fixed up use of == to test for string equality rather than .equals().

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed some unused local variables (PMD reports).

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Replaced single-character strings in StringBuffer.append() and replaced StringBuffer by StringBuilder where appropriate.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Inlined test molecule creation from MoleculeFactory.java.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Inlined test molecule creation from MoleculeFactory.java.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added test to demonstrate bug where AtomPlacer3D().numberOfUnplacedHeavyAtoms() counts explicit hydrogens as heavy atoms.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed bug where AtomPlacer3D().numberOfUnplacedHeavyAtoms() counts explicit hydrogens as heavy atoms.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Internal static utility class for the upcoming generator.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Internal class for holding and modifying text represented as a Java 2D shape.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Enumeration of hydrogen positions and methods that decide this position.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Convex-hull for Java 2D shapes.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
An atom symbol for storing a displayed symbol.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
A predicate class that defines whether an atom symbol is visible. Could be reused in other generators.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Isotopes are also displayed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Access methods for attributes.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Generation of atom symbols.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Tracing out the structure of the StandardGenerator. Parameters need to be added.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
First part of bond generation, determine the order of rings to display double bonds inside.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Tracing out the methods for the standard bond generator and how the API is called from the StandardGenerator. Implementation and documentation to follow.

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