def test_distance(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', 1, '', x=1., y=2., z=2.,
occupancy=1., b_factor=0., element=None, mass=None)
atom2 = Atom()
assert_almost_equals(3.0, atom1.distance(atom2))
assert_almost_equals(3.0, atom2.distance(atom1))
def test_clone(self):
atom1 = Atom()
atom2 = atom1.clone()
assert atom1 == atom2
assert not atom1 != atom2
atom1.name = 'C'
assert atom1 != atom2
def test_reference_points_singular_matrix(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', x=2., y=2., z=2.)
atom2 = Atom(2, 'CB', '', 'A', 'ALA', x=0., y=0., z=0.)
atom3 = Atom(3, 'C', '', 'A', 'ALA', x=1., y=1., z=1.)
atoms = [atom1, atom2, atom3]
docking_model = DockingModel(atoms, SpacePoints([[2., 2., 2.], [0., 0., 0.], [1., 1., 1.]]))
expected_coordinates = SpacePoints([[1., 1., 1.]])
assert expected_coordinates == docking_model.reference_points
def test_clone(self):
atom1 = Atom()
atom2 = atom1.clone()
assert atom1 == atom2
assert not atom1 != atom2
atom1.name = 'C'
assert atom1 != atom2
def test_apply_restraints(self):
swarm_centers = [[13.861446721229493, -28.730453433364488, 0.024305878079852336],
[-29.427540743780476, -2.960299745528308, -5.168493906227671],
[24.244162925019417, 2.9322386764307304, -15.44286271885186],
[2.0463687050893857, -13.94537658944639, -24.099372234598455],
[-10.833120242061193, 13.517315520348813, -20.69794891072167],
[-10.934383879949547, 24.302392364266915, 4.508648686944662],
[-13.742376304140548, -18.137915011405447, 12.54861921589357],
[-6.5003433948735, 7.824777098389764, 23.942006739050495],
[17.345254847698744, 18.209853942307866, 6.384609403593564],
[13.837506572006518, -7.152838167487336, 18.165186863034638]]
distance_cutoff = 19.522956365520056
translation = [-21.630461302211305, -5.510320024570013, -20.27116646191647]
atoms = [Atom(atom_number=1, atom_name='N', x=25.344, y=-10.048, z=26.435),
Atom(atom_number=2, atom_name='CA', x=26.439, y=-10.798, z=26.994),
Atom(atom_number=3, atom_name='C', x=26.646, y=-12.135, z=26.328),
Atom(atom_number=4, atom_name='O', x=27.790, y=-12.531, z=26.028),
Atom(atom_number=5, atom_name='CB', x=26.230, y=-10.933, z=28.503),
Atom(atom_number=6, atom_name='CG', x=26.448, y=-9.540, z=29.191),
Atom(atom_number=7, atom_name='CD', x=26.283, y=-9.676, z=30.689),
Atom(atom_number=8, atom_name='CE', x=26.609, y=-8.392, z=31.454),
Atom(atom_number=9, atom_name='NZ', x=26.210, y=-8.498, z=32.884)]
receptor_restraints = [Residue('LYS', 239, atoms=atoms)]
expected_new_centers = [[13.861446721229493, -28.730453433364488, 0.024305878079852336],
[13.837506572006518, -7.152838167487336, 18.165186863034638]]
new_centers = apply_restraints(swarm_centers, receptor_restraints, [], distance_cutoff, translation)
assert np.allclose(expected_new_centers, new_centers)
def test_reference_points_minimum_volume_ellipsoid(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', x=1.2, y=-1., z=2.)
atom2 = Atom(2, 'CB', '', 'A', 'ALA', x=0., y=0., z=0.)
atom3 = Atom(3, 'C', '', 'A', 'ALA', x=0.5, y=3., z=0.5)
atom4 = Atom(4, 'N', '', 'A', 'ALA', x=0.85, y=-2.5, z=0.4)
atoms = [atom1, atom2, atom3, atom4]
docking_model = DockingModel(atoms, SpacePoints([[1.2, -1., 2.], [0., 0., 0.],
[0.5, 3., 0.5], [0.85, -2.5, 0.4]]))
# Only center is used now
expected_coordinates = SpacePoints([[0.6375, -0.125, 0.725]])
assert expected_coordinates == docking_model.reference_points
def test_get_atom(self):
atoms = [Atom(1, 'CA', '', 'A', 'ALA'), Atom(2, 'N', '', 'A', 'ALA')]
residue = Residue('ALA', 1, atoms)
atom1 = residue.get_atom('CA')
atom2 = residue.get_atom('N')
atom3 = residue.get_atom('CG')
assert 'CA' == atom1.name
assert 'N' == atom2.name
assert None == atom3
def test_backbone_sidechain(self):
atoms = [Atom(1, 'CA', '', 'A', 'ALA'),
Atom(2, 'N', '', 'A', 'ALA'),
Atom(3, 'C', '', 'A', 'ALA'),
Atom(4, 'O', '', 'A', 'ALA'),
Atom(5, 'CB', '', 'A', 'ALA')]
residue = Residue('ALA', 1, atoms)
assert 1 == len(residue.sidechain)
assert 'CB' == residue.sidechain[0].name
assert 4 == len(residue.backbone)
def test_get_atom(self):
atoms = [Atom(1, 'CA', '', 'A', 'ALA'), Atom(2, 'N', '', 'A', 'ALA')]
residue = Residue('ALA', 1, atoms)
atom1 = residue.get_atom('CA')
atom2 = residue.get_atom('N')
atom3 = residue.get_atom('CG')
assert atom1.name == "CA"
assert atom2.name == "N"
assert atom3 is None
def test_backbone_sidechain(self):
atoms = [
Atom(1, 'CA', '', 'A', 'ALA'),
Atom(2, 'N', '', 'A', 'ALA'),
Atom(3, 'C', '', 'A', 'ALA'),
Atom(4, 'O', '', 'A', 'ALA'),
Atom(5, 'CB', '', 'A', 'ALA')
]
residue = Residue('ALA', 1, atoms)
assert len(residue.sidechain) == 1
assert residue.sidechain[0].name == "CB"
assert len(residue.backbone) == 4
def test_translate(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', x=2., y=2., z=2.)
atom2 = Atom(2, 'CB', '', 'A', 'ALA', x=0., y=0., z=0.)
residues = [Residue('ALA', 1, [atom1, atom2])]
docking_model = DockingModel(residues, SpacePoints([[2., 2., 2.], [0, 0, 0]]))
docking_model.translate([-2, -2, -2])
expected_coordinates = SpacePoints([[0, 0, 0], [-2, -2, -2]])
assert expected_coordinates == docking_model.coordinates[0]
expected_coordinates = SpacePoints([[-1, -1, -1]])
assert np.allclose(expected_coordinates, docking_model.reference_points)
def test_translate(self):
atom1 = Atom(2, 'C', '', 'A', 'ALA', x=2., y=2., z=2.)
atom2 = Atom(2, 'C', '', 'A', 'ALA', x=0., y=0., z=0.)
residue = Residue('ALA', 1, [atom1, atom2])
chains = [Chain('A', [residue])]
protein = Complex(chains)
com = protein.center_of_mass()
protein.translate([c * -1 for c in com])
expected_coordinates = np.array([[1, 1, 1], [-1, -1, -1]])
assert (expected_coordinates == protein.atom_coordinates).all()
def setUp(self):
self.atoms1 = [
Atom(1, 'CA', '', 'A', 'ALA', x=1., y=1., z=1.),
Atom(2, 'N', '', 'A', 'ALA', x=2., y=2., z=2.)
]
self.atoms2 = [
Atom(3, 'CA', '', 'A', 'HIS', x=1.1, y=1.2, z=1.3),
Atom(4, 'N', '', 'A', 'HIS', x=2.9, y=2.8, z=2.7)
]
self.residues = [
Residue('ALA', 1, self.atoms1),
Residue('HIS', 2, self.atoms2)
]
def test_null_rotation(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', x=2., y=2., z=2.)
atom2 = Atom(2, 'CB', '', 'A', 'ALA', x=0., y=0., z=0.)
atom3 = Atom(3, 'C', '', 'A', 'ALA', x=0.5, y=0.5, z=0.5)
atoms = [atom1, atom2, atom3]
docking_model = DockingModel(atoms, SpacePoints([[2., 2., 2.], [0., 0., 0.], [0.5, 0.5, 0.5]]))
q = Quaternion()
docking_model.rotate(q)
expected_coordinates = SpacePoints([[2., 2., 2.], [0., 0., 0.], [0.5, 0.5, 0.5]])
assert expected_coordinates == docking_model.coordinates[0]
expected_coordinates = SpacePoints([[0.833333333333, 0.833333333333, 0.833333333333]])
assert np.allclose(expected_coordinates, docking_model.reference_points)
def test_move_to_origin(self):
atom1 = Atom(2, 'C', '', 'A', 'ALA', x=0., y=0., z=0.)
atom2 = Atom(2, 'C', '', 'A', 'ALA', x=2., y=2., z=2.)
atom3 = Atom(2, 'C', '', 'A', 'ALA', x=4., y=4., z=4.)
residue = Residue('ALA', 1, [atom1, atom2, atom3])
chains = [Chain('A', [residue])]
protein = Complex(chains)
protein.move_to_origin()
expected_coordinates = np.array([[-2., -2., -2.], [0, 0, 0],
[2., 2., 2.]])
assert (expected_coordinates == protein.atom_coordinates).all()
def test_null_rotation_one_atom(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', x=2., y=2., z=2.)
atoms = [atom1]
docking_model = DockingModel(atoms, SpacePoints([[2., 2., 2.]]))
q = Quaternion()
docking_model.rotate(q)
expected_coordinates = np.array([[2., 2., 2.]])
assert (expected_coordinates == docking_model.coordinates).all()
def read_atom_line(line, line_type='', atoms_to_ignore=[]):
"""Parses a PDB file line starting with 'ATOM' or 'HETATM'"""
element = cstrip(line[76:78])
try:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
if math.isnan(x) or math.isnan(y) or math.isnan(z):
raise Exception()
except:
raise PDBParsingError("Wrong coordinates in '%s'" % line)
try:
atom_number = int(line[6:11])
except ValueError:
raise PDBParsingError("Wrong atom number in '%s'" % line)
atom_name = cstrip(line[12:16])
atom_alternative = cstrip(line[16])
residue_name = cstrip(line[17:21])
chain_id = cstrip(line[21])
residue_ext = line[26]
try:
residue_number = int(line[22:26])
except ValueError:
raise PDBParsingError("Wrong residue number in '%s'" % line)
if ('H' in atoms_to_ignore and atom_name[0] == 'H') or atom_name in atoms_to_ignore:
raise PDBParsingWarning("Ignored atom %s.%s.%s %s" % (chain_id,
residue_name,
residue_number,
atom_name))
try:
occupancy = float(line[54:60])
except:
occupancy = 1.0
try:
b_factor = float(line[60:66])
except:
b_factor = 0.0
if not line_type:
line_type = line[0:6].strip()
if line_type == 'ATOM':
return Atom(atom_number, atom_name, atom_alternative, chain_id,
residue_name, residue_number, residue_ext,
x, y, z, occupancy, b_factor, element)
else:
return HetAtom(atom_number, atom_name, atom_alternative, chain_id,
residue_name, residue_number, residue_ext,
x, y, z, occupancy, b_factor, element)
def test_apply_restraints_only_blocking(self):
swarm_centers = [
[13.861446721229493, -28.730453433364488, 0.024305878079852336],
[-29.427540743780476, -2.960299745528308, -5.168493906227671],
[24.244162925019417, 2.9322386764307304, -15.44286271885186],
[2.0463687050893857, -13.94537658944639, -24.099372234598455],
[-10.833120242061193, 13.517315520348813, -20.69794891072167],
[-10.934383879949547, 24.302392364266915, 4.508648686944662],
[-13.742376304140548, -18.137915011405447, 12.54861921589357],
[-6.5003433948735, 7.824777098389764, 23.942006739050495],
[17.345254847698744, 18.209853942307866, 6.384609403593564],
[13.837506572006518, -7.152838167487336, 18.165186863034638]
]
distance_cutoff = 19.522956365520056
translation = [
-21.630461302211305, -5.510320024570013, -20.27116646191647
]
atoms = [
Atom(atom_number=1, atom_name='N', x=30.795, y=-14.563, z=19.577),
Atom(atom_number=2, atom_name='CA', x=30.969, y=-13.948, z=18.287),
Atom(atom_number=3, atom_name='C', x=32.148, y=-12.988, z=18.291),
Atom(atom_number=4, atom_name='O', x=32.601, y=-12.684, z=19.413),
Atom(atom_number=5, atom_name='CB', x=29.742, y=-13.163, z=17.861),
Atom(atom_number=6, atom_name='CG', x=28.586, y=-14.066, z=17.510),
Atom(atom_number=7, atom_name='OD1', x=28.470, y=-14.548,
z=16.359),
Atom(atom_number=8, atom_name='ND2', x=27.742, y=-14.322, z=18.456)
]
blocking_restraints = [Residue('ASN', 245, atoms=atoms)]
expected_new_centers = [
[-29.427540743780476, -2.960299745528308, -5.168493906227671],
[24.244162925019417, 2.9322386764307304, -15.44286271885186],
[2.0463687050893857, -13.94537658944639, -24.099372234598455],
[-10.833120242061193, 13.517315520348813, -20.69794891072167],
[-10.934383879949547, 24.302392364266915, 4.508648686944662],
[-13.742376304140548, -18.137915011405447, 12.54861921589357],
[-6.5003433948735, 7.824777098389764, 23.942006739050495],
[17.345254847698744, 18.209853942307866, 6.384609403593564],
[13.837506572006518, -7.152838167487336, 18.165186863034638]
]
new_centers = apply_restraints(swarm_centers, [], blocking_restraints,
distance_cutoff, translation)
assert np.allclose(expected_new_centers, new_centers)
def test_to_string(self):
atom1 = Atom(1,
'CA',
'',
'A',
'ALA',
1,
'',
x=1.,
y=2.,
z=2.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
assert " CA 1.000 2.000 2.000" == str(atom1)
def test_assign_element_and_mass_of_not_recognized_element(self):
atom = Atom(1,
'Ty',
'',
'A',
'BSG',
1,
'',
x=0.,
y=0.,
z=0.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
assert atom.name != 'Ty'
def test_assign_element_and_mass(self):
atom = Atom(1,
'CA',
'',
'A',
'ALA',
1,
'',
x=0.,
y=0.,
z=0.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
assert 'C' == atom.element
assert_almost_equals(Atom.MASSES[atom.element], atom.mass)
def test_create_atom_not_given_element(self):
atom = Atom(1,
'PB',
'',
'A',
'ALA',
1,
'',
x=0.,
y=0.,
z=0.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
assert 'PB' == atom.element
assert_almost_equals(Atom.MASSES[atom.element], atom.mass)
def test_not_recognized_element(self):
"""Test if Tylium is recognized"""
atom = Atom(1,
'Ty',
'',
'A',
'BSG',
1,
'',
x=0.,
y=0.,
z=0.,
occupancy=1.,
b_factor=0.,
element='Ty',
mass=None)
assert atom.name != 'Ty'
def test_is_hydrogen(self):
atom1 = Atom(1,
'CA',
'',
'A',
'ALA',
1,
'',
x=1.,
y=2.,
z=-3.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
atom2 = Atom()
assert not atom1.is_hydrogen() and atom2.is_hydrogen()
def test_distance(self):
atom1 = Atom(1,
'CA',
'',
'A',
'ALA',
1,
'',
x=1.,
y=2.,
z=2.,
occupancy=1.,
b_factor=0.,
element=None,
mass=None)
atom2 = Atom()
assert_almost_equals(3.0, atom1.distance(atom2))
assert_almost_equals(3.0, atom2.distance(atom1))
def setUp(self):
self.atoms1 = [
Atom(1, 'CA', '', 'A', 'ALA', x=1., y=1., z=1.),
Atom(2, 'N', '', 'A', 'ALA', x=2., y=2., z=2.)
]
self.atoms2 = [
Atom(3, 'CA', '', 'A', 'HIS', x=1.1, y=1.2, z=1.3),
Atom(4, 'N', '', 'A', 'HIS', x=2.9, y=2.8, z=2.7)
]
self.residues = [
Residue('ALA', 1, self.atoms1),
Residue('HIS', 2, self.atoms2)
]
self.chains = [Chain('A', self.residues)]
self.atoms3 = [
Atom(1, 'N', '', 'A', 'CYS', 3, x=2.496, y=13.096, z=10.611),
Atom(2, 'CA', '', 'A', 'CYS', 3, x=2.787, y=12.161, z=9.557),
Atom(3, 'C', '', 'A', 'CYS', 3, x=4.052, y=11.431, z=9.896),
Atom(4, 'O', '', 'A', 'CYS', 3, x=5.120, y=12.044, z=9.912),
Atom(5, 'CB', '', 'A', 'CYS', 3, x=2.879, y=12.853, z=8.246),
Atom(6, 'SG', '', 'A', 'CYS', 3, x=3.492, y=11.911, z=6.838)
]
self.atoms4 = [
Atom(7, 'N', '', 'A', 'PRO', 4, x=3.987, y=10.183, z=10.286),
Atom(8, 'CA', '', 'A', 'PRO', 4, x=5.219, y=9.484, z=10.695),
Atom(9, 'C', '', 'A', 'PRO', 4, x=6.277, y=9.424, z=9.662),
Atom(10, 'O', '', 'A', 'PRO', 4, x=5.993, y=9.385, z=8.431),
Atom(11, 'CB', '', 'A', 'PRO', 4, x=4.664, y=8.140, z=11.092),
Atom(12, 'CG', '', 'A', 'PRO', 4, x=3.295, y=8.087, z=10.812),
Atom(13, 'CD', '', 'A', 'PRO', 4, x=2.797, y=9.351, z=10.427)
]
self.residues2 = [
Residue('CYS', 1, self.atoms3),
Residue('PRO', 2, self.atoms4)
]
self.chains2 = [Chain('A', self.residues2)]
self.path = os.path.dirname(os.path.realpath(__file__))
self.test_path = self.path + '/scratch/'
try:
shutil.rmtree(self.test_path)
except:
pass
os.mkdir(self.test_path)
self.golden_data_path = os.path.normpath(
os.path.dirname(os.path.realpath(__file__))) + '/golden_data/'
def test_create_empty_atom(self):
atom = Atom()
assert_almost_equals(0.0, atom.x)
def __init__(self):
self.atoms1 = [
Atom(1, 'CA', '', 'A', 'ALA', x=1., y=1., z=1.),
Atom(2, 'N', '', 'A', 'ALA', x=2., y=2., z=2.)
]
self.atoms2 = [
Atom(3, 'CA', '', 'A', 'HIS', x=1.1, y=1.2, z=1.3),
Atom(4, 'N', '', 'A', 'HIS', x=2.9, y=2.8, z=2.7)
]
self.residues = [
Residue('ALA', 1, self.atoms1),
Residue('HIS', 2, self.atoms2)
]
self.chains = [Chain('A', self.residues)]
self.atoms3 = [
Atom(1, 'N', '', 'A', 'CYS', 3, x=2.496, y=13.096, z=10.611),
Atom(2, 'CA', '', 'A', 'CYS', 3, x=2.787, y=12.161, z=9.557),
Atom(3, 'C', '', 'A', 'CYS', 3, x=4.052, y=11.431, z=9.896),
Atom(4, 'O', '', 'A', 'CYS', 3, x=5.120, y=12.044, z=9.912),
Atom(5, 'CB', '', 'A', 'CYS', 3, x=2.879, y=12.853, z=8.246),
Atom(6, 'SG', '', 'A', 'CYS', 3, x=3.492, y=11.911, z=6.838)
]
self.atoms4 = [
Atom(7, 'N', '', 'A', 'PRO', 4, x=3.987, y=10.183, z=10.286),
Atom(8, 'CA', '', 'A', 'PRO', 4, x=5.219, y=9.484, z=10.695),
Atom(9, 'C', '', 'A', 'PRO', 4, x=6.277, y=9.424, z=9.662),
Atom(10, 'O', '', 'A', 'PRO', 4, x=5.993, y=9.385, z=8.431),
Atom(11, 'CB', '', 'A', 'PRO', 4, x=4.664, y=8.140, z=11.092),
Atom(12, 'CG', '', 'A', 'PRO', 4, x=3.295, y=8.087, z=10.812),
Atom(13, 'CD', '', 'A', 'PRO', 4, x=2.797, y=9.351, z=10.427)
]
self.residues2 = [
Residue('CYS', 1, self.atoms3),
Residue('PRO', 2, self.atoms4)
]
self.chains2 = [Chain('A', self.residues2)]
self.path = Path(__file__).absolute().parent
self.test_path = self.path / 'scratch_complex'
self.golden_data_path = self.path / 'golden_data'
def test_to_string(self):
atoms = [Atom(1, 'CA', '', 'A', 'ALA'), Atom(2, 'N', '', 'A', 'ALA')]
residue = Residue('ALA', 1, atoms)
assert "ALA.1 CA 0.000 0.000 0.000\nALA.1 N 0.000 0.000 0.000" == str(residue)
def test_create_residue_with_atoms(self):
residue = Residue('ALA', 1, [Atom(), Atom()])
assert residue.name == 'ALA' and residue.number == 1 and len(residue.atoms) == 2
def dummy(x=0., y=0., z=0.):
atom = Atom(atom_name='CA', residue_name='DUM', x=x, y=y, z=z)
return Residue(residue_name='DUM', residue_number=0, atoms=[atom])
def test_is_backbone(self):
atom1 = Atom(1, 'CA', '', 'A', 'ALA', 1, '', x=1., y=2., z=-3.,
occupancy=1., b_factor=0., element=None, mass=None)
atom2 = Atom()
assert atom1.is_backbone() and not atom2.is_backbone()
