Changelog

Additions

• More functionality for structure.BondList
  • __contains__() method to test whether a bond exists
  • find_connected() identifies systems of connected atoms (aka molecules)
• Added frame wise iteration of trajectory files for saving memory
  • structure.io.TrajectoryFile.read_iter() yields coordinates, box and time for each frame
  • structure.io.TrajectoryFile.read_iter_structure() yields an structure.AtomArray for each frame
• Added ability to read entire biological assemblies from mmCIF files
  • structure.io.pdbx.list_assemblies() lists the available assemblies
  • structure.io.pdbx.get_assembly() returns the given assembly as
    structure.AtomArray or structure.AtomArrayStack
• Added the expect_looped parameter to
  structure.io.pdbx.PDBxFile.get_category
• structure.info.vdw_radius_single() provides VdW radii also for more
  uncommon elements
• Added structure.get_residue_masks(), which masks all residues to which the
  given atoms belong
• Added structure.repeat() functions to repeat atoms multiple times in the
  same model with different coordinates
• Added a bunch of new examples to the gallery

Changes

• temp_file() and temp_dir() is deprecated, use the Python standard library
  module tempfile instead
• For all File classes, read() is now a class method,
  e.g. pdbx_file = PDBxFile.read(), the old instance method is deprecated
• database.rcsb.fetch() and database.enrez.fetch() overwrite an existing
  file if it is empty

Fixes

• A newline character is appended to the end of file, when writing text files
• Fixed structure.CellList when using the periodic parameter in combination
  with the selection parameter; before unallocated memory was potentially
  accessed