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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

  andreasprlic

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

  

  Andreas Prlic

  committed
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Commits on Aug 13, 2013

• Have ChemCompConsumer respond to newChemCompAtom

  ucarion

  committed
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• Add ChemCompAtoms to ChemComp

  ucarion

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

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  andreasprlic

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

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  ucarion

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

  

  Andreas Prlic

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

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  andreasprlic

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Commits on Aug 12, 2013

• #31 adding a junit test

  

  Andreas Prlic

  committed
  e4f7d65

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• fixing missing bracket

  

  Andreas Prlic

  committed
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• #31 adding support for synthetic constructs via EntitySrcSyn

  

  Andreas Prlic

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

  

  Andreas Prlic

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

  

  Andreas Prlic

  committed
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• Add human-friendly toStrings for SSBond and LinkRecord

  ucarion

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

  ucarion

  committed
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• Make more precise error reporting on bond-formation errors

  ucarion

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

  ucarion

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

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  ucarion

  committed
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• Bugfix: getAltLocGroup might need to return 'this'

  ucarion

  committed
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• Trim to size all bond arraylists after creating the bonds

  ucarion

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

  ucarion

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

  ucarion

  committed
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• Use the new bond constructor in PDBFileReader

  ucarion

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

  ucarion

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

  ucarion

  committed
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• Remove BondType from Bond

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  ucarion

  committed
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Commits on Aug 11, 2013

• Merge remote-tracking branch 'updates/master'

  

  Karl Nicholas

  authored and

  Karl Nicholas

  committed
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• More work on Genbank files, bringing them inline with interfaces.

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  Karl Nicholas

  authored and

  Karl Nicholas

  committed
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Commits on Aug 9, 2013

• Missed Andreas's recent changes.

  dmyersturnbull

  committed
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• Ran more conservative cleanup on AtomCache.

  dmyersturnbull

  committed
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• Ran cleanup on AtomCache; this time didn't sort members.

  dmyersturnbull

  committed
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Commits on Aug 8, 2013

• Merge pull request #37 from ulyssecarion/peptide-bond-007

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  andreasprlic

  committed
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• Only form bonds if params has createAtomBonds set to true

  ucarion

  committed
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• Add a createAtomBonds flag to FileParsingParameters

  ucarion

  committed
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• Add bond-parsing to PDBFileParser

  ucarion

  committed
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