def minimum_covering_sphere(self, epsilon=None):
if (epsilon is None): epsilon = 1.e-3
points = flex.vec3_double()
orth = self.unit_cell.orthogonalize
for vertex in self.shape_vertices():
points.append(orth([float(e) for e in vertex]))
return minimum_covering_sphere(points=points, epsilon=epsilon)
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,
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 __init__(self, *args, **kwds): super(MyGLWindow, self).__init__(*args, **kwds) self.points = flex.vec3_double([ (-5,-5,-5), (-4,0,0), (0,-8,0), (0,0,-11) ]) self.line_i_seqs = [ (0,1), (0,2), (0,3), (1,2), (1,3), (2,3) ] self.spheres = [ ((0,0,0), 1) ] self.flag_show_minimum_covering_sphere = False self.minimum_covering_sphere = minimum_covering_sphere(self.points)
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 __init__(self, *args, **kwds):
wxGLWindow.__init__(self, *args, **kwds)
self.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
self.Bind(wx.EVT_ERASE_BACKGROUND, lambda evt: None)
# FIXME orthographic is definitely best for this application, but it isn't
# working properly right now
#self.orthographic = True
parent = self.GetParent()
if (parent is None):
parent = kwds.get("parent")
assert (parent is not None)
self.settings = parent.settings
self.buffer_factor = 2.0
self.min_slab = 4
self.min_viewport_use_fraction = 0.1
self.min_dist = 4.0
self.flag_show_fog = True
self.flag_use_lights = True
self.flag_use_quadrics = False
self.minimum_covering_sphere = None
self.spheres_display_list = None
self.points_display_list = None
self.labels_display_list = None
self.miller_array = None
self.d_min = None
self.scene = None
self.animation_time = 0
#self.fps = gltbx.viewer_utils.fps_monitor()
# XXX prevent exception when no data are loaded
from scitbx.math import minimum_covering_sphere
from scitbx.array_family import flex
points = flex.vec3_double([(0.0, 0.0, 0.0), (1.0, 1.0, 1.0)])
mcs = minimum_covering_sphere(points=points, epsilon=0.1)
self.minimum_covering_sphere = mcs
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 __init__ (self, *args, **kwds) :
wxGLWindow.__init__(self, *args, **kwds)
self.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
self.Bind(wx.EVT_ERASE_BACKGROUND, lambda evt: None)
# FIXME orthographic is definitely best for this application, but it isn't
# working properly right now
#self.orthographic = True
parent = self.GetParent()
if (parent is None) :
parent = kwds.get("parent")
assert (parent is not None)
self.settings = parent.settings
self.buffer_factor = 2.0
self.min_slab = 4
self.min_viewport_use_fraction = 0.1
self.min_dist = 4.0
self.flag_show_fog = True
self.flag_use_lights = True
self.flag_use_quadrics = False
self.minimum_covering_sphere = None
self.spheres_display_list = None
self.points_display_list = None
self.labels_display_list = None
self.miller_array = None
self.d_min = None
self.scene = None
self.animation_time = 0
#self.fps = gltbx.viewer_utils.fps_monitor()
# XXX prevent exception when no data are loaded
from scitbx.math import minimum_covering_sphere
from scitbx.array_family import flex
points = flex.vec3_double([(0.0,0.0,0.0),(1.0,1.0,1.0)])
mcs = minimum_covering_sphere(points=points, epsilon=0.1)
self.minimum_covering_sphere = mcs
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 __init__(self, *args, **kwds): super(MyGLWindow, self).__init__(*args, **kwds) self.points = flex.vec3_double([ (-5,-5,-5), (-4,0,0), (0,-8,0), (0,0,-11) ]) self.line_i_seqs = [ (0,1), (0,2), (0,3), (1,2), (1,3), (2,3) ] self.spheres = [ ((0,0,0), 1) ] self.flag_show_minimum_covering_sphere = False self.minimum_covering_sphere = minimum_covering_sphere(self.points)
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(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 construct_reciprocal_space(self, merge=None):
self.scene = hklview.scene(miller_array=self.miller_array,
merge=merge,
settings=self.settings)
from scitbx.math import minimum_covering_sphere
mcs = minimum_covering_sphere(points=self.scene.points, epsilon=0.1)
self.minimum_covering_sphere = mcs
self.spheres_display_list = None
self.points_display_list = None
self.labels_display_list = None
self.rotation_center = (0, 0, 0)
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 construct_reciprocal_space (self, merge=None) :
self.scene = hklview.scene(miller_array=self.miller_array,
merge=merge,
settings=self.settings)
from scitbx.math import minimum_covering_sphere
mcs = minimum_covering_sphere(points=self.scene.points,
epsilon=0.1)
self.minimum_covering_sphere = mcs
self.spheres_display_list = None
self.points_display_list = None
self.labels_display_list = None
self.rotation_center = (0,0,0)
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 __init__ (self, *args, **kwds) :
wx_viewer.wxGLWindow.__init__(self, *args, **kwds)
self.SetSize((400,400))
self.SetMinSize((400,400))
self.flag_draw_boxes = False
self.flag_log_scale = False
self._img = None
self.x_center = None
self.y_center = None
self.buffer_factor = 2.0
self.scale_factor = 100
self.rotation_center = (20,-20,0)
self.minimum_covering_sphere = minimum_covering_sphere(
flex.vec3_double([[0,0,0],[40,-40,40],[40,0,0],[0,-40,40]]))
self.zoom_level = 16
def __init__(self, *args, **kwds):
wx_viewer.wxGLWindow.__init__(self, *args, **kwds)
self.SetSize((400,400))
self.SetMinSize((400,400))
self.flag_draw_boxes = False
self.flag_log_scale = False
self._img = None
self.x_center = None
self.y_center = None
self.buffer_factor = 2.0
self.scale_factor = 100
self.rotation_center = (20,-20,0)
self.minimum_covering_sphere = minimum_covering_sphere(
flex.vec3_double([[0,0,0],[40,-40,40],[40,0,0],[0,-40,40]]))
self.zoom_level = 16
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 __init__ (self, *args, **kwds) :
if self.initialize_map_viewer_super :
wxGLWindow.__init__(self, *args, **kwds)
# various data objects
self.map_ids = []
self.map_objects = []
self.map_scenes = {}
self.show_object = {}
self.map_panel = None
# user settings
self.mesh_line_width = 0.25 # very buggy on OS X + NVidia (and ???)
self.selected_map_id = None
self.update_maps = False
self.flag_show_maps = True
self.flag_smooth_lines = True
self.flag_use_materials = False
self.flag_show_rotation_center = True
self.minimum_covering_sphere = minimum_covering_sphere(
flex.vec3_double([[0,0,0],[100,100,100],[100,0,0],[0,100,100]]))
def load_residue(self, *args, **kwargs):
self.points = flex.vec3_double(kwargs['atoms'])
self.colours = kwargs['colours']
self.line_i_seqs = kwargs['bonds']
self.labels = kwargs['labels']
self.blabels = kwargs['blabels']
self.uij = kwargs['uij']
self.minimum_covering_sphere = minimum_covering_sphere(points=self.points)
self.spheres_display_list = None
self.points_display_list = None
self.lines_display_list = None
self.labels_display_list = None
self.ellipsoid_display_list = None
self.blabels_display_list = None
if not self.GL_uninitialised:
self.move_rotation_center_to_mcs_center()
self.fit_into_viewport()
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 update_minimum_covering_sphere(self):
n_points = min(1000, self.points.size())
isel = flex.random_permutation(self.points.size())[:n_points]
self.minimum_covering_sphere = minimum_covering_sphere(
self.points.select(isel))
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
def set_ensemble_b_factors_to_xyz_displacement(
pdb_hierarchy,
include_hydrogens=False,
include_waters=False,
use_c_alpha_values=False,
method="rmsf",
selection=None,
substitute_b_value=-1.0,
logarithmic=False,
log=None,
):
"""
Given an ensemble (multi-MODEL PDB hierarchy), calculate the deviation
between copies of each atom (defined here as either the root-mean-square
fluctuation, or the radius of the minimum covering sphere) and set the
isotropic B-factors to this value.
"""
if log is None:
log = null_out()
assert method in ["rmsf", "mcs"]
from scitbx.math import minimum_covering_sphere
from scitbx.array_family import flex
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
xyz_by_atom = {}
def get_key(atom):
labels = atom.fetch_labels()
return (labels.chain_id, labels.resid(), labels.altloc, atom.name)
def get_c_alpha(atom):
if (atom.name.strip() == "CA") and (atom.element.strip() == "C"):
return atom
for other in atom.parent().atoms():
if (other.name.strip() == "CA") and (other.element.strip() == "C"):
return other
return None
for model in pdb_hierarchy.models():
for atom in model.atoms():
if selection is not None:
if not selection[atom.i_seq]:
continue
elif (not include_hydrogens) and (atom.element.strip() in ["H", "D"]):
continue
elif (not include_waters) and (atom.parent().resname in ["HOH"]):
continue
if (use_c_alpha_values) and (atom.name.strip() != "CA"):
continue
atom_key = get_key(atom)
if atom_key in xyz_by_atom:
xyz_by_atom[atom_key].append(atom.xyz)
else:
xyz_by_atom[atom_key] = flex.vec3_double([atom.xyz])
dev_by_atom = {}
for atom_key, xyz in xyz_by_atom.iteritems():
if method == "mcs":
mcs = minimum_covering_sphere(points=xyz, epsilon=0.1)
radius = mcs.radius()
if logarithmic:
radius = math.log(radius + 1.0)
dev_by_atom[atom_key] = radius
else:
mean_array = flex.vec3_double(xyz.size(), xyz.mean())
rmsf = xyz.rms_difference(mean_array)
dev_by_atom[atom_key] = rmsf
all_dev = flex.double(dev_by_atom.values())
if method == "mcs":
print >> log, "Distribution of sphere radii:"
else:
print >> log, "Distribution of root-mean-square fluctuation values:"
flex.histogram(all_dev, n_slots=20).show(f=log, prefix=" ", format_cutoffs="%.2f")
for model in pdb_hierarchy.models():
for atom in model.atoms():
if use_c_alpha_values:
c_alpha = get_c_alpha(atom)
if c_alpha is None:
atom.b = substitute_b_value
else:
atom_key = get_key(c_alpha)
atom.b = dev_by_atom.get(atom_key, substitute_b_value)
else:
atom_key = get_key(atom)
atom.b = dev_by_atom.get(atom_key, substitute_b_value)
def update_minimum_covering_sphere(self):
n_points = min(1000, self.points.size())
isel = flex.random_permutation(self.points.size())[:n_points]
self.minimum_covering_sphere = minimum_covering_sphere(
self.points.select(isel))
def set_ensemble_b_factors_to_xyz_displacement(pdb_hierarchy,
include_hydrogens=False,
include_waters=False,
use_c_alpha_values=False,
method="rmsf",
selection=None,
substitute_b_value=-1.0,
logarithmic=False,
log=None):
"""
Given an ensemble (multi-MODEL PDB hierarchy), calculate the deviation
between copies of each atom (defined here as either the root-mean-square
fluctuation, or the radius of the minimum covering sphere) and set the
isotropic B-factors to this value.
"""
if (log is None): log = null_out()
assert (method in ["rmsf", "mcs"])
from scitbx.math import minimum_covering_sphere
from scitbx.array_family import flex
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
xyz_by_atom = {}
def get_key(atom):
labels = atom.fetch_labels()
return (labels.chain_id, labels.resid(), labels.altloc, atom.name)
def get_c_alpha(atom):
if (atom.name.strip() == "CA") and (atom.element.strip() == "C"):
return atom
for other in atom.parent().atoms():
if (other.name.strip() == "CA") and (other.element.strip() == "C"):
return other
return None
for model in pdb_hierarchy.models():
for atom in model.atoms():
if (selection is not None):
if (not selection[atom.i_seq]): continue
elif (not include_hydrogens) and (atom.element.strip()
in ["H", "D"]):
continue
elif (not include_waters) and (atom.parent().resname in ["HOH"]):
continue
if (use_c_alpha_values) and (atom.name.strip() != "CA"):
continue
atom_key = get_key(atom)
if (atom_key in xyz_by_atom):
xyz_by_atom[atom_key].append(atom.xyz)
else:
xyz_by_atom[atom_key] = flex.vec3_double([atom.xyz])
dev_by_atom = {}
for atom_key, xyz in six.iteritems(xyz_by_atom):
if (method == "mcs"):
mcs = minimum_covering_sphere(points=xyz, epsilon=0.1)
radius = mcs.radius()
if (logarithmic):
radius = math.log(radius + 1.0)
dev_by_atom[atom_key] = radius
else:
mean_array = flex.vec3_double(xyz.size(), xyz.mean())
rmsf = xyz.rms_difference(mean_array)
dev_by_atom[atom_key] = rmsf
# NOTE it seems flex.double handles list generators, not sure about funky python3 dict.values() though
all_dev = flex.double(list(dev_by_atom.values()))
if (method == "mcs"):
print("Distribution of sphere radii:", file=log)
else:
print("Distribution of root-mean-square fluctuation values:", file=log)
flex.histogram(all_dev, n_slots=20).show(f=log,
prefix=" ",
format_cutoffs="%.2f")
for model in pdb_hierarchy.models():
for atom in model.atoms():
if (use_c_alpha_values):
c_alpha = get_c_alpha(atom)
if (c_alpha is None):
atom.b = substitute_b_value
else:
atom_key = get_key(c_alpha)
atom.b = dev_by_atom.get(atom_key, substitute_b_value)
else:
atom_key = get_key(atom)
atom.b = dev_by_atom.get(atom_key, substitute_b_value)
def update_minimum_covering_sphere(self):
self.minimum_covering_sphere = minimum_covering_sphere(
self.points, epsilon=1e-3)
def update_minimum_covering_sphere(self):
self.minimum_covering_sphere = minimum_covering_sphere(
self.points, epsilon=1e-3)