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Commits on Mar 2, 2016

• Updated to remove debug print

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• Updates to the parser to use the atom record asymid to authid mapping and not the ones parsed fron the header

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Commits on Mar 1, 2016

• Adding some logging for #398 that mitigatest the issue

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• Fixed bug: wasn't checking for server protocol properly

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

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Commits on Feb 29, 2016

• Added unit test for the asym id parsing functionality

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• Updates to allow for parsing mmCif files and producing chains based on internal chain ids.

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• Another fix: prefix can be too short

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• Making sure that the file is renamed properly, better logging

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• Slight change - makes a temp file first and then copies across

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• Updated code to bug fix - so when download fails it doesn't make an empty file

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Commits on Feb 24, 2016

• Merge remote-tracking branch 'upstream/master'

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• Fixing issues arising after making DownloadChemCompProvider the default

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Commits on Feb 23, 2016

• Added test for alternate location bonds

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• Updated the bond maker to make alternate locationo bonds

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Commits on Feb 20, 2016

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

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• new method for getting all ribosomes, some cleanup.

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Commits on Feb 19, 2016

• Fix NPE in the mmCIF parser when provided zero-length files.

  

  Matt Larson

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• Adding TER records to pdb file export.

  

  Matt Larson

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Commits on Feb 16, 2016

• Change print optimization history format in SymmOptimizer

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Commits on Feb 15, 2016

• Create method to update symmetry scores

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Commits on Feb 10, 2016

• adding try-with-resources

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

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• Merge pull request #407 from sbliven/fix81_squashed

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• A few fixes in RCSBUpdates

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• #397 changing default chem comp provider to DownloadChemCompProvider

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• Adding a new utility class that makes it easy to access to lists of PDB IDs.

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• Adding a new utility class that makes it easy to access to lists of PDB IDs.

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• Merge pull request #402 from abradle/master

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Commits on Feb 9, 2016

• Minor: removing extraneous try block

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• Merge remote-tracking branch 'biojava/master'

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• Removing broken test of home directory

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• Fix additional potential resource leaks in DownloadChemCompProvider

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• Include test for StructureImpl object linking

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• Clearing ChemComp cache whenever provider changes

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