def test_encodes_short_residue_id_without_sequence(self):
val = encode({
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_number': '50',
})
ans = '2AVY|1|A||50'
self.assertEqual(val, ans)
def test_encodes_short_residue_id_without_sequence(self):
val = encode({
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_number': '50',
})
ans = '2AVY|1|A||50'
self.assertEqual(val, ans)
def test_encodes_residue_id_with_numbers(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
})
ans = '2AVY|1|A|C|50'
self.assertEqual(val, ans)
def test_encodes_residue_id_with_numbers(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
})
ans = '2AVY|1|A|C|50'
self.assertEqual(val, ans)
def unit_id(self):
"""Get the unit id for this structure
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'symmetry': self.symmetry
})
def test_encodes_residue_id_without_sequence(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_number': 50,
'symmetry': '6_555'
})
ans = '2AVY|1|A||50||||6_555'
self.assertEqual(val, ans)
def test_encodes_full_residue_id_using_defaults(self):
val = encode({
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_id': 'C',
'component_number': '50',
}, full=True)
ans = '2AVY|1|A|C|50||||1_555'
self.assertEqual(val, ans)
def test_encodes_residue_id_without_sequence(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_number': 50,
'symmetry': '6_555'
})
ans = '2AVY|1|A||50||||6_555'
self.assertEqual(val, ans)
def unit_id(self):
"""Get the unit id for this structure
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'symmetry': self.symmetry
})
def test_encodes_short_residue_id_with_default_symmetry(self):
val = encode({
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_id': 'C',
'component_number': '50',
'symmetry': '1_555'
})
ans = '2AVY|1|A|C|50'
self.assertEqual(val, ans)
def test_encodes_short_residue_id_with_default_symmetry(self):
val = encode({
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_id': 'C',
'component_number': '50',
'symmetry': '1_555'
})
ans = '2AVY|1|A|C|50'
self.assertEqual(val, ans)
def test_can_generate_full_atom_id_missing_stuff(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'symmetry': '6_555'
}, full=True)
ans = "2AVY|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_encodes_full_residue_id_using_defaults(self):
val = encode(
{
'pdb': '2AVY',
'model': '1',
'chain': 'A',
'component_id': 'C',
'component_number': '50',
},
full=True)
ans = '2AVY|1|A|C|50||||1_555'
self.assertEqual(val, ans)
def test_can_generate_short_atom_id(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'alt_id': '',
'insertion_code': '',
'symmetry': '1_555'
})
ans = "2AVY|1|A|C|50|C1'"
self.assertEqual(val, ans)
def test_can_generate_short_atom_id(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'alt_id': '',
'insertion_code': '',
'symmetry': '1_555'
})
ans = "2AVY|1|A|C|50|C1'"
self.assertEqual(val, ans)
def test_encodes_full_residue_id(self):
val = encode({
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
}, full=True)
ans = '2AVY|1|A|C|50||||1_555'
self.assertEqual(val, ans)
def test_can_generate_full_atom_id_missing_stuff(self):
val = encode(
{
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'symmetry': '6_555'
},
full=True)
ans = "2AVY|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_generate_short_with_missing_and_extra(self):
val = encode({
'pdb': '1GID',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'symmetry': '6_555',
'x': -1,
'y': 0,
'z': 0,
})
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def unit_id(self):
"""Create the unit id for this Atom.
:returns: The unit id string.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.component_id,
'component_number': self.component_number,
'atom_name': self.name,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def test_generate_short_with_missing_and_extra(self):
val = encode({
'pdb': '1GID',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': "C1'",
'symmetry': '6_555',
'x': -1,
'y': 0,
'z': 0,
})
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def unit_id(self):
"""Create the unit id for this Atom.
:returns: The unit id string.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.component_id,
'component_number': self.component_number,
'atom_name': self.name,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def unit_id(self):
"""Compute the unit id of this Component.
:returns: The unit id.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.sequence,
'component_number': self.number,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def test_encodes_full_residue_id(self):
val = encode(
{
'pdb': '2AVY',
'model': 1,
'chain': 'A',
'component_id': 'C',
'component_number': 50,
'atom_name': None,
'alt_id': None,
'insertion_code': None,
'symmetry': '1_555'
},
full=True)
ans = '2AVY|1|A|C|50||||1_555'
self.assertEqual(val, ans)
def component_unit_id(self):
"""Generate the unit id of the component this atom belongs to.
:returns: A string of the unit id for this atom's component.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.component_id,
'component_number': self.component_number,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def component_unit_id(self):
"""Generate the unit id of the component this atom belongs to.
:returns: A string of the unit id for this atom's component.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.component_id,
'component_number': self.component_number,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def unit_id(self):
"""Compute the unit id of this Component.
:returns: The unit id.
"""
return encode({
'pdb': self.pdb,
'model': self.model,
'chain': self.chain,
'component_id': self.sequence,
'component_number': self.number,
'alt_id': self.alt_id,
'insertion_code': self.insertion_code,
'symmetry': self.symmetry
})
def test_round_trips_an_id(self):
ans = '2AVY|1|A|C|50'
val = encode(decode(ans))
self.assertEqual(val, ans)
def test_round_trips_an_id(self):
ans = '2AVY|1|A|C|50'
val = encode(decode(ans))
self.assertEqual(val, ans)
