def test_sf_from_map(self):
hmax, kmax, lmax = self.reflections.maxHKL()
density_map = ElectronDensityMap.fromUniverse(self.reflections.cell,
4 * hmax, 4 * kmax,
4 * lmax, self.universe,
self.adps)
sf_from_map = StructureFactor.fromElectronDensityMap(
self.reflections, density_map)
sf_from_universe = StructureFactor.fromUniverse(
self.reflections, self.universe, self.adps)
self.assert_(sf_from_universe.rFactor(sf_from_map) < 1.e-3)
d = N.absolute(sf_from_universe.array - sf_from_map.array)
self.assert_(N.maximum.reduce(d) < 0.13)
self.assert_(N.average(d) < 0.02)
map_from_sf = ElectronDensityMap.fromStructureFactor(
self.reflections.cell, 4 * hmax, 4 * kmax, 4 * lmax,
sf_from_universe)
sf_from_test_map = StructureFactor.fromElectronDensityMap(
self.reflections, map_from_sf)
d = N.absolute(sf_from_universe.array - sf_from_test_map.array)
self.assert_(sf_from_universe.rFactor(sf_from_test_map) < 1.e-15)
self.assert_(N.maximum.reduce(d) < 1.e-13)
def test_sf_from_map(self):
asu_atoms = sum(([atom for atom in residue] for residue in self.s), [])
unit_cell_atom_data = []
for tr in self.s.cs_transformations:
for atom in asu_atoms:
unit_cell_atom_data.append(
(atom, atom['element'], tr(atom['position']) * Units.Ang,
atom['temperature_factor'] * Units.Ang**2 /
(8. * N.pi**2), atom['occupancy']))
hmax, kmax, lmax = self.reflections.maxHKL()
density_map = ElectronDensityMap.fromUnitCellAtoms(
self.reflections.cell, 4 * hmax, 4 * kmax, 4 * lmax,
unit_cell_atom_data)
sf_from_map = StructureFactor.fromElectronDensityMap(
self.reflections, density_map)
sf_from_unit_cell = StructureFactor.fromUnitCellAtoms(
self.reflections, unit_cell_atom_data)
self.assert_(sf_from_unit_cell.rFactor(sf_from_map) < 1.e-3)
d = N.absolute(sf_from_unit_cell.array - sf_from_map.array)
self.assert_(N.maximum.reduce(d) < 0.13)
self.assert_(N.average(d) < 0.02)
map_from_sf = ElectronDensityMap.fromStructureFactor(
self.reflections.cell, 4 * hmax, 4 * kmax, 4 * lmax,
sf_from_unit_cell)
sf_from_test_map = StructureFactor.fromElectronDensityMap(
self.reflections, map_from_sf)
d = N.absolute(sf_from_unit_cell.array - sf_from_test_map.array)
self.assert_(sf_from_unit_cell.rFactor(sf_from_test_map) < 1.e-15)
self.assert_(N.maximum.reduce(d) < 1.e-13)
