[Cdk-devel] merging from branches.miguelrojasch-CMLReact to trunk

[Miguel R. C. <mig...@ya...>]

Hi,


I was creating parallel to trunk the branch: miguelrojasch-CMLReact and I would to merge now again
to trunk which I think they resolve some of the bugs and are created new
methods.

branches.miguelrojasch-CMLReaction contains

-The CML module has been implemented to read and to write schemeReaction
definitions in JUMBO project and in the papers CML. For that it has been
created a new ISchemeReaction and the sufficient tools to handle the concept in CDK.

-The reaction module is more flexible. The parameters defined in each
reaction are written from a owl dictionary. Furthermore, it is checked
that each reaction entry is included in the dictionary and backwards.

-All reactions are generated from a mechanism. The mechanism can handle more of one reaction.

-The StructureResonanceGenerator es more robust. Distinguishing
resonance structure in aromatic objects.

- More tests.

Applying the example from egon: http://chem-bla-ics.blogspot.com/2007/11/comparing-junit-test-results-between.html
to compare between trunk and branch to look the differences, I obtain the follow result:

$ diff -u trunk.results branch.results | grep "^-Testcase" | wc -l
241
$ diff -u trunk.results branch.results | grep "^+Testcase" | wc -l 
0

The first gives the number of JUnit tests which are now no longer failing, while the second
gives the number of tests which are new fails. Meaning very good expectations. Too much I think. 

Please take a look to confirm the result and to make possible the merging to trunk.

Best regards,
 Miquel



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