def test_isInvariant_tolerance(self):
pg3barHex = PointGroupFactory.createPointGroup('-3')
pg3barRh = PointGroupFactory.createPointGroup('-3 r')
cellHex = UnitCell(3, 3, 6, 90, 90, 120)
cellRh = UnitCell(3, 3, 3, 75, 75, 75)
self.assertTrue(pg3barHex.isInvariant(cellHex.getG()))
self.assertFalse(pg3barHex.isInvariant(cellRh.getG()))
self.assertTrue(pg3barRh.isInvariant(cellRh.getG()))
self.assertFalse(pg3barRh.isInvariant(cellHex.getG()))
def test_isEquivalent(self):
hkl1 = V3D(1, 1, 1)
hkl2 = V3D(-1, -1, -1)
hkl3 = V3D(-1, -1, 2)
pg = PointGroupFactory.createPointGroup("m-3m")
self.assertTrue(pg.isEquivalent(hkl1, hkl2))
self.assertFalse(pg.isEquivalent(hkl1, hkl3))
def test_getEquivalents(self):
hkl1 = V3D(1, 0, 0)
hkl2 = V3D(-1, 0, 0)
pg = PointGroupFactory.createPointGroup("-1")
equivalents = pg.getEquivalents(hkl1)
self.assertTrue(hkl1 in equivalents)
self.assertTrue(hkl2 in equivalents)
self.assertEquals(len(equivalents), 2)
def test_getEquivalents(self):
hkl1 = V3D(1, 0, 0)
hkl2 = V3D(-1, 0, 0)
pg = PointGroupFactory.createPointGroup("-1")
equivalents = pg.getEquivalents(hkl1)
self.assertTrue(hkl1 in equivalents)
self.assertTrue(hkl2 in equivalents)
self.assertEquals(len(equivalents), 2)
def test_to_string(self):
pg = PointGroupFactory.createPointGroup("m-3m")
expected_str = "Point group with:\nLattice system: Cubic"\
"\nCrystal system: Cubic\nSymbol: m-3m"
expected_repr = "PointGroupFactory.createPointGroup(\"m-3m\")"
self.assertEqual(expected_str, str(pg))
self.assertEqual(expected_repr, pg.__repr__())
newPg = eval(pg.__repr__())
self.assertEqual(pg.getHMSymbol(), newPg.getHMSymbol())
def test_to_string(self):
pg = PointGroupFactory.createPointGroup("m-3m")
expected_str = "Point group with:\nLattice system: Cubic"\
"\nCrystal system: Cubic\nSymbol: m-3m"
expected_repr = "PointGroupFactory.createPointGroup(\"m-3m\")"
self.assertEqual(expected_str, str(pg))
self.assertEqual(expected_repr, pg.__repr__())
newPg = eval(pg.__repr__())
self.assertEqual(pg.getHMSymbol(), newPg.getHMSymbol())
def _get_point_group(self, space_group):
return PointGroupFactory.createPointGroup(space_group[1:].replace(
'_', '/'))
def test_getInfo(self):
pg = PointGroupFactory.createPointGroup("m-3m")
self.assertEqual(pg.getName(), "m-3m (Cubic)")
self.assertEqual(pg.getHMSymbol(), "m-3m")
self.assertEqual(pg.getCrystalSystem(), PointGroup.CrystalSystem.Cubic)
def test_creation(self):
self.assertRaises(ValueError, PointGroupFactory.createPointGroup,
"none")
PointGroupFactory.createPointGroup("m-3m")
def test_creation(self):
self.assertRaises(ValueError, PointGroupFactory.createPointGroup, "none")
PointGroupFactory.createPointGroup("m-3m")
def test_getReflectionFamily(self):
hkl1 = V3D(0, 0, 1)
hkl2 = V3D(-1, 0, 0)
pg = PointGroupFactory.createPointGroup("m-3m")
self.assertEquals(pg.getReflectionFamily(hkl1), pg.getReflectionFamily(hkl2))
def test_getReflectionFamily(self):
hkl1 = V3D(0, 0, 1)
hkl2 = V3D(-1, 0, 0)
pg = PointGroupFactory.createPointGroup("m-3m")
self.assertEquals(pg.getReflectionFamily(hkl1), pg.getReflectionFamily(hkl2))
def test_getInfo(self):
pg = PointGroupFactory.createPointGroup("m-3m")
self.assertEquals(pg.getName(), "m-3m (Cubic)")
self.assertEquals(pg.getHMSymbol(), "m-3m")
self.assertEquals(pg.getCrystalSystem(), PointGroup.CrystalSystem.Cubic)
def test_getLatticeSystem(self):
pg_rhombohedral = PointGroupFactory.createPointGroup("3m r")
pg_hexagonal = PointGroupFactory.createPointGroup("3m")
self.assertEquals(pg_rhombohedral.getLatticeSystem(), PointGroup.LatticeSystem.Rhombohedral)
self.assertEquals(pg_hexagonal.getLatticeSystem(), PointGroup.LatticeSystem.Hexagonal)
peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
ellipseFile = '/SNS/users/ntv/integrate/corelli_beryl/combined_hexagonal_indexedonly.integrate'
pg = PointGroupFactory.createPointGroup("6/mmm")
'''
#Beta lactamase mutant
sampleRuns = range(5921, 5931 + 1)
workDir = '/SNS/users/ntv/dropbox/'
descriptorBVG = 'beta_lac_3D_mbvg_mutant_newppl'
descriptorTOF = 'beta_lac_lab_highres_mut2'
peaksFile = '%s%s/peaks_combined_good.integrate' % (workDir, descriptorTOF)
#peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
#ellipseFile = '/SNS/users/ntv/integrate/mandi_betalactamase/MANDI_betalactamase_2.integrate'
#ellipseFile = '/SNS/users/ntv/integrate/mandi_betalactamase/combined_triclinic.integrate'
ellipseFile = '/SNS/users/ntv/integrate/mandi_beta_lactamase3/combined.integrate'
sg = SpaceGroupFactory.createSpaceGroup("P 32 2 1")
pg = PointGroupFactory.createPointGroupFromSpaceGroup(sg)
'''
#pth
sampleRuns = [870,872,873,874,875,876]
workDir = '/SNS/users/ntv/dropbox/'
descriptorBVG = 'pth_3d'
descriptorTOF = 'pth_tof_secondRun'
peaksFile = '%s%s/peaks_combined_good.integrate'%(workDir,descriptorTOF)
#peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
ellipseFile = '/SNS/users/ntv/integrate/mandi_pth/peaks_combined.integrate'
sg = SpaceGroupFactory.createSpaceGroup("P 61 2 2")
pg = PointGroupFactory.createPointGroupFromSpaceGroup(sg)
'''
'''
#gfp
sampleRuns = range(599,607+1)
def _get_point_group(self, space_group):
return PointGroupFactory.createPointGroup(space_group[1:].replace('_', '/'))
def test_getLatticeSystem(self):
pg_rhombohedral = PointGroupFactory.createPointGroup("3m r")
pg_hexagonal = PointGroupFactory.createPointGroup("3m")
self.assertEquals(pg_rhombohedral.getLatticeSystem(), PointGroup.LatticeSystem.Rhombohedral)
self.assertEquals(pg_hexagonal.getLatticeSystem(), PointGroup.LatticeSystem.Hexagonal)