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_cellstring(self):
""" Test intialising with string of lattice parameters """
self.Crystal = readcoords.Crystal(cell=str(self.cell['a'])+" "+\
str(self.cell['b'])+" "+\
str(self.cell['c'])+" "+\
str(self.cell['alp'])+" "+\
str(self.cell['bet'])+" "+\
str(self.cell['gam']), atoms=None, atomtypes=None)
self.assertEqual(self.Crystal.cell, self.cell)
def test_celllist(self):
""" Test intialising with list of lattice parameters """
self.Crystal = readcoords.Crystal(cell=[
self.cell['a'], self.cell['b'], self.cell['c'], self.cell['alp'],
self.cell['bet'], self.cell['gam']
],
atoms=None,
atomtypes=None)
self.assertEqual(self.Crystal.cell, self.cell)
def test_celldict(self):
""" Test intialising with dictionary of lattice parameters """
self.Crystal = readcoords.Crystal(cell=self.cell,
atoms=None,
atomtypes=None)
self.assertEqual(self.Crystal.cell, self.cell)