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Commits on Jul 29, 2016

• Complete new CATH file names #546 and #544

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  lafita

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  josemduarte

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Commits on Jul 28, 2016

• Fixing #544 and improving logging

  josemduarte

  committed
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• Some work towards fixing #544

  josemduarte

  committed
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• Back-porting cloning fix (see #541) into bugfixes-4.2

  josemduarte

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• #542 changing default SCOP download location to Berkeley- SCOP.

  

  andreasprlic

  authored and

  josemduarte

  committed
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Commits on Jul 13, 2016

• Fixing #533

  josemduarte

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Commits on Jul 1, 2016

• #505 switching to https for all NCBI utils traffic.

  andreasprlic

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Commits on Jun 22, 2016

• Adding some more ignore fields in beans

  josemduarte

  committed
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• Mmcic parsing with tags works for all beans now

  josemduarte

  committed
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• Started converting PdbxStructOperList, not working yet

  josemduarte

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• Now using the CIFLabel annotations from cif parser

  josemduarte

  committed
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• Introduce @CIFLabel(label="str") annotation

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  sbliven

  authored and

  josemduarte

  committed
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• Fix #480. Correct spelling of _symmetry.space_group_name_H-M in CIF output

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  sbliven

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Commits on Jun 14, 2016

• Merge pull request #504 from andreasprlic/bugfixes-4.2

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  josemduarte

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• Merge pull request #507 from sbliven/pointgroups2

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  andreasprlic

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• Use all repeats to calculate hierarchical axes in internal symmetry

  lafita

  committed
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• Merge branch 'pointgroups2' of https://github.com/sbliven/biojava-sbliven.git into pointgroups2

  lafita

  committed
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• Commit local changes

  lafita

  committed
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• Fix bug with >3-level deep axes

  sbliven

  committed
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• Fix bug with >3-level deep axes

  sbliven

  committed
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Commits on Jun 13, 2016

• Storing PdbCode in BioAssemblyIdentifier cannonical representation

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  sbliven

  committed
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• Avoid renaming chains when dividing structure into repeats

  lafita

  committed
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• Do not divide internal repeats into chains to calculate QS

  lafita

  committed
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• Handle short structures in the CeSymm iteration

  lafita

  committed
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• Adapt CeSymm code to new SymmetryAxes API

  lafita

  committed
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Commits on Jun 10, 2016

• removing method that is not in biojava 4.2

  andreasprlic

  committed
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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

  committed
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• merging in fixes related to PTMs into bug fix branch

  andreasprlic

  committed
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Commits on Jun 8, 2016

• Fix bug with open symmetry axis reconstruction

  sbliven

  committed
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Commits on Jun 7, 2016

• Fix chain ID duplication bug in repeats alignment

  lafita

  committed
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• Fix symmetry axes position bug

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  sbliven

  committed
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• Add information for construction of full list of symmetry axes.

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Commits on Jun 6, 2016

• Refactor SymmetryAxis class to encapsulate individual axes

  sbliven

  committed
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Commits on Jun 3, 2016

• Simplify SymmetryAxis implementation & fix getSymmetryAxes()

  sbliven

  committed
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• Adding TestSymmetryAxes prior to refactoring

  sbliven

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