Open for changes
Correcting development version number
Updated the signatures library to version 1.1 with one new method and corresponding test case

Change-Id: I2ab9d2783d1f5e6a6d680a2b532142bd4248b07a
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
automatically set atomic number when given an element symbol, fixes bug/1296

Change-Id: I5c7e79e1784935e4f0ab1feb7f7883dab940a154
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
updated DebugChemObjectBuilder to use the new DynamicFactory

Change-Id: I30d0ee29ec019d90d34bd3c7a2ef2e8704472ec6
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
resolves two NullPointerExcetions in cdk-forcefield

Change-Id: Ie47b7b0298b723ef521ae3e6864046690061a137
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
corrected assertion - the C02M atom type has 3 formal neighbors (line 23, mmff94.prm)

Change-Id: I9a37c29ffac2cf9cba112dbd23ba361cabfb2ef0
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Revert "automatically set atomic number when given an element symbol, fixes bug/1296"

This reverts commit 2d80a80f0d726cd07aa51cb46290f9543377dd94.
Added 'stereo-sensitive' hydrogen remove method to the AtomContainerManipulator.

Change-Id: I13cc413377c9f8fa31c3a62eb5ca885758e70371
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
eleminated linkedlist queue from ShortestPaths - small performance boost

Change-Id: I864172105f7bf7f4406f96836c7d741ed55ccb66
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Revert "resolving failing unit test in MDMoleculeTest, the MDMoleculeCustomizer invokes storeAtomData() on it's own which however the core module also invokes this method via (storeData) at the end. This resolution simply cleans up the existing data once the atoms or bonds have been stored. Invoking the method again does not store the atoms twice."

This reverts commit 80cc27babfd8a85da60def975367c251e4093283.

Change-Id: Id5cf60ae15b4ea765588424a6051960f926d9410
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
correctly clearing atom/bond data for MDMoleculeConvention

Change-Id: Ic8de0339ecfa57ca8c2d5ce643ead40b7e232979
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Encoding of 2D and 3D cumulative double bond configurations.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
removing stateless check, this isn't possible to guarantee

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
fixing failing unit tests

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

Change-Id: If284e854566b2cf50c85c03741953acb1489dace
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
JavaDoc fixes for the interfaces module

Change-Id: I4950c4992a13c8cf045d244f92bd34245e3f1486
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing @cdk.githash tags for core and standard

Change-Id: If4b9b7ae986642582dfd623d97e3b7375ba8ed1d
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed couple of commented code

Change-Id: I82647d14db435903168e30d9dfeda9c952881046
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Now properly tests the right class (fixes #3553754)

Change-Id: Id1a43219832241e57cab46c40941564f8b978187