Radicals assigned to wrong atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Linear placement of cumulated atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Represent and store extended tetrahedral stereochemistry.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Conversion of extended tetrahedral stereochemistry to/from InChI.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Extended tetrahedral support in SMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Latest version of Beam with support for parsing and encoding extended tetrahedral stereochemistry.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Perceive extended tetrahedral from 2D/3D coordinates.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Perceive allene stereochemistry from 2D and 3D depictions.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Clockwise sort should handle exactly opposite atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Explicit hydrogens invert winding.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Improved winding detection for tetrahedral centres.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Improved identification of tetrahedral elements. More improvements needed but now any non-planar bonds indicate a tetrahedral centre should be created in 2D depictions. In 3D depictions, we check the environment of each neighbour. The method is currently inadequant and fails to identifier interdependent stereocentres (as seen in test) but is required to avoid create tetrahedral configurations for non-stereogenic atoms (i.e. methane).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Accurate and efficient assignment of a Kekulé form to a compound with aromatic bond types.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Improved method naming, to set or add properties. addProperties implementation has been simplified and improved such as to use the existing putAll method on maps avoid NPEs.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Lots of redundant boiler plate in the debug object updated.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Existing invokers may depend on adding properties.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
setProperties removes existing properties.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use a Maven properties file

Change-Id: Ic26a63a29ed12cf27c1393defefc1c02eeac1746
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Restored some error messages

Change-Id: If23acef5f7fa19b868d75c41f604819afe872d18
Signed-off-by: John May <john.wilkinsonmay@gmail.com>