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1. Commits on Sep 22, 2015

   • Fixed DBRef#toPDB() method to give 80 characters line

     sroughley

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   • Modified PBBFileParser to ensure all lines are 80 chars prior to parsing

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2. Commits on Sep 18, 2015

   • Modified StructureTools#getGroupsWithinShell method to return a Set not

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     sroughley

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3. Commits on Sep 17, 2015

   • cleanup

     andreasprlic

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   • #326 test for issue and fix

     andreasprlic

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4. Commits on Sep 16, 2015

   • Removing warnings.

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     sbliven

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   • don;t use Java 8 specific method names

     andreasprlic

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   • work around if ReducedChemCompProvider is getting used

     andreasprlic

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   • adding support for parsing sequence mismatched into Chain class

     andreasprlic

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   • additional test for parsing SIFTs files

     andreasprlic

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5. Commits on Sep 15, 2015

   • Fix #321. Optimized completeGroup() for large groups.

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     sbliven

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6. Commits on Sep 14, 2015

   • Use random seed unless specified in CeSymm optimization

     lafita

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   • Method to get the principal axis index from a RotationGroup

     lafita

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   • Fix bug when an empty alignment is produced in CeSymm

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     lafita

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7. Commits on Sep 11, 2015

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

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     andreasprlic

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   • #322 starting to add support for struct_ref_seq_dif category

     andreasprlic

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   • Fix ArrayIndexOutOfBounds due to iterating over too-short proteins

     sbliven

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8. Commits on Aug 28, 2015

   • #320 updating API

     andreasprlic

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   • #320 updating API

     andreasprlic

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9. Commits on Aug 14, 2015

   • Bond and SSBond now implemented as interfaces backed by BondImpl and SSBondImpl, respectively.

     jacob-litman

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   • Merge pull request #318 from sbliven/master

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     sbliven

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   • Merge branch 'itasser'

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     sbliven

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   • Change logger messages of CeSymm to info level

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     lafita

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   • Fix NullPointer bug in CeSymm

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     lafita

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   • Add all scores to non-optimized symmetry results

     lafita

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10. Commits on Aug 13, 2015

    • Fix small bug with short non-symmetric alignments

      lafita

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    • Fix bug when result was not symmetric in CeSymm

      lafita

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    • Disallow MC optimization in parallel

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      lafita

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    • Method to clone parameters in CeSymm

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      lafita

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11. Commits on Aug 12, 2015

    • Port two tests for internal symmetry package

      lafita

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    • Improve symmetry error messages

      lafita

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    • Check for symmetry significance in MultipleAlignment

      lafita

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    • Add new parameter for distance cutoff to MC optimization

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      lafita

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12. Commits on Aug 11, 2015

    • Fix bug in CeSymm iteration process

      lafita

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    • Add demo for point group internal symmetry calculation

      lafita

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