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1. Commits on Jun 24, 2018

   • Fixing issue with duplicate altlocs in writing to mmcif. Improved docs.

     josemduarte

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2. Commits on Mar 12, 2018

   • Removing deprecations from v4

     josemduarte

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3. Commits on Mar 7, 2018

   • Removing jgrapht library warnings, UndirectedGraph -> Graph

     josemduarte

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4. Commits on Mar 1, 2018

   • cleaning up and adding tags

     

     Dmytro Guzenko

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   • NCS-aware CrystalBuilder object

     

     Dmytro Guzenko

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5. Commits on Jun 29, 2017

   • Make other structure classes serializable

     lafita

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6. Commits on Apr 4, 2017

   • Refactoring FileDownload util to be a part of biojava-core project

     valasatava

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7. Commits on Mar 21, 2017

   • Create a test for the new parameters of the SmithWaterman3Daligner #552

     lafita

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8. Commits on Nov 7, 2016

   • Update to biojava 5.0 ligand and chain model

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     sbliven

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9. Commits on Nov 2, 2016

   • Moved addGroupToStructure methods to StructureTools

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     sbliven

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10. Commits on Oct 3, 2016

    • Ignore waters when calculating ligand proximity

      sbliven

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    • Reducing DEFAULT_LIGAND_PROXIMITY_CUTOFF to 5A

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      sbliven

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    • Show ligands by proximity in CE-Symm

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      sbliven

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    • Add StructureTools.getLigandsByProximity

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      sbliven

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    • Add model-specific iteration over Groups and Atoms

      sbliven

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11. Commits on Sep 15, 2016

    • Solving a compilation problem, making Grid usable for Point3d #545

      josemduarte

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    • Some more work towards #545, some cleanup

      josemduarte

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12. Commits on Aug 18, 2016

    • Deprecating methods that got used to the Chain interface.

      andreasprlic

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    • moving utility classes to detect type of Chain to the Chain interface level (used to be StructureTools).

      andreasprlic

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13. Commits on Aug 11, 2016

    • Using the new checks for polymer type in Group, instead of similar checks in StructureTools.

      andreasprlic

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14. Commits on Jun 9, 2016

    • Merge pull request #499 from DevFactory/release--primitives-should-not-be-boxed-just-for-String-conversion-fix-1

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      andreasprlic

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15. Commits on Jun 7, 2016

    • Refactored getChain(int chainIndex) and getChain(int modelNr, int chainIndex) to getChainByIndex().

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      abradle

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16. Commits on Jun 5, 2016

    • squid:S2131 - Primitives should not be boxed just for String conversion

      

      Mohamed Ezzat

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17. Commits on May 25, 2016

    • Updates for bond creation for deuterium atoms.

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      abradle

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18. Commits on May 12, 2016

    • Fixed some bugs in pdb parsing: now TestLongPdbVsMmCifParsing passes!

      josemduarte

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    • Fixing more problems with pdb parsing: water chains weren't split out

      josemduarte

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19. Commits on May 10, 2016

    • Fixed part of a test

      josemduarte

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20. Commits on May 5, 2016

    • Clean up of warnings and removed some old deprecations

      josemduarte

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    • Fixes on top of Andreas' patch

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      abradle

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21. Commits on May 4, 2016

    • #469 fixing more broken unit tests

      andreasprlic

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    • addressing several broken unit tests.

      andreasprlic

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22. Commits on Apr 29, 2016

    • Implemented method to expand ncs ops as new chains

      josemduarte

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23. Commits on Apr 28, 2016

    • Fixed a couple of bugs in structure tools about empty arrays

      abradle

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24. Commits on Apr 1, 2016

    • Updated the MMCIF, PDB and MMTF consumer,parser,decoder to use the same function for cleaning up alt locs.

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      abradle

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25. Commits on Mar 31, 2016

    • Removal of warnings and further refactoring

      abradle

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