All tests pass in the CIP module but the CIPTool needs updating to handle the implicit hydrogen / lone pair scheme. For the meantime we have a sanity check incase such a case is attempted.

Change-Id: Ia4fc8cfca0fca122b039356ab761af3cd425eb26
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in SMSD - it seems to be that the existing code won't match a aromatic double bond with an aromatic single bond (i.e. they both have to be single).

Change-Id: Ib47b2aa3d17649424a53bfeddafa10cee427acca
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in tautomer.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve stuctgen regressions - we no longer need to add implicit hydrogens.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in reaction.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in qsarionpot.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in qsaratomic.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolving regressions in fragment.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added missing JavaDoc in the atomtype module

Change-Id: I8178412b0080530de525b68a0d5e80a5490cad21
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing JavaDoc in the cip module

Change-Id: I0deb9dda09f04ec3de81576ac068c4c2fb65b95a
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing JavaDoc in the core module

Change-Id: I3e93e7f8748a9385363cc969688499f8c22f60ef
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Cleared the JavaDoc errors in the datadebug module: mostly explicit @Override and @inheritedDoc, but also a @cdk.githash or two

Change-Id: I698043c91c4670d006a7e6682fb09d9b6f4f3e2b
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing @cdk.githash tags

Change-Id: I6694f45e69bd59ff8f03396abdc5220516e42ed4
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added missing JavaDoc in the render and renderbasic modules

Change-Id: I1479d7f0304387498c1d4eff50c29f397adf1061
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Reformat to enable better visualisation of changes.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Beam version 0.2-SNAPSHOT - some minor tweaks to performance (more likely).

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