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Commits on Dec 14, 2009

• Updated fingerprinter to fix bug 2819557. Updated JUnit tests to take into account new fingerprints. Also cleaned up the template extractor code and regenerated fingerprints for builder3d. Also upd…

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  rajarshi

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• Added a datafile entry for the standard module to store the VDW radii etc for the periodic table

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  rajarshi

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Commits on Dec 10, 2009

• Fixed reading of SD file properties

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  egonw

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• Added unit test for a MDL SD file with mutliple data fields

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  egonw

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• Added unit test for data fields to allow to start with '>' (bug #2911300).

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  egonw

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• Added testing that properties are read from test6.sdf

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  egonw

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Commits on Dec 9, 2009

• Updated license info of third party libraries

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• Fixed JavaDoc: added missing period at end of first sentence, removed useless @throws clause, added missing @cdk.bug tag

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Commits on Dec 2, 2009

• Added changelog for 1.3.1

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• Merged in 1.2.4.1

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• Bumped version to denote post 1.2.4.1

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• Package fixing release: fixed building JavaDoc from source dist

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• Added missing references file to the source dist (full and pure)

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Commits on Dec 1, 2009

• Removed source folders of Doclets, which are not part of the release, and should not be compiled for JavaDoc generation anyway

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Commits on Nov 30, 2009

• Removed java pkg removed by the periodic table patch from the Eclipse project classpath

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Commits on Nov 29, 2009

• Made the unit test more informative

  rajarshi

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• Added test case for bug 2819557

  rajarshi

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• The AtomType(String) constructor is updated so that only formal charge is set to 0 as indicated in the Javadocs. All other fields are set ot UNSET. Javadocs were updated to make this explicit

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• Updated canonical labeler to make use of the PeriodicTable class so that even if an input molecule was not configured we can still get a valid atomic number. This makes SMILES generation a little m…

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• Added OpenJavaDocCheck library (new BSD licensed) and written a custom JavaDoc checks.

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• Additional constant

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  Stefan Kuhn

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• added a constant for untyped atoms

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  Stefan Kuhn

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• Updated to avoid use of deprecated StringBufferInputStream

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• added a test for single-line inchi with several branches

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  Stefan Kuhn

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• the inchi reader was written in such a way that it 1) needed a further line after the inchi=, which was not read, but needed to avoid npes 2) It could only process one branch on a level 3) it requi…

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  Stefan Kuhn

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• Start angles should be different for different size rings

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  mark_rynbeek

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• Sorting of containers in a AtomContainerSet

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  mark_rynbeek

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• Added new test class to the module suite

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• New comparators for AtomContainer

  

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Commits on Nov 28, 2009

• Refactored periodic table element to be a standalone class, so independent of the data module. This is OK, since the class is really just a struct to hold PT data for a given element. As opposed to…

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  rajarshi

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• Some minor code clean up

  

  rajarshi

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• Updated to remove Symbols and all associated tests and usages. Replaced with PeriodicTable

  

  rajarshi

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• Moved PT related tests to their own package. Updated test suites

  

  rajarshi

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• Added method (and test) to get symbol from atomic number and also get element counts

  

  rajarshi

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• Updated module membership. Also made everything bu tmain PT class package private

  

  rajarshi

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