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import utils
import os
import unittest
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.startmodel
class Tests(unittest.TestCase):
def test_template(self):
"""Test Template class"""
class MockObject:
pass
dataset = MockObject()
p = ihm.startmodel.Template(
dataset=dataset, asym_id='G', seq_id_range=(1, 90),
template_seq_id_range=(30, 90), sequence_identity=42.)
self.assertEqual(p.asym_id, 'G')
def test_pdb_helix(self):
"""Test PDBHelix class"""
p = ihm.startmodel.PDBHelix(
"HELIX 10 10 ASP A 607 GLU A 624 1"
" 18 ")
self.assertEqual(p.helix_id, '10')
self.assertEqual(p.start_asym, 'A')
self.assertEqual(p.start_resnum, 607)
self.assertEqual(p.end_asym, 'A')
self.assertEqual(p.end_resnum, 624)
self.assertEqual(p.helix_class, 1)
self.assertEqual(p.length, 18)
def test_starting_model(self):
"""Test StartingModel class, no templates"""
e1 = ihm.Entity('AAAA')
asym = ihm.AsymUnit(e1)
s = ihm.startmodel.StartingModel(asym, 'mock_dataset', 'A', offset=10)
self.assertEqual(s.get_atoms(), [])
self.assertEqual(s.get_seq_dif(), [])
def test_seq_dif(self):
"""Test SeqDif class"""
sd = ihm.startmodel.SeqDif(db_seq_id=10, seq_id=20, db_comp_id='PHE')
self.assertEqual(sd.db_seq_id, 10)
def test_mse_seq_dif(self):
"""Test MSESeqDif class"""
sd = ihm.startmodel.MSESeqDif(db_seq_id=10, seq_id=20)
self.assertEqual(sd.db_comp_id, 'MSE')
self.assertEqual(sd.details,
'Conversion of modified residue MSE to MET')
def test_add_atom(self):
"""Test StartingModel.add_atom()"""
atoms = ['atom1', 'atom2']
e1 = ihm.Entity('AAAA')
asym = ihm.AsymUnit(e1)
s = ihm.startmodel.StartingModel(asym, 'mock_dataset', 'A', offset=10)
s.add_atom(atoms[0])
s.add_atom(atoms[1])
self.assertEqual(s._atoms, atoms)
def test_add_seq_dif(self):
"""Test StartingModel.add_seq_dif()"""
seq_difs = ['sd1', 'sd2']
e1 = ihm.Entity('AAAA')
asym = ihm.AsymUnit(e1)
s = ihm.startmodel.StartingModel(asym, 'mock_dataset', 'A', offset=10)
s.add_seq_dif(seq_difs[0])
s.add_seq_dif(seq_difs[1])
self.assertEqual(s._seq_difs, seq_difs)
if __name__ == '__main__':
unittest.main()
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