These atoms need to be recognised for creating extended tetrahedral (allene) stereo elements.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Additional commit to fix still failing test. The previous example was hitting a heuristic in the code, where there is more than one hydrogen the type is automatically set to non-stereogenic. This was the case for the terminal atoms in this extended tetrahedral example.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
MMFF aromatic types are assigned by updating the existing symbolic types.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
MMFF atom type assignment, unit and validation tests. The atom types are assign using simple SMARTS patterns and the previously implemented aromatic mapping. This provides correct assignment of all symbolic types in the validation suite.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Circumvent '*' not matching explicit hydrogens.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
The expected value is for chloropropane and not chlorobutane. The SMILES 'CCCCl' was mistakenly misread as 'CCCCCl' in commit db9a311.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Inline method invocations and avoid using reflection (error prone).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove test reporting "This descriptor is not tested". Test coverage is reported using jacoco. The abstract descriptor test is still running some useful assertions (i.e. hydrogen representation) and so we leave the class in place.

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