Discrepancies in entities assignment

[aozalevsky]

XL residues have an empty entity attribute, but it can be accessed as asym.entity (see example below). Is this intended behavior? It can be puzzling if the user is unfamiliar with the python-ihm.

fname = 'PDBDEV_00000016.cif'
try:
    with open(fname, 'r') as f:
        mmcif, = ihm.reader.read(f)
except UnicodeDecodeError:
    with open(fname, 'r', encoding='latin-1') as f:
        mmcif, = ihm.reader.read(f)

restraint = mmcif.restraints[0]
xl = restraint.cross_links[0]

print(xl.residue1.entity)
>>> None

print(xl.residue1.asym.entity)
>>> <ihm.Entity(Nup133)>

[benmwebb]

This is as designed, but I agree it is a little confusing. Residues can represent both

• "real" residues in a chain, in which asym points to the chain and entity is None, or
• residues in an entity (e.g. an experimentally-identified cross link), in which case asym is None and entity points to the Entity.

I'll change entity in real residues to be a synonym for asym.entity.