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PDB file lines read in as Models, throws "AttributeError: 'Model' object has no attribute 'decode'" #237
Comments
decode
method, throws "AttributeError: 'Model' object has no attribute 'decode'"
I just tried the line you quoted and it worked correctly. What PDB file are you trying to load? Possibly the problem is specific to that PDB ID. |
fixer = PDBFixer(pdbid = '3uo4')
|
That's odd. I was able to get this to run on
Could you do a complete conda environment dump ( |
Attaching the output for conda env export. |
You have very old versions of both PDBFixer and OpenMM. You can update them with
|
In pdbfixer 1.6, 1.7 and 1.8 and openmm 7.5.1 (and 7.6 running pdbfixer 1.8), The following line:
fails with the trace (using pdbfixer 1.7 and openmm 7.5.1):
The relevant line in
_load(self, input_stream)
is discussed in #81, though I don't understand where_load
is called here. On line 285, aPdbStructure
is passed toPDBFile
, but thePdbStructure
constructor isn't then called with thisPdbStructure
instance as an argument. Does the error actually happen on 284?Thank you!
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