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1. Commits on Nov 30, 2016

   • addressing requested changes re. throwing exceptions.

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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 'bugfixes-4.2'

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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

   • 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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8. 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.

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9. Commits on Jun 1, 2016

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

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10. Commits on May 12, 2016

    • Merge pull request #479 from josemduarte/asymChainIds

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11. Commits on May 11, 2016

    • Fixed modfinder tests

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12. Commits on May 10, 2016

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

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13. 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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14. 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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15. Commits on Mar 8, 2016

    • Removing loadChemCompInfo, some tests don't pass yet

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16. Commits on Oct 6, 2015

    • Converting all line endings to Unix.

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      sbliven

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17. Commits on Jan 30, 2015

    • more updates of wrong resource paths

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    • updating some hard coded paths

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    • Refactoring of all package names according to #245 #242 #240

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18. Commits on Jan 29, 2015

    • Ran Optimize Imports across the whole project.

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