Unit test to expose a NPE happening when IAtoms do not have formal charges set

Change-Id: I22b4eb3c30bf23f0f80c6d92bf33b15f9d1c65d0
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fix the NPE: 0 formal charges is the common CDK default if unset

Change-Id: I66ef745de55acbe2b6c18672cd3dc45c67794699
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Expose another NPE source

Change-Id: I8a4eacd72d3da1a5de2424c50a54d8817511b2a0
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Deal with null charges on 'this' too

Change-Id: I94f5cea8fef424c597bd00390f056d87782a2247
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Reverse order of test to avoid having a potentially unreachable null check.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Replace occurrences of String.indexOf(String) by String.indexOf(Char) for single-char strings (PMD report).

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fix incorrect spelling of 'pseudo' in comments and variable name. Original variable deprecated and left in place.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add recognition of ACDLabs ChemSketch atom label property.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add reading of ACDLabs ChemSketch atom label property from V2000 molfiles.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Relocate resource files to the cdk-io module.
Fixed up a bunch of typos/misspellings in javadoc.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Exclude generated sources from PMD reports.
Correct PMD exclude for javacc source.
Duplicate PMD configuration in reporting section.
Add all missing @Override annotations.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add all missing @Override annotations.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add all missing @Override annotations.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add all missing @Override annotations.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add all missing @Override annotations.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Add all missing @Override annotations.

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