When a reaction references a molecule which is unknown - automatically create one with that Id. This happens when the set of molecules is defined after the reaction. This commit resolve the test in error 'CML2Test. testBug2697568'

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Backport for cdk-1.4.x: use IMolecule in IMoleculeSet

Change-Id: I110f4bc5078de535f8840eae811ad69752503b39