def set_points_and_lines(self,
tardy_model,
velocity_scaling=False,
e_kin_per_dof=1,
minimum_covering_sphere_view_scale=1.3,
show_loop_edge_bendings=True,
long_labels=None):
self.tardy_model = tardy_model
temperature_dof = len(tardy_model.sites) * 3
if (e_kin_per_dof is None):
self.e_kin_target = tardy_model.e_kin() / max(1, temperature_dof)
else:
self.e_kin_target = e_kin_per_dof * temperature_dof
tardy_model.assign_random_velocities(
e_kin_target=self.e_kin_target)
self.velocity_scaling = velocity_scaling
self.long_labels = long_labels
self.labels = self.tardy_model.labels
self.set_points()
for line, color in tardy_model.tardy_tree.viewer_lines_with_colors(
include_loop_edge_bendings=show_loop_edge_bendings):
self.line_i_seqs.append(line)
self.line_colors[line] = color
print("\n".join(
tardy_model.tardy_tree.viewer_lines_with_colors_legend(
include_loop_edge_bendings=show_loop_edge_bendings)))
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius() * minimum_covering_sphere_view_scale)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 1
self.show_key_stroke_help()
def set_points_and_lines(self):
self.sim_as = simulation()
self.sim_ac = simulation()
self.points = flex.vec3_double(self.sim_as.sites_cart_moved_F01)
self.points.extend(flex.vec3_double(self.sim_ac.sites_cart_moved_F01))
self.points.extend(flex.vec3_double(self.sim_as.sites_cart_wells_F01))
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
n = len(self.sim_as.sites_cart_F1)
offs = 0
for prefix,color in [("S",(1,0,0)),("C",(0,0,1)),("W",(0,1,0))]:
for i in range(n):
add_line(offs+i, offs+(i+1)%n, color)
self.labels.append(prefix+str(i))
offs += n
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius()*1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 8
print("Press and hold Tab key to run the simulation.")
print("Press Shift-Tab to increase speed.")
print("Press Ctrl-Tab to decrease speed.")
def set_points_and_lines(self, simulation_factory_index, n_zigzag):
if (simulation_factory_index == 0):
self.sim = tst_molecules.simulation_zigzag(NB=n_zigzag)
else:
self.sim = tst_molecules.simulation_factories[
simulation_factory_index]()
self.points = flex.vec3_double()
self.set_points()
def add_line(i, j, color):
line = (i, j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
B_off = []
for B in self.sim.bodies:
B_off.append(len(self.labels))
self.labels.extend(B.labels)
def add_off(i):
if (i < 0): return B_off[B.parent + 1] + i
else: return B_off[-1] + i
for bond in B.bonds:
i, j = [add_off(b) for b in bond]
add_line(i, j, (1, 0, 0))
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(center=mcs.center(),
radius=mcs.radius() * 1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 1
self.show_key_stroke_help()
def set_points_and_lines(self, simulation_factory_index, n_zigzag):
if (simulation_factory_index == 0):
self.sim = tst_molecules.simulation_zigzag(NB=n_zigzag)
else:
self.sim = tst_molecules.simulation_factories[simulation_factory_index]()
self.points = flex.vec3_double()
self.set_points()
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
B_off = []
for B in self.sim.bodies:
B_off.append(len(self.labels))
self.labels.extend(B.labels)
def add_off(i):
if (i < 0): return B_off[B.parent+1] + i
else: return B_off[-1] + i
for bond in B.bonds:
i,j = [add_off(b) for b in bond]
add_line(i, j, (1,0,0))
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius()*1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 1
self.show_key_stroke_help()
def set_points_and_lines(self):
NB = 3
self.sim = revolute_simulation(mersenne_twister=None,
NB=NB,
config="zigzag")
self.points = flex.vec3_double()
self.set_points()
assert self.points.size() == NB * 3
def add_line(i, j, color):
line = (i, j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
p, n, s = 0, 1, 2
for ib in range(NB):
self.labels.extend(["p%d" % ib, "n%d" % ib, "s%d" % ib])
add_line(p, n, (1, 0, 0))
add_line(p, s, (0, 1, 0))
add_line(n, s, (0, 0, 1))
p, n, s = p + 3, n + 3, s + 3
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(center=mcs.center(),
radius=mcs.radius() * 1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 8
print("Press and hold Tab key to run the simulation.")
print("Press Shift-Tab to increase speed.")
print("Press Ctrl-Tab to decrease speed.")
def set_points_and_lines(self):
self.sim_as = simulation()
self.sim_ac = simulation()
self.points = flex.vec3_double(self.sim_as.sites_cart_moved_F01)
self.points.extend(flex.vec3_double(self.sim_ac.sites_cart_moved_F01))
self.points.extend(flex.vec3_double(self.sim_as.sites_cart_wells_F01))
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
self.labels = []
n = len(self.sim_as.sites_cart_F1)
offs = 0
for prefix,color in [("S",(1,0,0)),("C",(0,0,1)),("W",(0,1,0))]:
for i in xrange(n):
add_line(offs+i, offs+(i+1)%n, color)
self.labels.append(prefix+str(i))
offs += n
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius()*1.3)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 8
print "Press and hold Tab key to run the simulation."
print "Press Shift-Tab to increase speed."
print "Press Ctrl-Tab to decrease speed."
def set_points_and_lines(O, app, minimum_covering_sphere_view_scale=1.3):
pdb_atoms = app.pdb_atoms
pdb_atoms.set_chemical_element_simple_if_necessary()
atom_tmp_sentinel = pdb_atoms.reset_tmp(first_value=0, increment=0)
for i, rg in enumerate(app.pdb_hierarchy.residue_groups()):
for atom in rg.atoms():
atom.tmp = i
O.points = pdb_atoms.extract_xyz()
if (app.co.serial_labels):
m = ""
need_m = (app.pdb_hierarchy.models_size() != 1)
for mdl in app.pdb_hierarchy.models():
if (need_m): m = mdl.id.strip() + ":"
for i in range(mdl.atoms_size()):
O.labels.append(m + str(i))
assert len(O.labels) == O.points.size()
else:
rg_done = set()
for atom in pdb_atoms:
i = atom.tmp
if (i not in rg_done):
rg_done.add(i)
l = atom.id_str()
else:
l = atom.name
O.labels.append(l)
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
bond_sets = build_simple_two_way_bond_sets(
sites_cart=O.points, elements=pdb_atoms.extract_element())
for i, bond_set in enumerate(bond_sets):
for j in bond_set:
if (i < j):
line = (i, j)
ai, aj = [pdb_atoms[_] for _ in line]
if (ai.is_in_same_conformer_as(aj)):
O.line_i_seqs.append(line)
if (ai.tmp == aj.tmp):
if (ai.tmp % 2 == 0):
color = (0, 0, 1)
else:
color = (0, 1, 0)
else:
color = (1, 0, 0)
O.line_colors[line] = color
del atom_tmp_sentinel
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius() * minimum_covering_sphere_view_scale)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
_ = app.co.labels_threshold
O.flag_show_labels = (_ == 0 or len(O.points) <= _)
O.labels_display_list = None
O.lines_display_list = None
O.points_display_list = None
def update_mcs(self, points, recenter_and_zoom=True, buffer=0):
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(points=points, epsilon=0.1)
if buffer > 0:
self.minimum_covering_sphere = sphere_3d(center=mcs.center(),
radius=mcs.radius() +
buffer)
else:
self.minimum_covering_sphere = mcs
if (recenter_and_zoom) and (not self.GL_uninitialised):
self.move_rotation_center_to_mcs_center()
self.fit_into_viewport()
def update_mcs (self, points, recenter_and_zoom=True, buffer=0) :
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(points=points,
epsilon=0.1)
if buffer > 0 :
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius() + buffer)
else :
self.minimum_covering_sphere = mcs
if (recenter_and_zoom) and (not self.GL_uninitialised) :
self.move_rotation_center_to_mcs_center()
self.fit_into_viewport()
def first_motion_callback(self, points):
self.points = flex.vec3_double(points)
self.labels = ["A", "B", "C"]
def add_line(i, j, color):
line = (i,j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
add_line(0, 1, (1,0,0))
add_line(1, 2, (0,1,0))
add_line(2, 0, (0,0,1))
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=matrix.col(mcs.center())+matrix.col((0.5,0.5,0.5)),
radius=mcs.radius()*2.0)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
def first_action_callback(O, tardy_model, rmsd_calculator):
O.tardy_model = tardy_model
tpo = tardy_model.potential_obj
O.draw_map.set_unit_cell_and_density_map(
unit_cell=tpo.geo_manager.crystal_symmetry.unit_cell(),
density_map=tpo.density_map)
O.points = tardy_model.sites_moved().deep_copy()
if (tpo.ideal_sites_cart is not None):
O.points.extend(tpo.ideal_sites_cart)
if (O.points.size() < 20):
if (tpo.ideal_sites_cart is None):
O.labels = tardy_model.labels
else:
O.labels = tardy_model.labels + [""] * len(tardy_model.labels)
def draw_ideal_line():
if (tpo.ideal_sites_cart is None): return
n = tardy_model.tardy_tree.n_vertices
ideal_line = tuple([i + n for i in line])
O.line_i_seqs.append(ideal_line)
O.line_colors[ideal_line] = [0.6] * 3
if (tardy_model.potential_obj.reduced_geo_manager is not None):
for line, color in tardy_model.tardy_tree.viewer_lines_with_colors(
include_loop_edge_bendings=False):
draw_ideal_line()
O.line_i_seqs.append(line)
O.line_colors[line] = color
print "\n".join(
tardy_model.tardy_tree.viewer_lines_with_colors_legend(
include_loop_edge_bendings=False))
else:
for line in tardy_model.potential_obj.geo_manager.simple_edge_list(
):
draw_ideal_line()
O.line_i_seqs.append(line)
O.line_colors[line] = (1, 0, 0)
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(center=mcs.center(),
radius=mcs.radius() * 2.0)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
O.show_key_stroke_help()
if (O.first_first): O.first_first = False
else: O.action_callback()
def first_motion_callback(self, points):
self.points = flex.vec3_double(points)
self.labels = ["A", "B", "C"]
def add_line(i, j, color):
line = (i, j)
self.line_i_seqs.append(line)
self.line_colors[line] = color
add_line(0, 1, (1, 0, 0))
add_line(1, 2, (0, 1, 0))
add_line(2, 0, (0, 0, 1))
mcs = minimum_covering_sphere(self.points, epsilon=1.e-2)
self.minimum_covering_sphere = sphere_3d(
center=matrix.col(mcs.center()) + matrix.col((0.5, 0.5, 0.5)),
radius=mcs.radius() * 2.0)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
def first_action_callback(O, tardy_model, rmsd_calculator):
O.tardy_model = tardy_model
tpo = tardy_model.potential_obj
O.draw_map.set_unit_cell_and_density_map(
unit_cell=tpo.geo_manager.crystal_symmetry.unit_cell(),
density_map=tpo.density_map)
O.points = tardy_model.sites_moved().deep_copy()
if (tpo.ideal_sites_cart is not None):
O.points.extend(tpo.ideal_sites_cart)
if (O.points.size() < 20):
if (tpo.ideal_sites_cart is None):
O.labels = tardy_model.labels
else:
O.labels = tardy_model.labels + [""] * len(tardy_model.labels)
def draw_ideal_line():
if (tpo.ideal_sites_cart is None): return
n = tardy_model.tardy_tree.n_vertices
ideal_line = tuple([i+n for i in line])
O.line_i_seqs.append(ideal_line)
O.line_colors[ideal_line] = [0.6]*3
if (tardy_model.potential_obj.reduced_geo_manager is not None):
for line,color in tardy_model.tardy_tree.viewer_lines_with_colors(
include_loop_edge_bendings=False):
draw_ideal_line()
O.line_i_seqs.append(line)
O.line_colors[line] = color
print "\n".join(tardy_model.tardy_tree.viewer_lines_with_colors_legend(
include_loop_edge_bendings=False))
else:
for line in tardy_model.potential_obj.geo_manager.simple_edge_list():
draw_ideal_line()
O.line_i_seqs.append(line)
O.line_colors[line] = (1,0,0)
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius()*2.0)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
O.show_key_stroke_help()
if (O.first_first): O.first_first = False
else: O.action_callback()
def set_points_and_lines(
self,
tardy_model,
velocity_scaling=False,
e_kin_per_dof=1,
minimum_covering_sphere_view_scale=1.3,
show_loop_edge_bendings=True,
long_labels=None,
):
self.tardy_model = tardy_model
temperature_dof = len(tardy_model.sites) * 3
if e_kin_per_dof is None:
self.e_kin_target = tardy_model.e_kin() / max(1, temperature_dof)
else:
self.e_kin_target = e_kin_per_dof * temperature_dof
tardy_model.assign_random_velocities(e_kin_target=self.e_kin_target)
self.velocity_scaling = velocity_scaling
self.long_labels = long_labels
self.labels = self.tardy_model.labels
self.set_points()
for line, color in tardy_model.tardy_tree.viewer_lines_with_colors(
include_loop_edge_bendings=show_loop_edge_bendings
):
self.line_i_seqs.append(line)
self.line_colors[line] = color
print "\n".join(
tardy_model.tardy_tree.viewer_lines_with_colors_legend(include_loop_edge_bendings=show_loop_edge_bendings)
)
mcs = minimum_covering_sphere(self.points, epsilon=1.0e-2)
self.minimum_covering_sphere = sphere_3d(
center=mcs.center(), radius=mcs.radius() * minimum_covering_sphere_view_scale
)
self.flag_show_minimum_covering_sphere = False
self.flag_show_rotation_center = False
self.steps_per_tab = 1
self.show_key_stroke_help()
def set_points_and_lines(
O,
app,
minimum_covering_sphere_view_scale=1.3):
pdb_atoms = app.pdb_atoms
pdb_atoms.set_chemical_element_simple_if_necessary()
atom_tmp_sentinel = pdb_atoms.reset_tmp(first_value=0, increment=0)
for i,rg in enumerate(app.pdb_hierarchy.residue_groups()):
for atom in rg.atoms():
atom.tmp = i
O.points = pdb_atoms.extract_xyz()
if (app.co.serial_labels):
m = ""
need_m = (app.pdb_hierarchy.models_size() != 1)
for mdl in app.pdb_hierarchy.models():
if (need_m): m = mdl.id.strip() + ":"
for i in xrange(mdl.atoms_size()):
O.labels.append(m+str(i))
assert len(O.labels) == O.points.size()
else:
rg_done = set()
for atom in pdb_atoms:
i = atom.tmp
if (i not in rg_done):
rg_done.add(i)
l = atom.id_str()
else:
l = atom.name
O.labels.append(l)
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
bond_sets = build_simple_two_way_bond_sets(
sites_cart=O.points,
elements=pdb_atoms.extract_element())
for i,bond_set in enumerate(bond_sets):
for j in bond_set:
if (i < j):
line = (i,j)
ai, aj = [pdb_atoms[_] for _ in line]
if (ai.is_in_same_conformer_as(aj)):
O.line_i_seqs.append(line)
if (ai.tmp == aj.tmp):
if (ai.tmp % 2 == 0):
color = (0,0,1)
else:
color = (0,1,0)
else:
color = (1,0,0)
O.line_colors[line] = color
del atom_tmp_sentinel
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius()*minimum_covering_sphere_view_scale)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
_ = app.co.labels_threshold
O.flag_show_labels = (_ == 0 or len(O.points) <= _)
O.labels_display_list = None
O.lines_display_list = None
O.points_display_list = None
