def test_add_remove(self):
st = gemmi.read_pdb_string(SSBOND_FRAGMENT)
st.add_model(st[0])
st.renumber_models()
res = st[0].sole_residue('A', gemmi.SeqId('310'))
self.assertEqual(len(res), 1)
res.remove_atom('SG', ' ')
self.assertEqual(len(res), 0)
res = st[1].sole_residue('A', gemmi.SeqId('310'))
self.assertEqual(len(res), 1)
self.assertEqual(len(st[0]['A']), 7)
del st[0]['A'][3]
self.assertEqual(len(st[0]['A']), 6)
self.assertEqual(len(st), 2)
self.assertEqual(st[0].name, '1')
del st['1']
self.assertEqual(len(st), 1)
self.assertEqual(st[0].name, '2')
st.renumber_models()
self.assertEqual(st[0].name, '1')
st.add_model(st[0])
st.add_model(st[0])
st.renumber_models()
self.assertEqual(st[0].name, '1')
self.assertEqual(st[-1].name, '3')
del st[:-1]
self.assertEqual(len(st), 1)
self.assertEqual(st[0].name, '3')
del st[0]
self.assertEqual(len(st), 0)
def test_ncs(self):
st = gemmi.read_structure(full_path('5cvz_final.pdb'))
self.assertEqual(st.resolution, 3.29)
first_atom = st[0].sole_residue('A', gemmi.SeqId(17, ' '))[0]
ne2 = st[0].sole_residue('A', gemmi.SeqId('63')).sole_atom('NE2')
direct_dist = first_atom.pos.dist(ne2.pos)
self.assertAlmostEqual(direct_dist, 34.89, delta=1e-2)
nearest_image = st.cell.find_nearest_image(first_atom.pos, ne2.pos)
nearest_dist = nearest_image.dist()
self.assertAlmostEqual(nearest_dist, 8.02, delta=1e-2)
def test_first_conformer(self):
model = gemmi.read_structure(full_path('1pfe.cif.gz'))[0]
b = model['B']
self.assertEqual([res.name for res in b if not res.is_water()], [
'DSN', 'ALA', 'N2C', 'NCY', 'MVA', 'DSN', 'ALA', 'NCY', 'N2C',
'MVA', 'QUI', 'QUI'
])
self.assertEqual(
[res.name for res in b.first_conformer() if not res.is_water()], [
'DSN', 'ALA', 'N2C', 'MVA', 'DSN', 'ALA', 'NCY', 'MVA', 'QUI',
'QUI'
])
polymer = b.get_polymer()
self.assertEqual([res.name for res in polymer], [
'DSN', 'ALA', 'N2C', 'NCY', 'MVA', 'DSN', 'ALA', 'NCY', 'N2C',
'MVA'
])
self.assertEqual(
[res.name for res in polymer.first_conformer()],
['DSN', 'ALA', 'N2C', 'MVA', 'DSN', 'ALA', 'NCY', 'MVA'])
self.assertEqual(len(polymer), 10)
self.assertEqual(polymer.length(), 8)
# The bond between 4 MVA(v) and 5 DSN(s) is betwenn C and OG
# (so it's not a peptide bond as expected). Depending on the heuristic
# used to determine gaps, this sequence could have a gap in the middle.
self.assertEqual(polymer.make_one_letter_sequence(), 'sAXvsAXv')
self.assertEqual([res.name for res in b.get_ligands()], ['QUI', 'QUI'])
res1 = model.sole_residue('A', gemmi.SeqId('1'))
self.assertEqual([atom.name for atom in res1.first_conformer()],
[atom.name for atom in res1 if atom.altloc != 'B'])
def test_pdb_misaligned_element(self):
pdb_line = "ATOM 7 S SUB A 7 34.489 -14.293 34.343" \
" 0.29 43.77 S"
for line in [pdb_line, pdb_line + '\n', pdb_line + '\r\n']:
st = gemmi.read_pdb_string(line)
atom = st[0].sole_residue('A', gemmi.SeqId('7')).sole_atom('S')
self.assertEqual(atom.element.name, 'S')
def test_ncs(self):
st = gemmi.read_structure(full_path('5cvz_final.pdb'))
self.assertEqual(st.resolution, 3.29)
first_atom = st[0].sole_residue('A', gemmi.SeqId(17, ' '))[0]
ne2 = st[0].sole_residue('A', gemmi.SeqId('63')).sole_atom('NE2')
direct_dist = first_atom.pos.dist(ne2.pos)
self.assertAlmostEqual(direct_dist, 34.89, delta=1e-2)
nearest_image = st.cell.find_nearest_image(first_atom.pos, ne2.pos)
nearest_dist = nearest_image.dist()
self.assertAlmostEqual(nearest_dist, 8.02, delta=1e-2)
# test __getitem__(splice) - unrelated to NCS (sometimes we put
# unrelated tests together to avoid the same file again)
chain = st[0]['A']
res = chain.next_residue(chain[:5][0])
self.assertTrue(res is chain[1])
def test_first_conformer(self):
model = gemmi.read_structure(full_path('1pfe.cif.gz'))[0]
b = model['B']
self.assertEqual([res.name for res in b if not res.is_water()], [
'DSN', 'ALA', 'N2C', 'NCY', 'MVA', 'DSN', 'ALA', 'NCY', 'N2C',
'MVA', 'QUI', 'QUI'
])
self.assertEqual(
[res.name for res in b.first_conformer() if not res.is_water()], [
'DSN', 'ALA', 'N2C', 'MVA', 'DSN', 'ALA', 'NCY', 'MVA', 'QUI',
'QUI'
])
polymer = b.get_polymer()
self.assertEqual([res.name for res in polymer], [
'DSN', 'ALA', 'N2C', 'NCY', 'MVA', 'DSN', 'ALA', 'NCY', 'N2C',
'MVA'
])
self.assertEqual(
[res.name for res in polymer.first_conformer()],
['DSN', 'ALA', 'N2C', 'MVA', 'DSN', 'ALA', 'NCY', 'MVA'])
self.assertEqual(len(polymer), 10)
self.assertEqual(polymer.length(), 8)
self.assertEqual(polymer.make_one_letter_sequence(), 'sAXvsAXv')
self.assertEqual([res.name for res in b.get_ligands()], ['QUI', 'QUI'])
res1 = model.sole_residue('A', gemmi.SeqId('1'))
self.assertEqual([atom.name for atom in res1.first_conformer()],
[atom.name for atom in res1 if atom.altloc != 'B'])
def test_pdb_element_names(self):
pdb_line = "HETATM 4154 MG MG A 341 1.384 19.340 11.968" \
" 1.00 67.64 MG"
for line in [pdb_line, pdb_line.strip(' MG'), pdb_line[:-2] + ' ']:
st = gemmi.read_pdb_string(line)
residue = st[0].sole_residue('A', gemmi.SeqId(341, ' '))
mg_atom = residue.sole_atom('MG')
self.assertEqual(mg_atom.element.name, 'Mg')
self.assertAlmostEqual(mg_atom.b_iso, 67.64, delta=1e-6)
mg_atom.element = gemmi.Element('Cu')
self.assertEqual(mg_atom.element.name, 'Cu')
def test_1gtv(self):
st = gemmi.read_pdb_string(FRAGMENT_1GTV)
a1 = st[0].sole_residue('A', gemmi.SeqId(85, ' '))[0]
ns = gemmi.NeighborSearch(st[0], st.cell, 5)
ns.populate()
marks = ns.find_atoms(a1.pos, a1.altloc, 3)
self.assertEqual(len(marks), 2)
for mark in marks:
d = ns.dist(a1.pos, mark.pos())
self.assertAlmostEqual(d, 0, delta=5e-6)
marks2 = ns.find_neighbors(a1, 0.1, 3)
self.assertEqual(len(marks2), 0)
def test_5a11(self, use_populate=True):
st = gemmi.read_pdb_string(FRAGMENT_5A11)
a1 = st[0].sole_residue('A', gemmi.SeqId(37, ' '))[0]
ns = gemmi.NeighborSearch(st[0], st.cell, 5)
if use_populate:
ns.populate()
else:
for n_ch, chain in enumerate(st[0]):
for n_res, res in enumerate(chain):
for n_atom, atom in enumerate(res):
ns.add_atom(atom, n_ch, n_res, n_atom)
marks = ns.find_atoms(a1.pos, a1.altloc, 3)
m1, m2 = sorted(marks, key=lambda m: ns.dist(a1.pos, m.pos()))
self.assertAlmostEqual(ns.dist(a1.pos, m1.pos()), 0, delta=5e-6)
self.assertAlmostEqual(ns.dist(a1.pos, m2.pos()), 0.13, delta=5e-3)
cra2 = m2.to_cra(st[0])
self.assertEqual(cra2.chain.name, 'B')
self.assertEqual(str(cra2.residue.seqid), '37')
self.assertEqual(cra2.atom.name, 'SG')
marks2 = ns.find_neighbors(a1, 0.1, 3)
self.assertEqual(len(marks2), 1)
self.assertEqual(marks2[0], m2)
