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Commits on Nov 30, 2016

addressing requested changes re. throwing exceptions.
andreasprlic
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cc56288
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moving to Java 7
andreasprlic
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4ee39f8
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now also accepting old header line
andreasprlic
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8210484
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#610 switching test to junit version 4
andreasprlic
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e1dbb04
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Commits on Nov 29, 2016

creating local dir, if it does not exist.
andreasprlic
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1ce3e1e
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fix for #610
andreasprlic
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6f28672
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Commits on Aug 18, 2016

making output less verbose
andreasprlic
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56e81e6
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setting default log level to warn
andreasprlic
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07f244a
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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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46560c7
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Commits on Jun 15, 2016

Merge branch 'master' of github.com:biojava/biojava
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andreasprlic
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ea722c2
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some formatting improvements.
andreasprlic
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80dd887
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Merge branch 'bugfixes-4.2'
sbliven
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1206ace
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Commits on Jun 14, 2016

merging in latest ptm modifications from master branch
pwrose
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8b08584
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Updating ptm list.
pwrose
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3fa10a9
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Added list of chromophores to ptm_list.xml file, updated unit tests
pwrose
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417e2da
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Commits on Jun 10, 2016

Reverting some changes to be compliant with the "old" way of doing chain IDs.
andreasprlic
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cba1ca2
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Merge pull request #502 from andreasprlic/master
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josemduarte
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3509775
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merging in updated ptm_list.xml
andreasprlic
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84c1e9c
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merging in updated ptm_list.xml
andreasprlic
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de6d033
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merging in updated ptm_list.xml
andreasprlic
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80dc3a9
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distance have to be looked up by element name, not atom name
andreasprlic
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2798876
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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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f8ac919
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merging in fixes related to PTMs into bug fix branch
andreasprlic
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849001f
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update for 2VH3 TY2
andreasprlic
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58c6743
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updating legacy chemical component and atom names to current naming conventions.
andreasprlic
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913d1ef
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distance have to be looked up by element name, not atom name
andreasprlic
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ad192d9
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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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b39840a
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Commits on Jun 5, 2016

squid:S2131 - Primitives should not be boxed just for String conversion
Mohamed Ezzat
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fa52fd8
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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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c561c3a
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Commits on May 17, 2016

Updating change log in PTM definitions file to reflect most recent changes.
andreasprlic
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f1c3f97
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Commits on May 12, 2016

Merge pull request #479 from josemduarte/asymChainIds
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andreasprlic
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aa37b02
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Commits on May 11, 2016

Fixed modfinder tests
josemduarte
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8459e6f
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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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e814b32
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Commits on May 4, 2016

Fix the compile errors - mainly by changin "setChainId" "setChainName"
abradle
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a4f8795
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Commits on Mar 10, 2016

Light cleanup:
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sbliven
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38fbae1
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