def test_unit_cell_volume():
from pyxmolpp2 import UnitCell, XYZ, Degrees
cell = UnitCell(1, 1, 1, Degrees(90), Degrees(90), Degrees(90))
assert cell.volume == 1
cell.scale_by(2)
assert cell.volume == 8
cell.scale_to_volume(27)
assert cell[0].distance(XYZ(3, 0, 0)) == pytest.approx(0)
assert cell[1].distance(XYZ(0, 3, 0)) == pytest.approx(0)
assert cell[2].distance(XYZ(0, 0, 3)) == pytest.approx(0)
def test_shorthands():
import numpy as np
from pyxmolpp2 import Rotation, Translation, XYZ, Degrees, Frame, calc_alignment
frame = make_polyglycine([("A", 20)])
for a in frame.atoms:
a.r = XYZ(*np.random.random(3))
frame2 = Frame(frame)
assert frame2 != frame
print(frame, frame2)
asel = frame.atoms
asel2 = frame2.atoms
asel.coords.mean()
# asel.mass_center([1.0] * asel.size) # todo: enable
# asel.inertia_tensor([1.0] * asel.size) # todo: enable
asel.coords.inertia_tensor()
T = Translation(XYZ(1, 0, 0))
asel2.coords.apply(T)
print(asel.coords.rmsd(asel2.coords))
assert np.isclose(asel.coords.rmsd(asel2.coords), 1.0)
assert np.isclose(asel.coords.rmsd(asel2.coords), 1.0)
asel2.coords.apply(T.inverted())
assert np.isclose(asel.coords.rmsd(asel2.coords), 0.0)
T = Translation(XYZ(1, 0, 0)) * Rotation(XYZ(1, 1, 1), Degrees(45))
asel.coords.apply(asel.coords.alignment_to(asel2.coords))
assert np.isclose(asel.coords.rmsd(asel2.coords), 0)
asel2.coords.apply(T)
asel.align_to(asel2)
assert np.isclose(asel.coords.rmsd(asel2.coords), 0)
asel2.coords.apply(T)
asel2.guess_mass()
asel.guess_mass()
asel.align_to(asel2, weighted=True)
assert np.isclose(asel.rmsd(asel2), 0)
assert np.isclose(asel.rmsd(asel2, weighted=True), 0)
T = Translation(XYZ(1, 0, 0)) * Rotation(XYZ(1, 1, 1), Degrees(45))
asel2.coords.apply(T)
assert np.allclose(
T.matrix3d(),
calc_alignment(asel2.coords.values, asel.coords.values).matrix3d())
assert np.allclose(T.matrix3d(), asel.alignment_to(asel2).matrix3d())
def test_conversions():
from pyxmolpp2 import Degrees, Radians, radians_to_degrees, degrees_to_radians
deg = Degrees(10)
rad = Radians(100)
assert rad.radians == pytest.approx(100)
assert deg.degrees == pytest.approx(10)
assert rad.degrees == pytest.approx(radians_to_degrees(100))
assert deg.radians == pytest.approx(degrees_to_radians(10))
def test_calc_alignment():
from pyxmolpp2 import calc_alignment, XYZ, calc_rmsd, Rotation, Translation, Degrees
a = np.array([(1, 2, 3), (1, 2, 5), (4, 2, 7), (8, 1, 4)])
G = Rotation(XYZ(7, 6, 5), Degrees(12)) * Translation(XYZ(8, -9, 1))
b = np.array([G.transform(XYZ(*x)).values for x in a])
G2 = calc_alignment(a, b)
assert calc_rmsd(a, b) > 1
c = np.array([G2.transform(XYZ(*x)).values for x in b])
assert calc_rmsd(a, c) == pytest.approx(0)
def test_composition():
from pyxmolpp2 import XYZ, Rotation, Translation, Degrees, UniformScale
R = Rotation(XYZ(1, 1, 1), Degrees(39))
T = Translation(XYZ(7, 1, 2))
S = UniformScale(1.5)
G = R * T * S * R * T
def check(G):
r = XYZ(5, 6, 4)
assert ((G * G.inverted()).transform(r) - r).len() == pytest.approx(0)
check(R)
check(T)
check(S)
check(G)
for a in [R, T, S, G]:
for b in [R, T, S, G]:
check(a * b)
def test_transformation_3d():
import numpy as np
from pyxmolpp2 import XYZ, Rotation, Translation, Degrees
R = Rotation(XYZ(1, 0, 0), Degrees(45))
T = Translation(XYZ(1, 2, 5))
G = T * R
m = G.matrix3d()
v = G.vector3d()
assert pytest.approx(m[0, 0]) == 1
assert pytest.approx(m[0, 1]) == 0
assert pytest.approx(m[0, 2]) == 0
assert pytest.approx(np.sqrt(2) / 2) == m[2, 1]
assert v.x == 1
assert v.y == 2
assert v.z == 5
def test_rotation_decomposition():
import numpy as np
from pyxmolpp2 import XYZ, Rotation, Degrees
for ax, theta in [
(XYZ(0, 0, 1), Degrees(30)),
(XYZ(0, 0, 1), Degrees(70)),
(XYZ(0, 1, 0), Degrees(70)),
(XYZ(1, 0, 0), Degrees(70)),
(XYZ(1, 1, 0), Degrees(70)),
(XYZ(1, 1, 1), Degrees(70)),
(XYZ(1, 0, 1), Degrees(0)),
(XYZ(1, 1, 1), Degrees(0)),
]:
R = Rotation(ax, theta)
ax1, theta1 = R.axis(), R.theta()
R2 = Rotation(ax1, theta1)
assert np.allclose(R.matrix3d(), R2.matrix3d()), ("\n".join(
map(lambda x: "%25.18e" % x,
(R.matrix3d() - R2.matrix3d()).flatten())))
def test_read_frame():
from pyxmolpp2 import PdbFile, UnitCell, Degrees
cells = [
UnitCell(36.633, 36.633, 79.254, Degrees(90), Degrees(90),
Degrees(120.00)),
UnitCell(50.840, 42.770, 28.950, Degrees(90), Degrees(90.00),
Degrees(90.00)),
UnitCell(52.323, 79.498, 52.406, Degrees(90), Degrees(90.14),
Degrees(90.00)),
UnitCell(25.037, 37.194, 49.217, Degrees(90), Degrees(90.00),
Degrees(90.00)),
]
for pdb_code, cell in zip(['1PGB', '1UBQ', '5BMG', '5BMH'], cells):
frames = PdbFile(os.environ["TEST_DATA_PATH"] +
f"/pdb/rcsb/{pdb_code}.pdb").frames()
for frame in frames:
for i in range(3):
assert cell[i].distance(frame.cell[i]) == pytest.approx(0)
assert frame.atoms.size > 0