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1. Commits on Aug 14, 2013

   • #31 now tracking expression system for proteins that were not isolated directly from a natural tissue

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

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

     

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   • adding some null value tests

     

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2. Commits on Aug 13, 2013

   • Merge pull request #46 from ulyssecarion/chemcomp-atoms

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   • Have ChemCompConsumer respond to newChemCompAtom

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   • Add ChemCompAtoms to ChemComp

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   • Merge pull request #45 from ulyssecarion/heavy-water

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   • Consider Deuterium and Tritium not to be heavy elements by Element#isHeavyAtom

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

     

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   • Merge pull request #39 from ulyssecarion/bond-efficiency

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   • Merge pull request #44 from karlnicholas/master

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   • Added GenbankCookbookTest test case.

     

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3. Commits on Aug 12, 2013

   • #31 adding a junit test

     

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   • fixing missing bracket

     

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   • #31 adding support for synthetic constructs via EntitySrcSyn

     

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   • #31 starting to work on parsing organism and expression system

     

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   • #31 starting to work on parsing organism and expression system

     

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   • Add human-friendly toStrings for SSBond and LinkRecord

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   • Do not fail "silently" on error while PDB parsing

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   • Make more precise error reporting on bond-formation errors

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   • Skip sequence residues that aren't amino acids or are missing atoms for intra-residue bonds

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   • Bugfix: off-by-one error in the SSBOND handler

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   • Bugfix: getAltLocGroup might need to return 'this'

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   • Add tests for IDs that make formBonds crash

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   • Merge branch 'bond-efficiency' of https://github.com/ulyssecarion/biojava into ulyssecarion-bond-efficiency

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   • Merge branch 'master' of https://github.com/karlnicholas/biojava into karl

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

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   • Trim to size all bond arraylists after creating the bonds

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   • By default, keep the bond arraylist as small as possible

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   • Loop through all non-water groups for intra-residue bonds, not just sequence residues

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   • Add a test making sure ligands get bonds too

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   • Use the new bond constructor in PDBFileReader

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   • For LINK records, work strictly with atoms that aren't alt locs

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   • By default, Bonds will now add themselves to their Atoms' bond lists.

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