#631 Fix for the atom type matcher testing stack, bug #1299

[Egon Willighagen]

This patch updates the stack to use @AfterClass for counting the tested atom types, rather than relying on the last method in the source code to be called last. This fixes the "regression" introduced by updating the JUnit stack which no longer keeps the test method order.

Two additional patches fixes two problems exposed by this fix:

1. incorrect casting to cdk.Atom
2. a fix in counting the tested atoms, and in particular if types are being tested which are not defined in the ontology

[Egon Willighagen]

1. a fix in counting the tested atoms, and in particular if types are being tested which are not defined in the ontology

[Egon Willighagen]

1. incorrect casting to cdk.Atom

[John May]

@cdk.module test-core

is missing from the new interface, I'm going to go ahead and add this.

[John May]

compiles and no new test fails, applied and pushed