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JavaMuller
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biojava
biojava-structure
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biojava-ffx
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Commits on Aug 14, 2015
Merging from master to biojava-ffx integration branch.
jacob-litman
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Commits on Aug 4, 2015
Updated POMs in preparation for hosting as separate Maven repository; a few comments and log messages also got slightly refactored. Everything seems ready for public Biojava-FFX integration (with t…
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Jacob Litman
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Merge remote-tracking branch 'upstream/master'
josemduarte
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Merge pull request #311 from lafita/cesymm
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andreasprlic
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Fix StructureToolsTest to pass according to changes
lafita
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Allow non-refined result, only self-alignment
lafita
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Fix demo issues
lafita
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Commits on Aug 3, 2015
Make getRepresentative Atoms consistent
lafita
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Fixing issue in getAlignedResIndex, now the mapping will work for
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josemduarte
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Add Demo for CeSymm
lafita
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Port CeSymm for internal symmetry detection code to BioJava
lafita
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Commits on Jul 31, 2015
fix for #306 - now checks provided URL if it contains the string ".cif" and switches to mmCif parsing accordingly.
andreasprlic
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Minor fix
josemduarte
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Commits on Jul 29, 2015
Extended the interface-implementation paradigm to Bonds and SSBonds. Renamed chain.getParent() and chain.setParent() to chain.getStructure() and chain.setStructure() to deconflict with other APIs. …
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Jacob Litman
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Commits on Jul 28, 2015
Some cosmetics
josemduarte
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Commits on Jul 27, 2015
Merge pull request #304 from sbliven/master
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Adding some more non-deposited files tests, #305.
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Reverting parser change: removing pure non-poly chains is a bad idea.
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More parsing fixes, #305
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Commits on Jul 24, 2015
Merge remote-tracking branch 'upstream/master'
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Better parsing of COMPND lines in PDB files, #305
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Fixing tests: order of AbstractScoresCache.getScores wasn't guaranteed
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Fix bug with flexible MultipleAlignments
lafita
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Commits on Jul 23, 2015
Rename and move Tests for consistency
lafita
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Merge branch 'master' of https://github.com/biojava/biojava.git
lafita
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Remove the 3D transformations in MultipleAlignment
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lafita
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Updating SCOPe to version 2.05
sbliven
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Factor out Subunits definition in quaternary symmetry
lafita
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Adding sortBlocks method
sbliven
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Commits on Jul 22, 2015
Calc.transform() documentation and testing
lafita
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Commits on Jul 20, 2015
Unify Vecmath to JAMA conversion methods in Calc
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lafita
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Fix bug in jama to vecmath conversion
lafita
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Core length used as the the min block length
lafita
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Commits on Jul 17, 2015
New parameter to control the threads used for Multiple Alignments
lafita
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Commits on Jul 16, 2015
Fix bug in MultipleAlignmentEnsemble, now Atoms are not cloned
lafita
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Jacob Litman