More efficient suppression of hydrogen atoms. We use a different name as not break the existing behaviour (of cloning) but that method will also be updated.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updates existing methods to call the new copyAndSuppressHydrogens method. There will likely be a few regressions as the method complains about unset hydrogen counts.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
null != 0 - consider this a methane where one hydrogen is explicit, removing that hydrogen could set the h count to 1 when it should have been 4.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Zeroing hydrogen counts in other AtomContainerManipulatorTests.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Bridged hydrogens are no longer removed - this is because we can not put them back in and so we would lose information. Removing bridged hydrogens is useful though but should be done a separate normalisation step such as disconnected metals.

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