Biotite 0.34.0

Changelog

Additions

• Support for new RCSB search API (#408)
  • Added case_sensitive parameter in database.rcsb.FieldQuery
• structure.info.mass() support deuterium
• structure.connect_via_distances() can connect atoms over periodic boundaries
• Added more chain-level utilities consistent with residue-level utilities
  • structure.apply_chain_wise()
  • structure.spread_chain_wise()
  • structure.get_chain_masks()
  • structure.get_chain_starts_for()
  • structure.get_chain_positions()
• structure.superimpose() supports also pure coordinates

Changes

• structure.hbond() uses an associated structure.BondList to find hydrogen atoms to potential hydrogen bond donors
• Lines depicting bonds in structure.graphics.plot_atoms() and structure.graphics.plot_ball_and_stick_model() use rounded tips

Fixes

• Fixed structure.io.pdbx.get_assembly missing chains in some structures (#387)
• Added a more meaningful error, if Matplotlib is required, but not installed (#302)
• Added more descriptive error, if a structure.io.pdb.PDBFile has erroneous atom IDs (#379)
• structure.io.pdb.PDBFile pads lines always to 80 characters
• Allow empty attribute string in sequence.io.GFFFile
• Fixed wrong similarity scores, if a sequence.align.SubstitutionMatrix with two different alphabets is read from string or file
• Fixed application.mafft.MafftApp runs for more than 10 sequences.