def calcfromcif(CIF,
centres,
radius,
allligtypes=[],
alllignames=[],
**kwargs):
""" Main routine for computing ellipsoids from CIF file. """
# kwargs should be valid arguments for polyhedron.makeellipsoid(), primarily designed for tolerance and maxcycles
from pieface import readcoords
logger.debug('Starting file %s', CIF)
cell, atomcoords, atomtypes, spacegp, symmops, symmid = readcoords.readcif(
CIF)
allatoms = readcoords.makeP1cell(atomcoords, symmops, symmid)
phase = readcoords.Crystal(cell=cell, atoms=allatoms, atomtypes=atomtypes)
for cen in centres:
if cen not in list(allatoms.keys()):
logger.info("Centre %s is not present in atom labels: skipping",
cen)
continue
validligtyps = list(
set(allligtypes).intersection(set(atomtypes.values())))
validlignames = list(
set(alllignames).intersection(set(atomtypes.keys())))
if len(validligtyps) == 0 and len(validlignames) == 0:
raise ValueError(
"No ligands of type(s) or name(s) '{0}' are present in file {1}. Valid types are {2}"
.format(", ".join(allligtypes) + ", ".join(alllignames), CIF,
", ".join([str(p) for p in set(atomtypes.values())])))
elif len(validligtyps) != len(allligtypes):
logger.info("Not all types %s are present in %s; using %s",
", ".join(allligtypes), CIF, ", ".join(validligtyps))
elif len(validlignames) != len(alllignames):
logger.info("Not all labels %s are present in %s; using %s",
", ".join(alllignames), CIF, ", ".join(validlignames))
# Calculate ligands for current centre: the coordinates returned may be in a different unit cell to those in allatoms
ligands, ligtypes = readcoords.findligands(cen,
phase.atoms,
phase.orthomatrix(),
radius=radius,
types=validligtyps,
names=validlignames,
atomtypes=phase.atomtypes)
phase.makepolyhedron({cen: allatoms[cen]},
ligands,
atomdict=None,
ligtypes=ligtypes)
polynm = cen + "_poly"
getattr(phase, polynm).makeellipsoid(phase.orthomatrix(), **kwargs)
logger.debug('Finishing file %s', CIF)
return phase
def test_read_CIFS(self):
""" Test CIF reads correctly"""
for cif in self.CIFS:
returnvals = readcoords.readcif(self.CIFS[cif])
self.assertDictEqual(returnvals[0], self.results[cif]['cell'])
# Test atomcoords are equal
self.assertItemsEqual(list(returnvals[1].keys()),
list(self.results[cif]['atomcoords'].keys()))
for k in list(returnvals[1].keys()):
np.testing.assert_array_almost_equal(
returnvals[1][k], self.results[cif]['atomcoords'][k])
self.assertDictEqual(returnvals[2], self.results[cif]['atomtypes'])
self.assertEqual(returnvals[3], self.results[cif]['spacegrp'])
self.assertListEqual(returnvals[4], self.results[cif]['symmops'])
self.assertListEqual(returnvals[5], self.results[cif]['symmid'])
def test_read_internet_CIF(self):
""" Check that we can read a CIF online from COD (requires an internet connection). """
ciffile = 'http://www.crystallography.net/cod/1004021.cif'
cif = '1004021'
returnvals = readcoords.readcif(ciffile)
self.assertDictEqual(returnvals[0], self.results[cif]['cell'])
# Test atomcoords are equal
self.assertItemsEqual(list(returnvals[1].keys()),
list(self.results[cif]['atomcoords'].keys()))
for k in list(returnvals[1].keys()):
np.testing.assert_array_almost_equal(
returnvals[1][k], self.results[cif]['atomcoords'][k])
self.assertDictEqual(returnvals[2], self.results[cif]['atomtypes'])
self.assertEqual(returnvals[3], self.results[cif]['spacegrp'])
self.assertListEqual(returnvals[4], self.results[cif]['symmops'])
self.assertListEqual(returnvals[5], self.results[cif]['symmid'])
def _alltyplbls(CIF):
""" Return all allowed labels and corresponding types in CIF file. """
from pieface.readcoords import readcif
cell, atomcoords, atomtypes, spacegp, symmops, symmid = readcif(CIF)
# Just return atomtypes dict {label: type} direct from readcif
return atomtypes
def _alllabels(CIF, phase=0):
""" Return all allowed labels in CIF file. """
from pieface.readcoords import readcif
cell, atomcoords, atomtypes, spacegp, symmops, symmid = readcif(CIF, phase)
return atomcoords.keys()