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1. Commits on Jul 6, 2013

   • Made AstralSet.getId() and AstralSet.getUrl() public.

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2. Commits on Jul 3, 2013

   • Oops. Shouldn't have pushed. Fix "org.biojava.structure" -->

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   • Added Log4J configurations.

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   • Use Log4J logging instead.

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   • Set ScopFactory to 1.75B to prevent test failure.

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   • Fixed demo: can't use same structure.

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   • Created classes for RCSB ligands (should have committed this a while

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   • Moved general XML utilities to a new class ReadUtils.

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   • Comments.

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   • Added support for Astral sets.

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   • Added Log4J to POM.

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   • Return an empty list when sunId is not listed, rather than null.

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   • Created tests for ScopInstallation and BerkeleyScopInstallation.

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   • Added support for SCOP com files. ScopDatabase now has a getComments()

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3. Commits on Jul 1, 2013

   • Merge branch 'master' of https://github.com/biojava/biojava

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   • Added another CP factory method.

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4. Commits on Jun 28, 2013

   • adding cleaner logging and new option to disable domain based alignments

     

     Andreas Prlic

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   • making sure cache can't be null

     

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5. Commits on Jun 27, 2013

   • Merge branch 'master' of github.com:biojava/biojava

     

     Andreas Prlic

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   • catching NPE

     

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   • Merge pull request #29 from ulyssecarion/master

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   • Merge pull request #30 from ulyssecarion/non-verbose

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   • Get rid of a few debugging println calls

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6. Commits on Jun 26, 2013

   • Have StructureIO set the atom cache of getBioUnitDataProvider

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   • Replace all uses of waternames with isWater(); move waternames into HetatomImpl

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   • Add an isWater method to Group; add water names to GroupType

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   • Merge pull request #28 from ulyssecarion/master

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   • Revert "Remove useless StructureExceptions in Calc"

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   • Revert "Remove @throws from methods no longer throwing StructureExceptions"

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   • Remove @throws from methods no longer throwing StructureExceptions

     ucarion

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   • Deprecate skalarProduct for scalarProduct (fix typo)

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   • Remove useless StructureExceptions in Calc

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   • Merge branch 'master' of https://github.com/biojava/biojava

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7. Commits on Jun 25, 2013

   • Merge branch 'master' of github.com:biojava/biojava

     

     Andreas Prlic

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   • cleanup

     

     Andreas Prlic

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