Stripping out existing implementation - leaving only the public API.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Encapsulating parser and documenting fields and constructor.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Invert logical condition - new parser will automatically assign bond orders. This also allows us to throw a condition for cases just as invalid pyrrole (c1nccc1) which is one of the existing (and failing) units.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using Beam to read the SMILES string.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Convenience method for writing new tests.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Atom typing not longer automatically applied.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added missing aromatic bond 'C:1C:C:C:C:C1' is not the same as 'C:1:C:C:C:C:C1'. Also added an additionally test to show if loading normally the correct structure 'cyclo-hexane' is obtained.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Documenting ITetrahedralChirality with the fact that one if the chiral atom is present in the ligands it indicates an implicit hydrogen or lone pair.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Convert tetrahedral centres with an implicit hydrogen or lone-pair to the CDK ITetrahedralChirality.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Beam gives the configuration in the absolute order of the atoms - tests were updated to account for this. Also atom objects were tested instead of symbols.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Static import of assertTrue/assertFalse - no other changes.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Kekule molecule is loaded - but we can apply the aromaticity if required.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Typos and check bond orders.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Chiral hydrogens are no long converted to explicit atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Bond order sums are now correct (once the molecule is kekulised)

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Input was invalide (amine nitrogen) added another test for the invalid case.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Many tests which check atom types are present or that aromaticity is set are resolved.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Beam will (currently) allow bare 'H', 'D' and 'T'. These are common mistakes and is no extra effort to parse it. Note D and T are auto-corrected to a hydrogen with a mass number '[2H]' and '[3H]'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
'Co' is invalid - show we can load it if needed and that also we can kekulise an acrylic molecule with 'Co' at the front.

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