Also include the dependencies of the smiles module

Change-Id: If99d6d17afec08c6a75f7bbfd53e5c5304c281d2
Update header/copyright information
Aromaticity requires atom typing.

Change-Id: If676dddd2f0cf414557475af68e31e7443d39f35
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't check for aromatic atoms before checking charge. Carbon, 'C.plus' cation can also be aromatic and so the charge types should be checked first.

Change-Id: I5c75fabcb004f1cb6839733f0d92c1b3187045da
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Correctly consider the heavy bonds and hydrogen counts. When connectedHeavyAtoms == 2 the full bond list was checked for the aromatic bonds. As the full bond list could contain an explicit hydrogen we should filter it to ensure the aromatic bond checking works correctly.

Change-Id: Ie9952a4da175996acf6f7bf4af5d93aa7c95cc5d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure non-negative height is passed when drawing a rectangle - bug #1163.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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
Using the pattern *Visitor.java ignores adding a cdk module tag to a generated class - avoid this by specifying the full the names of those we actually want to ignore.

Change-Id: Ic5126c300a21bb75265d61981021501450d1ee58
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>