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_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)