test_mr_alphafold.py
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| Last edited time |
wrote to Adam 26/04/2023 and 07/06/2023
test_mr_alphafold.py::test_calculate_quality_scores FAILED [100%]
==================================================================================== FAILURES =====================================================================================
__________________________________________________________________________ test_calculate_quality_scores __________________________________________________________________________
get_2uvo_alphafold_test_hits = OrderedDict([('Q0JF21_1', <mrparse.mr_hit.SequenceHit object at 0x117afea50>), ('Q7Y1Z1_2', <mrparse.mr_hit.SequenceHi...<mrparse.mr_hit.SequenceHit object at 0x117b04090>), ('B6TT00_2', <mrparse.mr_hit.SequenceHit object at 0x117b04150>)])
def test_calculate_quality_scores(get_2uvo_alphafold_test_hits):
"""Test the quality scoring methods"""
hits = get_2uvo_alphafold_test_hits
hit = hits['Q0JF21_1']
database_version = get_afdb_version()
pdb_name = f"AF-{hit.pdb_id}-F1-model_{database_version}.pdb"
pdb_struct = PdbStructure()
pdb_string = download_model(pdb_name)
pdb_struct.structure = gemmi.read_pdb_string(pdb_string)
seqid_range = range(hit.hit_start, hit.hit_stop + 1)
> pdb_struct.select_residues(to_keep_idx=seqid_range)
test_mr_alphafold.py:37:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <simbad.util.pdb_util.PdbStructure object at 0x117af9bd0>, delete = None, to_keep = None, delete_idx = None, to_keep_idx = range(30, 198)
def select_residues(self, delete=None, to_keep=None, delete_idx=None, to_keep_idx=None):
self.keep_first_model_only()
self.keep_first_chain_only()
to_remove = []
> chain = self.structure[0][0]
E IndexError
../../../Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/simbad/util/pdb_util.py:160: IndexError