def test_clone(self):
chain1 = Chain('A', [Residue('ALA', 1), Residue('MET', 2)])
chain2 = chain1.clone()
assert len(chain1.residues) == len(chain2.residues) and \
chain1.residues[0].name == chain2.residues[0].name
chain1.residues[0].name = 'MET'
assert chain1.residues[0].name != chain2.residues[0].name
def test_clone(self):
chain1 = Chain('A', [Residue('ALA',1), Residue('MET',2)])
chain2 = chain1.clone()
assert len(chain1.residues) == len(chain2.residues) and \
chain1.residues[0].name == chain2.residues[0].name
chain1.residues[0].name = 'MET'
assert chain1.residues[0].name != chain2.residues[0].name
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 parse_complex_from_file(input_file_name,
atoms_to_ignore=[],
verbose=False):
"""Reads and parses a given input_file_name PDB file.
TODO: Check if chain have been already created and insert it into the first one
"""
lines = open(input_file_name).readlines()
atoms = []
residues = []
chains = []
num_models = 0
last_chain_id = '#'
last_residue_name = '#'
last_residue_number = '#'
current_chain = None
current_residue = None
for line in lines:
# Only first model is going to be read
if num_models <= 1:
line_type = line[0:6].strip()
if line_type == "MODEL":
num_models += 1
if num_models > 1:
log.warning(
'Multiple models found in %s. Only first model will be used.'
% input_file_name)
elif line_type == "ATOM" or line_type == "HETATM":
try:
atom = read_atom_line(line, line_type, atoms_to_ignore)
atoms.append(atom)
except PDBParsingWarning as warning:
if verbose:
print(warning)
continue
if last_chain_id != atom.chain_id:
last_chain_id = atom.chain_id
current_chain = Chain(last_chain_id)
chains.append(current_chain)
if last_residue_name != atom.residue_name or last_residue_number != atom.residue_number:
last_residue_name = atom.residue_name
last_residue_number = atom.residue_number
current_residue = Residue(atom.residue_name,
atom.residue_number)
residues.append(current_residue)
current_chain.residues.append(current_residue)
current_residue.atoms.append(atom)
# Set backbone and side-chain atoms
for residue in residues:
residue.set_backbone_and_sidechain()
try:
residue.check()
except Exception as e:
log.warning("Possible problem: %s" % str(e))
return atoms, residues, chains
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_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 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__to_string(self):
chain = Chain('A', [Residue('ALA', 1), Residue('MET', 2)])
assert "[Chain A]\nALA.1\nMET.2" == str(chain)
def test_create_chain(self):
chain = Chain('A', [Residue('ALA', 1), Residue('MET', 2)])
assert chain.cid == 'A' and len(chain.residues) == 2
def test_create_empty_chain(self):
chain = Chain()
assert chain.cid == '' and chain.peptide and len(chain.residues) == 0