def test_dimer_tags(self):
"""Checks the DSSP data tagged to a coiled-coil dimer."""
cc_di = specs.CoiledCoil(2)
cc_packed = pack_side_chains_scwrl(cc_di, cc_di.basis_set_sequences)
tag_dssp_data(cc_packed)
for residue in cc_packed.get_monomers():
self.assertTrue('dssp_data' in residue.tags)
def test_helix_non_canonical_lower(self, sequence):
"""Test Scwrl sidechain packing using upper and lower case labels."""
helix = ampal.Assembly(specs.Helix(5))
helix = pack_side_chains_scwrl(helix, [sequence])
r_seq = sequence[:]
non_can = [x for x in sequence if x.upper() not in cannonical_labels]
if non_can:
for aa in non_can:
r_seq = r_seq.replace(aa, 'G')
self.assertEqual(helix.sequences, [r_seq.upper()])
else:
self.assertEqual(helix.sequences, [r_seq.upper()])
def test_helix_non_canonical(self, sequence):
"""Test Scwrl sidechain packing when given non-cannonical residue labels."""
helix = ampal.Assembly(specs.Helix(5))
helix = pack_side_chains_scwrl(helix, [sequence])
non_can = [x for x in sequence if x not in cannonical_labels]
r_seq = sequence
if non_can:
for aa in non_can:
r_seq = r_seq.replace(aa, 'G')
self.assertEqual(helix.sequences, [r_seq])
else:
self.assertEqual(helix.sequences, [r_seq])
def test_convert_pro_to_hyp(self):
col = specs.CoiledCoil.tropocollagen(aa=21)
col = pack_side_chains_scwrl(col, ['GPPGPPGPPGPPGPPGPPGPP'] * 3)
to_convert = [
res for (i, res) in enumerate(col.get_monomers())
if not (i + 1) % 3
]
ori_pros = copy.deepcopy(to_convert)
for pro in to_convert:
convert_pro_to_hyp(pro)
self.assertEqual(col.sequences, ['GPXGPXGPXGPXGPXGPXGPX'] * 3)
hyps = to_convert
self.assertEqual(len(hyps), 7 * 3)
hyp_atom_labels = ('N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OD1')
common_atoms = ('N', 'CA', 'C', 'O', 'CB')
for (pro, hyp) in zip(ori_pros, hyps):
for (label, atom) in hyp.atoms.items():
self.assertTrue(label in hyp_atom_labels)
if label in common_atoms:
self.assertTrue(
numpy.allclose(atom.array, hyp[label].array))
def test_basis_set_tetramer(self):
"""Test packing basis set tetramer model."""
cc_tet = specs.CoiledCoil(4)
cc_packed = pack_side_chains_scwrl(cc_tet, cc_tet.basis_set_sequences)
self.assertEqual(cc_packed.sequences, cc_tet.basis_set_sequences)
def test_basis_set_dimer(self):
"""Test packing basis set dimer model."""
cc_di = specs.CoiledCoil(2)
cc_packed = pack_side_chains_scwrl(cc_di, cc_di.basis_set_sequences)
self.assertEqual(cc_packed.sequences, cc_di.basis_set_sequences)
def test_helix_seq_packing(self, sequence):
"""Test Scwrl sidechain packing using a small helix."""
helix = ampal.Assembly(specs.Helix(5))
helix = pack_side_chains_scwrl(helix, [sequence])
self.assertEqual(helix.sequences, [sequence])