Python f_000 Examples

Example #1

def exercise_f_000():
    pdb_str = """
CRYST1    5.000    5.000    5.000  90.00  90.00  90.00 P 1
HETATM    1  C    C      1       0.000   0.000   0.000  1.00  5.00           C
END
"""
    xrs = iotbx.pdb.input(source_info=None,
                          lines=pdb_str).xray_structure_simple()
    #
    f = utils.f_000(xray_structure=xrs, mean_solvent_density=0)
    assert approx_equal(f.f_000, 6, 1.e-3)
    #
    f = utils.f_000(mean_solvent_density=1, unit_cell_volume=125)
    assert approx_equal(f.f_000, 125)
    #
    f = utils.f_000(mean_solvent_density=0.25,
                    unit_cell_volume=125,
                    solvent_fraction=0.3,
                    xray_structure=xrs)
    assert approx_equal(f.f_000, 0.25 * 125 * 0.3 + 6, 1.e-3)
    assert approx_equal(f.solvent_fraction, 0.3)
    #
    f = utils.f_000(mean_solvent_density=0.25,
                    unit_cell_volume=125,
                    xray_structure=xrs)
    assert approx_equal(f.f_000, 0.25 * 125 * 0.687355324074 + 6, 1.e-3)

Example #2

File: tst_utils.py Project: keitaroyam/cctbx_fork

def exercise_f_000():
    pdb_str = """
CRYST1    5.000    5.000    5.000  90.00  90.00  90.00 P 1
HETATM    1  C    C      1       0.000   0.000   0.000  1.00  5.00           C
END
"""
    xrs = iotbx.pdb.input(source_info=None, lines=pdb_str).xray_structure_simple()
    #
    f = utils.f_000(xray_structure=xrs, mean_solvent_density=0)
    assert approx_equal(f.f_000, 6, 1.0e-3)
    #
    f = utils.f_000(mean_solvent_density=1, unit_cell_volume=125)
    assert approx_equal(f.f_000, 125)
    #
    f = utils.f_000(mean_solvent_density=0.25, unit_cell_volume=125, solvent_fraction=0.3, xray_structure=xrs)
    assert approx_equal(f.f_000, 0.25 * 125 * 0.3 + 6, 1.0e-3)
    assert approx_equal(f.solvent_fraction, 0.3)
    #
    f = utils.f_000(mean_solvent_density=0.25, unit_cell_volume=125, xray_structure=xrs)
    assert approx_equal(f.f_000, 0.25 * 125 * 0.687355324074 + 6, 1.0e-3)