def exercise_2():
symmetry = crystal.symmetry(
unit_cell=(5.67, 10.37, 10.37, 90, 135.49, 90),
space_group_symbol="C2")
structure = xray.structure(crystal_symmetry=symmetry)
atmrad = flex.double()
xyzf = flex.vec3_double()
for k in xrange(100):
scatterer = xray.scatterer(
site = ((1.+k*abs(math.sin(k)))/1000.0,
(1.+k*abs(math.cos(k)))/1000.0,
(1.+ k)/1000.0),
scattering_type = "C")
structure.add_scatterer(scatterer)
atmrad.append(van_der_waals_radii.vdw.table[scatterer.element_symbol()])
xyzf.append(scatterer.site)
miller_set = miller.build_set(
crystal_symmetry=structure,
d_min=1.0,
anomalous_flag=False)
step = 0.5
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure.unit_cell(),
step=step)
nxyz = crystal_gridding.n_real()
shrink_truncation_radius = 1.0
solvent_radius = 1.0
m1 = around_atoms(
structure.unit_cell(),
structure.space_group().order_z(),
structure.sites_frac(),
atmrad,
nxyz,
solvent_radius,
shrink_truncation_radius)
assert m1.solvent_radius == 1
assert m1.shrink_truncation_radius == 1
assert flex.max(m1.data) == 1
assert flex.min(m1.data) == 0
assert m1.data.size() == m1.data.count(1) + m1.data.count(0)
m2 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
gridding_n_real=nxyz,
ignore_zero_occupancy_atoms = False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m2.data.all_eq(m1.data)
m3 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
grid_step=step,
ignore_zero_occupancy_atoms = False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m3.data.all_eq(m1.data)
f_mask2 = m2.structure_factors(miller_set=miller_set)
f_mask3 = m3.structure_factors(miller_set=miller_set)
assert approx_equal(f_mask2.data(), f_mask3.data())
assert approx_equal(flex.sum(flex.abs(f_mask3.data())), 1095.17999134)
def exercise_2():
symmetry = crystal.symmetry(unit_cell=(5.67, 10.37, 10.37, 90, 135.49, 90),
space_group_symbol="C2")
structure = xray.structure(crystal_symmetry=symmetry)
atmrad = flex.double()
xyzf = flex.vec3_double()
for k in xrange(100):
scatterer = xray.scatterer(site=((1. + k * abs(math.sin(k))) / 1000.0,
(1. + k * abs(math.cos(k))) / 1000.0,
(1. + k) / 1000.0),
scattering_type="C")
structure.add_scatterer(scatterer)
atmrad.append(
van_der_waals_radii.vdw.table[scatterer.element_symbol()])
xyzf.append(scatterer.site)
miller_set = miller.build_set(crystal_symmetry=structure,
d_min=1.0,
anomalous_flag=False)
step = 0.5
crystal_gridding = maptbx.crystal_gridding(unit_cell=structure.unit_cell(),
step=step)
nxyz = crystal_gridding.n_real()
shrink_truncation_radius = 1.0
solvent_radius = 1.0
m1 = around_atoms(structure.unit_cell(),
structure.space_group().order_z(),
structure.sites_frac(), atmrad, nxyz, solvent_radius,
shrink_truncation_radius)
assert m1.solvent_radius == 1
assert m1.shrink_truncation_radius == 1
assert flex.max(m1.data) == 1
assert flex.min(m1.data) == 0
assert m1.data.size() == m1.data.count(1) + m1.data.count(0)
m2 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
gridding_n_real=nxyz,
ignore_zero_occupancy_atoms=False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m2.data.all_eq(m1.data)
m3 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
grid_step=step,
ignore_zero_occupancy_atoms=False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m3.data.all_eq(m1.data)
f_mask2 = m2.structure_factors(miller_set=miller_set)
f_mask3 = m3.structure_factors(miller_set=miller_set)
assert approx_equal(f_mask2.data(), f_mask3.data())
assert approx_equal(flex.sum(flex.abs(f_mask3.data())), 1095.17999134)
def exercise_1():
#------------------------------------------------------------------------TEST-1
if(1):
r=(1.67,0.68,0.0,0.5,-0.31,-0.64,-1.63)
d = 2.0*van_der_waals_radii.vdw.table["C"]
a = (d/2.) * (4./3.*math.pi*2.)**(1./3.)
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init((x,y,z),
"P1",
(a, a, a, 90, 90, 90))
step = 0.1
crystal_gridding = maptbx.crystal_gridding(
unit_cell = structure.unit_cell(),
step = step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(
structure.unit_cell(),
structure.space_group().order_z(),
xyzf,
atmrad,
crystal_gridding.n_real(),
solvent_radius,
shrink_truncation_radius)
assert m.solvent_radius == 0
assert m.shrink_truncation_radius == 0
assert approx_equal(1./m.accessible_surface_fraction, 2.0, 1e-2)
assert approx_equal(1./m.contact_surface_fraction, 2.0, 1e-2)
assert flex.max(m.data) == 1
assert flex.min(m.data) == 0
assert m.data.size() == m.data.count(1) + m.data.count(0)
#------------------------------------------------------------------------TEST-2
if(1):
r=(-2.0,-1.0,-0.5,0.0,0.5,1.0,2.0)
asf=[]
csf=[]
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init((x,y,z),
"C2",
(5.0, 5.5, 7.0, 90, 80, 90))
step = 0.25
crystal_gridding = maptbx.crystal_gridding(
unit_cell = structure.unit_cell(),
step = step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(
structure.unit_cell(),
structure.space_group().order_z(),
xyzf,
atmrad,
crystal_gridding.n_real(),
solvent_radius,
shrink_truncation_radius)
asf.append(m.accessible_surface_fraction)
csf.append(m.contact_surface_fraction)
assert m.accessible_surface_fraction == m.contact_surface_fraction
assert approx_equal(min(asf),max(asf))
#------------------------------------------------------------------------TEST-3
if(1):
r=(1.673,0.685,-0.315,-0.649,-1.637)
asf=[]
csf=[]
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init((x,y,z),
"P1",
(5.0, 5.5, 6.0, 70, 80, 100))
step = 0.1
crystal_gridding = maptbx.crystal_gridding(
unit_cell = structure.unit_cell(),
step = step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(
structure.unit_cell(),
structure.space_group().order_z(),
xyzf,
atmrad,
crystal_gridding.n_real(),
solvent_radius,
shrink_truncation_radius)
asf.append(m.accessible_surface_fraction)
csf.append(m.contact_surface_fraction)
assert m.accessible_surface_fraction == m.contact_surface_fraction
assert approx_equal(min(asf),max(asf), 1e-3)
def tst2_run(angles, nspacing, af ):
rad = van_der_waals_radii.vdw.table["C"]
a = (2.0*rad)*2.0*af;
pos1=(0.25,0.25,0.25)
pos2=(0.25+0.9*2.0*rad/a,0.25,0.25)
solvent_radius1 = rad*0.5
solvent_radius2 = rad*3.1
# shrink_truncation_radius = 1.3*solvent_radius2
shrink_truncation_radius = 0.0
cell = [a,a,a, angles[0], angles[1], angles[2] ]
structure1, xyzf1, atmrad1 = structure_init2(pos1,pos2, "P1", cell)
structure2, xyzf2, atmrad2 = structure_init2(pos1,pos2, "P1", cell)
step = (1.0/nspacing) * a
#
crystal_gridding = maptbx.crystal_gridding(
unit_cell = structure1.unit_cell(),
step = step)
#
m1 = around_atoms(
structure1.unit_cell(),
structure1.space_group().order_z(),
xyzf1,
atmrad1,
crystal_gridding.n_real(),
solvent_radius1,
shrink_truncation_radius, explicit_distance=False, debug=True )
#
m2 = around_atoms(
structure2.unit_cell(),
structure2.space_group().order_z(),
xyzf2,
atmrad2,
crystal_gridding.n_real(),
solvent_radius2,
shrink_truncation_radius, explicit_distance=False, debug=True )
#
m3 = around_atoms(
structure1.unit_cell(),
structure1.space_group().order_z(),
xyzf1,
atmrad1,
crystal_gridding.n_real(),
solvent_radius1,
shrink_truncation_radius, explicit_distance=True, debug=True)
#
m4 = around_atoms(
structure2.unit_cell(),
structure2.space_group().order_z(),
xyzf2,
atmrad2,
crystal_gridding.n_real(),
solvent_radius2,
shrink_truncation_radius, explicit_distance=True, debug=True)
#
assert m3.n_atom_points == m4.n_atom_points
mx1 = max(abs(m1.n_atom_points),abs(m2.n_atom_points))
mx2 = max(abs(m1.n_atom_points),abs(m3.n_atom_points))
mx3 = max(abs(m2.n_atom_points),abs(m3.n_atom_points))
if mx1!=0:
assert float(abs(m1.n_atom_points - m2.n_atom_points))/float(mx1) < 0.01
if mx2!=0:
assert float(abs(m1.n_atom_points - m3.n_atom_points))/float(mx2) < 0.01
if mx3!=0:
assert float(abs(m2.n_atom_points - m3.n_atom_points))/float(mx3) < 0.01
def exercise_1():
#------------------------------------------------------------------------TEST-1
if (1):
r = (1.67, 0.68, 0.0, 0.5, -0.31, -0.64, -1.63)
d = 2.0 * van_der_waals_radii.vdw.table["C"]
a = (d / 2.) * (4. / 3. * math.pi * 2.)**(1. / 3.)
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init(
(x, y, z), "P1", (a, a, a, 90, 90, 90))
step = 0.1
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure.unit_cell(), step=step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(structure.unit_cell(),
structure.space_group().order_z(), xyzf,
atmrad, crystal_gridding.n_real(),
solvent_radius, shrink_truncation_radius)
assert m.solvent_radius == 0
assert m.shrink_truncation_radius == 0
assert approx_equal(1. / m.accessible_surface_fraction,
2.0, 1e-2)
assert approx_equal(1. / m.contact_surface_fraction, 2.0,
1e-2)
assert flex.max(m.data) == 1
assert flex.min(m.data) == 0
assert m.data.size() == m.data.count(1) + m.data.count(0)
#------------------------------------------------------------------------TEST-2
if (1):
r = (-2.0, -1.0, -0.5, 0.0, 0.5, 1.0, 2.0)
asf = []
csf = []
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init(
(x, y, z), "C2", (5.0, 5.5, 7.0, 90, 80, 90))
step = 0.25
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure.unit_cell(), step=step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(structure.unit_cell(),
structure.space_group().order_z(), xyzf,
atmrad, crystal_gridding.n_real(),
solvent_radius, shrink_truncation_radius)
asf.append(m.accessible_surface_fraction)
csf.append(m.contact_surface_fraction)
assert m.accessible_surface_fraction == m.contact_surface_fraction
assert approx_equal(min(asf), max(asf))
#------------------------------------------------------------------------TEST-3
if (1):
r = (1.673, 0.685, -0.315, -0.649, -1.637)
asf = []
csf = []
for x in r:
for y in r:
for z in r:
structure, xyzf, atmrad = structure_init(
(x, y, z), "P1", (5.0, 5.5, 6.0, 70, 80, 100))
step = 0.1
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure.unit_cell(), step=step)
shrink_truncation_radius = 0.0
solvent_radius = 0.0
m = around_atoms(structure.unit_cell(),
structure.space_group().order_z(), xyzf,
atmrad, crystal_gridding.n_real(),
solvent_radius, shrink_truncation_radius)
asf.append(m.accessible_surface_fraction)
csf.append(m.contact_surface_fraction)
assert m.accessible_surface_fraction == m.contact_surface_fraction
assert approx_equal(min(asf), max(asf), 1e-3)
def tst2_run(angles, nspacing, af):
rad = van_der_waals_radii.vdw.table["C"]
a = (2.0 * rad) * 2.0 * af
pos1 = (0.25, 0.25, 0.25)
pos2 = (0.25 + 0.9 * 2.0 * rad / a, 0.25, 0.25)
solvent_radius1 = rad * 0.5
solvent_radius2 = rad * 3.1
# shrink_truncation_radius = 1.3*solvent_radius2
shrink_truncation_radius = 0.0
cell = [a, a, a, angles[0], angles[1], angles[2]]
structure1, xyzf1, atmrad1 = structure_init2(pos1, pos2, "P1", cell)
structure2, xyzf2, atmrad2 = structure_init2(pos1, pos2, "P1", cell)
step = (1.0 / nspacing) * a
#
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure1.unit_cell(), step=step)
#
m1 = around_atoms(structure1.unit_cell(),
structure1.space_group().order_z(),
xyzf1,
atmrad1,
crystal_gridding.n_real(),
solvent_radius1,
shrink_truncation_radius,
explicit_distance=False,
debug=True)
#
m2 = around_atoms(structure2.unit_cell(),
structure2.space_group().order_z(),
xyzf2,
atmrad2,
crystal_gridding.n_real(),
solvent_radius2,
shrink_truncation_radius,
explicit_distance=False,
debug=True)
#
m3 = around_atoms(structure1.unit_cell(),
structure1.space_group().order_z(),
xyzf1,
atmrad1,
crystal_gridding.n_real(),
solvent_radius1,
shrink_truncation_radius,
explicit_distance=True,
debug=True)
#
m4 = around_atoms(structure2.unit_cell(),
structure2.space_group().order_z(),
xyzf2,
atmrad2,
crystal_gridding.n_real(),
solvent_radius2,
shrink_truncation_radius,
explicit_distance=True,
debug=True)
#
assert m3.n_atom_points == m4.n_atom_points
mx1 = max(abs(m1.n_atom_points), abs(m2.n_atom_points))
mx2 = max(abs(m1.n_atom_points), abs(m3.n_atom_points))
mx3 = max(abs(m2.n_atom_points), abs(m3.n_atom_points))
if mx1 != 0:
assert float(
abs(m1.n_atom_points - m2.n_atom_points)) / float(mx1) < 0.01
if mx2 != 0:
assert float(
abs(m1.n_atom_points - m3.n_atom_points)) / float(mx2) < 0.01
if mx3 != 0:
assert float(
abs(m2.n_atom_points - m3.n_atom_points)) / float(mx3) < 0.01