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base repository: biopython/biopython
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head repository: BiPUJ/biopython
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  • 11 commits
  • 3 files changed
  • 1 contributor

Commits on Sep 26, 2016

  1. Merge remote-tracking branch 'refs/remotes/biopython/master'

    @dadoskawina
    dadoskawina committed Sep 26, 2016
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  2. Update Bio.PDB.PDBList module 

    1. Possibility to download structures in PDBx/mmCif, PDB, PDBML/XML and
mmtf formats
2. Possibility to download large structures in PDB-like formatted
bundles
3. New function: download specified set of structures
4. Code python 3.x comatible
5. Unit tests added.

Note. The default download format changed from (deprecated) PDB to
(recommended by RCSB) PDBx/mmCIf.
    @dadoskawina
    dadoskawina committed Sep 26, 2016
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  3. Merge pull request #1 from BiPUJ/Bio.PDBList 

    Update Bio.PDB.PDBList module
    @dadoskawina
    dadoskawina authored Sep 26, 2016
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Commits on Oct 7, 2016

  1. Corrected according to comments. 

    Rewritten retrieve_pdb_file tests to be more explicit.
    @dadoskawina
    dadoskawina committed Oct 7, 2016
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  2. Prevent form creating "obsolete" folder during tests. One new test.

    @dadoskawina
    dadoskawina committed Oct 7, 2016
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  3. Corrections according to review.

    @dadoskawina
    dadoskawina committed Oct 7, 2016
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  4. Corrected the issue with downloading the same structure twice into di… 

    …fferent directories.

Due to the urlretrieve implementation in python 2.7, two consecutive calls for the same structure to be downloaded into different directories failed. This fix correct it.
    @dadoskawina
    dadoskawina committed Oct 7, 2016
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Commits on Feb 1, 2017

  1. Correct unicode issues 

    The error occured while trying to download all entries or all obsolete
entries in python 3.x
    @dadoskawina
    dadoskawina committed Feb 1, 2017
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  2. Fix issue with parameters while running from command line 

    The file_format parameter was missing in some functions.
    @dadoskawina
    dadoskawina committed Feb 1, 2017
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Commits on Feb 28, 2017

  1. Corrections according to comments 

    1. change `dir` variable to `directory`
2. add "deprecation warning"
    @dadoskawina
    dadoskawina committed Feb 28, 2017
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Commits on Mar 1, 2017

  1. Correction according to PEP8/PEP257 standard

    @dadoskawina
    dadoskawina committed Mar 1, 2017
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