def test_repr(self):
frame = Frame()
self.assertEqual(frame.__repr__(), "Frame with 0 atoms")
frame.resize(4)
self.assertEqual(frame.__repr__(), "Frame with 4 atoms")
self.assertEqual(frame.atoms.__repr__(), "[Atom(''), Atom(''), Atom(''), Atom('')]")
def test_iter(self):
frame = Frame()
frame.resize(3)
for i, atom in enumerate(frame.atoms):
self.assertEqual(atom.name, "")
self.assertEqual(i, 2)
def test_repr(self):
frame = Frame()
self.assertEqual(frame.__repr__(), "Frame with 0 atoms")
frame.resize(4)
self.assertEqual(frame.__repr__(), "Frame with 4 atoms")
self.assertEqual(frame.atoms.__repr__(),
"[Atom(''), Atom(''), Atom(''), Atom('')]")
def test_atoms_count(self):
frame = Frame()
self.assertEqual(len(frame.atoms), 0)
frame.resize(4)
self.assertEqual(len(frame.atoms), 4)
frame.remove(2)
self.assertEqual(len(frame.atoms), 3)
def test_atoms_count(self):
frame = Frame()
self.assertEqual(len(frame.atoms), 0)
frame.resize(4)
self.assertEqual(len(frame.atoms), 4)
frame.remove(2)
self.assertEqual(len(frame.atoms), 3)
def test_copy(self):
frame = Frame()
cloned = copy.copy(frame)
self.assertEqual(len(frame.atoms), 0)
self.assertEqual(len(cloned.atoms), 0)
frame.resize(6)
self.assertEqual(len(frame.atoms), 6)
self.assertEqual(len(cloned.atoms), 0)
def test_copy(self):
frame = Frame()
cloned = copy.copy(frame)
self.assertEqual(len(frame.atoms), 0)
self.assertEqual(len(cloned.atoms), 0)
frame.resize(6)
self.assertEqual(len(frame.atoms), 6)
self.assertEqual(len(cloned.atoms), 0)
def test_iter(self):
frame = Frame()
frame.resize(3)
for i, atom in enumerate(frame.atoms):
self.assertEqual(atom.name, "")
self.assertEqual(i, 2)
for i, atom in enumerate(frame.topology.atoms):
self.assertEqual(atom.name, "")
self.assertEqual(i, 2)
def test_topology(self):
frame = Frame()
frame.resize(2)
topology = Topology()
topology.atoms.append(Atom("Zn"))
topology.atoms.append(Atom("Ar"))
frame.topology = topology
self.assertEqual(frame.atoms[0].name, "Zn")
self.assertEqual(frame.atoms[1].name, "Ar")
def test_topology(self):
frame = Frame()
frame.resize(2)
topology = Topology()
topology.atoms.append(Atom("Zn"))
topology.atoms.append(Atom("Ar"))
frame.topology = topology
self.assertEqual(frame.topology.atoms[0].name, "Zn")
self.assertEqual(frame.topology.atoms[1].name, "Ar")
self.assertEqual(frame.atoms[0].name, "Zn")
self.assertEqual(frame.atoms[1].name, "Ar")
def test_positions(self):
frame = Frame()
frame.resize(4)
expected = np.array(
[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]],
np.float64,
)
np.copyto(frame.positions, expected)
self.assertEqual(frame.positions.all(), expected.all())
frame.positions[3, 2] = 42
self.assertEqual(frame.positions[3, 2], 42)
# Checking empty frame positions access
_ = Frame().positions
def test_positions(self):
frame = Frame()
frame.resize(4)
expected = np.array(
[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0],
[10.0, 11.0, 12.0]],
np.float64,
)
np.copyto(frame.positions, expected)
self.assertEqual(frame.positions.all(), expected.all())
frame.positions[3, 2] = 42
self.assertEqual(frame.positions[3, 2], 42)
# Checking empty frame positions access
_ = Frame().positions
def test_velocities(self):
frame = Frame()
frame.resize(4)
self.assertFalse(frame.has_velocities())
frame.add_velocities()
self.assertTrue(frame.has_velocities())
expected = np.array(
[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]],
np.float64,
)
np.copyto(frame.velocities, expected)
self.assertEqual(frame.velocities.all(), expected.all())
frame.velocities[3, 2] = 42
self.assertEqual(frame.velocities[3, 2], 42)
# Checking empty frame velocities access
frame = Frame()
frame.add_velocities()
_ = frame.velocities
def test_velocities(self):
frame = Frame()
frame.resize(4)
self.assertFalse(frame.has_velocities())
frame.add_velocities()
self.assertTrue(frame.has_velocities())
expected = np.array(
[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0],
[10.0, 11.0, 12.0]],
np.float64,
)
np.copyto(frame.velocities, expected)
self.assertEqual(frame.velocities.all(), expected.all())
frame.velocities[3, 2] = 42
self.assertEqual(frame.velocities[3, 2], 42)
# Checking empty frame velocities access
frame = Frame()
frame.add_velocities()
_ = frame.velocities
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
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))
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/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:
def test_out_of_bounds(self):
frame = Frame()
frame.resize(3)
_ = frame.atoms[2]
with self.assertRaises(IndexError):
_ = frame.atoms[6]
def test_out_of_bounds(self):
frame = Frame()
frame.resize(3)
_ = frame.atoms[2]
with self.assertRaises(IndexError):
_ = frame.atoms[6]