def testCIFModels(self):
""" Test CIF parsing/writing NMR structure with 20 models (2koc) """
cif = download_CIF('2koc')
self.assertEqual(cif.get_coordinates('all').shape, (20, 451, 3))
self.assertEqual(len(cif.atoms), 451)
output = StringIO()
write_CIF(cif, output)
output.seek(0)
pdbfile2 = read_CIF(output)
self.assertEqual(len(pdbfile2.atoms), 451)
self.assertEqual(pdbfile2.get_coordinates('all').shape, (20, 451, 3))
def read_mmcif(f, reassign_chains=True):
"""Parse an mmCIF file (using the parmEd parser) and return a molecule
Args:
f (file): file-like object containing the mmCIF file
reassign_chains (bool): reassign chain IDs from ``auth_asym_id`` to ``label_asym_id``
Returns:
moldesign.Molecule: parsed molecule
"""
parmedmol = parmed.read_CIF(f)
mol = parmed_to_mdt(parmedmol)
if reassign_chains:
f.seek(0)
mol = _reassign_chains(f, mol)
mdt.helpers.assign_biopolymer_bonds(mol)
return mol
def read_mmcif(f, reassign_chains=True):
"""Parse an mmCIF file (using the parmEd parser) and return a molecule
Args:
f (file): file-like object containing the mmCIF file
reassign_chains (bool): reassign chain IDs from ``auth_asym_id`` to ``label_asym_id``
Returns:
moldesign.Molecule: parsed molecule
"""
parmedmol = parmed.read_CIF(f)
mol = parmed_to_mdt(parmedmol)
if reassign_chains:
f.seek(0)
mol = _reassign_chains(f, mol)
mdt.helpers.assign_biopolymer_bonds(mol)
return mol
def test4LZT(self):
""" Test CIF parsing on 4LZT (w/ ANISOU, altlocs, etc.) """
self._check4lzt(read_CIF(self.lzt))
def testWriteCIF(self):
""" Test CIF writing capabilities """
cif = read_CIF(self.lzt)
written = get_fn('test.cif', written=True)
cif.write_cif(written, renumber=False, write_anisou=True)
cif2 = read_CIF(written)
# cif and cif2 should have equivalent atom properties (basically,
# everything should be the same except the metadata)
self.assertEqual(len(cif.atoms), len(cif2.atoms))
self.assertEqual(len(cif.residues), len(cif2.residues))
# Check residue properties
for res1, res2 in zip(cif.residues, cif2.residues):
self.assertEqual(len(res1), len(res2))
self.assertEqual(res1.name, res2.name)
self.assertEqual(res1.chain, res2.chain)
self.assertEqual(res1.insertion_code, res2.insertion_code)
self.assertEqual(res1.number, res2.number)
# Check atom properties
for a1, a2 in zip(cif.atoms, cif2.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.number, a2.number)
self.assertEqual(a1.element, a2.element)
self.assertEqual(a1.altloc, a2.altloc)
self.assertEqual(a1.xx, a2.xx)
self.assertEqual(a1.xy, a2.xy)
self.assertEqual(a1.xz, a2.xz)
self.assertEqual(len(a1.anisou), 6)
self.assertEqual(len(a2.anisou), 6)
for x, y in zip(a1.anisou, a2.anisou):
self.assertEqual(x, y)
# Check box
self.assertEqual(len(cif.box), len(cif2.box))
for x, y in zip(cif.box, cif2.box):
self.assertEqual(x, y)
# Now check CIF writing without anisotropic B-factors and with
# renumbering
io = StringIO()
cif.write_cif(io)
io.seek(0)
cif3 = read_CIF(io)
# cif and cif3 should have equivalent atom properties (basically,
# everything should be the same except the metadata)
self.assertEqual(len(cif.atoms), len(cif3.atoms))
self.assertEqual(len(cif.residues), len(cif3.residues))
# Check residue properties
i = 1
for res1, res2 in zip(cif.residues, cif3.residues):
self.assertEqual(len(res1), len(res2))
self.assertEqual(res1.name, res2.name)
self.assertEqual(res1.chain, res2.chain)
self.assertEqual(res1.insertion_code, res2.insertion_code)
self.assertEqual(res2.number, i)
i += 1
# Check atom properties
i = 1
for a1, a2 in zip(cif.atoms, cif3.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a2.number, i)
self.assertEqual(a1.element, a2.element)
self.assertEqual(a1.altloc, a2.altloc)
self.assertEqual(a1.xx, a2.xx)
self.assertEqual(a1.xy, a2.xy)
self.assertEqual(a1.xz, a2.xz)
self.assertIs(a2.anisou, None)
i += 1 + len(a2.other_locations)
# Check box
self.assertEqual(len(cif.box), len(cif3.box))
for x, y in zip(cif.box, cif3.box):
self.assertEqual(x, y)