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onbiojava-4.2.1

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Commits on Apr 29, 2016

• Added handling of '?' and other non integer string for the charge.

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  abradle

  authored and

  josemduarte

  committed
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• Refactored ChargeAdder and fixed bugs where it wasn't adding charges to all groups.

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  abradle

  authored and

  josemduarte

  committed
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Commits on Apr 11, 2016

• Fixing bug in mmcif writing: ins codes were written as ascii code

  josemduarte

  committed
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Commits on Apr 6, 2016

• Fix #449 by copying SEQRES to new chains

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  sbliven

  committed
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Commits on Mar 14, 2016

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

  

  Anthony Bradley

  authored and

  josemduarte

  committed
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Commits on Mar 10, 2016

• Light cleanup:

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  sbliven

  committed
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• Running spacestotabs on recent changes

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  sbliven

  committed
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• Run addlicense

  sbliven

  committed
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Commits on Mar 9, 2016

• Merge branch 'master' into removeLoadChemCompInfo

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  josemduarte

  committed
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• More whitespace fixes

  sbliven

  committed
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• Converting initial spaces to tabs.

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  sbliven

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• Removing template messages

  sbliven

  committed
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• Remove trailing whitespace globally from .java files

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  sbliven

  committed
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• Running addlicense.sh

  sbliven

  committed
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• Merge branch 'master' into removeLoadChemCompInfo

  josemduarte

  committed
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Commits on Mar 8, 2016

• Fixing a few bugs that arose after loadChemCompInfo removal, #426

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  josemduarte

  committed
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• Fix PDBFileParser bug with missing trailing spaces.

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  sbliven

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

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  sroughley

  authored and

  sbliven

  committed
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• Merge branch 'master' into removeLoadChemCompInfo

  josemduarte

  committed
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• Merge remote-tracking branch 'biojava/master'

  sbliven

  committed
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• Honor prefixes for StructureNames

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  sbliven

  committed
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• Tests pass now, except for TestLongPdbVsMmcif

  josemduarte

  committed
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• Removing loadChemCompInfo, some tests don't pass yet

  josemduarte

  committed
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Commits on Mar 7, 2016

• Changing TestBond to use mmcif

  josemduarte

  committed
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• Merge pull request #424 from edlunde-dnastar/zipchem

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  josemduarte

  committed
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• Use the SLF4J for logging rather than Java logger for ZipChemCommpProvider and unit test.

  

  Matt Larson

  committed
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• Merge pull request #421 from josemduarte/bondsRewrite

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  josemduarte

  committed
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• ZipChemCompProvider cleanup:

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  larsonmattr

  committed
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Commits on Mar 4, 2016

• Fix #385. Support BIO: identifiers

  sbliven

  committed
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• Refactoring BioUnitDataProviderFactory to take class arguments

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  sbliven

  committed
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• Implementing #408

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  josemduarte

  committed
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• Refactoring of Structure ssbonds interface, as described in #341

  josemduarte

  committed
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Commits on Mar 3, 2016

• Removed some warnings and Structure.getConnections calls

  josemduarte

  committed
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• Correct significance criteria for internal symmetry

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  lafita

  committed
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• Better name

  josemduarte

  committed
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