Changelog

Additions

• Support for unit cells and simulation boxes
  • Added box attribute for structure.AtomArray and structure.AtomArrayStack that represents the three box vectors
  • The box attribute is automatically read from and written into all supported structure file formats
  • Added methods for handling boxes in structure package
    • vectors_from_unitcell() and unitcell_from_vectors() faciliate the conversion between box vectors and lengths/angles
    • coord_to_fraction() and fraction_to_coord allow expressing coordinates as fraction of box vectors
    • repeat_box() and repeat_box_coord() create periodic copies of coordinates or an atom array (stack).
    • box_volume() calculates the volume of a box
    • is_orthogonal() is used to check whether a box is orthogonal
    • check_in_box() checks whether atoms of a structure are outside the box
  • Added structure.index_xxx() versions of functions for geometric measurements (e.g. structure.index_distance())
    • The functions take an atom array (stack) and referring indices, similar to MDTraj.
    • Optionally use a minimum-image convention based on the box attribute
    • displacement() and index_displacement() are used for calculation of displacement vectors
  • structure.CellList optionally uses minimum-image convention for distance calculation based on the box attribute
• Added structure.io.pdb.get_structure() and structure.io.pdb.set_structure() as thin wrappers around the corresponding methods of structure.io.pdb.PDBFile

Changes

• structure.io.mmtf.MMTFFile and structure.io.pdbx.PDBxFile implement MutableMapping, offering a wider range of dictionary-like methods
• Cython language level is set to 3

Fixes

• A single model can now be read from a structure.io.pdb.PDBFile, if the models in the file have a different amount of atoms
• Clarified in the documentation that Biotite uses Å as base unit