Changelog

Additions

Support stack-wise iteration over trajectory files (#420)
Support Path objects in File.read()
Improved filters for different types of residues in structure subpackage (#425)
- filter_amino_acids() now also filters for non-canonical amino acids
- filter_nucleotides() uses an updated list of nucleotides
- New filter_carbohydrates() filters for saccharides
- filter_canonical_amino_acids() and filter_canonical_nucleotides() filter the respective canonical residues
- New structure.info.carbohydrate_names() and structure.info.amino_acid_names() give a list of residue names considered as carbohydrates and amino acids, respectively
application.LocalApp now supports input to STDIN
Improved ViennaRNA interfaces (#435)
- Added application.viennarna.RNAalifoldApp interface to RNAalifold
- Secondary structure constraints can be given to application.viennarna.RNAfoldApp and application.viennarna.RNAalifoldApp

The residues that are recognized by structure.filter_amino_acids() have changed (see above)
Deprecated application.viennarna.RNAfoldApp.get_mfe() and replaced it by application.viennarna.RNAfoldApp.get_free_energy()

Support PDB format dialect with inverted charge column (X+ instead of +X)
in structure.io.PDBFile(#421)
Fixed erroneous atom parsing in strutcure.io.mmtf.MMTFFile, if an MMTF file
has multiple different groupType entries for the same residue name and the same number of atoms (#426)
Fixed angle condition in structure.base_stacking() (#432)
Fixed TypeError in database.muscle.Muscle5App
Fixed bond_line_style parameter in structure.graphics.plot_secondary_structure()
Fixed error in pseudoknots() and base_pairs_from_dot_bracket() in cases the secondary structure had no base pairs
Update identification of error messages from server in database.entrez.fetch()