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Commits on Jun 24, 2016

• Include a second structure clustering after internal symmetry

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  lafita

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• Simplify and rename Demo for Quaternary Symmetry in structure-gui

  lafita

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• Add a test for helical symmetry detection

  lafita

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• Port the ScanSymmetry script to the symmetry project

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  lafita

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• Create an ENUM for the symmetry perception methods

  lafita

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• Adapt test for Quaternary Symmetry detection with same examples

  lafita

  committed
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• Complete refactoring of QuatSymmetryDetector into static methods

  lafita

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• Expand test on Subunit Clustering classes

  lafita

  committed
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• Replace the CombinationGenerator with a PowerSet generator

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Commits on Jun 23, 2016

• Create a conversion method from List SubunitCluster to Subunits

  lafita

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• Refactor QuatSymmetryParameters to have only symmetry params

  lafita

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• Deprecate old Chain Clustering classes

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  lafita

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Commits on Jun 22, 2016

• Implement and test for dividing SubunitClusters with internal symmetry

  lafita

  committed
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• Test for bio assemblies in Subunit Extractor

  lafita

  committed
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• Move Subunits back to the symmetry.core package

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  lafita

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• Create static SubunitClusterer equivalent to ChainClusterer

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  lafita

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• Create SubunitCluster class and test with methods to merge clusters

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  lafita

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• Create basic Subunit Class as elementary unit replacing Chain

  lafita

  committed
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• Create static class SubunitExtractor

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  lafita

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• Rename classes to be consistent with Subunit

  lafita

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Commits on Jun 20, 2016

• Replace verbose by logger.info and unify methods with StructureTools

  lafita

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• Merge remote-tracking branch 'main/master' into quatsymm

  lafita

  committed
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• Move ChainClusterer test to new package

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  lafita

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• Document and add parameters for ChainClusterer

  lafita

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• Merge pull request #516 from DevFactory/release--Iterator.next()-methods-should-throw-NoSuchElementException-fix-1

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  sbliven

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• Merge pull request #514 from DevFactory/release--equals(Object-obj)-and-hashCode()-should-be-overridden-in-pairs-fix-1

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  sbliven

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Commits on Jun 17, 2016

• Create ChainClusterParameters from QuaternarySymmetry

  lafita

  committed
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• Organize symmetry packages and classes

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  lafita

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• Use default file format (MMTF) for QuatSymmetry test and demo

  lafita

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Commits on Jun 16, 2016

• squid:S2272 - "Iterator.next()" methods should throw "NoSuchElementException"

  

  Mohamed Ezzat

  committed
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• squid:S1206 - "equals(Object obj)" and "hashCode()" should be overridden in pairs

  

  Mohamed Ezzat

  committed
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• Added some tests on the structures.

  abradle

  committed
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• Fix to add chemComp info for the Basic MMTF test.

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Commits on Jun 15, 2016

• A test that round trips mmtf files

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  abradle

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• Fix for the MmtfStructureReader to handle altLoc being a null byte.

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