def moveSystem(self, moveVector):
"""move all the atoms in the loaded file
Args:
moveVector (np.array, 3, float): the vector of moving
"""
allAtoms = self.uObject.select_atoms('all')
transformations.translate(moveVector)(allAtoms)
def test_translate_coords(translate_universes):
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans = translate(vector)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_translate_coords(translate_universes):
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans = translate(vector)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_translate_transformations_api(translate_universes):
# test if the translate transformation works when using the
# on-the-fly transformations API
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans_u.trajectory.add_transformations(translate(vector))
assert_array_almost_equal(trans_u.trajectory.ts.positions, ref.positions, decimal=6)
def test_translate_transformations_api(translate_universes):
# test if the translate transformation works when using the
# on-the-fly transformations API
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans_u.trajectory.add_transformations(translate(vector))
assert_array_almost_equal(trans_u.trajectory.ts.positions,
ref.positions,
decimal=6)
def transformed(ref):
transformed = ref.reader(ref.trajectory)
transformed.add_transformations(translate([1, 1, 1]),
translate([0, 0, 0.33]))
return transformed
def transformed(ref):
return mda.Universe(PSF,
[DCD, CRD, DCD, CRD, DCD, CRD, CRD],
transformations=[translate([10,10,10])])
def transformed(ref):
transformed = ref.reader(ref.trajectory, convert_units=False)
transformed.add_transformations(translate([1, 1, 1]),
translate([0, 0, 0.33]))
return transformed
def test_translate_vector(translate_universes, vector):
# what happens if the vector argument is of wrong size?
ts = translate_universes[0].trajectory.ts
with pytest.raises(ValueError):
translate(vector)(ts)
def test_add_another_transformations_raises_ValueError(self, transformed):
# After defining the transformations, the workflow cannot be changed
with pytest.raises(ValueError):
transformed.add_transformations(translate([2,2,2]))
def test_list(self):
workflow = [translate([10, 10, 0]), translate([0, 0, 10])]
u = mda.Universe(PSF, DCD, transformations=workflow)
uref = mda.Universe(PSF, DCD)
ref = translate([10, 10, 10])(uref.trajectory.ts)
assert_almost_equal(u.trajectory.ts.positions, ref, decimal=6)
def test_translate_vector(translate_universes, vector):
# what happens if the vector argument is of wrong size?
ts = translate_universes[0].trajectory.ts
with pytest.raises(ValueError):
translate(vector)(ts)
def test_list(self):
workflow = [translate([10,10,0]), translate([0,0,10])]
u = mda.Universe(PSF,DCD, transformations=workflow)
uref = mda.Universe(PSF,DCD)
ref = translate([10,10,10])(uref.trajectory.ts)
assert_almost_equal(u.trajectory.ts.positions, ref, decimal=6)
def test_callable(self):
u = mda.Universe(PSF,DCD, transformations=translate([10,10,10]))
uref = mda.Universe(PSF,DCD)
ref = translate([10,10,10])(uref.trajectory.ts)
assert_almost_equal(u.trajectory.ts.positions, ref, decimal=6)
import sys import numpy as np import MDAnalysis as mda from MDAnalysis.analysis import align import MDAnalysis.transformations as trans from MDAnalysis.analysis.leaflet import LeafletFinder u = mda.Universe(sys.argv[1] + '.data', sys.argv[1] + '.xtc') ref = mda.Universe(sys.argv[1] + '.data') # Get box dimensions from first frame b = u.trajectory[0].dimensions[0:3] bbox = np.array([0, 0, 0, b[0], b[1], b[2]]).reshape(2, 3) # Align all frames to first frame on PH beads alignment = mda.analysis.align.AlignTraj(u, ref, select='type 2') alignment.run() # Translate box to centre buckle translator = [0.5 * bbox[1, 0], 0.5 * bbox[1, 1], 0.5 * bbox[1, 2]] # Feed transformations to trajectory wf = [trans.translate(translator), trans.wrap(u.atoms, compound='residues')] u.trajectory.add_transformations(*wf) # Write output u.atoms.write(sys.argv[1] + '_wrap.xtc', frames=u.trajectory[:])
def test_add_another_transformations_raises_ValueError(self, transformed):
# After defining the transformations, the workflow cannot be changed
with pytest.raises(ValueError):
transformed.add_transformations(translate([2, 2, 2]))
def test_callable(self):
u = mda.Universe(PSF, DCD, transformations=translate([10, 10, 10]))
uref = mda.Universe(PSF, DCD)
ref = translate([10, 10, 10])(uref.trajectory.ts)
assert_almost_equal(u.trajectory.ts.positions, ref, decimal=6)
def transformed(ref):
transformed = ref.reader(ref.trajectory, convert_units=False)
transformed.add_transformations(translate([1,1,1]), translate([0,0,0.33]))
return transformed
def transformed(ref):
return mda.Universe(PSF,
[DCD, CRD, DCD, CRD, DCD, CRD, CRD],
transformations=[translate([10,10,10])])
def transformed(ref):
transformed = ref.reader(ref.trajectory)
transformed.add_transformations(translate([1,1,1]), translate([0,0,0.33]))
return transformed
