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
def test_load_topology_sybyl(self):
"""
Load topology including Tripos SYBYL atom types from mol2
"""
top = System(self.pdb_file, mol2file=self.mol_file).topology
self.assertTrue('attype' in top.columns)
def test_load_topology_instance(self):
"""
Check if returned object is instance of DataFrame, TopologyDataFrame
"""
top = System(self.pdb_file).topology
self.assertIsInstance(top, DataFrame)
self.assertIsInstance(top, TopologyDataFrame)
def setUpClass(cls):
"""
Prepare TopologyDataFrame once for every test
"""
cls.top = System(cls.pdb_file, mol2file=cls.mol_file).topology
# Build distance matrix
cls.top.distances()
def test_load_topology_pdb(self):
"""
Load PDB file
"""
top = System(self.pdb_file).topology
self.assertEqual(len(top), 5202)
self.assertEqual(list(top.columns), ['serial', 'name', 'element', 'resSeq', 'resName',
'chainID', 'segmentID'])
def test_topdataframe_neighbours_exceptions(self):
"""
Neighbours method exceptions
"""
# Method requires pairwise distance matrix
top = System(self.pdb_file, mol2file=self.mol_file).topology
sel = top[top['resName'] == 'THA']
self.assertRaises(AttributeError, sel.neighbours)
# Target selection should be contained in parent
sel.distances()
target = top[top['resSeq'].isin(
[72, 80, 81, 84, 85, 117, 118, 119, 121, 122])]
parent = top[top['resSeq'].isin([84, 85, 117, 118, 119, 121, 122])]
sel._parent = parent
self.assertRaises(TypeError, sel.neighbours, target)
def setUpClass(cls):
"""
Prepare TopologyDataFrame once for every test
"""
pdb_file = '{0}/{1}.pdb'.format(filepath, cls.ref['pdb_id'])
mol_file = '{0}/{1}.mol2'.format(filepath, cls.ref['pdb_id'])
# Load structures (PDB + MOL2) and calculate distance matrix
trajectory = System(pdb_file, mol2file=mol_file)
cls.top = trajectory.topology
cls.top.distances()
# Select ligand and neighbours, build contact frame
if 'chain' in cls.ref:
ligand_selection = cls.top[
(cls.top['resSeq'] == cls.ref['ligand'])
& (cls.top['chainID'] == cls.ref['chain'])]
else:
ligand_selection = cls.top[cls.top['resSeq'] == cls.ref['ligand']]
cls.neighbour_selection = ligand_selection.neighbours()
cls.cf = ligand_selection.contacts(cls.neighbour_selection)
def setUp(self):
"""
Prepare TopologyDataFrame once for every test
"""
self.top = System(self.pdb_file, mol2file=self.mol_file).topology
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)
def setUpClass(cls):
"""
Prepare TopologyDataFrame once for every test
"""
cls.top = System(cls.pdb_file, mol2file=cls.mol_file).topology