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Commits on Jul 22, 2013

• Some of the URLs and Ids were swapped; critical fix.

  dmyersturnbull

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• Critical null check of soft reference.

  dmyersturnbull

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Commits on Jul 21, 2013

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

  dmyersturnbull

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• Added caching using soft references in a multiton pattern. Commented.

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  dmyersturnbull

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Commits on Jul 15, 2013

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

  

  Andreas Prlic

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• [maven-release-plugin] prepare release biojava-3.0.6

  

  Andreas Prlic

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

  

  Andreas Prlic

  committed
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• now using 4HHB as a standard example

  

  Andreas Prlic

  committed
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• adding new calcRotationAngleInDegrees

  

  Andreas Prlic

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Commits on Jul 12, 2013

• Added an argument strictLigandHandling to getStructureForDomains, and

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  dmyersturnbull

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• Made getStructureForScopDomain correctly handle ligands in multi-chain

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  dmyersturnbull

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• Made AtomPositionMap constructor take a GroupMatcher, which is a new

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  dmyersturnbull

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• Added a match(String) method, and added some argument checks.

  dmyersturnbull

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Commits on Jul 11, 2013

• Don't allow a period (.) as a range specifier. Really we should reserve

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  dmyersturnbull

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• Made AtomPositionMap work with chain Ids of more than 1 character.

  dmyersturnbull

  committed
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• 1. Added support for chain Ids of more than 1 character. This deprecates

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  dmyersturnbull

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• Added methods that take SCOP Ids rather than SCOPDomains.

  dmyersturnbull

  committed
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Commits on Jul 10, 2013

• Added a getStructureForDomain that takes a ScopDatabase.

  dmyersturnbull

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Commits on Jul 8, 2013

• Ran cleanup and fixed comments.

  dmyersturnbull

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• 1. Made RCSBLigandsFactory handle describeHet queries. 2. Wrote helper

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  dmyersturnbull

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Commits on Jul 6, 2013

• Made AstralSet.getId() and AstralSet.getUrl() public.

  dmyersturnbull

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Commits on Jul 3, 2013

• Oops. Shouldn't have pushed. Fix "org.biojava.structure" -->

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  dmyersturnbull

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• Added Log4J configurations.

  dmyersturnbull

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• Use Log4J logging instead.

  dmyersturnbull

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• Set ScopFactory to 1.75B to prevent test failure.

  dmyersturnbull

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• Created classes for RCSB ligands (should have committed this a while

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• Moved general XML utilities to a new class ReadUtils.

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• Comments.

  dmyersturnbull

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• Added support for Astral sets.

  dmyersturnbull

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• Added Log4J to POM.

  dmyersturnbull

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• Return an empty list when sunId is not listed, rather than null.

  dmyersturnbull

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• Created tests for ScopInstallation and BerkeleyScopInstallation.

  dmyersturnbull

  committed
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• Added support for SCOP com files. ScopDatabase now has a getComments()

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Commits on Jul 1, 2013

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

  dmyersturnbull

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• Added another CP factory method.

  dmyersturnbull

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