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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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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

  

  Andreas Prlic

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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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Commits on Aug 12, 2013

• #31 adding a junit test

  

  Andreas Prlic

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• fixing missing bracket

  

  Andreas Prlic

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• #31 adding support for synthetic constructs via EntitySrcSyn

  

  Andreas Prlic

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

  

  Andreas Prlic

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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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