New API for match ChemFormats - instead of checking line-by-line the entire header is passed. The matcher then indicates whether it matched, where it matched and what format it is.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updating abstract test to use new API.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replacing mock method with new implementation.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using new API to guess format

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Default implementation to easily adapt existing matchers.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving old API method from interface to abstract super-class.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Adapting existing formats to new API.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updating PubChem Compound XML format to not match PubChem Compounds (plural).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow PubChem Substance to not match PubChem Substances (plural).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing matching state from MDLRXN3000 format.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Dependencies not inherited from ioformats.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Performance improvements to exteneded connectivity computation (morgan numbers).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
As described in the original publication only use the connectivity value of non-hydrogen atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Linear search (getAtomicNumber(IAtom)) is fast enough to avoid precomputing the index map.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Extended documentation suggesting better approaches to what the exteneded connectivity was traditionally used for. Also explicitly made clear the numbers are not the canoniclal labelling as described in the original article and mearly the exteneded connectivity which is used in computing the lexicographic smallest unique labelling (canonical).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Reformat - removing tab indents.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Dependencies not inherited by ant.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Timeout to long running test - the test currently errors due to to much GC. Adding a timeout doesn't convert the error to a failure but does allow the 'cdk-standard' suite to run twice as quick.

Change-Id: If8db442080406d08b68fff7f9fbf5e8f307f64cf
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>