def test_graph_radial_hub_fingerprint(self):
db = DBMolecules('test/radial/',
radial=True,
fingerprint=True,
fast=True,
hub="ejm_46.mol2")
strict, loose = db.build_matrices()
graph = db.build_graph()
mol2_graph = nx.read_gpickle(
"test/radial/radial_hub_fingerprint_fast.gpickle")
dic1_nodes = graph.nodes(data=True)
dic1_edges = graph.edges(data=True)
dic2_nodes = mol2_graph.nodes(data=True)
dic2_edges = mol2_graph.edges(data=True)
self.assertEqual(True, dic1_nodes == dic2_nodes)
self.assertEqual(True, dic2_edges == dic2_edges)
nm = iso.categorical_node_match(['fname_comp', 'ID'], ['noname', -1])
em = iso.categorical_edge_match(['strict_flag', 'similarity'],
[False, -1.0])
self.assertEqual(
True,
nx.is_isomorphic(graph, mol2_graph, node_match=nm, edge_match=em))
def test_serial_parallel(self):
db = DBMolecules('test/basic')
s_strict, s_loose = db.build_matrices()
db.options.paralell = multiprocessing.cpu_count()
p_strict, p_loose = db.build_matrices()
self.assertEqual(True, all(s_strict == p_strict))
self.assertEqual(True, all(s_loose == p_loose))
def setUp(self):
self.inst = DBMolecules('test/basic/',
parallel=1,
verbose='off',
output=False,
time=20,
ecrscore=0.0,
name='out',
display=False,
max=6,
cutoff=0.4)
class TestLomap(unittest.TestCase):
def setUp(self):
self.inst = DBMolecules('test/basic/',
parallel=1,
verbose='off',
output=False,
time=20,
ecrscore=0.0,
name='out',
display=False,
max=6,
cutoff=0.4)
# Test class Inizialitazion
# Check wrong number of argumetns or wrong options
def test_InsufficientArgs(self):
self.assertRaises(TypeError, self.inst.__init__)
# Check passed input Types
def test_TypeArgs(self):
self.assertRaises(argparse.ArgumentTypeError, self.inst.__init__,
'test/nodir/')
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
time=-1)
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
parallel=-1)
self.assertRaises(SystemExit,
self.inst.__init__,
'test/basic',
parallel=-1.5)
self.assertRaises(SystemExit,
self.inst.__init__,
'test/basic',
verbose='err_option')
self.assertRaises(SystemExit,
self.inst.__init__,
'test/basic',
time=-1.5)
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
ecrscore=-1.5)
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
ecrscore=2.0)
self.assertRaises(TypeError,
self.inst.__init__,
'test/basic',
output=-5.0)
self.assertRaises(TypeError,
self.inst.__init__,
'test/basic',
display=-5.0)
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
max=-5)
self.assertRaises(SystemExit,
self.inst.__init__,
'test/basic',
max=-5.0)
self.assertRaises(argparse.ArgumentTypeError,
self.inst.__init__,
'test/basic',
cutoff=-5)
self.assertRaises(SystemExit,
self.inst.__init__,
'test/basic',
max='string')
# Test class methods
# Check iter and next
def test_iter_next(self):
for i in range(0, self.inst.nums()):
self.inst.next()
self.assertRaises(StopIteration, self.inst.next)
# Check get, set and add
def test_get_set_add(self):
self.assertRaises(IndexError, self.inst.__getitem__,
self.inst.nums() + 1)
self.assertRaises(IndexError, self.inst.__setitem__,
self.inst.nums() + 1, self.inst[1])
self.assertRaises(ValueError, self.inst.__setitem__, 0, 'no_mol_obj')
self.assertRaises(ValueError, self.inst.__add__, 'no_mol_obj')
# Check read mol2 files
def test_read_mol2_files(self):
db = DBMolecules('test/basic')
db.options.directory = 'test/'
self.assertRaises(IOError, db.read_mol2_files)
# Check serial and parallel mode
def test_serial_parallel(self):
db = DBMolecules('test/basic')
s_strict, s_loose = db.build_matrices()
db.options.paralell = multiprocessing.cpu_count()
p_strict, p_loose = db.build_matrices()
self.assertEqual(True, all(s_strict == p_strict))
self.assertEqual(True, all(s_loose == p_loose))
# Check Graph
def test_graph(self):
db = self.inst
strict, loose = db.build_matrices()
graph = db.build_graph()
self.assertRaises(IOError, nx.nx_agraph.write_dot, graph, '/check.dot')
mol2_graph = nx.read_gpickle("test/basic/molecules.gpickle")
dic1_nodes = graph.nodes(data=True)
dic1_edges = graph.edges(data=True)
dic2_nodes = mol2_graph.nodes(data=True)
dic2_edges = mol2_graph.edges(data=True)
self.assertEqual(True, dic1_nodes == dic2_nodes)
self.assertEqual(True, dic2_edges == dic2_edges)
nm = iso.categorical_node_match(['fname_comp', 'ID'], ['noname', -1])
em = iso.categorical_edge_match(['strict_flag', 'similarity'],
[False, -1.0])
self.assertEqual(
True,
nx.is_isomorphic(graph, mol2_graph, node_match=nm, edge_match=em))
def test_mcs(self):
f = open('test/basic/MCS.pickle', 'rb')
data = pickle.load(f)
data_no_hydrogens = data[0]
data_hydrogens = data[1]
db = self.inst
nohyds = {}
hyds = {}
lg = RDLogger.logger()
lg.setLevel(RDLogger.CRITICAL)
for i in range(0, db.nums()):
for j in range(i + 1, db.nums()):
MCS_no_hyds = MCS.getMapping(db[i].getMolecule(),
db[j].getMolecule())
MCS_hyds = MCS.getMapping(db[i].getMolecule(),
db[j].getMolecule(),
hydrogens=True)
nohyds[(i, j)] = MCS_no_hyds
hyds[(i, j)] = MCS_hyds
self.assertEqual(True, nohyds == data_no_hydrogens)
self.assertEqual(True, hyds == data_hydrogens)
def test_read_mol2_files(self):
db = DBMolecules('test/basic')
db.options.directory = 'test/'
self.assertRaises(IOError, db.read_mol2_files)