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1. Commits on Nov 30, 2016

   • addressing requested changes re. throwing exceptions.

     andreasprlic

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   • moving to Java 7

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   • now also accepting old header line

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   • #610 switching test to junit version 4

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2. Commits on Nov 29, 2016

   • creating local dir, if it does not exist.

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   • fix for #610

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3. Commits on Aug 18, 2016

   • making output less verbose

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   • setting default log level to warn

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4. Commits on Aug 8, 2016

   • new utility classes to detect if a Group is polymeric, an amino acid, or a nucleotide group.

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5. Commits on Jun 15, 2016

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

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     andreasprlic

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   • some formatting improvements.

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

     

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   • [maven-release-plugin]prepare release biojava-5.0.0-alpha4

     

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   • Merge branch 'bugfixes-4.2'

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

     

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   • [maven-release-plugin]prepare release biojava-4.2.2

     

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   • [maven-release-plugin] rollback the release of biojava-4.2.2

     

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

     

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   • [maven-release-plugin]prepare release biojava-4.2.2

     

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   • [maven-release-plugin] rollback the release of biojava-4.2.2

     

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   • [maven-release-plugin]prepare release biojava-4.2.2

     

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6. Commits on Jun 14, 2016

   • merging in latest ptm modifications from master branch

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   • Updating ptm list.

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   • Added list of chromophores to ptm_list.xml file, updated unit tests

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7. Commits on Jun 10, 2016

   • Reverting some changes to be compliant with the "old" way of doing chain IDs.

     andreasprlic

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   • Merge pull request #502 from andreasprlic/master

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     josemduarte

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   • merging in updated ptm_list.xml

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   • merging in updated ptm_list.xml

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   • merging in updated ptm_list.xml

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   • distance have to be looked up by element name, not atom name

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   • Adds a new definitions file so the code can correctly detect Metal bonds. Slightly more efficient representation of standard amino acids.

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   • merging in fixes related to PTMs into bug fix branch

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   • update for 2VH3 TY2

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   • updating legacy chemical component and atom names to current naming conventions.

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   • distance have to be looked up by element name, not atom name

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