Problematic residue indices

[aozalevsky]

ID: 9a0j
crosslinking restraint is assigned to a residue beyond sequence

ERROR:root:Missing residue
ERROR:root:Residue 493 out of range for <ihm.Entity(fancF)> (1-350)
ERROR:root:Missing residue
ERROR:root:Residue 493 out of range for <ihm.Entity(fancF)> (1-350)
ERROR:root:Missing residue
ERROR:root:Residue 367 out of range for <ihm.Entity(fancF)> (1-350)
ERROR:root:Missing residue
ERROR:root:Residue 362 out of range for <ihm.Entity(fancF)> (1-350)

352 353 4 F 314 LYS 5 F 493 LYS . . 'upper bound' . by-residue 29 . . . NO 
353 354 4 F 317 LYS 5 F 493 LYS . . 'upper bound' . by-residue 29 . . . NO 
354 355 4 F 345 LYS 6 F 367 LYS . . 'upper bound' . by-residue 29 . . . NO 
<...>
356 357 4 F 345 LYS 6 F 362 LYS . . 'upper bound' . by-residue 29 . . . NO 

IDs: 9a1z, 9a21, 9a22, 9a23, 9a24, 9a26, 9a27, 9a28, 9a29, 9a3u
water molecules are assigned residue indices pointing outside of the entity seq range. Other non-polymeric entities (like SODIUM ION in 9a3u) work fine.
code:

for a in system.state_groups[0][0][0][0].get_atoms():
    try:
        a.asym_unit.residue(a.seq_id)
    except IndexError as e:
        print(e)

output:

Residue 2 out of range for <ihm.Entity(water)> (1-1)
Residue 3 out of range for <ihm.Entity(water)> (1-1)
Residue 4 out of range for <ihm.Entity(water)> (1-1)
Residue 5 out of range for <ihm.Entity(water)> (1-1)

[aozalevsky]

@benmwebb The first issue is probably related to the data (how did ihm.dumper let it pass, though?), but the water issue is pure python-ihm.

[benmwebb]

python-ihm is only supposed to do range checks for polymeric entities, since seq_id is not as well defined for non-polymers and waters, but it looks like I missed a check when referencing individual residues. That's an easy fix.

Alternatively, you can disable residue range checks entirely by setting e._range_check = False for every Entity e.