def test_calculate_starting_points_no_need_to_minimize(self):
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1PPE_rec.pdb')
receptor = Complex(chains, atoms)
atoms, residues, chains = parse_complex_from_file(
self.golden_data_path + '1PPE_lig.pdb')
ligand = Complex(chains, atoms)
# Move structures to origin
receptor_center = receptor.center_of_coordinates()
ligand_center = ligand.center_of_coordinates()
receptor_translation = [-1. * c for c in receptor_center]
ligand_translation = [-1. * c for c in ligand_center]
receptor.translate(receptor_translation)
ligand.translate(ligand_translation)
poses = FTDockCoordinatesParser.get_list_of_poses(
self.golden_data_path + '1PPE.ftdock', ligand_center)
assert 10000 == len(poses)
for i in range(5):
assert self.quaternions[i] == poses[i].q
for j in range(3):
assert_almost_equal(self.translations[i][j],
poses[i].translation[j])
def test_calculate_starting_points_no_need_to_minimize(self):
atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_rec.pdb')
receptor = Complex(chains, atoms)
atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_lig.pdb')
ligand = Complex(chains, atoms)
# Move structures to origin
receptor_center = receptor.center_of_coordinates()
ligand_center = ligand.center_of_coordinates()
receptor_translation = [-1.*c for c in receptor_center]
ligand_translation = [-1.*c for c in ligand_center]
receptor.translate(receptor_translation)
ligand.translate(ligand_translation)
poses = FTDockCoordinatesParser.get_list_of_poses(self.golden_data_path + '1PPE.ftdock',
ligand_center)
assert 10000 == len(poses)
for i in range(5):
assert self.quaternions[i] == poses[i].q
for j in range(3):
assert_almost_equal(self.translations[i][j], poses[i].translation[j])
def test_center_of_coordinates_zero_atoms(self):
protein = Complex(chains=[])
cc = protein.center_of_coordinates()
assert_almost_equals(0.0, cc[0])
assert_almost_equals(0.0, cc[1])
assert_almost_equals(0.0, cc[2])
def test_center_of_coordinates(self):
protein = Complex(chains=self.chains)
cc = protein.center_of_coordinates()
assert_almost_equals(1.75, cc[0])
assert_almost_equals(1.75, cc[1])
assert_almost_equals(1.75, cc[2])
def test_center_of_coordinates_zero_atoms(self):
protein = Complex(chains=[])
cc = protein.center_of_coordinates()
assert_almost_equals(0.0, cc[0])
assert_almost_equals(0.0, cc[1])
assert_almost_equals(0.0, cc[2])
def test_center_of_coordinates(self):
protein = Complex(chains=self.chains)
cc = protein.center_of_coordinates()
assert_almost_equals(1.75, cc[0])
assert_almost_equals(1.75, cc[1])
assert_almost_equals(1.75, cc[2])
