Changelog

Additions

• Added MMTF writing functionality
  • Added set_array() method for structure.io.mmtf.MMTFFile allows for array encoding
  • write() method for structure.io.mmtf.MMTFFile is now implemented
  • structure.io.mmtf.set_structure() is used for writing an
    structure.AtomArray or structure.AtomArrayStack instance
    to the fields of an structure.io.mmtf.MMTFFile instance
• Added structure.get_residue_starts()
  • Returns the indices of residue starts in an atom array (stack)
  • Internally used by all other residue level functions, simplifying the code base
• Added structure.BondList
  • Stores indices and bond types of bonded atoms in a corresponding atom array (stack)
  • Can be associated to an atom array (stack) using the bonds attribute
  • Indexing behaves in accordance to the atom array (stack)
  • C-accelerated operations
  • Can be loaded from and written to an MMTF file
• Added convenience function structure.io.save_structure()
• Added visualization capabilities based on matplotlib figures
  • Using Visualizer as base class
  • sequence.graphics.FeatureMap for visualization of sequence annotations
  • sequence.graphics.SequenceLogo for creation of sequence logos
  • sequence.graphics.AlignmentVisualizer for displaying alignments
    • sequence.graphics.AlignmentSimilarityVisualizer colors symbols
      based on similarities in alignment column
    • sequence.graphics.AlignmentSymbolVisualizer colors symbols
      based on a color scheme
  • Color schemes that can be loaded from JSON files
  • Biotite standard colors via colors list
• Added support of NCBI Entrez search service
  • database.entrez.Query instances that can be combined using boolean operators
  • database.entrez.Query objects a re submitted via database.entrez.search()
• Added sequence.io.genbank.MultiFile for Genbank or Genpept files with multiple contents
• Added get_order() method to application.MSAApp
• Added PEP 8 compliant __author__ attribute for each module
• Added example gallery to documentation

Changes

• Higher performance of structure.superimpose()
• Renamed structure.io.get_structure from() to structure.io.load_structure()
• sequence.Alphabet objects are hashable

Fixes

• Superimposition was not working for structure.AtomArrayStack instances
  with more models than atoms
• Input value checks were missing in structure.AdjacencyMap constructor
• box_size parameter in structure.AdjacencyMap constructor
  was restricted to integer values
• alphabet checks in application.MSAApp constructor were missing
• \\ was required at the end of Genbank files
• Index arrays did not work as second index for sequence.align.Alignment objects
• Enum types are now properly documented

Notes

Currently no wheels are provided for Python 3.5 on Windows due to issues with openssl in the install process.