def test_angle(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
self.assertEqual(frame.angle(0, 1, 2), math.pi / 2.0)
def test_distance(self):
frame = Frame()
frame.cell = UnitCell(3.0, 4.0, 5.0)
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (1, 2, 6))
self.assertEqual(frame.distance(0, 1), math.sqrt(6.0))
def test_distance(self):
frame = Frame()
frame.cell = UnitCell(3.0, 4.0, 5.0)
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (1, 2, 6))
self.assertEqual(frame.distance(0, 1), math.sqrt(6.0))
def test_angle(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
self.assertEqual(frame.angle(0, 1, 2), math.pi / 2.0)
def test_out_of_plane(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (0, 0, 3))
self.assertEqual(frame.out_of_plane(1, 3, 0, 2), 3.0)
def test_out_of_plane(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (0, 0, 3))
self.assertEqual(frame.out_of_plane(1, 3, 0, 2), 3.0)
def test_add_atom(self):
frame = Frame()
frame.add_atom(Atom("F"), (3, 4, 5))
self.assertEqual(len(frame.atoms), 1)
self.assertEqual(list(frame.positions[0]), [3, 4, 5])
frame.add_velocities()
frame.add_atom(Atom("F"), (-3, -4, 5), (1, 0, 1))
self.assertEqual(list(frame.positions[1]), [-3, -4, 5])
self.assertEqual(list(frame.velocities[1]), [1, 0, 1])
def test_add_atom(self):
frame = Frame()
frame.add_atom(Atom("F"), (3, 4, 5))
self.assertEqual(len(frame.atoms), 1)
self.assertEqual(list(frame.positions[0]), [3, 4, 5])
frame.add_velocities()
frame.add_atom(Atom("F"), (-3, -4, 5), (1, 0, 1))
self.assertEqual(list(frame.positions[1]), [-3, -4, 5])
self.assertEqual(list(frame.velocities[1]), [1, 0, 1])
def test_indexes(self):
# Create an input file
frame = Frame()
for i in range(120):
frame.add_atom(Atom('X'), [i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("filename.xyz", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "indexes.py")
# disable output
exec(open(path).read(), globals(), {'print': lambda _: None})
def testing_frame():
frame = Frame()
frame.add_atom(Atom("H"), [0, 0, 0])
frame.add_atom(Atom("O"), [0, 0, 0])
frame.add_atom(Atom("O"), [0, 0, 0])
frame.add_atom(Atom("H"), [0, 0, 0])
frame.add_bond(0, 1)
frame.add_bond(1, 2)
frame.add_bond(2, 3)
return frame
def test_select(self):
# Create an input file
frame = Frame()
NAMES = ["N", "Zn", "C", "O"]
for i in range(120):
frame.add_atom(Atom(NAMES[i % 4]),
[i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("input.arc", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "select.py")
exec(open(path).read(), globals())
def test_write(self):
frame = Frame()
for i in range(4):
frame.add_atom(Atom("X"), [1, 2, 3])
with Trajectory("test-tmp.xyz", "w") as fd:
fd.write(frame)
expected_content = """4
Written by the chemfiles library
X 1 2 3
X 1 2 3
X 1 2 3
X 1 2 3
"""
with open("test-tmp.xyz") as fd:
self.assertEqual(fd.read(), expected_content)
os.unlink("test-tmp.xyz")
def test_write(self):
frame = Frame()
for i in range(4):
frame.add_atom(Atom("X"), [1, 2, 3])
with Trajectory("test-tmp.xyz", "w") as fd:
fd.write(frame)
expected_content = """4
Written by the chemfiles library
X 1 2 3
X 1 2 3
X 1 2 3
X 1 2 3
"""
with open("test-tmp.xyz") as fd:
self.assertEqual(fd.read(), expected_content)
os.unlink("test-tmp.xyz")
def test_bonds(self):
frame = Frame()
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_bond(0, 1)
frame.add_bond(3, 4)
frame.add_bond(2, 1, BondOrder.Qintuplet)
self.assertEqual(
frame.topology.bonds.all(), np.array([[0, 1], [1, 2], [3, 4]]).all()
)
self.assertEqual(
frame.topology.bonds_orders,
[BondOrder.Unknown, BondOrder.Qintuplet, BondOrder.Unknown]
)
frame.remove_bond(3, 4)
# Also try to remove non-existing bonds
frame.remove_bond(3, 4)
frame.remove_bond(0, 4)
self.assertEqual(
frame.topology.bonds.all(), np.array([[0, 1], [1, 2]]).all()
)
def test_bonds(self):
frame = Frame()
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_bond(0, 1)
frame.add_bond(3, 4)
frame.add_bond(2, 1, BondOrder.Qintuplet)
self.assertEqual(frame.topology.bonds.all(),
np.array([[0, 1], [1, 2], [3, 4]]).all())
self.assertEqual(
frame.topology.bonds_orders,
[BondOrder.Unknown, BondOrder.Qintuplet, BondOrder.Unknown])
frame.remove_bond(3, 4)
# Also try to remove non-existing bonds
frame.remove_bond(3, 4)
frame.remove_bond(0, 4)
self.assertEqual(frame.topology.bonds.all(),
np.array([[0, 1], [1, 2]]).all())
def test_dihedral(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (-1, 1, 0))
self.assertEqual(frame.dihedral(0, 1, 2, 3), math.pi)
def test_dihedral(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (-1, 1, 0))
self.assertEqual(frame.dihedral(0, 1, 2, 3), math.pi)
import numpy as np
from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
topology = Topology()
topology.add_atom(Atom("H"))
topology.add_atom(Atom("O"))
topology.add_atom(Atom("H"))
topology.add_bond(0, 1)
topology.add_bond(2, 1)
frame = Frame()
frame.resize(3)
frame.set_topology(topology)
positions = frame.positions()
positions[0, :] = np.array([1.0, 0.0, 0.0])
positions[1, :] = np.array([0.0, 0.0, 0.0])
positions[2, :] = np.array([0.0, 1.0, 0.0])
frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
frame.add_bond(3, 4)
frame.add_bond(4, 5)
frame.set_cell(UnitCell(10, 10, 10))
trajectory = Trajectory("water-co2.pdb", 'w')
trajectory.write(frame)
#!/usr/bin/env python
import numpy as np
from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
topology = Topology()
topology.atoms.append(Atom("H"))
topology.atoms.append(Atom("O"))
topology.atoms.append(Atom("H"))
topology.add_bond(0, 1)
topology.add_bond(2, 1)
frame = Frame()
frame.resize(3)
frame.topology = topology
frame.positions[0, :] = np.array([1.0, 0.0, 0.0])
frame.positions[1, :] = np.array([0.0, 0.0, 0.0])
frame.positions[2, :] = np.array([0.0, 1.0, 0.0])
frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
frame.add_bond(3, 4)
frame.add_bond(4, 5)
frame.cell = UnitCell(10, 10, 10)
with Trajectory("water-co2.pdb", 'w') as trajectory:
trajectory.write(frame)
if state < 7:
x1, y1, x2, y2, x3, y3, z3 = coordinate_si(
ring, column, state)
if state > 6 and ring % 4 == 1 and column % 2 == 0: #up (vert)
x1, y1, x2, y2, x3, y3, z3 = coordinate_up(
ring, column, state)
if state > 6 and ring % 4 == 1 and column % 2 == 1: #down (rouge)
x1, y1, x2, y2, x3, y3, z3 = coordinate_down(
ring, column, state)
if state > 6 and ring % 4 == 3 and column % 2 == 1: #up (vert)
x1, y1, x2, y2, x3, y3, z3 = coordinate_up(
ring, column, state)
if state > 6 and ring % 4 == 3 and column % 2 == 0: #down (rouge)
x1, y1, x2, y2, x3, y3, z3 = coordinate_down(
ring, column, state)
if state < 7 and state > 0:
atom1 = Atom("Si", "Si")
atom2 = Atom("O", "O")
atom3 = Atom("H", "H")
frame.add_atom(atom1, [x1, y1, 0])
frame.add_atom(atom2, [x2, y2, height])
frame.add_atom(atom3, [x3, y3, height])
if state > 7:
atom1 = Atom("Ow", "O")
atom2 = Atom("Hw", "H")
atom3 = Atom("Hw", "H")
frame.add_atom(atom1, [x1, y1, height])
frame.add_atom(atom2, [x2, y2, height])
frame.add_atom(atom3, [x3, y3, z3])
ring += 1