Custom CCDs and CIF round trips

Register your ligand before writing. Here ligand is one complete LG1 residue with correct atom names, elements, charges, bonds, and a nonempty chain ID; atoms is the structure containing it (or just ligand).

from atomworks.io import parse
from atomworks.io.config import ParseConfig
from atomworks.io.utils.ccd import custom_ccd_residues
from atomworks.io.utils.io_utils import to_cif_file

with custom_ccd_residues({"LG1": ligand}):
    to_cif_file(atoms, "structure.cif")

config = ParseConfig.from_preset(
    "minimal", build_assembly=None, cif_ccd_on_mismatch="ignore",
    return_atom_array_plus=True,
)
restored = parse("structure.cif", config=config)["asym_unit"][0]

register_custom_ccd_entry("LG1", ligand) also works, but persists globally. The writer generates all three chem_comp* tables. Missing chem_comp_type is inferred from atom names; override it if the heuristic is wrong. An existing annotation is used directly as chem_comp.type.

"minimal" avoids atom rebuilding/filtering; "ignore" permits intentional CCD-code collisions. The file is self-contained; no registration is needed to read it. return_atom_array_plus=True retains its definitions for rewriting. Coordinates are rounded to 0.001 Å; this is not exact object serialization.