inconsistent reduced representation of 5ijo

[speleo3]

The reduced model for 5ijo has numBonds=0, but len(bondOrderList)=2 and len(bondAtomList)=4.

>>> import simplemmtf
>>> d = simplemmtf.from_url('http://mmtf.rcsb.org/v1.0/reduced/5ijo')
>>> d.get('numBonds')
0
>>> d.get('bondOrderList')
array('b', [1, 1])
>>> d.get('bondAtomList')
array('i', [2959, 1342, 7253, 1812])

Expected: len(bondOrderList)=0 and len(bondAtomList)=0 or numBonds=2 (though there should really be no bonds in a CA-only model)

[pwrose]

There are two covalent CA-CA bonds specified in the 5ijo.cif file. I'll file an issue with PDB to check these bond definitions.

covale1 covale none ? C PRO 173 CA ? ? ? 1_555 D ILE 1688 CA ? ? C PRO 173 D ILE 1688 1_555 ? ? ? ? ? ? ? 1.628 ? covale32 covale none ? C SER 680 CA ? ? ? 1_555 K ASP 853 CA ? ? C SER 680 K ASP 853 1_555 ? ? ? ? ? ? ? 1.591 ?

[speleo3]

Apparently this has been fixed, closing the case.

>>> import simplemmtf
>>> d = simplemmtf.from_url('http://mmtf.rcsb.org/v1.0/reduced/5ijo')
>>> d.get('numBonds')
0
>>> 
>>> d.get('bondOrderList')
array('b')
>>> 
>>> d.get('bondAtomList')
array('i')