Including the beam library in the SMILES module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Conversion of the CDK object model to Beam.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Conversion from Beam to CDK objects.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Iodine only belongs to the aliphatic and not the aromatic subset - it can not be lower case and this test does not work as intended. A correct example is to have an aliphatic carbon and an aromatic oxygen which make the symbol of Cobalt (non organic subset atom).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing redundant bracket. Generally such an error indicates something deeper is wrong. This test was checking hydrogen counts though so we can safely remove it.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Noticeable performance improvement by avoiding invoking the factory each time. We cache a template atom/bond/container and then clone these when we need them. On large datasets provides a noticeable difference.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Missing license headers and removal of a duplicate line.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Only set aromatic flags if the atoms are aromatic AND the bond was implicit.

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