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Merge pull request #147 from rigdenlab/gemmi_fix
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Fixes to code/tests broken by changes to gemmi
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@hlasimpk
hlasimpk authored Dec 12, 2024
2 parents 9aa7836 + 9ac5d34 commit e791d8c
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Showing 4 changed files with 24 additions and 24 deletions.
2 changes: 1 addition & 1 deletion simbad/parsers/tests/test_phaser_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def test_phaser_parser_1(self):

self.assertEqual(pp.llg, 1419)
self.assertEqual(pp.tfz, 28.9)
self.assertEqual(pp.rfz, None)
self.assertEqual(pp.rfz, 0)


if __name__ == "__main__":
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4 changes: 2 additions & 2 deletions simbad/util/pdb_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,14 +131,14 @@ def keep_first_chain_only(self):
self.select_chain_by_idx(0)

def keep_first_model_only(self):
models = [m.name for m in self.structure]
models = [m.num for m in self.structure]
for model in models[1:]:
del self.structure[model]

def remove_empty_models(self):
for model in self.structure:
if len(model.subchains()) == 0:
del self.structure[model.name]
del self.structure[model.num]

def select_chain_by_idx(self, chain_idx):
self.keep_first_model_only()
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40 changes: 20 additions & 20 deletions simbad/util/tests/test_pdb_util.py
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Expand Up @@ -213,16 +213,16 @@ def test_standardise_1(self):
os.unlink("tmp.pdb")

reference_data = [
"CRYST1 64.820 78.560 39.050 90.00 90.00 90.00 P 21 21 21 0 \n",
"ATOM 1 N ASP A 1 45.025 12.898 8.789 1.00 20.71 N \n",
"ATOM 2 CA ASP A 1 45.101 12.554 7.385 1.00 21.13 C \n",
"ATOM 3 C ASP A 1 46.569 12.441 6.994 1.00 18.35 C \n",
"ATOM 4 O ASP A 1 47.443 13.016 7.624 1.00 23.34 O \n",
"ATOM 5 CB ASP A 1 44.385 13.622 6.515 1.00 27.06 C \n",
"ATOM 6 CG ASP A 1 42.911 13.800 6.841 1.00 40.10 C \n",
"ATOM 7 OD1 ASP A 1 42.374 12.978 7.610 1.00 48.03 O \n",
"ATOM 8 OD2 ASP A 1 42.292 14.768 6.325 1.00 52.96 O \n",
"ATOM 9 N VAL A 2 46.810 11.649 5.958 1.00 20.56 N \n",
'CRYST1 64.820 78.560 39.050 90.00 90.00 90.00 P 21 21 21 8 \n',
'MTRIX1 1 0.972240 0.229670 0.044780 -33.28425 1 \n',
'MTRIX2 1 -0.042920 0.363160 -0.930740 21.22728 1 \n',
'MTRIX3 1 -0.230030 0.902980 0.362930 18.74696 1 \n',
'ATOM 1 N ASP A 1 44.945 12.883 8.824 1.00 19.69 N \n',
'ATOM 2 CA ASP A 1 45.082 12.376 7.484 1.00 22.49 C \n',
'ATOM 3 C ASP A 1 46.551 12.322 7.040 1.00 20.41 C \n',
'ATOM 4 O ASP A 1 47.413 12.994 7.593 1.00 22.53 O \n',
'ATOM 5 CB ASP A 1 44.383 13.428 6.514 1.00 34.50 C \n',
'ATOM 6 CG ASP A 1 42.999 13.726 7.124 1.00 45.87 C \n'
]

self.assertEqual(data, reference_data)
Expand All @@ -249,16 +249,16 @@ def test_standardise_2(self):
os.unlink("tmp.pdb")

reference_data = [
"CRYST1 64.200 77.800 38.280 90.00 90.00 90.00 P 21 21 21 0 \n",
"ATOM 1 N ASP A 1 44.435 13.209 8.556 1.00 13.65 N \n",
"ATOM 2 CA ASP A 1 44.447 13.005 7.125 1.00 14.15 C \n",
"ATOM 3 C ASP A 1 45.889 12.781 6.697 1.00 13.17 C \n",
"ATOM 4 O ASP A 1 46.791 13.376 7.261 1.00 15.94 O \n",
"ATOM 5 CB ASP A 1 43.901 14.237 6.415 1.00 19.04 C \n",
"ATOM 6 CG ASP A 1 42.489 14.626 6.758 1.00 23.36 C \n",
"ATOM 7 OD1 ASP A 1 41.913 14.024 7.665 1.00 25.96 O \n",
"ATOM 8 OD2 ASP A 1 41.957 15.540 6.115 1.00 33.92 O \n",
"ATOM 9 N VAL A 2 46.062 11.964 5.669 1.00 14.26 N \n",
'CRYST1 64.200 77.800 38.280 90.00 90.00 90.00 P 21 21 21 8 \n',
'ATOM 1 N ASP A 1 44.437 13.199 8.551 1.00 14.05 N \n',
'ATOM 2 CA ASP A 1 44.452 12.952 7.124 1.00 14.52 C \n',
'ATOM 3 C ASP A 1 45.912 12.766 6.723 1.00 12.79 C \n',
'ATOM 4 O ASP A 1 46.786 13.402 7.273 1.00 17.99 O \n',
'ATOM 5 CB ASP A 1 43.905 14.169 6.325 1.00 22.32 C \n',
'ATOM 6 CG ASP A 1 42.555 14.639 6.688 1.00 28.30 C \n',
'ATOM 7 OD1 ASP A 1 42.038 15.680 6.186 1.00 42.93 O \n',
'ATOM 8 OD2 ASP A 1 41.915 14.081 7.579 1.00 26.74 O \n',
'ATOM 9 N VAL A 2 46.081 11.961 5.697 1.00 14.42 N \n'
]

self.assertEqual(data, reference_data)
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2 changes: 1 addition & 1 deletion simbad/version.py
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Expand Up @@ -2,7 +2,7 @@

# Maintain sematantic versioning. Further information can
# be found here [http://semver.org/]
__version_info__ = (0, 2, 8, 1)
__version_info__ = (0, 2, 8, 3)

# ======================================================
# Do __NOT__ change anything below here
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