Commits

Commit history

1. Commits on Nov 30, 2016

   • addressing requested changes re. throwing exceptions.

     andreasprlic

     committed
     cc56288View commit details

     Copy full SHA for cc56288

     View code at this pointBrowse repository at this point

   • moving to Java 7

     andreasprlic

     committed
     4ee39f8View commit details

     Copy full SHA for 4ee39f8

     View code at this pointBrowse repository at this point

   • now also accepting old header line

     andreasprlic

     committed
     8210484View commit details

     Copy full SHA for 8210484

     View code at this pointBrowse repository at this point

   • #610 switching test to junit version 4

     andreasprlic

     committed
     e1dbb04View commit details

     Copy full SHA for e1dbb04

     View code at this pointBrowse repository at this point
2. Commits on Nov 29, 2016

   • creating local dir, if it does not exist.

     andreasprlic

     committed
     1ce3e1eView commit details

     Copy full SHA for 1ce3e1e

     View code at this pointBrowse repository at this point

   • fix for #610

     andreasprlic

     committed
     6f28672View commit details

     Copy full SHA for 6f28672

     View code at this pointBrowse repository at this point
3. Commits on Aug 18, 2016

   • making output less verbose

     andreasprlic

     committed
     56e81e6View commit details

     Copy full SHA for 56e81e6

     View code at this pointBrowse repository at this point

   • setting default log level to warn

     andreasprlic

     committed
     07f244aView commit details

     Copy full SHA for 07f244a

     View code at this pointBrowse repository at this point
4. Commits on Aug 8, 2016

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

     andreasprlic

     committed
     46560c7View commit details

     Copy full SHA for 46560c7

     View code at this pointBrowse repository at this point
5. Commits on Jun 15, 2016

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

     Show description for ea722c2
     andreasprlic

     committed
     ea722c2View commit details

     Copy full SHA for ea722c2

     View code at this pointBrowse repository at this point

   • some formatting improvements.

     andreasprlic

     committed
     80dd887View commit details

     Copy full SHA for 80dd887

     View code at this pointBrowse repository at this point

   • Merge branch 'bugfixes-4.2'

     sbliven

     committed
     1206aceView commit details

     Copy full SHA for 1206ace

     View code at this pointBrowse repository at this point
6. Commits on Jun 14, 2016

   • merging in latest ptm modifications from master branch

     pwrose

     committed
     8b08584View commit details

     Copy full SHA for 8b08584

     View code at this pointBrowse repository at this point

   • Updating ptm list.

     pwrose

     committed
     3fa10a9View commit details

     Copy full SHA for 3fa10a9

     View code at this pointBrowse repository at this point

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

     pwrose

     committed
     417e2daView commit details

     Copy full SHA for 417e2da

     View code at this pointBrowse repository at this point
7. Commits on Jun 10, 2016

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

     andreasprlic

     committed
     cba1ca2View commit details

     Copy full SHA for cba1ca2

     View code at this pointBrowse repository at this point

   • Merge pull request #502 from andreasprlic/master

     Show description for 3509775
     josemduarte

     authored
     3509775View commit details

     Copy full SHA for 3509775

     View code at this pointBrowse repository at this point

   • merging in updated ptm_list.xml

     andreasprlic

     committed
     84c1e9cView commit details

     Copy full SHA for 84c1e9c

     View code at this pointBrowse repository at this point

   • merging in updated ptm_list.xml

     andreasprlic

     committed
     de6d033View commit details

     Copy full SHA for de6d033

     View code at this pointBrowse repository at this point

   • merging in updated ptm_list.xml

     andreasprlic

     committed
     80dc3a9View commit details

     Copy full SHA for 80dc3a9

     View code at this pointBrowse repository at this point

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

     andreasprlic

     committed
     2798876View commit details

     Copy full SHA for 2798876

     View code at this pointBrowse repository at this point

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

     andreasprlic

     committed
     f8ac919View commit details

     Copy full SHA for f8ac919

     View code at this pointBrowse repository at this point

   • merging in fixes related to PTMs into bug fix branch

     andreasprlic

     committed
     849001fView commit details

     Copy full SHA for 849001f

     View code at this pointBrowse repository at this point

   • update for 2VH3 TY2

     andreasprlic

     committed
     58c6743View commit details

     Copy full SHA for 58c6743

     View code at this pointBrowse repository at this point

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

     andreasprlic

     committed
     913d1efView commit details

     Copy full SHA for 913d1ef

     View code at this pointBrowse repository at this point

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

     andreasprlic

     committed
     ad192d9View commit details

     Copy full SHA for ad192d9

     View code at this pointBrowse repository at this point
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.

     andreasprlic

     committed
     b39840aView commit details

     Copy full SHA for b39840a

     View code at this pointBrowse repository at this point
9. Commits on Jun 5, 2016

   • squid:S2131 - Primitives should not be boxed just for String conversion

     

     Mohamed Ezzat

     committed
     fa52fd8View commit details

     Copy full SHA for fa52fd8

     View code at this pointBrowse repository at this point
10. Commits on Jun 1, 2016

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

      andreasprlic

      committed
      c561c3aView commit details

      Copy full SHA for c561c3a

      View code at this pointBrowse repository at this point
11. Commits on May 17, 2016

    • Updating change log in PTM definitions file to reflect most recent changes.

      andreasprlic

      committed
      f1c3f97View commit details

      Copy full SHA for f1c3f97

      View code at this pointBrowse repository at this point
12. Commits on May 12, 2016

    • Merge pull request #479 from josemduarte/asymChainIds

      Show description for aa37b02
      andreasprlic

      committed
      aa37b02View commit details

      Copy full SHA for aa37b02

      View code at this pointBrowse repository at this point
13. Commits on May 11, 2016

    • Fixed modfinder tests

      josemduarte

      committed
      8459e6fView commit details

      Copy full SHA for 8459e6f

      View code at this pointBrowse repository at this point
14. Commits on May 10, 2016

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

      pwrose

      committed
      e814b32View commit details

      Copy full SHA for e814b32

      View code at this pointBrowse repository at this point
15. Commits on May 4, 2016

    • Fix the compile errors - mainly by changin "setChainId" "setChainName"

      abradle

      committed
      a4f8795View commit details

      Copy full SHA for a4f8795

      View code at this pointBrowse repository at this point
16. Commits on Mar 10, 2016

    • Light cleanup:

      Show description for 38fbae1
      sbliven

      committed
      38fbae1View commit details

      Copy full SHA for 38fbae1

      View code at this pointBrowse repository at this point