Changelog

Additions

structure.hbond() supports periodic boundary conditions
Added structure.remove_pbc() and structure.remove_pbc_coord(), that sanitize structures that are segmented due to periodic boundaries
Write support for trajectory files
- This includes structure.io.save_structure()
Support for DCD and NetCDF trajectory formats (structure.io.dcd and structure.io.netcdf)

The coord and box attribute in structure.AtomArray and structure.AtomArrayStack are stored as float32 arrays
- File readers are changed accordingly
- Previously, both float64 and float32 were allowed, which made type conversions necessary for some functions
- If an atom array (stack) is provided with an float64 array, the type is implicitly converted.
Faster encoding and decoding in sequence.LetterAlphabet
- Internally uses bytes instead of str for symbols
- sequence.LetterAlphabet does only accept ASCII characters
Discontinued support for Python type annotations
- May be re-enabled when official type annotations for NumPy arrive
Changed protected abstract methods in structure.io.TrajectoryFile
structure.filter_solvent() regards only the res_name and ignores the hetero field

structure.io.mmtf.MMTFFile fields can be set with ndarray objects for non-encoded fields
- The ndarray objects are implicitly converted into list objects
The box attribute of structure.AtomArrayStack objects are correctly sliced when slicing the atom array stack
structure.displacement(), structure.distance(), structure.angle() and structure.dihedral() accept structure.Atom instances as parameter