subcluster_radius_thresholds = set(
[ens['subcluster_radius_threshold'] for ens in ensembles_data if ens['cluster_num'] == i])
self.assertTrue(side_chain_treatments.issubset(sidechains), side_chain_treatments)
self.assertTrue(subcluster_radius_thresholds.issubset(radii), subcluster_radius_thresholds)
self.assertTrue(self.AMPLE_DICT['AMPLE_finished'])
self.assertGreater(len(self.AMPLE_DICT['mrbump_results']), 0, "No MRBUMP results")
SHELXE_CC = 15 # use lower as we can't guarantee it will succeed but should check something sensible is produced
self.assertGreater(self.AMPLE_DICT['mrbump_results'][0]['SHELXE_CC'], SHELXE_CC, "SHELXE_CC criteria not met")
# Check some random benchmarking data
self.assertTrue(os.path.isfile(os.path.join(self.AMPLE_DICT['benchmark_dir'], 'results.csv')),
"Missing benchmark results.csv")
result = self.AMPLE_DICT['benchmark_results'][0]
self.assertTrue(result['MR_program'], 'PHASER')
self.assertTrue(result['native_pdb_solvent_content'], 47.67)
TEST_DICT['coiled_coil_existing_models'] = {
'args': args_coiled_coil_existing,
'test': AMPLETest,
}
###############################################################################
#
# End Test Setup
#
###############################################################################
if __name__ == '__main__':
test_funcs.parse_args(TEST_DICT)
# Test class that holds the functions to test the RESULTS_PKL file that will be passed in
class AMPLETest(AMPLEBaseTest):
def test_from_quark_models(self):
self.assertTrue(self.AMPLE_DICT['AMPLE_finished'])
nmodels = len(glob.glob(
os.path.join(self.AMPLE_DICT['models_dir'], "*.pdb")
))
self.assertEqual(nmodels, 200, "Only {0} models produced".format(nmodels))
self.assertIn('ensembles', self.AMPLE_DICT)
nensembles = len(self.AMPLE_DICT['ensembles'])
# number was 35 - changed 19/10/17 with CCP4 7.0.44 linux
# number was 30 - changed 10/5/18 with CCP4 7.0.55 linux
ref_nensembles = 18 if self.AMPLE_DICT["use_scwrl"] else 35 # unmod ensembles without side-chains - Scwrl4 required
msg = "Incorrect number of ensembles produced: {0} vs {1}".format(nensembles, ref_nensembles)
self.assertEqual(nensembles, ref_nensembles, msg)
TEST_DICT['from_quark_models'] = {
'args': args_from_quark_models,
'test': AMPLETest,
}
###############################################################################
#
# End Test Setup
#
###############################################################################
if __name__ == '__main__':
test_funcs.parse_args(TEST_DICT)
