def test_residue(self):
res = gemmi.Residue()
self.assertEqual(res.label_seq, None)
self.assertEqual(res.seqid.num, None)
res.label_seq = 1
self.assertEqual(res.label_seq, 1)
res.seqid.num = 2
self.assertEqual(res.seqid.num, 2)
res.label_seq = None
self.assertEqual(res.label_seq, None)
res.seqid.num = None
self.assertEqual(res.seqid.num, None)
for name in ['HOH', 'hoh', 'DOD', 'h2o', 'H2O', 'WAT']:
res.name = name
self.assertTrue(res.is_water())
for name in ['SO4', '', 'HO', 'hoho', 'oho']:
res.name = name
self.assertFalse(res.is_water())
def test_model_all(self):
model = gemmi.Model('1')
for name in 'ABCDEFG':
model.add_chain(gemmi.Chain(name))
expected = []
for cname in 'BCF':
chain = model[cname]
for _ in range(7):
chain.add_residue(gemmi.Residue())
for (r, name) in [(2, '0'), (2, '1'), (3, '2'), (5, '3')]:
a = gemmi.Atom()
a.name = cname + name
expected.append(a.name)
chain[r].add_atom(a)
self.assertEqual([cra.atom.name for cra in model.all()], expected)
st = gemmi.Structure()
st.add_model(model)
st.remove_empty_chains()
self.assertEqual([cra.atom.name for cra in model.all()], expected)
def get_masked_pdb(pdb: gemmi.Structure,
coord: Coord,
radius: float = 8.0) -> gemmi.Structure:
event_centoid = gemmi.Position(
coord.x,
coord.y,
coord.z,
)
new_structure = gemmi.Structure()
for model_i, model in enumerate(pdb):
new_model = gemmi.Model(model.name)
new_structure.add_model(new_model, pos=-1)
for chain_i, chain in enumerate(model):
new_chain = gemmi.Chain(chain.name)
new_structure[model_i].add_chain(new_chain, pos=-1)
for residue_i, residue in enumerate(chain):
new_residue = gemmi.Residue()
new_residue.name = residue.name
new_residue.seqid = residue.seqid
new_residue.subchain = residue.subchain
new_residue.label_seq = residue.label_seq
new_residue.het_flag = residue.het_flag
new_structure[model_i][chain_i].add_residue(new_residue,
pos=-1)
for atom_i, atom in enumerate(residue):
pos = atom.pos
if pos.dist(event_centoid) > radius:
new_structure[model_i][chain_i][residue_i].add_atom(
atom, pos=-1)
for model_i, model in enumerate(pdb):
pdb.add_model(new_structure[model_i], pos=-1)
del pdb[0]
return pdb