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()

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

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