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from pymol import cmd, testing, stored
@testing.requires_version('1.7.1')
class TestCIF(testing.PyMOLTestCase):
def testPYMOL1737(self):
cmd.load(self.datafile('ice_IV.cif'))
self.assertTrue('ice_IV' in cmd.get_object_list())
def testPYMOL1533(self):
cmd.load(self.datafile('1v5a-3models.cif'))
self.assertEqual(cmd.count_states(), 3)
@testing.requires_version('1.7.7')
def test_models_diff_atom_count(self):
cmd.load(self.datafile('1v5a-2models-1st-trunc.cif'), 'm1')
self.assertEqual(cmd.count_states(), 2)
self.assertEqual(cmd.count_atoms(), 387)
self.assertEqual(cmd.count_atoms('state 1'), 139)
@testing.requires_version('1.7.7')
def test_chemical_conn_bond(self):
cmd.load(self.datafile('1519159.cif'), 'm1')
model = cmd.get_model()
self.assertEqual(len(model.atom), 26)
self.assertEqual(len(model.bond), 35)
@testing.requires_version('1.7.7')
def test_CCDC(self):
cmd.load(self.datafile('CAFINE.cif'), 'm1')
self.assertEqual(cmd.count_atoms(), 25)
sym = cmd.get_symmetry('m1')
self.assertEqual(sym[6], 'P 21/a')
self.assertArrayEqual(sym[:6], [14.8, 16.7, 3.97, 90., 97., 90.], delta=1e-4)
@testing.requires_version('1.7.7')
def test_components_multiplex(self):
cmd.load(self.datafile('components-000-001-002.cif'))
for name, natoms, nbonds in [
('002', 67, 67),
('001', 87, 90),
('000', 9, 8),
]:
model = cmd.get_model(name)
self.assertEqual(len(model.atom), natoms)
self.assertEqual(len(model.bond), nbonds)
# for 000, test bond orders
self.assertEqual([b.order for b in model.bond], [1, 2, 1, 1, 1, 1, 1, 1])
@testing.requires_version('1.7.7')
def test_assembly(self):
cmd.load(self.datafile('4m4b-minimal-w-assembly.cif'))
self.assertEqual(cmd.count_states(), 1)
self.assertEqual(cmd.get_chains(), ['A', 'B'])
cmd.delete('*')
cmd.set('assembly', '1')
cmd.load(self.datafile('4m4b-minimal-w-assembly.cif'))
self.assertEqual(cmd.count_states(), 2)
self.assertEqual(cmd.get_chains(), ['B'])
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