def test_write_gromacs():
water = Molecule(
[
Atom("O", [0.0, 0.0, 0.0], export={"grotype": "OW"}),
Atom("H", [0.1, 0.0, 0.0], export={"grotype": "HW1"}),
Atom("H", [-0.03333, 0.09428, 0.0], export={"grotype": "HW2"}),
],
export={"groname": "SOL"},
)
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile("/tmp/dummy.gro", mode="w")
df.write("system", sys)
with assert_raises(Exception):
df = datafile("/tmp/dummy.gro")
df.write("system", sys)
df = datafile("/tmp/dummy.gro")
sread = df.read("system")
assert all(sread.type_array == sys.type_array)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write("system", sys)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
water.r_array += 0.1
sys.add(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty()
with sys.batch() as b:
for i in range(200):
water.r_array += 0.1
b.append(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty()
with sys.batch() as b:
for i in range(200):
water.r_array += 0.1
b.append(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3)*2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_write_pdb():
water = Molecule(
[
Atom("O", [0.0, 0.0, 0.0], export={"pdb.type": "O"}),
Atom("H", [0.1, 0.0, 0.0], export={"pdb.type": "H"}),
Atom("H", [-0.03333, 0.09428, 0.0], export={"pdb.type": "H"}),
],
export={"groname": "SOL"},
)
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
water.r_array += 0.1
sys.add(water.copy())
df = datafile("/tmp/dummy.pdb", mode="w")
df.write("system", sys)
def test_write_gromacs():
water = Molecule([
Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})
],
export={'groname': 'SOL'})
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
