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Commits on Mar 29, 2016

• Ugly, basic MMTF support in AtomCache

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Commits on Mar 24, 2016

• [maven-release-plugin] prepare for next development iteration

  abradle

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• [maven-release-plugin] prepare release biojava-5.0.0-alpha2

  abradle

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• Updated pom to build off alpha2

  abradle

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Commits on Mar 22, 2016

• Update the decoder to work with the new interface

  abradle

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• Develop off the snaspshot.

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• Build biojava against the alpha release of mmtf

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Commits on Mar 21, 2016

• Merge remote-tracking branch 'fork/mmtf' into alt_loc_bonds

  abradle

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• Merge remote-tracking branch 'fork/entity_features' into alt_loc_bonds

  abradle

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• Alternate locations now contain all atoms in a group.

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Commits on Mar 17, 2016

• Upstream refactoring of mmtf specification

  abradle

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• Updates to the biojava structure decoder due to an API change in the interrface

  abradle

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• Added a fairly poor and basic test

  abradle

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• Update to consider the new API versioning

  abradle

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• Updates to for the new mmtf format

  abradle

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• Minor

  abradle

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• Added a new MMTF parsing module in biojava

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Commits on Mar 15, 2016

• Updates to the tests to fix for new manner of parsing entity

  abradle

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• Updated test becuase we now consider non-polymeric compounds

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Commits on Mar 14, 2016

• Updates to the Biojava code to include imporved handling of Entity information.

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• Added a new test file for entity information

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Commits on Mar 12, 2016

• Fixed a bug where nucleotide bonds were not being generated. Added a test to ensure nucleotide bonds are being generated.

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Commits on Mar 10, 2016

• [maven-release-plugin] prepare for next development iteration

  andreasprlic

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• [maven-release-plugin] prepare release biojava-4.2.0

  andreasprlic

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• Light cleanup:

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  sbliven

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• Running spacestotabs on recent changes

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  sbliven

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• Run addlicense

  sbliven

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• Another serializable, we should revise at some point all

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  josemduarte

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• Fixing issue in cloning: was adding same group several times

  josemduarte

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Commits on Mar 9, 2016

• Merge branch 'master' into removeLoadChemCompInfo

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• Docs

  josemduarte

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• Fixing issues with bonds in 3th3 and better logging

  josemduarte

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• More whitespace fixes

  sbliven

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• Automatically adding missing @Override

  sbliven

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• Converting initial spaces to tabs.

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