Biotite 0.26.0

Changelog

Additions

• Added interface to some programs of the ViennaRNA software package
  • application.viennarna.RNAfoldApp uses RNAfold to predict the minimum
    free energy secondary structure of an RNA sequence
  • application.viennarna.RNAplotApp uses RNAplot to calculate the
    2D coordinates for base symbols in a secondary structure plot
• Added structure.graphics.plot_nucleotide_secondary_structure() for
  visualization of an RNA secondary structure via Matplotlib
  • Internally uses RNAplot
  • Optional visualization of pseudoknots
• Increased performance of structure.find_connected()
• Increased performance of structure.partial_charges()
• Added structure.BondList.remove_bonds_to
• Added molecule-level atom selections
  • structure.get_molecule_indices(), structure.get_molecule_masks() and
    structure.molecule_iter select atoms belong to a single molecule, i.e.
    atoms that are connected via bonds
• Added interface to NetworkX package
  • Added as_graph() method to sequence.phylo.Tree and structure.BondList
    for conversion into a NetworkX Graph
  • The find_rotatable_bonds() function uses NetworkX to identify
    rotatable bonds, i.e. single bonds that are not part of a cycle,
    in structures with a structure.BondList()

Changes

• Add support for Python 3.9, remove support for Python 3.6
• Add networkx package as dependency
• structure.io.pdbx.set_structure() does not convert the residue ID -1
  to "." anymore

Fixes

• Fixed missing check for string length of chain ID, residue name
  and atom name when setting a structure in a structure.io.pdb.PDBFile
• structure.io.pdbx.set_structure() supports now atom IDs larger than
  one million
• Fixed application.dssp.DsspApp unable to work with multicharacter chain
  identifiers (#264)
• Fixed application.muscle.MuscleApp sometimes not finishing for long
  alignments (#273)
• Fixed the creation an AtomArray from atoms with optional annotations (#279)
• Fixed deletion of annotation arrays in `structure.AtomArray
• Fixed structure.BondList potentially ending in a broken state after
  indexing it with an unordered index array
• structure.partial_charges() uses bond order instead of number of bond
  partners to calculate correct charges for atoms with positive or negative
  formal charge