def load_topology(self, pdb_id):
pdb_file = os.path.abspath(
os.path.join(currpath, '../files/{0}.pdb'.format(pdb_id)))
mol_file = os.path.abspath(
os.path.join(currpath, '../files/{0}.mol2'.format(pdb_id)))
top = System(pdb_file, mol2file=mol_file).topology
top.distances()
return top
class DistanceMatrixTests(UnittestPythonCompatibility):
currpath = os.path.dirname(__file__)
pdb_file = os.path.abspath(os.path.join(currpath, '../files/1acj.pdb'))
mol_file = os.path.abspath(os.path.join(currpath, '../files/1acj.mol2'))
def setUp(self):
"""
Prepare TopologyDataFrame once for every test
"""
self.top = System(self.pdb_file, mol2file=self.mol_file).topology
def test_distmat_overflow_exception(self):
"""
Test OverflowError exception for (too) large distance matrix
"""
# Unable to compute distance matrix > max_distmat_size
self.assertRaises(OverflowError,
self.top.distances,
max_distmat_size=10000)
def test_distmat_attribute_exception(self):
"""
Test AttributeError on missing or incomplete coordinates
"""
# No coordinates
self.top._coordinates = None
self.assertRaises(AttributeError, self.top.distances)
def test_distmat_square(self):
"""
Test computation of default square matrix
"""
distmat = self.top.distances()
self.assertIsInstance(distmat, DataFrame)
self.assertEqual(distmat.shape[0], distmat.shape[1])
self.assertEqual(list(distmat.columns), list(distmat.index))
def test_distmat_target(self):
"""
Test computation of matrix with custom source and target selection
"""
source = self.top[self.top['resSeq'] == 999]
target = self.top[self.top['resName'] == 'HIS']
distmat = source.distances(target=target)
self.assertIsInstance(distmat, DataFrame)
self.assertEqual(distmat.shape, (17, 138))
self.assertEqual(len(distmat.columns), len(target))
self.assertEqual(len(distmat.index), len(source))
def test_distmat_empty_selection(self):
"""
Test compuation of matrix when (one of) the input selections is empty
"""
source = self.top[self.top['resSeq'] == 9999]
target = self.top[self.top['resName'] == 'HIS']
self.assertTrue(source.distances().empty)
self.assertTrue(source.distances(target=target).empty)