def test_calc_alignment():
from pyxmolpp2.geometry import calc_alignment, XYZ, VectorXYZ, calc_rmsd, Rotation3d, Translation3d, Degrees
a = VectorXYZ([XYZ(1, 2, 3), XYZ(1, 2, 5), XYZ(4, 2, 7), XYZ(8, 1, 4)])
G = Rotation3d(XYZ(7, 6, 5), Degrees(12)) * Translation3d(XYZ(8, -9, 1))
b = VectorXYZ([G.transform(x) for x in a])
G2 = calc_alignment(a, b)
assert calc_rmsd(a, b) > 1
assert calc_rmsd(a, b, G2) == pytest.approx(0)
def test_alignment_exception():
from pyxmolpp2.geometry import calc_alignment, XYZ, VectorXYZ, calc_rmsd, AlignmentError
a = [XYZ(1, 2, 3)] * 10
with pytest.raises(AlignmentError):
calc_alignment(VectorXYZ(a[:2]), VectorXYZ(a[:2]))
calc_alignment(VectorXYZ(a[:3]), VectorXYZ(a[:3]))
with pytest.raises(AlignmentError):
calc_alignment(VectorXYZ(a[:4]), VectorXYZ(a))
def test_shorthands():
import numpy as np
from pyxmolpp2.geometry import Rotation3d, Translation3d, XYZ, Degrees, calc_alignment
frame = make_polyglycine([("A", 20)])
for a in frame.asAtoms:
a.r = XYZ(*np.random.random(3))
frame2 = frame.copy()
asel = frame.asAtoms
asel2 = frame2.asAtoms
asel.geom_center()
asel.mass_center([1.0] * asel.size)
asel.inertia_tensor([1.0] * asel.size)
asel.geom_inertia_tensor()
T = Translation3d(XYZ(1, 0, 0))
asel2.transform(T)
assert np.isclose(asel.rmsd(asel2), 1.0)
assert np.isclose(asel.rmsd(asel2.toCoords), 1.0)
assert np.isclose(asel.rmsd(asel2.toCoords.transform(T.inverted())), 0.0)
T = Translation3d(XYZ(1, 0, 0)) * Rotation3d(XYZ(1, 1, 1), Degrees(45))
asel.align_to(asel2)
assert np.isclose(asel.rmsd(asel2), 0)
asel2.transform(T)
asel.align_to(asel2.toCoords)
assert np.isclose(asel.rmsd(asel2), 0)
T = Translation3d(XYZ(1, 0, 0)) * Rotation3d(XYZ(1, 1, 1), Degrees(45))
asel2.transform(T)
assert np.allclose(T.matrix3d(), calc_alignment(asel2.toCoords, asel.toCoords).matrix3d())
assert np.allclose(T.matrix3d(), asel.alignment_to(asel2).matrix3d())
assert np.allclose(T.matrix3d(), asel.alignment_to(asel2.toCoords).matrix3d())
def test_rmsd():
from pyxmolpp2.polymer import AtomName
from pyxmolpp2.pdb import PdbFile
from pyxmolpp2.geometry import calc_rmsd, calc_alignment, calc_geom_center
import glob
filenames = sorted(glob.glob("tests_dataset/pdb/rcsb/*.pdb"))
for i in range(len(filenames) - 1):
frame_1 = PdbFile(filenames[i]).get_frame()
residues_1 = [
a.rId for a in frame_1.asChains[0].asAtoms.filter(
lambda a: a.name.str == "CA")
]
for j in range(i + 1, len(filenames)):
frame_2 = PdbFile(filenames[j]).get_frame()
residues_2 = [
a.rId for a in frame_2.asChains[0].asAtoms.filter(
lambda a: a.name.str == "CA")
]
common = set(residues_1) & set(residues_2)
ats1 = frame_1.asChains[0].asAtoms.filter(lambda a: (
a.id == a.residue[AtomName("CA")].id) and a.rId in common)
ats2 = frame_2.asChains[0].asAtoms.filter(lambda a: (
a.id == a.residue[AtomName("CA")].id) and a.rId in common)
assert ats1.size == len(common)
assert ats2.size == len(common)
assert ats1.size == ats2.size
assert len(ats1) > 3
assert len(ats2) > 3
aligment = calc_alignment(ats1.toCoords, ats2.toCoords)
not_aligned_rmsd = calc_rmsd(ats1.toCoords, ats2.toCoords)
aligned_rmsd = calc_rmsd(ats1.toCoords, ats2.toCoords, aligment)
# Number of residues in chains must be same (strip water, ions, etc.)
N = 0
for i in range(frame.size):
if frame.asChains[i].size != frame.asChains[0].size:
break
N += 1
##############################################################################
# Print RMSD matrix for all deposited chains:
for i in range(0, N):
chain_i_ca = frame.asChains[i].asAtoms.filter(aName == "CA")
for j in range(0, i + 1):
chain_j_ca = frame.asChains[j].asAtoms.filter(aName == "CA")
alignment = calc_alignment(chain_i_ca.toCoords, chain_j_ca.toCoords)
rmsd = calc_rmsd(chain_i_ca.toCoords, chain_j_ca.toCoords, alignment)
print("%5.1f" % rmsd, end=" ")
print()
##############################################################################
# Calculate RMSF per residue
from pyxmolpp2.geometry import UniformScale3d
first_chain_ca = frame.asChains[0].asAtoms.filter(aName == "CA")
# initialize average coordinates with (0,0,0)