def initialise_opengl(self):
self.ellipsoid_proto = quadrics.proto_ellipsoid(slices=32, stacks=32)
self.principal_ellipses_tex = \
quadrics.ellipsoid_principal_sections_texture(darkening=0.75,
n_s=64, n_t=64)
self.cylindre_proto = quadrics.proto_cylinder(slices=16)
self.bond_material = gl_managed.material_model(
ambient_front_colour=(0.2, ) * 3, diffuse_front_colour=(0.1, ) * 3)
glEnable(GL_TEXTURE_2D)
glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE)
def initialise_opengl(self):
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
self.material = gl_managed.material_model(
ambient_front_colour=(0, 0.25, 0, 1),
ambient_back_colour=(0., 0.25, 0, 1),
diffuse_front_colour=(0, 1, 0, 1),
diffuse_back_colour=(0, 0.75, 0, 1),
specular_front_colour=(0.5, 0, 0.5, 1),
specular_focus=100)
self.wire_colour = (0, 1, 0, 1)
def initialise_opengl(self):
glEnableClientState(GL_VERTEX_ARRAY)
glEnableClientState(GL_NORMAL_ARRAY)
self.material = gl_managed.material_model(
ambient_front_colour=(0, 0.25, 0, 1),
ambient_back_colour=(0., 0.25, 0, 1),
diffuse_front_colour=(0, 1, 0, 1),
diffuse_back_colour=(0, 0.75, 0, 1),
specular_front_colour=(0.5, 0, 0.5, 1),
specular_focus=100)
self.wire_colour = (0, 1, 0, 1)
def initialise_opengl(self):
self.ellipsoid_proto = quadrics.proto_ellipsoid(
slices=32, stacks=32)
self.principal_ellipses_tex = \
quadrics.ellipsoid_principal_sections_texture(darkening=0.75,
n_s=64, n_t=64)
self.cylindre_proto = quadrics.proto_cylinder(slices=16)
self.bond_material = gl_managed.material_model(
ambient_front_colour=(0.2,)*3,
diffuse_front_colour=(0.1,)*3)
glEnable(GL_TEXTURE_2D)
glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE)
class xray_structure_viewer(qttbx.widget):
material_for = (
[
('Br', (0.97, 0.86, 0.03), (1, 0.5, 0)),
('C', (0.32, ) * 3, (0.75, ) * 3),
('N', (0, 0, 1), (0.37, 0.37, 0.63)),
('O', (0.91, 0, 0), (0.63, 0.37, 0.37)),
('F', (0, 1, 0), (0.07, 0.35, 0.07)),
('Al', (0, 0.5, 0.5), (0.37, 0.87, 0.87)),
('Si', (0.98, 0.42, 0.01), (0.62, 0.62, 0.37)),
('P', (0.5, 0, 0.5), (0.5, ) * 3),
('S', (0.97, 0.85, 0.03), (0.5, ) * 3),
('Cl', (0, 0.25, 0), (0.13, 0.65, 0.13)),
('Br', (0.51, 0, 0), (0.72, 0.53, 0.53)),
('I', (0.27, 0, 0.27), (0.87, 0.37, 0.87)),
]
# Metals (1st row)
+ [(elt, (0, 0, 0.49), (0.37, 0.37, 0.62))
for elt in ('Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn')])
default_material = gl_managed.material_model(
ambient_front_colour=(0.2, ) * 3, diffuse_front_colour=(0.1, ) * 3)
material_for = dict([(elt,
gl_managed.material_model(ambient_front_colour=a,
diffuse_front_colour=b))
for (elt, a, b) in material_for])
covalent_bond_tolerance = 0.5 # Angstrom
distance_cutoff = None
bonding = "covalent"
def __init__(self, xray_structure, name='??', **kwds):
super(xray_structure_viewer,
self).__init__(unit_cell=xray_structure.unit_cell(),
orthographic=True,
light_position=(-1, 1, 1, 0),
**kwds)
assert self.bonding in ("covalent", "all")
assert self.bonding != "all" or self.distance_cutoff is not None
self.xray_structure = xs = xray_structure
self.setWindowTitle("%s in %s" %
(name, xs.space_group().type().hall_symbol()))
sites_frac = xs.sites_frac()
self.set_extent(sites_frac.min(), sites_frac.max())
self.is_unit_cell_shown = False
sites_cart = self.sites_cart = xs.sites_cart()
thermal_tensors = xs.extract_u_cart_plus_u_iso()
self.ellipsoid_to_sphere_transforms = {}
self.scatterer_indices = flex.std_string()
self.scatterer_labels = flex.std_string()
for i, (sc, site, u_cart) in enumerate(
zip(xs.scatterers(), sites_cart, thermal_tensors)):
t = quadrics.ellipsoid_to_sphere_transform(site, u_cart)
self.ellipsoid_to_sphere_transforms.setdefault(
sc.element_symbol(),
quadrics.shared_ellipsoid_to_sphere_transforms()).append(t)
self.scatterer_indices.append("# %i" % i)
self.scatterer_labels.append(sc.label)
self.labels = None
self.label_font = QtGui.QFont("Arial Black", pointSize=18)
if self.bonding == "covalent":
radii = [
covalent_radii.table(elt).radius() for elt in
xs.scattering_type_registry().type_index_pairs_as_dict()
]
buffer_thickness = 2 * max(radii) + self.covalent_bond_tolerance
asu_mappings = xs.asu_mappings(buffer_thickness=buffer_thickness)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_covalent_pairs(
xs.scattering_types(), tolerance=self.covalent_bond_tolerance)
elif self.bonding == "all":
asu_mappings = xs.asu_mappings(
buffer_thickness=self.distance_cutoff)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_all_pairs(self.distance_cutoff)
pair_sym_table = bond_table.extract_pair_sym_table(
all_interactions_from_inside_asu=True)
self.bonds = flex.vec3_double()
self.bonds.reserve(len(xs.scatterers()))
uc = self.xray_structure.unit_cell()
frac = mat.rec(uc.fractionalization_matrix(), (3, 3))
inv_frac = frac.inverse()
site_symms = xs.site_symmetry_table()
scatt = self.xray_structure.scatterers()
for i, neighbours in enumerate(pair_sym_table):
x0 = sites_cart[i]
sc0 = scatt[i]
for j, ops in neighbours.items():
sc1 = scatt[j]
if sc0.scattering_type == 'H' and sc1.scattering_type == 'H':
continue
for op in ops:
if op.is_unit_mx():
x1 = sites_cart[j]
else:
x1 = uc.orthogonalize(op * sites_frac[j])
op_cart = inv_frac * mat.rec(op.r().as_double(),
(3, 3)) * frac
u1 = (op_cart * mat.sym(sym_mat3=thermal_tensors[j]) *
op_cart.transpose())
t = quadrics.ellipsoid_to_sphere_transform(
x1, u1.as_sym_mat3())
self.ellipsoid_to_sphere_transforms[
sc1.element_symbol()].append(t)
self.sites_cart.append(x1)
op_lbl = (" [%s]" % op).lower()
self.scatterer_indices.append("# %i%s" % (j, op_lbl))
self.scatterer_labels.append("%s%s" %
(sc1.label, op_lbl))
self.bonds.append(x0)
self.bonds.append(x1)
def initialise_opengl(self):
self.ellipsoid_proto = quadrics.proto_ellipsoid(slices=32, stacks=32)
self.principal_ellipses_tex = \
quadrics.ellipsoid_principal_sections_texture(darkening=0.75,
n_s=64, n_t=64)
self.cylindre_proto = quadrics.proto_cylinder(slices=16)
self.bond_material = gl_managed.material_model(
ambient_front_colour=(0.2, ) * 3, diffuse_front_colour=(0.1, ) * 3)
glEnable(GL_TEXTURE_2D)
glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE)
def draw_object_in_cartesian_coordinates(self):
self.principal_ellipses_tex.bind()
for element, transforms in six.iteritems(
self.ellipsoid_to_sphere_transforms):
material = self.material_for.get(element, self.default_material)
material.execute()
transforms.draw(self.ellipsoid_proto)
self.principal_ellipses_tex.unbind()
self.bond_material.execute()
for i in range(0, len(self.bonds), 2):
start, end = self.bonds[i], self.bonds[i + 1]
self.cylindre_proto.draw(start, end, base_radius=0.05)
if self.labels is not None:
glPushAttrib(GL_LIGHTING_BIT)
glDisable(GL_LIGHTING)
glPushAttrib(GL_DEPTH_BUFFER_BIT)
glDisable(GL_DEPTH_TEST)
glColor3f(1, 1, 1)
e = 0.1
for x, lbl in zip(self.sites_cart, self.labels):
self.renderText(x[0] - e, x[1] + e, x[2] - e, lbl,
self.label_font)
glPopAttrib()
glPopAttrib()
def set_labels_type(self, kind):
self.labels = getattr(self, str(kind).lower().replace(' ', '_'), None)
self.updateGL()
def set_font_size(self, s):
self.label_font.setPointSize(s)
self.updateGL()