def setUp(self):
metadata = Metadata(atomname=np.array(("A", "A", "B", "B"),
dtype="<U4"),
resname=np.array(("MOLA", "MOLA", "MOLB", "MOLB"),
dtype="<U4"),
ressize=np.array((1, 1, 2, 0)))
self.simple_system = Molecules(metadata=metadata)
def setUp(self):
''' Sets up a molecule with equivalent fields to the reference files used for reading tests. Not just
loading a molecule directly from file because if the reading gets broken then the writing tests would
likely break too
'''
metadata = Metadata(atomname=np.array(("A", "B", "A"), dtype="<U4"),
resname=np.array(("MOLA", "MOLA", "MOLB"),
dtype="<U4"),
ressize=np.array((2, 0, 1)))
coords = np.array([[0.000, -5.000, 0.500], [5.000, -10.000, 0.600],
[10.000, -20.000, 0.700]])
boxdims = np.array([100, 100, 80])
self.simple_system = Molecules(metadata=metadata,
coords=coords,
boxdims=boxdims)
class test_write_coordinates(unittest.TestCase):
def setUp(self):
''' Sets up a molecule with equivalent fields to the reference files used for reading tests. Not just
loading a molecule directly from file because if the reading gets broken then the writing tests would
likely break too
'''
metadata = Metadata(atomname=np.array(("A", "B", "A"), dtype="<U4"),
resname=np.array(("MOLA", "MOLA", "MOLB"),
dtype="<U4"),
ressize=np.array((2, 0, 1)))
coords = np.array([[0.000, -5.000, 0.500], [5.000, -10.000, 0.600],
[10.000, -20.000, 0.700]])
boxdims = np.array([100, 100, 80])
self.simple_system = Molecules(metadata=metadata,
coords=coords,
boxdims=boxdims)
def tearDown(self):
''' Removes temporary files generated during output tests '''
written_test_files = ["test_write_simple.pdb", "test_write_simple.gro"]
for file in written_test_files:
if os.path.exists(file):
os.remove(file)
def test_write_pdb(self):
''' Want exact match with reference PDB, turn off position changing'''
temporaryOutputPath = "test_write_simple.pdb"
self.simple_system.write_coordinates(temporaryOutputPath,
position=False,
reorder=False)
self.assertTrue(
PDBComp.compareAtomFields(temporaryOutputPath,
referenceFilePath + "read_pdb.pdb"))
def test_write_gro(self):
''' Want exact match with reference GRO, turn off position changing'''
temporaryOutputPath = "test_write_simple.gro"
self.simple_system.write_coordinates("test_write_simple.gro",
position=False,
reorder=False)
self.assertTrue(
GROComp.compareAtomFields(temporaryOutputPath,
referenceFilePath + "read_gro.gro"))
def test_raises_execeptions(self):
flat_reference = Molecules(
get_relative_path("reference_files/test_classes/reference.pdb"))
baseshape = shapes.shape()
with self.assertRaises(NotImplementedError):
baseshape.gen_shape(flat_reference, 0)
with self.assertRaises(NotImplementedError):
baseshape.dimension_requirements()
with self.assertRaises(NotImplementedError):
baseshape.final_dimensions()
class test_shapes_run(unittest.TestCase):
def setUp(self):
self.flat_reference = Molecules(
get_relative_path("reference_files/test_classes/reference.pdb"))
self.flat_reference.duplicate_laterally(
3, 3) # should be large enough for all shapes
def test_shapes_run(self):
shapes.buckle.gen_shape(self.flat_reference, (10, 10),
r_buckle=50,
l_buckle=50)
shapes.capped_cylinder.gen_shape(self.flat_reference, (10, 10),
r_cylinder=50,
l_cylinder=50)
shapes.cylinder.gen_shape(self.flat_reference, (10, 10),
r_cylinder=50,
l_cylinder=50)
shapes.double_bilayer_cylinder.gen_shape(self.flat_reference, (10, 10),
r_cylinder=50,
l_cylinder=50,
r_junction=50,
l_flat=200)
shapes.inner_quarter_torus.gen_shape(self.flat_reference, (10, 10),
r_tube=50,
r_torus=75)
shapes.outer_quarter_torus.gen_shape(self.flat_reference, (10, 10),
r_tube=50,
r_torus=75)
shapes.semicylinder_plane.gen_shape(self.flat_reference, (10, 10),
r_cylinder=50,
l_cylinder=50,
r_junction=50,
l_flat=100)
shapes.semisphere.gen_shape(self.flat_reference, (10, 10), r_sphere=50)
shapes.semisphere_plane.gen_shape(self.flat_reference, (10, 10),
r_sphere=50,
r_junction=50,
l_flat=200)
shapes.sphere.gen_shape(self.flat_reference, (10, 10), r_sphere=50)
shapes.torus.gen_shape(self.flat_reference, (10, 10),
r_tube=50,
r_torus=150)
def test_ignore_resnames(self):
inputPDBPath = referenceFilePath + "read_pdb.pdb"
testMolecule = Molecules(infile=inputPDBPath, ignore="MOLB")
self.assertEqual(testMolecule.coords.shape, (2, 3))
self.assertAlmostEqual(testMolecule.coords[0, 0], 0)
self.assertAlmostEqual(testMolecule.coords[1, 1], -10)
# test atomnames
self.assertEqual(testMolecule.metadata.atomname[0].strip(), "A")
self.assertEqual(testMolecule.metadata.atomname[1].strip(), "B")
# test resnames
self.assertEqual(testMolecule.metadata.resname[0], "MOLA")
self.assertEqual(testMolecule.metadata.resname[1], "MOLA")
class test_write_topology(unittest.TestCase):
def setUp(self):
metadata = Metadata(atomname=np.array(("A", "A", "B", "B"),
dtype="<U4"),
resname=np.array(("MOLA", "MOLA", "MOLB", "MOLB"),
dtype="<U4"),
ressize=np.array((1, 1, 2, 0)))
self.simple_system = Molecules(metadata=metadata)
def tearDown(self):
''' Removes temporary files generated during output tests '''
written_test_files = ["test_write_simple.top"]
for file in written_test_files:
if os.path.exists(file):
os.remove(file)
def test_basic_functionality(self):
temporaryOutputPath = "test_write_simple.top"
self.simple_system.write_topology(temporaryOutputPath)
self.assertTrue(
filecmp.cmp(temporaryOutputPath,
referenceFilePath + "reference_basic_top.top"))
def test_read_gro(self):
inputGROPath = referenceFilePath + "read_gro.gro"
testMolecule = Molecules(infile=inputGROPath)
# test coordinates
self.assertEqual(testMolecule.coords.shape, (3, 3))
self.assertAlmostEqual(testMolecule.coords[0, 0], 0)
self.assertAlmostEqual(testMolecule.coords[1, 1], -10)
self.assertAlmostEqual(testMolecule.coords[2, 2], 0.7)
# test atomnames
self.assertEqual(testMolecule.metadata.atomname[0].strip(), "A")
self.assertEqual(testMolecule.metadata.atomname[1].strip(), "B")
self.assertEqual(testMolecule.metadata.atomname[2].strip(), "A")
# test resnames
self.assertEqual(testMolecule.metadata.resname[0], "MOLA")
self.assertEqual(testMolecule.metadata.resname[1], "MOLA")
self.assertEqual(testMolecule.metadata.resname[2], "MOLB")
class test_write_index(unittest.TestCase):
def setUp(self):
metadata = Metadata(atomname=np.array(("A", "A", "B", "B"),
dtype="<U4"),
resname=np.array(("MOLA", "MOLA", "MOLB", "MOLB"),
dtype="<U4"),
leaflets=np.array((0, 1, 1, 1)),
ressize=np.array((1, 1, 2, 0)))
self.simple_system = Molecules(metadata=metadata)
def tearDown(self):
written_test_files = [
"test_write_simple.ndx", "test_write_top_leaflet_only.ndx",
"test_write_molB_as_dummy.ndx"
]
for file in written_test_files:
if os.path.exists(file):
os.remove(file)
def test_writes_fields(self):
temporaryOutputPath = "test_write_simple.ndx"
self.simple_system.write_index(temporaryOutputPath)
self.assertTrue(
filecmp.cmp(temporaryOutputPath,
referenceFilePath + "reference_basic_index.ndx"))
def test_handles_zero_indices(self):
temporaryOutputPath = "test_write_top_leaflet_only.ndx"
self.simple_system.metadata.leaflets = np.array((1, 1, 1, 1))
self.simple_system.write_index(temporaryOutputPath)
self.assertTrue(
filecmp.cmp(temporaryOutputPath,
referenceFilePath + "reference_top_index_only.ndx"))
def test_writes_dummy_particles(self):
# In this case, we'll just treat MOL B as a dummy particle
temporaryOutputPath = "test_write_molB_as_dummy.ndx"
self.simple_system.write_index(temporaryOutputPath, dummy_name="MOLB")
self.assertTrue(
filecmp.cmp(temporaryOutputPath,
referenceFilePath + "reference_dummy_index.ndx"))
def setUp(self):
self.flat_reference = Molecules(
get_relative_path("reference_files/test_classes/reference.pdb"))
self.flat_reference.duplicate_laterally(
3, 3) # should be large enough for all shapes