Minimising the scope of SMARTS parser classes. These classes are specific to the parser and don't need to be exposed in the public API. The atom matchers in isomorphism.matchers.smarts are still public but could also be hidden behind a factory. This commit removes about 50 classes from the JavaDoc making it easier to find other parts.

Change-Id: I01d6ae9b713c36fd521c7dacf089b71cd5315869
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't repurpose SMARTS query atoms for other uses. We can define our own matchers internally.

Change-Id: I7b690d148c67413a64eaa40f4a7ee86303d0538b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move SMARTSAtoms back to the smarts module.
Three classes already have explicit @cdk.module annotation

Change-Id: Icf9c8c297bb048fb62230bf2a1c00c3cd2bb81e7