def setUp(self):
self.nt1 = Component(atoms=[
Atom(x=0, y=0, z=1, name='C1'),
Atom(x=0, y=0, z=0, name='C2'),
Atom(x=1, y=0, z=1, name='N'),
], sequence='A', model=1, chain='A', number=1, polymeric=True)
self.nt2 = Component(atoms=[
Atom(x=5, y=5, z=5, name='C1'),
Atom(x=5, y=5, z=5, name='C2'),
Atom(x=5, y=5, z=5, name='N'),
], sequence='U', model=1, chain='A', number=2, polymeric=True)
self.nt3 = Component(atoms=[
Atom(x=-5, y=-5, z=-5, name='C1'),
Atom(x=-5, y=-5, z=-5, name='C2'),
Atom(x=-5, y=-5, z=-5, name='N'),
], sequence='C', model=1, chain='A', number=3, polymeric=True)
self.nt4 = Component(atoms=[
Atom(x=0, y=0, z=3, name='C1'),
Atom(x=0, y=0, z=3, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='U', model=1, chain='A', number=4, polymeric=True)
self.nt5 = Component(atoms=[
Atom(x=0, y=0, z=8, name='C1'),
Atom(x=0, y=0, z=8, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='G', model=1, chain='A', number=5, polymeric=True)
structure = Structure([self.nt1, self.nt2, self.nt3, self.nt4,
self.nt5], pdb='0000', model='1')
self.pairs = Pairs(structure)
def pairs(self, first={}, second={}, distance={}):
"""Create an iterator for all pairs in the structure. The first and
second arguments are selectors, that is a dictionary that can contain
the same arguments given to the residues method. The third argument
distance is a dictionary
:first: A selector for the first item in the pair.
:second: A selector for the second item in the pair.
:distance: A
:returns: A iterator that will go over all matching pairs in the
structure.
"""
pairs = Pairs(self)
pairs.first(**first)
pairs.second(**second)
pairs.distance(**distance)
return pairs
def pairs(self, first={}, second={}, distance={}):
"""Create an iterator for all pairs in the structure. The first and
second arguments are selectors, that is a dictionary that can contain
the same arguments given to the residues method. The third argument
distance is a dictionary
:first: A selector for the first item in the pair.
:second: A selector for the second item in the pair.
:distance: A
:returns: A iterator that will go over all matching pairs in the
structure.
"""
pairs = Pairs(self)
pairs.first(**first)
pairs.second(**second)
pairs.distance(**distance)
return pairs
class PairsTest(ut.TestCase):
def setUp(self):
self.nt1 = Component(atoms=[
Atom(x=0, y=0, z=1, name='C1'),
Atom(x=0, y=0, z=0, name='C2'),
Atom(x=1, y=0, z=1, name='N'),
], sequence='A', model=1, chain='A', number=1, polymeric=True)
self.nt2 = Component(atoms=[
Atom(x=5, y=5, z=5, name='C1'),
Atom(x=5, y=5, z=5, name='C2'),
Atom(x=5, y=5, z=5, name='N'),
], sequence='U', model=1, chain='A', number=2, polymeric=True)
self.nt3 = Component(atoms=[
Atom(x=-5, y=-5, z=-5, name='C1'),
Atom(x=-5, y=-5, z=-5, name='C2'),
Atom(x=-5, y=-5, z=-5, name='N'),
], sequence='C', model=1, chain='A', number=3, polymeric=True)
self.nt4 = Component(atoms=[
Atom(x=0, y=0, z=3, name='C1'),
Atom(x=0, y=0, z=3, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='U', model=1, chain='A', number=4, polymeric=True)
self.nt5 = Component(atoms=[
Atom(x=0, y=0, z=8, name='C1'),
Atom(x=0, y=0, z=8, name='C2'),
Atom(x=0, y=0, z=3, name='N'),
], sequence='G', model=1, chain='A', number=5, polymeric=True)
structure = Structure([self.nt1, self.nt2, self.nt3, self.nt4,
self.nt5], pdb='0000', model='1')
self.pairs = Pairs(structure)
def test_can_get_all_pairs_by_attributes(self):
self.pairs.first(sequence='A')
self.pairs.second(sequence='U')
val = list(self.pairs)
ans = [(self.nt1, self.nt2), (self.nt1, self.nt4)]
self.assertEquals(ans, val)
def test_can_get_using_center_distance(self):
self.pairs.distance(use='center', cutoff=3.0)
val = list(self.pairs)
ans = [(self.nt1, self.nt4), (self.nt4, self.nt1)]
self.assertEquals(ans, val)
def test_can_get_using_atom_atom_distance(self):
self.pairs.distance(use='atoms', cutoff=3.0)
val = list(self.pairs)
ans = [(self.nt1, self.nt4), (self.nt1, self.nt5),
(self.nt4, self.nt1), (self.nt4, self.nt5),
(self.nt5, self.nt1), (self.nt5, self.nt4)]
self.assertEquals(ans, val)
def test_can_get_using_specific_atoms(self):
self.pairs.distance(use='atoms', cutoff=3.0, first_atoms=['C1', 'C2'],
second_atoms=['C2'])
val = list(self.pairs)
ans = [(self.nt1, self.nt4), (self.nt4, self.nt1)]
self.assertEquals(ans, val)
def test_can_get_using_atoms_by_definition_name(self):
self.pairs.distance(use='atoms', cutoff=4.0, first_atoms='base',
second_atoms='base')
val = list(self.pairs)
ans = [(self.nt1, self.nt4), (self.nt4, self.nt1)]
self.assertEquals(ans, val)
def test_can_get_using_definition_name(self):
self.pairs.distance(use='center', cutoff=3.0, first_atoms='base')
val = list(self.pairs)
ans = [(self.nt1, self.nt4), (self.nt4, self.nt1)]
self.assertEquals(ans, val)