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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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Commits on Sep 18, 2015

• Modified StructureTools#getGroupsWithinShell method to return a Set not

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Commits on Sep 17, 2015

• cleanup

  andreasprlic

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• #326 test for issue and fix

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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

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Commits on Sep 15, 2015

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

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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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Commits on Sep 11, 2015

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

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• #322 starting to add support for struct_ref_seq_dif category

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• Fix ArrayIndexOutOfBounds due to iterating over too-short proteins

  sbliven

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Commits on Aug 28, 2015

• #320 updating API

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• #320 updating API

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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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• Merge branch 'itasser'

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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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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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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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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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