class ResiduesTest(ut.TestCase):
def setUp(self):
self.structure = Structure([nts.nt77_9, nts.nt78_9, nts.nt79_9,
nts.nt80_9], pdb="1S72")
def test_can_get_sequence_from_all_residues(self):
self.assertEquals(['A', 'G', 'U', 'A'], self.structure.sequence)
def test_can_iterate_over_all_residues(self):
val = list(self.structure.residues())
self.assertEquals([nts.nt77_9, nts.nt78_9, nts.nt79_9, nts.nt80_9],
val)
def test_can_select_residues(self):
val = list(self.structure.residues(sequence='A'))
self.assertEquals([nts.nt77_9, nts.nt80_9], val)
def test_skip_iterating_over_nonpolymeric_by_default(self):
self.structure._residues.append(nts.nt212_0)
val = list(self.structure.residues())
self.assertEquals([nts.nt77_9, nts.nt78_9, nts.nt79_9, nts.nt80_9],
val)
def test_giving_polymeric_is_none_iterates_overall(self):
self.structure._residues.append(nts.nt212_0)
val = list(self.structure.residues(polymeric=None))
ans = [nts.nt77_9, nts.nt78_9, nts.nt79_9, nts.nt80_9, nts.nt212_0]
self.assertEquals(ans, val)
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 structure(self):
"""Get the structure from the Cif file.
:returns: The first structure in the cif file.
"""
pdb = self.data.getName()
residues = self.__residues__(pdb)
return Structure(list(residues), pdb=pdb)
class FindingAResidueTest(ut.TestCase):
def setUp(self):
self.structure = Structure([nts.nt77_9, nts.nt78_9, nts.nt79_9,
nts.nt80_9], pdb="1S72")
def test_can_find_residue_by_unit_id(self):
val = self.structure.residue('1S72||9|U|79')
self.assertEquals(nts.nt79_9, val)
def test_can_find_residue_by_index(self):
val = self.structure.residue(1)
self.assertEquals(nts.nt78_9, val)
def test_can_find_residues_by_negative_index(self):
val = self.structure.residue(-1)
self.assertEquals(nts.nt80_9, val)
def test_can_find_by_unit_id_residue_even_when_unordered(self):
shuffle(self.structure._residues)
val = self.structure.residue('1S72||9|U|79')
self.assertEquals(nts.nt79_9, val)
def test_raises_exception_if_missing_unit_id(self):
self.assertRaises(IndexError, lambda: self.structure.residue('bob'))
def test_raises_exception_if_missing_index(self):
self.assertRaises(IndexError, lambda: self.structure.residue(1000000))
def coordinates(self, pdb, residue):
"""Compute a string of the coordinates in CIF format (the atom_site
block) for the given residue. Exclude the header and trailing lines
that are part of the atom_site entries, because these entries are meant
to be concatenated together for the coordinate server later.
Parameters
----------
pdb : str
The PDB id to use.
residue : fr3d.data.Component
The residue to convert.
Returns
-------
coordinates : str
A string that represents CIF-formatted data for the given residue.
"""
structure = Structure([residue], pdb=pdb)
sio = StringIO()
writer = CifAtom(sio, unit_ids=False, protect_lists_of_lists=True)
writer(structure)
raw = sio.getvalue()
coords = []
for line in raw.split('\n'):
# Exclude header/comment lines that start with: 1) "data_",
# 2) "loop_", 3) "_", or 4) "#".
if not line or \
line.startswith('data_') or \
line.startswith('loop_') or \
line[0] in set('_#'):
continue
coords.append(line)
return '\n'.join(coords)
def test_empty_structure_is_false(self):
val = Structure([])
self.assertFalse(bool(val))
def setUp(self):
self.structure = Structure([nts.nt77_9, nts.nt78_9, nts.nt79_9,
nts.nt80_9], pdb="1S72")
def test_selecting_a_subset_updates_unit_id(self):
val = Structure([], pdb='1S72').select(model=1).unit_id()
self.assertEquals('1S72|1', val)
def test_has_a_unit_id(self):
val = Structure([], pdb='1S72').unit_id()
self.assertEquals('1S72', val)
def test_no_residues_is_0_length(self):
val = Structure([])
self.assertEquals(0, len(val))
def test_length_is_number_of_residues(self):
val = Structure([1])
self.assertEquals(1, len(val))
def test_non_empty_structure_is_true(self):
val = Structure([1])
self.assertTrue(bool(val))