def setUp(self):
self.x = array([[51.65, -1.90, 50.07], [50.40, -1.23, 50.65],
[50.68, -0.04, 51.54], [50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58],
[52.36, -1.20, 48.03], [52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
def setUp(self):
self.x = array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
def align(self, structure, transform=True):
"""Align the input structure onto the reference structure.
Parameters
----------
transform: bool, optional
If True (default), apply the rotation/translation that minimizes
the RMSD between the two structures to the input structure. If
False, the structure is not modified but the optimal RMSD will
still be calculated.
"""
self.rms = None # clear before aligning
coord = self.get_guide_coord_from_structure(structure)
if len(coord) < self.window_size * 2:
n_atoms = len(coord)
msg = (f"Too few atoms in the mobile structure ({n_atoms}). "
"Try reducing the window_size parameter.")
raise PDBException(msg)
# Run CEAlign
# CEAlign returns the best N paths, where each path is a pair of lists
# with aligned atom indices. Paths are not guaranteed to be unique.
paths = run_cealign(self.refcoord, coord, self.window_size,
self.max_gap)
unique_paths = {(tuple(pA), tuple(pB)) for pA, pB in paths}
# Iterate over unique paths and find the one that gives the lowest
# corresponding RMSD. Use QCP to align the molecules.
best_rmsd, best_u = 1e6, None
for u_path in unique_paths:
idxA, idxB = u_path
coordsA = np.array([self.refcoord[i] for i in idxA])
coordsB = np.array([coord[i] for i in idxB])
aln = QCPSuperimposer()
aln.set(coordsA, coordsB)
aln.run()
if aln.rms < best_rmsd:
best_rmsd = aln.rms
best_u = (aln.rot, aln.tran)
if best_u is None:
raise RuntimeError("Failed to find a suitable alignment.")
if transform:
# Transform all atoms
rotmtx, trvec = best_u
for chain in structure.get_chains():
for resid in chain.get_unpacked_list():
for atom in resid.get_unpacked_list():
atom.transform(rotmtx, trvec)
self.rms = best_rmsd
def calc_rmsd(self, source_atoms, target_atoms):
from math import sqrt
import numpy as np
from Bio.PDB.QCPSuperimposer import QCPSuperimposer
if len(source_atoms) != len(target_atoms):
return -1
source_arr = []
for atom in source_atoms:
xyz = [atom.coord[0], atom.coord[1], atom.coord[2]]
source_arr.append(xyz)
source_arr = np.array(source_arr)
target_arr = []
for atom in target_atoms:
xyz = [atom.coord[0], atom.coord[1], atom.coord[2]]
target_arr.append(xyz)
target_arr = np.array(target_arr)
sup = QCPSuperimposer()
sup.set(source_arr, target_arr)
sup.run()
return sup.get_rms()
"C module in Bio.QCPSuperimposer not compiled")
# start with two coordinate sets (Nx3 arrays - Float0)
x = array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]], 'f')
y = array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]], 'f')
sup = QCPSuperimposer()
# set the coords
# y will be rotated and translated on x
sup.set(x, y)
# do the qcp fit
sup.run()
# get the rmsd
rms = sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran = sup.get_rotran()
# rotate y on x manually
"Install NumPy if you want to use Bio.QCPSuperimposer.")
from Bio import BiopythonExperimentalWarning
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio.PDB.QCPSuperimposer import QCPSuperimposer
# start with two coordinate sets (Nx3 arrays - Float0)
x = array([[51.65, -1.90, 50.07], [50.40, -1.23, 50.65], [50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]], 'f')
y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58], [52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]], 'f')
sup = QCPSuperimposer()
# set the coords
# y will be rotated and translated on x
sup.set(x, y)
# do the qcp fit
sup.run()
# get the rmsd
rms = sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran = sup.get_rotran()
# rotate y on x manually
class QCPSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07], [50.40, -1.23, 50.65],
[50.68, -0.04, 51.54], [50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58],
[52.36, -1.20, 48.03], [52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
# Public methods
def test_set(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
def test_run(self):
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3),
around(calc_rot, decimals=3)))
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3),
around(calc_tran, decimals=3)))
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.rms), calc_rms)
self.assertIsNone(self.sup.init_rms)
def test_get_transformed(self):
self.sup.run()
transformed_coords = array([[49.05456082, -1.23928381, 50.58427566],
[50.02204971, -0.39367917, 51.42494181],
[51.47738545, -0.57287128, 51.06760944],
[52.39602307, -0.98417088, 52.03318837]])
self.assertTrue(
array_equal(around(self.sup.get_transformed(), decimals=3),
around(transformed_coords, decimals=3)))
def test_get_init_rms(self):
x = array([[1.1, 1.2, 1.3], [1.4, 1.5, 1.6], [1.7, 1.8, 1.9]])
y = array([[1.0, 1.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = array([0.81, 0.9, 0.98])
self.assertTrue(
array_equal(around(self.sup.get_init_rms(), decimals=2),
around(init_rms, decimals=2)))
def test_get_rotran(self):
self.sup.run()
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
rot, tran = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot, decimals=3), around(calc_rot, decimals=3)))
self.assertTrue(
array_equal(around(tran, decimals=3), around(calc_tran,
decimals=3)))
def test_get_rms(self):
self.sup.run()
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.get_rms()), calc_rms)
# Old test from Bio/PDB/QCPSuperimposer/__init__.py
def test_oldTest(self):
x = array([[-2.803, -15.373, 24.556], [0.893, -16.062, 25.147],
[1.368, -12.371, 25.885], [-1.651, -12.153, 28.177],
[-0.440, -15.218, 30.068], [2.551, -13.273, 31.372],
[0.105, -11.330, 33.567]])
y = array([[-14.739, -18.673, 15.040], [-12.473, -15.810, 16.074],
[-14.802, -13.307, 14.408], [-17.782, -14.852, 16.171],
[-16.124, -14.617, 19.584], [-15.029, -11.037, 18.902],
[-18.577, -10.001, 17.996]])
self.sup.set(x, y)
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(y, decimals=3)))
self.sup.run()
rot = array([[0.72216358, 0.69118937, -0.0271479],
[-0.52038257, 0.51700833, -0.67963547],
[-0.45572112, 0.50493528, 0.73304748]])
tran = array([11.68878393, -4.13245037, 6.05208344])
rms = 0.7191064509622271
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3),
around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3),
around(tran, decimals=3)))
self.assertEqual(float('%.3f' % self.sup.rms), around(rms, decimals=3))
rms_get = self.sup.get_rms()
self.assertTrue(
array_equal(around(rms_get, decimals=3), around(rms, decimals=3)))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran,
decimals=3)))
y_on_x1 = dot(y, rot) + tran
y_x_solution = array([[3.90787281, -16.37976032, 30.16808376],
[3.58322456, -12.81122728, 28.91874135],
[1.3580194, -13.96815768, 26.05958411],
[-0.79347336, -15.93647897, 28.48288439],
[-1.27379224, -12.9456459, 30.78004989],
[-2.03519089, -10.6822696, 27.81728956],
[-4.72366028, -13.05646024, 26.54536695]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3),
around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3),
around(y_x_solution, decimals=3)))
class QCPSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
# Public methods
def test_set(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
def test_run(self):
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(calc_rot, decimals=3)))
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(calc_tran, decimals=3)))
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.rms), calc_rms)
self.assertIsNone(self.sup.init_rms)
def test_get_transformed(self):
self.sup.run()
transformed_coords = array([[49.05456082, -1.23928381, 50.58427566],
[50.02204971, -0.39367917, 51.42494181],
[51.47738545, -0.57287128, 51.06760944],
[52.39602307, -0.98417088, 52.03318837]])
self.assertTrue(
array_equal(around(self.sup.get_transformed(), decimals=3), around(transformed_coords, decimals=3)))
def test_get_init_rms(self):
x = array([[1.1, 1.2, 1.3],
[1.4, 1.5, 1.6],
[1.7, 1.8, 1.9]])
y = array([[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = array([0.81, 0.9, 0.98])
self.assertTrue(
array_equal(around(self.sup.get_init_rms(), decimals=2), around(init_rms, decimals=2)))
def test_get_rotran(self):
self.sup.run()
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
rot, tran = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot, decimals=3), around(calc_rot, decimals=3)))
self.assertTrue(
array_equal(around(tran, decimals=3), around(calc_tran, decimals=3)))
def test_get_rms(self):
self.sup.run()
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.get_rms()), calc_rms)
# Old test from Bio/PDB/QCPSuperimposer/__init__.py
def test_oldTest(self):
x = array([[-2.803, -15.373, 24.556],
[0.893, -16.062, 25.147],
[1.368, -12.371, 25.885],
[-1.651, -12.153, 28.177],
[-0.440, -15.218, 30.068],
[2.551, -13.273, 31.372],
[0.105, -11.330, 33.567]])
y = array([[-14.739, -18.673, 15.040],
[-12.473, -15.810, 16.074],
[-14.802, -13.307, 14.408],
[-17.782, -14.852, 16.171],
[-16.124, -14.617, 19.584],
[-15.029, -11.037, 18.902],
[-18.577, -10.001, 17.996]])
self.sup.set(x, y)
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(y, decimals=3)))
self.sup.run()
rot = array([[0.72216358, 0.69118937, -0.0271479],
[-0.52038257, 0.51700833, -0.67963547],
[-0.45572112, 0.50493528, 0.73304748]])
tran = array([11.68878393, -4.13245037, 6.05208344])
rms = 0.7191064509622271
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(tran, decimals=3)))
self.assertEqual(float('%.3f' % self.sup.rms), around(rms, decimals=3))
rms_get = self.sup.get_rms()
self.assertTrue(
array_equal(around(rms_get, decimals=3), around(rms, decimals=3)))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran, decimals=3)))
y_on_x1 = dot(y, rot) + tran
y_x_solution = array([[3.90787281, -16.37976032, 30.16808376],
[3.58322456, -12.81122728, 28.91874135],
[1.3580194, -13.96815768, 26.05958411],
[-0.79347336, -15.93647897, 28.48288439],
[-1.27379224, -12.9456459, 30.78004989],
[-2.03519089, -10.6822696, 27.81728956],
[-4.72366028, -13.05646024, 26.54536695]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3), around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3), around(y_x_solution, decimals=3)))
from Bio.PDB.QCPSuperimposer import QCPSuperimposer sup = QCPSuperimposer() # set the coords # y will be rotated and translated on x sup.set(x, y) # do the lsq fit sup.run() # get the rmsd rms = sup.get_rms()