updated PMD to version 5.0.1

Change-Id: Ibb369c1eefdf6e65ad5d32cc99495f82ad9c0908

2012-12-13 07:56:46 Tree
[cc2af0] by John May John May , pushed by Egon Willighagen Egon Willighagen

Corrected method call on DebugChemObject

Change-Id: I451223222e0e71b553672b484e55af90991449b0
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-12 23:44:41 Tree
[959f3f] by John May John May , pushed by Egon Willighagen Egon Willighagen

Added unit tests for the new getProperty(Object,Class) method.

Change-Id: Id0b619ae0eb77d4caba10a742b7ed43fd422bace
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2012-12-12 23:42:00 Tree
Older >