def test_rmsd_rotated_and_translated(self):
s1 = self.get_test_structure()
s2 = self.get_test_structure()
# rotate and translate s2
AXIS_DIRECTION = np.array([11, 2, 0])
AXIS_DIRECTION = AXIS_DIRECTION / np.linalg.norm(
AXIS_DIRECTION) # following code expects a unit vector
ANGLE = np.pi / 4
TRANSLATION = np.array([1, 200, 7])
atoms = list(s2.get_atoms())
coords = np.array([a.get_coord() for a in atoms])
rotation = Rotation.from_rotvec(ANGLE * AXIS_DIRECTION)
for atom, new_coord in zip(atoms,
rotation.apply(coords) + TRANSLATION):
atom.set_coord(new_coord)
# test rmsd is still 0
chain_a = ChainResidues.from_bio_chain(s1[0]['A'])
chain_a_rotated = ChainResidues.from_bio_chain(s2[0]['A'])
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rmsd = GetRMSD((get_centered_c_alpha_coords,
GetRotationMatrix(
(get_centered_c_alpha_coords, ))))
rmsd = get_rmsd(chain_a, chain_a_rotated)
self.assertAlmostEqual(0, rmsd, places=4)
def test_rmsd_pheromone_binding_protein_paper(self):
apo = self.load_test_structure('2fjy')
holo = self.load_test_structure('1dqe')
apo_chain = apo[0]['A']
holo_chain = holo[0]['A']
# # logging.root.setLevel(logging.INFO)
# self.assertTrue(sequences_same(apo_chain, holo_chain))
# chains also have leading and trailing residues not present in the other, remove them
apo_pp = chain_to_polypeptide(apo_chain)[:-5]
holo_pp = chain_to_polypeptide(holo_chain)[6:]
# analyze just A chain (like in the paper)
apo_residues = ChainResidues(list(apo_pp), apo.id, apo_chain.id)
holo_residues = ChainResidues(list(holo_pp), holo.id, holo_chain.id)
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rmsd = GetRMSD((get_centered_c_alpha_coords,
GetRotationMatrix(
(get_centered_c_alpha_coords, ))))
rmsd = get_rmsd(apo_residues, holo_residues)
self.assertAlmostEqual(7, rmsd,
delta=1) # todo 6.24 (vs 7.0 in the paper)
def test_rmsd_guanylate_kinase_paper(self):
apo = self.load_test_structure('1ex6')
holo = self.load_test_structure('1ex7')
apo_chain = apo[0][
'B'] # note that different chain (as by dyndom), why?
holo_chain = holo[0]['A']
logging.root.setLevel(logging.INFO)
self.assertTrue(sequences_same(apo_chain, holo_chain))
# analyze just A chain (like in the paper)
apo_residues = ChainResidues.from_bio_chain(apo_chain)
holo_residues = ChainResidues.from_bio_chain(holo_chain)
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rmsd = GetRMSD((get_centered_c_alpha_coords,
GetRotationMatrix(
(get_centered_c_alpha_coords, ))))
rmsd = get_rmsd(apo_residues, holo_residues)
self.assertAlmostEqual(4.4, rmsd,
delta=0.1) # 4.37 (vs 4.4 Å in the paper)
def run_analyses_for_isoform_group(
apo_codes: List[str], holo_codes: List[str], get_structure,
serializer_or_analysis_handler: AnalysisHandler):
# apo-holo analyses
get_main_chain = GetMainChain((GetChains(), ))
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rotation_matrix = GetRotationMatrix((get_centered_c_alpha_coords, ))
get_hinge_angle = GetHingeAngle(
(get_c_alpha_coords, get_centroid, get_rotation_matrix))
get_rmsd = GetRMSD((get_centered_c_alpha_coords, get_rotation_matrix))
get_ss = GetSecondaryStructureForStructure()
get_ss = mulproc_lru_cache(get_ss, m)
ss_a = CompareSecondaryStructure((get_ss, ))
interdomain_surface_a = GetInterfaceBuriedArea((GetSASAForStructure(), ))
comparators_of_apo_holo__residues_param = [get_rmsd, interdomain_surface_a]
comparators_of_apo_holo__residue_ids_param = [ss_a]
comparators_of_apo_holo_domains__residues_param = [
get_rmsd, interdomain_surface_a
]
comparators_of_apo_holo_domains__residue_ids_param = [ss_a]
comparators_of_apo_holo_2domains__residues_param = [get_hinge_angle]
get_domains = GetDomainsForStructure()
def test_interdomain_surface_paper(self):
s1, (s1_mapping,
s1_entity_poly_seqs) = self.load_test_structure('1vr6')
s2, (s2_mapping,
s2_entity_poly_seqs) = self.load_test_structure('1rzm')
# analyze just A chain (like in the paper)
s1_chain_a = s1[0]['A']
s2_chain_a = s2[0]['A']
c1_mapping = s1_mapping[0]['A']
c2_mapping = s2_mapping[0]['A']
# divide into domains exactly like in the paper
# todo check that label_seq_ids do correspond to those (changed it now) NO they dont, use bio residue mapping
# todo s1d1, ....
d1 = DomainResidueMapping(
'D1', 'A', [1], [64]
) # can reuse the domain for both structures (here for testing purposes)
d2 = DomainResidueMapping('D2', 'A', [65], [338])
s1d1 = DomainResidues.from_domain(d1, s1[0], c1_mapping)
s1d2 = DomainResidues.from_domain(d2, s1[0], c1_mapping)
s2d1 = DomainResidues.from_domain(d1, s2[0], c2_mapping)
s2d2 = DomainResidues.from_domain(d2, s2[0], c2_mapping)
interdomain_surface_computer = GetInterfaceBuriedArea(
(GetSASAForStructure(), ))
apo__domain_interface_area = interdomain_surface_computer(s1d1, s1d2)
holo__domain_interface_area = interdomain_surface_computer(s2d1, s2d2)
# *2 = 218, 933 vs paper -- 288, 1024 # oni to asi nedělej dvěma..., ale priblibzne to odpovida
self.assertAlmostEqual(288,
apo__domain_interface_area,
delta=0.3 * 288) # 218
self.assertAlmostEqual(1024,
holo__domain_interface_area,
delta=0.3 * 1024) # 933
# rmsd
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rotation_matrix = GetRotationMatrix(
(get_centered_c_alpha_coords, ))
get_rmsd = GetRMSD((get_centered_c_alpha_coords, get_rotation_matrix))
print(get_rmsd(
s1d1 + s1d2,
s2d1 + s2d2)) # 10.1 vs 8.0 in paper, todo celkem velky rozdil...
# hinge
get_hinge_angle = GetHingeAngle(
(get_c_alpha_coords, get_centroid, get_rotation_matrix))
screw_motion = get_hinge_angle(s1d1, s1d2, s2d1, s2d2)
self.assertAlmostEqual(147, 180 / np.pi * screw_motion.angle, delta=2)
def test_get_hinge_angle(self):
s1 = self.get_test_structure()
s2 = self.get_test_structure()
s2.id = f'{s1.id}_with_rotated_chain'
s1d1 = ChainResidues.from_bio_chain(s1[0]['A'])
s1d2 = ChainResidues.from_bio_chain(s1[0]['B'])
s2d1 = ChainResidues.from_bio_chain(s2[0]['A'])
s2d2 = ChainResidues.from_bio_chain(s2[0]['B'])
# rotate second domain over a defined screw axis, then check if GetHingeAngle indeed computes the correct parameters (angle, translation)
# define the screw axis
AXIS_DIRECTION = np.array([1, 2, 0])
AXIS_DIRECTION = AXIS_DIRECTION / np.linalg.norm(
AXIS_DIRECTION) # following code expects a unit vector
AXIS_LOCATION = np.array([
52.71183395385742, 44.92530822753906, -11.425999641418457
]) # a random pivot point (the axis goes through it)
ANGLE = np.pi / 4
TRANSLATION_IN_AXIS = 3
# move along the screw axis using scipy
s2d2_atoms = [atom for residue in s2d2 for atom in residue]
s2d2_atom_coords = np.array([atom.coord for atom in s2d2_atoms])
rotation = Rotation.from_rotvec(ANGLE * AXIS_DIRECTION)
rotated_s2d2_atom_coords = rotation.apply(
s2d2_atom_coords - AXIS_LOCATION) + AXIS_LOCATION
for atom, new_coord in zip(
s2d2_atoms, rotated_s2d2_atom_coords +
AXIS_DIRECTION * TRANSLATION_IN_AXIS):
atom.set_coord(new_coord)
# compute the hinge angle with GetHingeAngle
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_hinge_angle = GetHingeAngle((get_c_alpha_coords, get_centroid,
GetRotationMatrix(
(get_centered_c_alpha_coords, ))))
screw_motion = get_hinge_angle(s1d1, s1d2, s2d1, s2d2)
self.assertAlmostEqual(ANGLE, screw_motion.angle, places=3)
self.assertAlmostEqual(TRANSLATION_IN_AXIS,
screw_motion.translation_in_axis,
places=3)
def test_rmsd_translated(self):
s = self.get_test_structure()
chain_a_copy = s[0]['A'].copy()
# move the copy by 1 angstrom
for atom in chain_a_copy.get_atoms():
atom.coord += (1, 0, 0)
chain_a = ChainResidues([r for r in s[0]['A'] if is_aa(r)], s.id, 'A')
chain_a_copy = ChainResidues([r for r in chain_a_copy if is_aa(r)],
f'moved_{s.id}', 'A')
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rmsd = GetRMSD((get_centered_c_alpha_coords,
GetRotationMatrix(
(get_centered_c_alpha_coords, ))))
rmsd = get_rmsd(chain_a, chain_a_copy)
self.assertAlmostEqual(0, rmsd, places=5)
def test_hinge_guanylate_kinase_paper(self):
apo = self.load_test_structure('1ex6')
holo = self.load_test_structure('1ex7')
apo_chain = apo[0][
'B'] # note that different chain (as by dyndom), why?
holo_chain = holo[0]['A']
logging.root.setLevel(logging.INFO)
self.assertTrue(sequences_same(apo_chain, holo_chain))
apo_d1 = DomainResidues.from_domain(
DomainResidueMapping('D1', 'B', [200 + 1, 200 + 84],
[200 + 32, 200 + 186]), apo)
apo_d2 = DomainResidues.from_domain(
DomainResidueMapping('D2', 'B', [200 + 33], [200 + 83]), apo)
# zmena chainu preci nepomahala, tak kde je zakopany pes?
holo_d1 = DomainResidues.from_domain(
DomainResidueMapping('D1', 'A', [1, 84], [32, 186]), holo)
holo_d2 = DomainResidues.from_domain(
DomainResidueMapping('D2', 'A', [33], [83]), holo)
get_c_alpha_coords = GetCAlphaCoords()
get_centroid = GetCentroid((get_c_alpha_coords, ))
get_centered_c_alpha_coords = GetCenteredCAlphaCoords(
(get_c_alpha_coords, get_centroid))
get_rotation_matrix = GetRotationMatrix(
(get_centered_c_alpha_coords, ))
get_hinge_angle = GetHingeAngle(
(get_c_alpha_coords, get_centroid, get_rotation_matrix))
screw_motion = get_hinge_angle(apo_d1, apo_d2, holo_d1, holo_d2)
self.assertAlmostEqual(
47, 180 / np.pi * screw_motion.angle,
delta=0.2) # in paper: dyndom: 47°, their principal axes 43.9