def as_unit(self, unit_id):
"""Turn a unit id into a Unit.
:param str unit_id: The unit id.
"""
parts = fuid.decode(unit_id)
del parts['component_id']
del parts['atom_name']
return Unit(**parts)
def as_unit(self, unit_id):
"""Turn a unit id into a Unit.
:param str unit_id: The unit id.
"""
parts = fuid.decode(unit_id)
del parts['component_id']
del parts['atom_name']
return Unit(**parts)
def test_decodes_full_atom_id(self):
val = decode("2AVY|1|A|C|50|C1'|A|c|6_555")
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'alt_id': 'A',
'insertion_code': 'c',
'symmetry': '6_555'
}
self.assertEqual(val, ans)
def test_decodes_short_with_default_data(self):
val = decode('2AVY|1|A|C|50')
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
}
self.assertEqual(val, ans)
def test_decodes_full_atom_id(self):
val = decode("2AVY|1|A|C|50|C1'|A|c|6_555")
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'alt_id': 'A',
'insertion_code': 'c',
'symmetry': '6_555'
}
self.assertEqual(val, ans)
def test_decodes_a_full_residue_id(self):
val = decode('2AVY|1|A|C|50||||1_555')
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
}
self.assertEquals(val, ans)
def test_decodes_a_full_residue_id(self):
val = decode('2AVY|1|A|C|50||||1_555')
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
}
self.assertEquals(val, ans)
def test_decodes_short_with_default_data(self):
val = decode('2AVY|1|A|C|50')
ans = {
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
}
self.assertEqual(val, ans)
def too_many_sym_ops(self, loop):
"""Detect if we have only 1 symmetry operator in this loop. This is
an invalid loop.
:param dict loop: The loop to examine.
:returns: Bool, true if there is more symmetry operator.
"""
ops = set()
for unit in loop['nts']:
parts = decode(unit)
ops.add(parts['symmetry'])
if loop['type'] == 'HL':
return len(ops) != 1
if loop['type'] == 'IL':
return len(ops) > 2
if loop['type'] == 'J3':
return len(ops) > 3
def too_many_sym_ops(self, loop):
"""Detect if we have only 1 symmetry operator in this loop. This is
an invalid loop.
:param dict loop: The loop to examine.
:returns: Bool, true if there is more symmetry operator.
"""
ops = set()
for unit in loop['nts']:
parts = decode(unit)
ops.add(parts['symmetry'])
if loop['type'] == 'HL':
return len(ops) != 1
if loop['type'] == 'IL':
return len(ops) > 2
if loop['type'] == 'J3':
return len(ops) > 3
def compatabile_units(self, unit_id1, unit_id2):
unit1 = decode(unit_id1)
unit2 = decode(unit_id2)
return unit1['model'] == unit2['model'] and \
unit1['symmetry'] == unit2['symmetry']
def test_resets_the_index(self):
chain_of = lambda d: decode(d['unit_id'])['chain']
chain_a = [d['index'] for d in self.data if chain_of(d) == 'A']
chain_b = [d['index'] for d in self.data if chain_of(d) == 'B']
assert chain_a == range(0, 158)
assert chain_b == range(0, 158)
def test_can_get_for_both_chains(self):
ans = set('AB')
assert set(decode(d['unit_id'])['chain'] for d in self.data) == ans
assert set(d['seq_id'].split('|')[2] for d in self.data) == ans
def chain_of(self, uid):
return decode(uid)['chain']
def test_can_generate_mappings(self):
mapping = self.cif.experimental_sequence_mapping('1')
val = decode(next(mapping)[2])
self.assertEquals('P_1', val['symmetry'])
def test_round_trips_an_id(self):
ans = '2AVY|1|A|C|50'
val = encode(decode(ans))
self.assertEqual(val, ans)
def test_maps_both_symmetry_operators(self):
ops = set(decode(d['unit_id'])['symmetry'] for d in self.data)
assert ops == set(['P_P', 'P_1'])
def test_can_generate_mapping_to_model_0(self):
mapping = self.cif.experimental_sequence_mapping('B')
val = decode(next(mapping)[2])
self.assertEquals(0, val['model'])
def test_round_trips_an_id(self):
ans = '2AVY|1|A|C|50'
val = encode(decode(ans))
self.assertEqual(val, ans)
def test_can_generate_mappings(self):
mapping = self.cif.experimental_sequence_mapping('1')
val = decode(next(mapping)[2])
self.assertEquals('P_1', val['symmetry'])
def test_can_generate_mapping_to_model_0(self):
mapping = self.cif.experimental_sequence_mapping('B')
val = decode(next(mapping)[2])
self.assertEquals(0, val['model'])
def test_it_uses_a_single_symmetry_operator(self):
units = [pos.unit_id for pos in self.positions]
sym_ops = set(decode(uid)['symmetry'] for uid in units)
assert sym_ops == set(['1_555'])
