Commits on Jul 27, 2016
  1. @krdav @peterjc

    Unit test for the DSSP object

    Squashed commit from pull request #900.
    
    * Added pre-computed values for unit tests on the DSSP object.
    
    * Added unit test on the DSSP object.
    
    * Modified the DSSP class to accept DSSP files as input as well as PDB files.
    
    * Small comments
    
    * Casting map object as a list to allow list comparison
    
    * fixed python2.6 number of decimals error
    krdav committed with peterjc Jul 27, 2016
Commits on Jul 26, 2016
  1. @krdav @peterjc

    Wrong values for alanine ASA, ooops

    While fiddling around with the unit test i discovered this small mistake that should be corrected ASAP.
    krdav committed with peterjc Jul 25, 2016
Commits on Jul 25, 2016
  1. @peterjc
Commits on Jul 22, 2016
  1. @peterjc @peterjc

    Replacing SeqRecord .seq when have .letter_annotation

    In the special case where the new sequence is the same length,
    and there was per-letter-annotation, rather than a ValueError
    allow the sequence to be replaced and preserve the existing
    per-letter-annotation.
    
    This should resolve #880.
    peterjc committed with peterjc Jul 22, 2016
  2. @peterjc
  3. @peterjc
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  5. @peterjc

    Thank Kristian Davidsen for DSSP ASA work

    See GitHub pull request #876
    peterjc committed Jul 22, 2016
  6. @peterjc
  7. @peterjc
  8. @krdav @peterjc

    Additional ASA values in Bio.PDB.DSSP

    Adds Miller et al. 1987, and Wilke from Tien et al. 2013,
    in addition to existing Sander & Rost (1994) numbers.
    krdav committed with peterjc Jul 15, 2016
  9. @peterjc
  10. @twrightsman
Commits on Jul 21, 2016
  1. @peterjc

    Use .dev0 rather than .dev as the development version suffix.

    This avoids the "python setup.py build" warning:
    
    UserWarning: Normalizing '1.68.dev' to '1.68.dev0'
    
    See mailing list discussion where Eric Talevich suggested this.
    peterjc committed Jul 21, 2016
Commits on Jul 20, 2016
  1. @peterjc
  2. @peterjc @peterjc

    Remove SeqFeature sub_features

    Removing the code from the SeqFeature itself was the easy part.
    Updating all the tests and remaining legacy code still using it
    (preceeding commits) took a bit longer.
    peterjc committed with peterjc Jun 20, 2016
  3. @peterjc @peterjc
  4. @peterjc @peterjc
  5. @peterjc @peterjc

    Remove obsolete _insdc_feature_location_string function

    Had kept this until now for cross-validation against the
    newer CompoundLocation based GenBank/EMBL feature output.
    peterjc committed with peterjc Jun 20, 2016
  6. @peterjc @peterjc
  7. @peterjc @peterjc

    Remove .sub_features from tests

    peterjc committed with peterjc Jun 20, 2016
  8. @peterjc @peterjc
Commits on Jul 19, 2016
  1. @peterjc

    Tweak setuptools vs distutils to fix building manifest

    Previously this was failing (using setuptools):
    
    $ python setup.py sdist --manifest-only
    /Library/Python/2.7/site-packages/setuptools/dist.py:285: UserWarning: Normalizing '1.68.dev' to '1.68.dev0'
      normalized_version,
    usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: setup.py --help [cmd1 cmd2 ...]
       or: setup.py --help-commands
       or: setup.py cmd --help
    error: option --manifest-only not recognized
    
    Now works again:
    
    $ python setup.py sdist --manifest-only
    running sdist
    running check
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.py{}' found anywhere in distribution
    warning: no previously-included files matching '*.py-e' found anywhere in distribution
    writing manifest file 'MANIFEST'
    peterjc committed Jul 19, 2016
  2. @peterjc

    pep8 E265 and E302 whitespace

    peterjc committed Jul 19, 2016
  3. @peterjc
  4. @peterjc

    remove whitespace in overly long lines

    TODO: Check line wrapping just works with RST markup
    peterjc committed Jul 19, 2016
  5. @peterjc

    pep E213 and over-long lines

    peterjc committed Jul 19, 2016
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  8. @peterjc

    TravisCI: Update setuptools

    This should fix an indirect dependency installation problem
    noticed on a recent pull request:
    
    Collecting html5lib (from rdflib)
      Downloading html5lib-0.999999999.tar.gz (245kB)
        100% |████████████████████████████████| 245kB 5.3MB/s
        Complete output from command python setup.py egg_info:
        html5lib requires setuptools version 18.5 or above; please upgrade before installing (you have 12.0.5)
    peterjc committed Jul 19, 2016
Commits on Jul 18, 2016
  1. @peterjc

    Actually test parsing 4ZHL.mmtf and 1A8O.mmtf

    Just having a function named test_parser() would not work
    with how we import the unittest based classes in run_tests.py
    nor with our typical __main__ stub in test_mmtf.py
    peterjc committed Jul 18, 2016
  2. @peterjc
  3. @peterjc

    Refactor to avoid misleading test_xxx method names.

    With unittest, methods named with test_ prefix are special.
    Helper methods should be named differently to avoid any
    confusion, by convention we've used check_ as a prefix.
    peterjc committed Jul 18, 2016
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  5. @abradle @peterjc

    Added two more MMTK test files and tests reading them in

    Merge of pull request #871
    abradle committed with peterjc Jul 18, 2016