def testBadCif(self):
"""Make sure we can read all cif files."""
from pyobjcryst import ObjCrystException
fname = datafile('ni.stru')
infile = open(fname, 'rb')
self.assertRaises(ObjCrystException, CreateCrystalFromCIF, infile)
infile.close()
return
def testBadCif(self):
"""Make sure we can read all cif files."""
from pyobjcryst import ObjCrystException
fname = datafile('ni.stru')
infile = open(fname, 'rb')
self.assertRaises(ObjCrystException, CreateCrystalFromCIF, infile)
infile.close()
return
def _testPutAtomsInMolecule(self):
"""Make sure this utility method is correct."""
from math import floor
f = lambda v: v - floor(v)
import glob
from pyobjcryst.tests.pyobjcrysttestutils import datafile
pat = os.path.join(datafile(''), '*.cif')
for fname in glob.glob(pat):
print fname
c = CreateCrystalFromCIF(file(fname))
from diffpy.Structure import Structure
s = Structure(filename = fname)
# Get positions from unmodified structure
pos1 = []
scl = c.GetScatteringComponentList()
for s in scl:
xyz = map(f, [s.X, s.Y, s.Z])
xyz = c.FractionalToOrthonormalCoords(*xyz)
pos1.append(xyz)
# Get positions from molecular structure
putAtomsInMolecule(c)
pos2 = []
scl = c.GetScatteringComponentList()
for s in scl:
xyz = map(f, [s.X, s.Y, s.Z])
xyz = c.FractionalToOrthonormalCoords(*xyz)
pos2.append(xyz)
# Now compare positions
self.assertEqual(len(pos1), len(pos2))
for p1, p2 in zip(pos1, pos2):
for i in range(3):
self.assertAlmostEqual(p1[i], p2[i])
return
def _testPutAtomsInMolecule(self):
"""Make sure this utility method is correct."""
from math import floor
f = lambda v: v - floor(v)
import glob
from pyobjcryst.tests.pyobjcrysttestutils import datafile
pat = os.path.join(datafile(''), '*.cif')
for fname in glob.glob(pat):
print fname
c = CreateCrystalFromCIF(file(fname))
from diffpy.Structure import Structure
s = Structure(filename=fname)
# Get positions from unmodified structure
pos1 = []
scl = c.GetScatteringComponentList()
for s in scl:
xyz = map(f, [s.X, s.Y, s.Z])
xyz = c.FractionalToOrthonormalCoords(*xyz)
pos1.append(xyz)
# Get positions from molecular structure
putAtomsInMolecule(c)
pos2 = []
scl = c.GetScatteringComponentList()
for s in scl:
xyz = map(f, [s.X, s.Y, s.Z])
xyz = c.FractionalToOrthonormalCoords(*xyz)
pos2.append(xyz)
# Now compare positions
self.assertEqual(len(pos1), len(pos2))
for p1, p2 in zip(pos1, pos2):
for i in range(3):
self.assertAlmostEqual(p1[i], p2[i])
return
