Biotite 0.35.0

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

Changes

• 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()

Fixes

• 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()