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1. Commits on Mar 15, 2018

   • Converting junit3 to 4, thanks intellij

     josemduarte

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2. Commits on Mar 14, 2018

   • Add license to all files

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     sbliven

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3. Commits on Sep 8, 2017

   • Fixing phosphosite urls and changing default url timeout to 30s

     josemduarte

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4. Commits on Apr 26, 2017

   • Changing all line ending to unix (to match .gitattributes)

     sbliven

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5. Commits on Nov 30, 2016

   • addressing requested changes re. throwing exceptions.

     andreasprlic

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   • #610 switching test to junit version 4

     andreasprlic

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6. Commits on Nov 29, 2016

   • creating local dir, if it does not exist.

     andreasprlic

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   • fix for #610

     andreasprlic

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7. Commits on Aug 18, 2016

   • making output less verbose

     andreasprlic

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   • setting default log level to warn

     andreasprlic

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8. Commits on Aug 8, 2016

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

     andreasprlic

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9. Commits on Jun 15, 2016

   • Merge branch 'bugfixes-4.2'

     sbliven

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10. Commits on Jun 14, 2016

    • merging in latest ptm modifications from master branch

      pwrose

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    • Updating ptm list.

      pwrose

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

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11. Commits on Jun 10, 2016

    • merging in updated ptm_list.xml

      andreasprlic

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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

      andreasprlic

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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.

      andreasprlic

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    • merging in fixes related to PTMs into bug fix branch

      andreasprlic

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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

      andreasprlic

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12. Commits on Jun 9, 2016

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

      andreasprlic

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13. Commits on Jun 1, 2016

    • Allowing detection of PTMs that interact with Terbium, as reported by @epeisach . Also less verbose PTM junit test.

      andreasprlic

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14. Commits on May 12, 2016

    • Merge pull request #479 from josemduarte/asymChainIds

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      andreasprlic

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15. Commits on May 11, 2016

    • Fixed modfinder tests

      josemduarte

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16. Commits on May 10, 2016

    • Added definition for PLP (pyridoxin-5'-phosphate) protein modification to xml file and added unit test.

      pwrose

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17. Commits on Mar 10, 2016

    • Light cleanup:

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      sbliven

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    • Running spacestotabs on recent changes

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      sbliven

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18. Commits on Mar 9, 2016

    • Merge branch 'master' into removeLoadChemCompInfo

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      josemduarte

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    • Converting initial spaces to tabs.

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      sbliven

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    • Remove trailing whitespace globally from .java files

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      sbliven

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19. Commits on Mar 8, 2016

    • Removing loadChemCompInfo, some tests don't pass yet

      josemduarte

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20. Commits on Oct 6, 2015

    • Converting all line endings to Unix.

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      sbliven

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