Migrate PartialTChargeMMFF94DescriptorTest to a simpler, InChi input based approach

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Enumerate all molecules in table V of the MMFF94 paper II. Unit tests still failing.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Ignore tests in error.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Further explanation of ignored test.

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

Conflicts:
	tool/forcefield/src/main/java/org/openscience/cdk/charges/MMFF94PartialCharges.java
Allow compilation. 

Built okay the first time but jenkins doesn't like the Object -> double cast.
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>