Reinstate some PMD custom rulesets.
Correct PMD configuration. Rulesets are now accessed cdk-build-util on the classpath. They could also be hosted remotely but this way they can be run offline.
Plugin repository required for PMD to obtain cdk-build-util.
Unit test that shows that namespaces are no longer properly handled when reading CML

Change-Id: Ic1e0916c24a326fdbe25c498206e5ded13342a8d
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Also track the modules and thus with their states

Change-Id: I4cfad7da0aea5ac0d5a157411a0e1d8cbb2c98a6

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Ignore elements from other namespaces (but default to CML if not NS is defined)

Change-Id: I902b2fda8bbc841a2db26c324a0c4371ffbbcfc5
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Report the simple name, not the hashcode

Change-Id: I726d0aa1d1b7629307d01b326d84438fd9a6c84f

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Make sure to store the reaction set

Change-Id: Iaf7f8c36610ba9a89fe228363d168f1186641643

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Only store a cdk:Formula field if we really found formula

Change-Id: I860ad9a35c3d4c7caf1f87d159179986573f0050
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Be more explicit about source of reference values

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
testPartialTotalChargeDescriptor_Methylamine does not check final atom

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use the charge value from the paper for methanol

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
fix for The import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo collides with another import statement

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

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Enable logging for MMFF94PartialCharges

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Minor MMFF94charge LOG improvements

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
More logging improvements to MMFF94PartialCharges

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Formatting.
Log4J is invoked indirectly through the CDK LoggingTool.
Update README.md