#25 CDK should use the BO data lists

[Egon Willighagen]

Instead of using CDK based configuration data, it should
reuse the blue obelisk data repository. It requires some
looking into to wether or not they provide all data we need.

[Egon Willighagen]

Logged In: YES
user_id=25678

One possible problem might be the license. I think most BO
data currently has the GPL license, while CDK is LGPL...
this needs to be resolved first. Note that some copyright is
bye OpenEye!

[Egon Willighagen]

Logged In: YES
user_id=25678

OK, the licence for BODR has been set MIT, so CDK can start
use this data.

[Egon Willighagen]

Logged In: YES
user_id=25678

Rajarshi, thanx for addressing this. Might you please update
the JUnit tests too, by recalculating the correct values
manually:

http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-standard.html

[Rajarshi Guha]

Logged In: YES
user_id=349408

Fixed the errors. This leaves the element data
(chemicalElements.xml) to be updated. Whats the view on
that? The BO data misses some fields that are present in the
current CDK data

[Egon Willighagen]

Logged In: YES
user_id=25678

If we have element data not in BO yet, then we need to
contribute those bits. Which info is that? Is it atom type info?

[Rajarshi Guha]

Logged In: YES
user_id=349408

The only attribute in the chemicalElements.xml file of the
CDK that is not in elements.xml of the BODR is the phase.

Also the BODR its own atom type files - I'm not entirely
sure about replacing the CDK aomt typing files - AFAIK, the
CDK is using the Jmol atom types, the BODR has OpenBabel
atom types (which also is based on SMARTS patterns)