def test_frame_mdtraj_read_xtc(self):
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
self.assertEqual(663, frame.natoms)
# These are the coordinates from the gro file
np.testing.assert_allclose(np.array([0.696, 1.33, 1.211]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.89868, 1.89868, 1.89868]),
frame.box)
frame.next_frame()
# These coordinates are from the xtc file
np.testing.assert_allclose(np.array([1.176, 1.152, 1.586]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.9052, 1.9052, 1.9052]),
frame.box)
frame.next_frame()
np.testing.assert_allclose(np.array([1.122, 1.130, 1.534]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.90325272, 1.90325272, 1.90325272]),
frame.box)
def test_bondset_boltzmann_invert(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_bondset_boltzmann_invert(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_frame_write_xtc_mdtraj(self):
try:
os.remove("water_test2.xtc")
except IOError:
pass
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
while frame.next_frame():
frame.write_xtc("water_test2.xtc")
def test_frame_write_xtc_mdtraj(self):
try:
os.remove("water_test2.xtc")
except IOError:
pass
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
while frame.next_frame():
frame.write_xtc("water_test2.xtc")
def test_bondset_boltzmann_invert_mdtraj(self):
logging.disable(logging.WARNING)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
measure = BondSet("test/data/sugar.bnd", DummyOptions)
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_full_itp_sugar(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
logging.disable(logging.WARNING)
measure.write_itp("sugar_out.itp", mapping)
logging.disable(logging.NOTSET)
self.assertTrue(cmp_whitespace_float("sugar_out.itp", "test/data/sugar_out.itp", float_rel_error=0.001))
def test_bondset_boltzmann_invert_func_forms(self):
class FuncFormOptions(DummyOptions):
length_form = "CosHarmonic"
angle_form = "Harmonic"
dihedral_form = "MartiniDefaultLength"
measure = BondSet("test/data/sugar.bnd", FuncFormOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 3)
def test_bondset_boltzmann_invert_mdtraj(self):
logging.disable(logging.WARNING)
frame = Frame("test/data/sugar.gro",
xtc="test/data/sugar.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
measure = BondSet("test/data/sugar.bnd", DummyOptions)
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_bondset_boltzmann_invert_manual_default_fc(self):
class FuncFormOptions(DummyOptions):
length_form = "MartiniDefaultLength"
angle_form = "MartiniDefaultAngle"
dihedral_form = "MartiniDefaultDihedral"
measure = BondSet("test/data/sugar.bnd", FuncFormOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 2)
def test_full_itp_sugar(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
logging.disable(logging.WARNING)
measure.write_itp("sugar_out.itp", mapping)
logging.disable(logging.NOTSET)
self.assertTrue(
cmp_whitespace_float("sugar_out.itp",
"test/data/sugar_out.itp",
float_rel_error=0.001))
