def test_repr(self):
self.assertEqual(
UnitCell(3, 4, 5).__repr__(),
"UnitCell(3.0, 4.0, 5.0, 90.0, 90.0, 90.0)")
self.assertEqual(
UnitCell(3, 4, 5, 89.015, 120, 112).__repr__(),
"UnitCell(3.0, 4.0, 5.0, 89.015, 120.0, 112.0)")
def test_wrap(self):
cell = UnitCell(3, 4, 5)
wrapped = cell.wrap((1, 5, -5.5))
self.assertEqual(wrapped[0], 1.0)
self.assertEqual(wrapped[1], 1.0)
self.assertEqual(wrapped[2], -0.5)
def test_shape(self):
cell = UnitCell(3, 4, 5)
self.assertEqual(cell.shape, CellShape.Orthorhombic)
cell.shape = CellShape.Triclinic
self.assertEqual(cell.shape, CellShape.Triclinic)
cell = UnitCell(3, 4, 5, 100, 120, 130)
self.assertEqual(cell.shape, CellShape.Triclinic)
def test_copy(self):
cell = UnitCell(3, 4, 5)
cloned = copy.copy(cell)
self.assertEqual(cell.lengths, (3.0, 4.0, 5.0))
self.assertEqual(cloned.lengths, (3.0, 4.0, 5.0))
cell.lengths = 10, 11, 12
self.assertEqual(cell.lengths, (10.0, 11.0, 12.0))
self.assertEqual(cloned.lengths, (3.0, 4.0, 5.0))
def test_angles(self):
cell = UnitCell(3, 4, 5)
self.assertEqual(cell.angles, (90.0, 90.0, 90.0))
self.assertEqual(cell.shape, CellShape.Orthorhombic)
with remove_warnings:
with self.assertRaises(ChemfilesError):
cell.angles = [80, 89, 110]
cell.shape = CellShape.Triclinic
cell.angles = [80, 89, 110]
self.assertEqual(cell.angles, (80.0, 89.0, 110.0))
def test_matrix(self):
cell = UnitCell(3, 4, 5)
expected = [(3, 0, 0), (0, 4, 0), (0, 0, 5)]
matrix = cell.matrix
for i in range(3):
for j in range(3):
self.assertAlmostEqual(matrix[i][j], expected[i][j])
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_cell(self):
frame = Frame()
frame.cell = UnitCell(1, 2, 4)
self.assertEqual(frame.cell.lengths, (1, 2, 4))
self.assertEqual(frame.cell.angles, (90, 90, 90))
self.assertEqual(frame.cell.shape, CellShape.Orthorhombic)
frame.cell.lengths = (3, 4, 5)
self.assertEqual(frame.cell.lengths, (3, 4, 5))
def test_read(self):
trajectory = Trajectory(get_data_path("water.xyz"))
self.assertEqual(trajectory.nsteps, 100)
self.assertEqual(trajectory.path, get_data_path("water.xyz"))
frame = trajectory.read()
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.positions[0].all(),
np.array([0.417219, 8.303366, 11.737172]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.099554, -0.045104, 14.153846]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.atoms[0].name, "O")
self.assertEqual(frame.atoms[1].name, "H")
trajectory.set_cell(UnitCell(30, 30, 30))
frame = trajectory.read_step(41)
self.assertEqual(frame.cell.lengths, (30.0, 30.0, 30.0))
self.assertEqual(frame.positions[0].all(),
np.array([0.761277, 8.106125, 10.622949]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.13242, 0.079862, 14.194161]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.topology.bonds_count(), 0)
frame.guess_bonds()
self.assertEqual(frame.topology.bonds_count(), 181)
self.assertEqual(frame.topology.angles_count(), 87)
topology = Topology()
for i in range(297):
topology.atoms.append(Atom("Cs"))
trajectory.set_topology(topology)
frame = trajectory.read_step(10)
self.assertEqual(frame.atoms[10].name, "Cs")
trajectory.set_topology(get_data_path("topology.xyz"), "XYZ")
frame = trajectory.read()
self.assertEqual(frame.atoms[100].name, "Rd")
#!/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)
def test_volume(self):
cell = UnitCell(3, 4, 5)
self.assertEqual(cell.volume, 3 * 4 * 5)
def test_lengths(self):
cell = UnitCell(3, 4, 5)
self.assertEqual(cell.lengths, (3.0, 4.0, 5.0))
cell.lengths = [10, 11, 12]
self.assertEqual(cell.lengths, (10.0, 11.0, 12.0))
name = "nt12.opt"
a = 24.2
# Read the frame
frame = Trajectory(name + ".xyz").read()
# Set the topology
topo = Trajectory("topology.pdb").read()
frame.set_topology(topo.topology())
# Get the positions
positions = frame.positions()
# Set the cell
cell = UnitCell(a, a, 42.43, 90, 90, 120)
frame.set_cell(cell)
# Select all except hydroxyl groups
#selection = Selection("atoms: name Al or name Obr or name Si")
selection = Selection(
"atoms: name Hext or name Oext or name Al or name Obr or name Si")
framework = selection.evaluate(frame)
with open(name + ".cris", 'w') as cris:
with open(name + ".slice.xyz", 'w') as slic:
with open(name + ".framework.xyz", 'w') as out:
cris.write(" .false.\n")
cris.write('{} {} 8.486 90.0 90.0 120.0\n'.format(a, a))
cris.write('{}\n'.format(len(framework) / 5))