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>
Merge remote branch 'upstream/master'