CIF input and output

xtalforge_io::cif reads and writes CIF data blocks. read_cif(text) returns the first block as a Structure; read_cif_block(text, name) selects one; read_cif_all(text) returns every block. write_cif(structure) writes the cell, Hall symbol, operation loop and atom sites.

let structure = xtalforge::io::read_cif(&text)?;
let p1 = structure.p1()?;
let output = xtalforge::io::write_cif(&structure)?;

CifDocument::parse exposes the raw parse as CifDocument { blocks }, with CifBlock for a data block and CifLoop for its loops; the read_cif* functions are the typed shortcut.

The parser handles data blocks, tags, loops, single and double quoted values, semicolon-delimited text, comments, standard uncertainties (1.234(5)), ? and . values, atom sites, occupancy, Uiso/Uij, formal charges (including the _atom_type_oxidation_number fallback), disorder group and assembly, and symmetry operation loops (_symmetry_equiv_pos_as_xyz or _space_group_symop_operation_xyz). The operation loop is the setting when present; without one, the Hall or H-M symbol is resolved through the symmetry catalogue. Only an unknown symbol, or an operation loop whose count or operation set disagrees with the named symbol, records a symmetry_warning. The anisotropic loop is matched by _atom_site_aniso_label, so a subset of atoms is read correctly.

decode_text(bytes) strips a UTF-8 BOM, reads UTF-8 and falls back to Latin-1 byte by byte. read_text(path) is the file wrapper.

Status

The reader covers the corpus CIFs and malformed input returns a typed error. The writer emits the cell, Hall symbol, operation loop, occupancy, Uiso, Uij, disorder group/assembly, charge and the explicit-bond loop. Explicit bonds are written with the program's _xtal_bond_kind/_geom_bond_* tags and read back for P1 structures. A non-P1 row is mapped through its operation and image to P1 contacts (MIL53 matches the 36 golden contacts); an unmatched contact is not added to the graph. A non-P1 explicit set is written back as a _xtal_bond_p1_count plus _xtal_bond_atom_1/_xtal_bond_atom_2 index loop, and the reader checks the declared count against its own expansion. The fuzz target lives in crates/xtalforge-io/fuzz; inconsistency warnings beyond the unknown-symbol warning are not implemented.