Atoms are not added to IQueryAtomContainer causing an index out of bounds exception downstream. Adding the atoms fixes the issue.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Avoid erroneous aromaticity due to abnormal valence.

Change-Id: I4abbb2e203c07c2dbec27dfb0090d20e06e49a64
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Beam 0.5. - resolve a bug that would randomly fail when configuring double-bond stereochemistry (found from the new random order of IStereoElement sets). - parse tetrahedral selenium and sulphur cations (okay according to inchi tech manual) - parser arbitrary labels in bracket atoms - they are never generated output but instead placed in the ‘label’ of a pseudo atom if one wants to handle them.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Arbitrary labels in SMILES bracket atoms. The label is set in the pseudo atom.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity information is lost on descriptor execution unless the 'aromaticity parameter' is set to true. Already perceived -- pre-perceived -- aromaticity information should not be lost automatically if this parameter is set to false. Perception of unset parameters only via the helper method in the AtomContainerManipulator rectifies this issue. Three test cases: 1) Benzene with pre-perceived aromaticity and no aromaticity perception in the descriptor. 2) Benzene with no pre-perceived aromaticity and no aromaticity perception in the descriptor. 3) Benzene with no pre-perceived aromaticity and perception in the descriptor.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moved to cdk-build-util project

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving source files to separate source trees.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
@cdk.set files - note qsar set is now redundant and picked up from META-INF/services

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing old class from JChemPaint.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ignore maven build directory (target/).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Dependencies are now resolved using Maven. Version is now in root pom.xml instead of build.props.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using latest version of Beam.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving testdata resources to the correct location.
Added project names for each module (same as module name)

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Bumping copyright year.
Updating readme with maven instructions.

Needs more clean up but okay for now.
Update README