def align_centroids_using_pca(ref_frames, ref_frames_reference):
"""
Align the centroids of 2 sets of rigid bodyes using PCA using their
reference frames. returns the best rmsd and the ref_frames to get it.
"""
if(len(ref_frames) != len(ref_frames_reference)):
raise ValueError("The number of reference frames must be the same")
Ts1 = [r.get_transformation_to() for r in ref_frames]
vs1 = [T.get_translation() for T in Ts1]
Ts2 = [r.get_transformation_to() for r in ref_frames_reference]
vs2 = [T.get_translation() for T in Ts2]
# align with PCA
pc1 = alg.get_principal_components(vs1)
pc2 = alg.get_principal_components(vs2)
pcTs = alg.get_alignments_from_first_to_second(pc1, pc2)
best_refs = []
best_rmsd = 1e5
for j, pcT in enumerate(pcTs):
new_Ts1 = [alg.compose(pcT, T) for T in Ts1]
new_vs1 = [T.get_translation() for T in new_Ts1]
r = atom.get_rmsd(new_vs1, vs2)
if(r < best_rmsd):
best_rmsd = r
best_refs = [alg.ReferenceFrame3D(T) for T in new_Ts1]
return best_rmsd, best_refs
def test_relative_position_mover(self, ):
""" Test the RelativePositionMover """
log.info("test RelativePositionMover")
fn_rec1 = self.get_input_file_name("1suvA_xlinked.pdb")
fn_rec2 = self.get_input_file_name("1suvC_xlinked.pdb")
fn_lig = self.get_input_file_name("1suvE_xlinked.pdb")
fn_tr1 = \
self.get_input_file_name("transforms-1suvA-1suvE_reduced.txt")
fn_tr2 = \
self.get_input_file_name("transforms-1suvC-1suvE_filtered.txt")
m = IMP.kernel.Model()
sel = atom.ATOMPDBSelector()
h_rec1 = atom.read_pdb(fn_rec1, m, sel)
rb_rec1 = atom.create_rigid_body(h_rec1)
rec1_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_rec1)]
h_rec2 = atom.read_pdb(fn_rec2, m, sel)
rb_rec2 = atom.create_rigid_body(h_rec2)
rec2_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_rec2)]
h_ligand = atom.read_pdb(fn_lig, m, sel)
rb_lig = atom.create_rigid_body(h_ligand)
Ts = get_relative_transforms(fn_tr1)
Tis1 = []
for i, T in enumerate(Ts):
V = get_internal_transform3(T, rb_rec1, rb_lig)
Tis1.append(V)
docked_refs1 = get_docked_reference_frames(Ts, rb_lig)
Ts = get_relative_transforms(fn_tr2)
Tis2 = []
for i, T in enumerate(Ts):
V = get_internal_transform3(T, rb_rec2, rb_lig)
Tis2.append(V)
docked_refs2 = get_docked_reference_frames(Ts, rb_lig)
mv = em2d.RelativePositionMover(rb_lig, 10, 20)
mv.add_internal_transformations(rb_rec1, Tis1)
mv.add_internal_transformations(rb_rec2, Tis2)
for i in range(2):
# prob_random = 0
ref_before = rb_lig.get_reference_frame()
ps = mv.propose() #_move(prob_random)
ref_after = rb_lig.get_reference_frame()
found = False
current_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_ligand)]
# check all possible reference frames where the ligand could be
for r in itertools.chain(docked_refs1, docked_refs2):
rb_lig.set_reference_frame(r)
docked_coords = [core.XYZ(l) for l in atom.get_leaves(h_ligand)]
rmsd = atom.get_rmsd(current_coords, docked_coords)
if rmsd < 0.1:
found = True
self.assertTrue(found, msg= "the proposed move is not " \
"in the relative solutions")
mv.accept()
def get_rmsd(hierarchy1, hierarchy2):
xyz1 = [core.XYZ(l) for l in atom.get_leaves(hierarchy1)]
xyz2 = [core.XYZ(l) for l in atom.get_leaves(hierarchy2)]
return atom.get_rmsd(xyz1, xyz2)
def get_rmsd(hierarchy1, hierarchy2):
xyz1 = [core.XYZ(l) for l in atom.get_leaves(hierarchy1)]
xyz2 = [core.XYZ(l) for l in atom.get_leaves(hierarchy2)]
return atom.get_rmsd(xyz1, xyz2)