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Commits on Apr 28, 2017
  1. Thank Andrew for DSSP fix

    See preceeding commit from pull request #1194.
    peterjc committed Apr 28, 2017
  2. Fix DSSP error when MMCIF file contains non-standard residues (#1194)

    When running DSSP on the newer PDBx/mmCIF file format, the following error is observed when the structure contains non-standard residues (e.g. 1AS5.cif structure):
    
    Bio.PDB.PDBExceptions.PDBException: Structure/DSSP mismatch at <Residue HYP het= resseq=2 icode= >
    
    This is due to DSSP labelling any non-standard residues as X, whereas DSSP.py checks against a much larger dictionary of possible residue 3-letter codes (SCOPData.protein_letters_3_to_1). For example, the residue HYP gets interpreted as P, whereas DSSP returns this as X.
    
    Using the old PDB file format, these sorts of residues would be labelled as HETATOM, and hence get caught earlier in the DSSP.py code, but this isn't the case with mmCIF files.
    
    I'm proposing a simple change where anything that isn't a standard residue gets interpreted as X.
    
    I've added the relevant unit tests to test DSSP generation on mmCIF files that contain non-standard residues.
    andrewguy committed with peterjc Apr 28, 2017
Commits on Apr 27, 2017
  1. move self-test from Bio/PDB/Polypeptide.py

    Squashed commit of pull request #1190.
    
    See also issue #820.
    Gasta88 committed with peterjc Apr 27, 2017
  2. Enforce pydocstyle D404, don't start docstrings with 'This'.

    D404: First word of the docstring should not be `This`
    
    Cross reference GitHub issue #1170.
    peterjc committed Apr 27, 2017
  3. Avoid starting docstrings with 'This' (pydocstyle D404)

    Issues flagged using:
    
    $ pydocstyle Bio/ BioSQL/ Tests/ Scripts/ Doc/ --select D404 Bio BioSQL Tests/ Doc/ Scripts/
    
    I have also addressed some other docstring issues as I saw them
    while editing these docstrings.
    
    See GitHub issue #1170.
    peterjc committed Apr 27, 2017
  4. Thank Connor for BioSQL taxonomy tweak

    See preceeding commit from pull request #740.
    peterjc committed Apr 27, 2017
  5. BioSQL: NCBI Taxons without rank should be reported

    The current code for the DBSeq class removes any taxonomic name that
    has a rank of 'no rank'. This can change the returned taxonomy of the
    sequence significantly and is incorrect with what is reported at NCBI. It
    is further confusing as the taxonomic names are stored correctly in the
    database but are filtered out after their retrieval.
    
    Added in test for NCBI taxonomy retrieval for BioSQL.
    
    Squashed commit of #740
    ctSkennerton committed with peterjc Apr 27, 2017
  6. Bow has also contributed to the next release

    peterjc committed Apr 27, 2017
  7. Restriction: Bugfixes, Python 3 compatibility, PEP8/PEP257 issues, mo…

    …re tests.
    MarkusPiotrowski committed with peterjc Apr 26, 2017
Commits on Apr 26, 2017
  1. Add SearchIO test case for BLAT with protein query

    bow committed with bow Apr 26, 2017
Commits on Apr 25, 2017
  1. Deprecate Bio.PDB.Dice

    As discussed on #820, this was likely intended as an example
    script using PDBIO rather than as part of the Bio.PDB public
    API.
    
    Squashed commit of pull request #1166
    peterjc committed on GitHub Apr 25, 2017
  2. pydocstyle D413 blank line after last section

    Squashed commit of pull request #1170
    peterjc committed Apr 25, 2017
Commits on Apr 24, 2017
  1. flake8/pyflakes F821 passes now under Python 2

    It fails under Python 3 due to Bio.PDB having some
    legacy sorting code using the missing cmp function,
    see #1189.
    peterjc committed Apr 24, 2017
  2. Python 2 fix for recent DSSP work.

    Spotted via flake8/pyflakes under Python 2:
    
    $ python -m flake8 --config=/dev/null --select F821 Bio/PDB/
    Bio/PDB/DSSP.py:186:12: F821 undefined name 'FileNotFoundError'
    Bio/PDB/DSSP.py:355:20: F821 undefined name 'FileNotFoundError'
    peterjc committed Apr 24, 2017
  3. Bio.Restriction: Can't use cmp on Python 3

    peterjc committed Apr 24, 2017
  4. Fix variabel name type in exception

    Spotted via flake8 F821
    peterjc committed Apr 24, 2017
  5. Avoid lambda in Bio.MaxEntropy

    peterjc committed Apr 24, 2017
  6. Revert "TravisCI/Tox: flake8 F812 is passing on Bio/"

    This reverts commit 015182c.
    
    Not sure why it seemed to be OK locally...
    peterjc committed Apr 24, 2017
  7. Avoid import * in Bio.Cluster

    I have instead manually imported everything defined in the C module.
    
    This solves a flake8 warning, F405,
    
    $ flake8 Bio/Cluster/
    Bio/Cluster/__init__.py:265:16: F405 'treecluster' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:317:16: F405 'kcluster' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:363:16: F405 'somcluster' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:392:16: F405 'clustercentroids' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:439:16: F405 'clusterdistance' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:482:16: F405 'distancematrix' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:529:37: F405 'Tree' may be undefined, or defined from star imports: Bio.Cluster.cluster
    Bio/Cluster/__init__.py:542:36: F405 'Tree' may be undefined, or defined from star imports: Bio.Cluster.cluster
    peterjc committed Apr 24, 2017
  8. pep8 was renamed pycodestyle

    peterjc committed Apr 24, 2017
Commits on Apr 22, 2017
  1. Thank morrme; ignore case when sorting names

    peterjc committed Apr 22, 2017
  2. Fixes for pydocstyle rule D209

    morrme committed with peterjc Apr 22, 2017
  3. docstring capitalization changes per pydocstyle rule D403

    morrme committed with peterjc Apr 21, 2017
  4. Thank Max for QCPSuperimposer test updates.

    See preceeding commits from pull request #1186.
    peterjc committed Apr 22, 2017
  5. Delete test_QCPSuperimposer

    Additionally delete file Tests/output/test_QCPSuperimposer because it is no longer needed for the old printtest.
    MaxGreil committed with peterjc Apr 21, 2017
  6. Update __init__.py

    Deleted self-test. Old printtest can be found in already updated unittest-file Tests/test_QCPSuperimposer.py under function test_oldTest.
    MaxGreil committed with peterjc Apr 21, 2017
Commits on Apr 21, 2017
  1. removed D405 from ignore list

    morrme committed with peterjc Apr 21, 2017