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_iter(self):
frame = Frame()
frame.resize(3)
for i, atom in enumerate(frame.atoms):
self.assertEqual(atom.name, "")
self.assertEqual(i, 2)
def test_property(self):
frame = Frame()
frame["foo"] = 3
self.assertEqual(frame["foo"], 3.0)
frame["foo"] = False
self.assertEqual(frame["foo"], False)
with remove_warnings:
with self.assertRaises(ChemfilesError):
_ = frame["bar"]
with self.assertRaises(ChemfilesError):
frame[3] = "test"
with self.assertRaises(ChemfilesError):
_ = frame[3]
# Check that enabling indexing/__getitem__ did not enable iteration
with self.assertRaises(TypeError):
for i in frame:
pass
frame["bar"] = "baz"
self.assertEqual(frame.properties_count(), 2)
self.assertEqual(set(frame.list_properties()), {"bar", "foo"})
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_property(self):
frame = Frame()
frame["foo"] = 3
self.assertEqual(frame["foo"], 3.0)
frame["foo"] = False
self.assertEqual(frame["foo"], False)
with remove_warnings:
with self.assertRaises(ChemfilesError):
_ = frame["bar"]
with self.assertRaises(ChemfilesError):
frame[3] = "test"
with self.assertRaises(ChemfilesError):
_ = frame[3]
# Check that enabling indexing/__getitem__ did not enable iteration
with self.assertRaises(TypeError):
for i in frame:
pass
frame["bar"] = "baz"
self.assertEqual(frame.properties_count(), 2)
self.assertEqual(set(frame.list_properties()), {"bar", "foo"})
def test_residues(self):
frame = Frame()
frame.add_residue(Residue("Foo"))
frame.add_residue(Residue("Foo"))
frame.add_residue(Residue("Foo"))
self.assertEqual(len(frame.topology.residues), 3)
self.assertEqual(frame.topology.residues[0].name, "Foo")
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_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_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_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_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_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 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 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_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_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_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_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_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_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_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_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_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_residues(self):
frame = Frame()
frame.add_residue(Residue("Foo"))
frame.add_residue(Residue("Foo"))
frame.add_residue(Residue("Foo"))
self.assertEqual(len(frame.topology.residues), 3)
self.assertEqual(frame.topology.residues[0].name, "Foo")
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_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_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_out_of_bounds(self):
frame = Frame()
frame.resize(3)
_ = frame.atoms[2]
with self.assertRaises(IndexError):
_ = frame.atoms[6]
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_step(self):
frame = Frame()
self.assertEqual(frame.step, 0)
frame.step = 42
self.assertEqual(frame.step, 42)
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
# This file is an example for the chemfiles library
# 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)
def test_out_of_bounds(self):
frame = Frame()
frame.resize(3)
_ = frame.atoms[2]
with self.assertRaises(IndexError):
_ = frame.atoms[6]
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_step(self):
frame = Frame()
self.assertEqual(frame.step, 0)
frame.step = 42
self.assertEqual(frame.step, 42)
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()
)
# This file is an example for the chemfiles library
# 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))
return x, y, x - 0.866, y + 0.5, x, y, height + 1
if state == 11:
return x, y, x, y - 1, x + 0.866, y + 0.5, height
if state == 12:
return x, y, x - 0.866, y + 0.5, x + 0.866, y + 0.5, height
if state == 13:
return x, y, x - 0.866, y + 0.5, x, y - 1, height
with Trajectory('conf.xyz', 'w') as output:
with open('conf.dat', 'r') as conf:
ring = 0
skip = 0
for line in conf:
if line.startswith("Step:") and skip % 100 == 0:
frame = Frame()
ring = 0
elif line.startswith("####"):
if skip % 100 == 0:
output.write(frame)
skip += 1
elif skip % 100 == 0:
row = map(int, line.split())
for column, state in enumerate(row):
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)