def test_centering_broken_mol():
ref_struct_filepath = os.path.join(root_dir, 'test_data/ala_centered.gro')
ref_top_filepath = os.path.join(root_dir, 'test_data/top.tpr')
other_filepath = os.path.join(root_dir, 'test_data/ala_shifted_broken.gro')
ref_univ = MDAnalysis.Universe(ref_top_filepath, ref_struct_filepath)
other_univ = MDAnalysis.Universe(ref_top_filepath, other_filepath)
center_mol(other_univ)
np.testing.assert_array_almost_equal(ref_univ.atoms.positions,
other_univ.atoms.positions,
decimal=2)
def check_centering(ref_filepath, ref_toppath, other_glob):
u_ref = MDAnalysis.Universe(ref_toppath, ref_filepath)
ref_com = u_ref.select_atoms(sel_spec_nowall).center_of_mass()
try:
ref_close_atoms = u_ref.select_atoms('around {:.2f} ({})'.format(
DIST_CUTOFF, sel_spec_nowall))
ref_pos = ref_close_atoms.positions
except NoDataError:
ref_close_atoms = None
other_paths = glob.glob(other_glob)
for other_filepath in other_paths:
u_other = MDAnalysis.Universe(ref_toppath, other_filepath)
# apply centering or rotating function
center_mol(u_other)
other_com = u_other.select_atoms(sel_spec_nowall).center_of_mass()
err_msg = 'Center of masses of mol not equal within precision'
np.testing.assert_array_almost_equal(ref_com,
other_com,
err_msg=err_msg,
decimal=2)
np.testing.assert_array_almost_equal(
u_ref.select_atoms(sel_spec_nowall).positions,
u_other.select_atoms(sel_spec_nowall).positions,
decimal=2)
if ref_close_atoms is not None:
other_pos = u_other.atoms[ref_close_atoms.indices].positions
rms = np.sqrt((np.sum((ref_pos - other_pos)**2, axis=1)).mean())
assert rms < RMSD_TOL, "RMSD ({}) is greater than tolerance ({}) for atoms within {:.2f} A".format(
rms, RMSD_TOL, DIST_CUTOFF)
def test_align_prot_struct():
top_file_path = os.path.join(root_dir, 'test_data/ubiq/ubiq.tpr')
ref_struct_path = os.path.join(root_dir,
'test_data/ubiq/ubiq_reference.gro')
other_struct_path = os.path.join(root_dir, 'test_data/ubiq/ubiq_other.gro')
ref_univ = MDAnalysis.Universe(top_file_path, ref_struct_path)
other_univ = MDAnalysis.Universe(top_file_path, other_struct_path)
center_mol(ref_univ)
center_mol(other_univ)
# Rotationally align according to all protein heavies
rotate_mol(other_univ, ref_univ, mol_spec=sel_spec_heavies_nowall)
ref_mol = ref_univ.select_atoms(sel_spec_heavies_nowall)
other_mol = ref_univ.select_atoms(sel_spec_heavies_nowall)
rms = np.sqrt(
(np.sum((ref_mol.atoms.positions - other_mol.atoms.positions)**2,
axis=1)).mean())
assert rms < 5.0, "RMSD ({}) is greater than {} A".format(rms)
def test_align_prot_after_shift():
top_file_path = os.path.join(root_dir, 'test_data/ubiq/ubiq.tpr')
ref_struct_path = os.path.join(root_dir,
'test_data/ubiq/ubiq_reference.gro')
ref_univ = MDAnalysis.Universe(top_file_path, ref_struct_path)
center_mol(ref_univ)
box = ref_univ.dimensions[:3]
assert np.array_equal(ref_univ.dimensions[3:],
np.ones(3) * 90), "Not a cubic box!"
other_univ = MDAnalysis.Universe(top_file_path, ref_struct_path)
center_mol(other_univ)
com = other_univ.select_atoms(sel_spec_nowall).center_of_mass()
# Rotate the system randomly
rot_vector = np.random.random((3))
is_neg = np.random.random(3) > 0.5
rot_vector[is_neg] = -rot_vector[is_neg]
degree_to_rot = np.random.random() * 360.0
curr_rot_mat = rotation_matrix(rot_vector, degree_to_rot)
# Rotate about protein's COM
init_positions = other_univ.atoms.positions - com
new_positions = np.dot(init_positions, curr_rot_mat) + com
other_univ.atoms.positions = new_positions
# Shift all positions
shift_vec = np.random.random((3))
shift_vec /= np.sqrt(np.sum(shift_vec**2))
is_neg = np.random.random(3) > 0.5
shift_vec[is_neg] = -shift_vec[is_neg]
# Max shift of 10 A in any direction
dist_to_shift = np.random.random() * 5.0
shift_vec *= dist_to_shift
other_univ.atoms.positions += shift_vec
# ...and apply pbc
pbc(other_univ)
## No check we can retrieve original structure by centering
# and fitting the protein's heavy atoms
center_mol(other_univ)
new_com = other_univ.select_atoms(sel_spec_nowall).center_of_mass()
np.testing.assert_array_almost_equal(com, new_com, decimal=ARR_PREC_TIGHT)
rotate_mol(ref_univ, other_univ, sel_spec_heavies_nowall)
ref_mol = ref_univ.select_atoms(sel_spec_nowall)
other_mol = other_univ.select_atoms(sel_spec_nowall)
rmsd_mol = rmsd(ref_mol.positions, other_mol.positions)
assert rmsd_mol < 1e-4
## Make sure all waters within a reasonable distance of protein are still good
ref_close_waters = ref_univ.select_atoms(
'name OW and around {:.1f} {}'.format(PROT_DIST_CUTOFF,
sel_spec_nowall))
other_close_waters = other_univ.atoms[ref_close_waters.indices]
assert ref_close_waters.n_atoms > 1000
rmsd_waters = rmsd(ref_close_waters.positions,
other_close_waters.positions)
assert rmsd_waters < 1e-4
def go(self):
header_str = "fitspec: {}; rmsdspec: {}; fitspec_other: {}; rmsd_spec_other: {}".format(
self.sel_spec, self.rmsd_spec, self.sel_spec_other,
self.rmsd_spec_other)
n_frames = self.last_frame - self.start_frame
ndim = 2 if self.rmsd_spec is None else 3
self.rmsd_arr = np.zeros((self.n_frames, ndim))
self.ref_univ.atoms.write('fit_ref.gro')
if self.rmsd_spec is not None:
ref_struct = self.ref_univ.select_atoms(self.rmsd_spec)
other_struct = self.other_univ.select_atoms(self.rmsd_spec_other)
assert ref_struct.n_atoms == other_struct.n_atoms
self.rms_per_atom = np.zeros((self.n_frames, ref_struct.n_atoms))
if self.do_traj:
with MDAnalysis.Writer(self.outfile + ".xtc",
self.other_univ.atoms.n_atoms) as W:
for i_frame in range(self.start_frame, self.last_frame):
if i_frame % 100 == 0:
print("doing frame {} of {}".format(
i_frame, self.last_frame))
sys.stdout.flush()
curr_ts = self.other_univ.trajectory[i_frame]
center_mol(self.other_univ, do_pbc=False)
if not self.center_only:
rms = rotate_mol(self.ref_univ,
self.other_univ,
ref_spec=self.sel_spec,
other_spec=self.sel_spec_other)
self.rmsd_arr[i_frame - self.start_frame,
0] = curr_ts.time
self.rmsd_arr[i_frame - self.start_frame, 1] = rms
if i_frame == self.start_frame:
self.other_univ.atoms.write('first_frame_fit.gro')
W.write(self.other_univ.atoms)
if self.rmsd_spec is not None and not self.center_only:
rms_other = rmsd(ref_struct.atoms.positions,
other_struct.atoms.positions)
self.rmsd_arr[i_frame - self.start_frame,
2] = rms_other
self.rms_per_atom[i_frame -
self.start_frame, :] = np.sqrt(
np.sum(
(ref_struct.atoms.positions -
other_struct.atoms.positions
)**2,
axis=1))
else:
center_mol(self.other_univ, do_pbc=False, check_broken=False)
rms = rotate_mol(self.ref_univ,
self.other_univ,
ref_spec=self.sel_spec,
other_spec=self.sel_spec_other)
self.other_univ.atoms.write(self.outfile + ".gro")
self.rmsd_arr[0, 0] = 0.0
self.rmsd_arr[0, 1] = rms
if self.rmsd_spec is not None:
rms_other = rmsd(ref_struct.atoms.positions,
other_struct.atoms.positions)
self.rmsd_arr[0, 2] = rms_other
self.rms_per_atom[0, :] = np.sqrt(
np.sum((ref_struct.atoms.positions -
other_struct.atoms.positions)**2,
axis=1))
if self.rmsd_spec is not None:
avg_rms_per_atom = self.rms_per_atom.mean(axis=0)
self.other_univ.add_TopologyAttr('tempfactors')
other_struct.tempfactors = avg_rms_per_atom
other_struct.write('fit_per_atom_rmsd.pdb', bonds=None)
self.ref_univ.add_TopologyAttr('tempfactors')
ref_struct.tempfactors = avg_rms_per_atom
ref_struct.write('fit_ref_per_atom_rmsd.pdb', bonds=None)
# Save output
np.savetxt(self.rmsd_out, self.rmsd_arr, header=header_str)
np.savez_compressed('rms_per_atom.dat',
header=self.rmsd_spec,
rms_per_atom=self.rms_per_atom)