Removed FIXME.

Commit 061ea218 corrected this behaviour.
Added Alison Choy as new author

Change-Id: Ie7a66be569dccc7b34b0c2197d6cfccff5c21df2
Ensure writer.close() is invoked by CMLWriter.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Use StringBuilder to construct HTML formula string.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Display CH4 not C1H4 for HTML.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
A module for deprecated and legacy code.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Simplified access to a new aromaticity implementation that replicates the now deprecated CDKHuekelAromaticityDetector.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replacing usage of CDKHueckelAromaticityDetector.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move old aromaticity implementations to the legacy module.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Moving the deprecated DoubleBondAcceptingAromaticityDetector to 'cdk-legacy'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
SwissArmyKnife is not used and is moved to cdk-legacy.

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

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
New aromaticity perception complains on unset atom types - these tests are regressions as the atom types have not been set. That is, they were silently being ignored.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity was being silently skip for these tests - adding the correct setup in now means the expected data changed.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Aromaticity perception was previously being skipped on initial fragmentation. Now that aromaticity is set, some expected output has changed, note the specified single bonds in SMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Treat atomic number as symbol and leave set when other properties are cleared.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
To obtain correct output in the fragmenters we need to clear all existing configurations and reperceive atom types. Could be improved.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ensure atom types are percevied in fragmenter tests.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Default atom type is now "X" not null. This allows us to tell when something has been typed and when it hasn't.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Regressions in reaction module to new atom type behaviour. This similar code needed updating to check for untyped atoms.

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