class Notes(ModelObject):
info = ModelObjectInfo("plugins/basic/notes.svg")
authors = [authors.toon_verstraelen]
#
# Properties
#
def set_notes(self, notes, init=False):
self.notes = notes
properties = [
Property("notes", StringIO.StringIO(), lambda self: self.notes, set_notes)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo("Basic", (0, 10), fields.edit.TextView(
label_text="Notes",
attribute_name="notes",
))
])
class ConscanResults(ReferentBase):
info = ModelObjectInfo("plugins/builder/conscan_results.svg",
"ShowConscanResultsWindow")
authors = [authors.toon_verstraelen]
#
# State
#
def initnonstate(self):
ReferentBase.initnonstate(self)
self.set_children(
[Reference(prefix="First"),
Reference(prefix="Second")])
#
# Properties
#
def get_connections(self):
def get_index(node):
if node is None: return -1
node = node()
if node is None: return -1
if node.model != context.application.model: return -1
return node.get_index()
return [(quality, transformation, [
(get_index(node1), get_index(node2)) for node1, node2 in pairs
], [(get_index(node1), get_index(node2))
for node1, node2 in inverse_pairs]) for quality, transformation,
pairs, inverse_pairs in self.connections]
def set_connections(self, connections, init=False):
def get_ref(frame_index, index):
if index is -1:
return None
else:
return weakref.ref(
self.children[frame_index].target.children[index])
self.connections = [
(quality, transformation, [(get_ref(0, index1), get_ref(1, index2))
for index1, index2 in pairs],
[(get_ref(0, index1), get_ref(1, index2))
for index1, index2 in inverse_pairs])
for quality, transformation, pairs, inverse_pairs in connections
]
properties = [
Property("connections", [], get_connections, set_connections),
]
class UserColorMixin(gobject.GObject):
__metaclass__ = NodeClass
#
# Properties
#
def set_user_color(self, user_color, init=False):
self.user_color = user_color
if not init:
self.invalidate_draw_list()
properties = [
Property("user_color",
Undefined(numpy.array([0.7, 0.7, 0.7, 1.0])),
lambda self: self.user_color,
set_user_color,
signal=True)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Markup", (1, 7),
fields.optional.CheckOptional(
fields.edit.Color(
label_text="User defined color",
attribute_name="user_color",
))),
])
#
# Draw
#
def get_color(self):
if isinstance(self.user_color, Undefined):
return self.default_color
else:
return self.user_color
def draw(self):
context.application.vis_backend.set_color(*self.get_color())
class GLPeriodicContainer(GLContainerBase):
#
# Properties
#
def update_vectors(self):
for node in self.children:
if isinstance(node, GLReferentBase):
node.invalidate_draw_list()
node.invalidate_boundingbox_list()
def set_cell(self, cell, init=False):
self.cell = cell
if not init:
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
self.update_vectors()
#
# Properties
#
properties = [
Property("cell", default_unit_cell, lambda self: self.cell, set_cell),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Unit cell", (5, 0),
fields.composed.Cell(
label_text="Periodic cell",
attribute_name="cell",
)),
])
class ColorMixin(gobject.GObject):
__metaclass__ = NodeClass
#
# Properties
#
def set_color(self, color, init=False):
self.color = color
if not init:
self.invalidate_draw_list()
properties = [
Property("color", numpy.array([0.7, 0.7, 0.7, 1.0]),
lambda self: self.color, set_color)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Markup", (1, 0),
fields.edit.Color(
label_text="Color",
attribute_name="color",
))
])
#
# Draw
#
def draw(self):
context.application.vis_backend.set_color(*self.color)
class GLTransformationMixin(GLMixin):
#
# State
#
def initnonstate(self, Transformation):
GLMixin.initnonstate(self)
self.Transformation = Transformation
#
# Properties
#
def default_transformation(self):
return self.Transformation.identity()
def set_transformation(self, transformation, init=False):
if not transformation.__class__ == self.Transformation:
# create an object of the proper type and take only the attributes
# of interest.
if isinstance(transformation, Translation):
t = transformation.t
else:
t = None
if isinstance(transformation, Rotation):
r = transformation.r
else:
r = None
if self.Transformation == Translation:
if t is None:
transformation = Translation.identity()
else:
transformation = Translation(t)
elif self.Transformation == Rotation:
if r is None:
transformation = Rotation.identity()
else:
transformation = Rotation(r)
else: # self.Transformation == Complete:
if r is None:
r = numpy.identity(3, float)
if t is None:
t = numpy.zeros(3, float)
transformation = Complete(r, t)
self.transformation = transformation
if not init:
self.invalidate_transformation_list()
properties = [
Property("transformation", default_transformation,
lambda self: self.transformation, set_transformation)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Transformation", (3, 0),
fields.composed.Translation(
label_text="Translation with vector t",
attribute_name="transformation",
)),
DialogFieldInfo(
"Transformation", (3, 1),
fields.composed.Rotation(
label_text="Rotation around axis n",
attribute_name="transformation",
)),
DialogFieldInfo(
"Transformation", (3, 2),
fields.composed.Complete(
label_text=
"The transformation is a rotation followed by a translation.",
attribute_name="transformation",
)),
DialogFieldInfo("Transformation", (3, 3), fields.read.Handedness()),
])
#
# OpenGL
#
def initialize_gl(self):
vb = context.application.vis_backend
self.transformation_list = vb.create_list()
##print "Created transformation list (%i): %s" % (self.transformation_list, self.get_name())
self.transformation_list_valid = True
GLMixin.initialize_gl(self)
def cleanup_gl(self):
GLMixin.cleanup_gl(self)
vb = context.application.vis_backend
##print "Deleting transformation list (%i): %s" % (self.transformation_list, self.get_name())
vb.delete_list(self.transformation_list)
del self.transformation_list
del self.transformation_list_valid
#
# Invalidation
#
def invalidate_transformation_list(self):
##print "CALL %s: on-transformation-list-invalidated" % self.get_name()
if self.gl_active and self.transformation_list_valid:
self.transformation_list_valid = False
context.application.main.drawing_area.queue_draw()
context.application.scene.add_revalidation(
self.revalidate_transformation_list)
self.emit("on-transformation-list-invalidated")
##print "EMIT %s: on-transformation-list-invalidated" % self.get_name()
if isinstance(self.parent, GLMixin):
self.parent.invalidate_boundingbox_list()
def invalidate_all_lists(self):
self.invalidate_transformation_list()
GLMixin.invalidate_all_lists(self)
#
# Revalidation
#
def revalidate_transformation_list(self):
if self.gl_active:
vb = context.application.vis_backend
##print "Compiling transformation list (%i): %s" % (self.transformation_list, self.get_name())
vb.begin_list(self.transformation_list)
vb.transform(self.transformation)
vb.end_list()
self.transformation_list_valid = True
def revalidate_total_list(self):
if self.gl_active:
vb = context.application.vis_backend
##print "Compiling total list (%i): %s" % (self.total_list, self.get_name())
vb.begin_list(self.total_list)
if self.visible:
vb.push_name(self.draw_list)
vb.push_matrix()
vb.call_list(self.transformation_list)
self.draw_selection()
vb.call_list(self.draw_list)
vb.pop_matrix()
vb.pop_name()
vb.end_list()
self.total_list_valid = True
#
# Frame
#
def get_bounding_box_in_parent_frame(self):
return self.bounding_box.transformed(self.transformation)
def get_absolute_frame(self):
if not isinstance(self.parent, GLMixin):
return self.transformation
else:
return self.get_absolute_parentframe() * self.transformation
def get_frame_up_to(self, upper_parent):
if (upper_parent == self):
return Complete.identity()
elif (self.parent == upper_parent):
return self.transformation
else:
return self.get_parentframe_up_to(
upper_parent) * self.transformation
class Point(GLGeometricBase, ColorMixin):
info = ModelObjectInfo("plugins/basic/point.svg")
authors = [authors.toon_verstraelen]
def initnonstate(self):
GLGeometricBase.initnonstate(self, Translation)
#
# Properties
#
def set_spike_length(self, spike_length, init=False):
self.spike_length = spike_length
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_spike_thickness(self, spike_thickness, init=False):
self.spike_thickness = spike_thickness
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("spike_length", 0.3, lambda self: self.spike_length,
set_spike_length),
Property("spike_thickness", 0.1, lambda self: self.spike_thickness,
set_spike_thickness),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 7),
fields.faulty.Length(label_text="Spike length",
attribute_name="spike_length",
low=0.0,
low_inclusive=False)),
DialogFieldInfo(
"Geometry", (2, 8),
fields.faulty.Length(label_text="Spike thickness",
attribute_name="spike_thickness",
low=0.0,
low_inclusive=False))
])
#
# Draw
#
def draw_spike(self):
ColorMixin.draw(self)
vb = context.application.vis_backend
vb.draw_quad_strip(
(numpy.array([0.5773502692, -0.5773502692, -0.5773502692]), [
numpy.array(
[self.spike_length, self.spike_length, self.spike_length])
]), (numpy.array([1, 0, 0
]), [numpy.array([self.spike_thickness, 0, 0])]),
(numpy.array([-0.5773502692, 0.5773502692, -0.5773502692]), [
numpy.array(
[self.spike_length, self.spike_length, self.spike_length])
]), (numpy.array([0, 1, 0
]), [numpy.array([0, self.spike_thickness, 0])]),
(numpy.array([-0.5773502692, -0.5773502692, 0.5773502692]), [
numpy.array(
[self.spike_length, self.spike_length, self.spike_length])
]), (numpy.array([0, 0, 1
]), [numpy.array([0, 0, self.spike_thickness])]),
(numpy.array([0.5773502692, -0.5773502692, -0.5773502692]), [
numpy.array(
[self.spike_length, self.spike_length, self.spike_length])
]), (numpy.array([1, 0, 0
]), [numpy.array([self.spike_thickness, 0, 0])]))
def draw(self):
GLGeometricBase.draw(self)
vb = context.application.vis_backend
vb.push_matrix()
for i in range(2):
for i in range(4):
self.draw_spike()
vb.rotate(90, 1.0, 0.0, 0.0)
vb.rotate(180, 0.0, 1.0, 0.0)
vb.pop_matrix()
#
# Revalidation
#
def revalidate_bounding_box(self):
GLGeometricBase.revalidate_bounding_box(self)
self.bounding_box.extend_with_corners(
numpy.array(
[[-self.spike_length, -self.spike_length, -self.spike_length],
[self.spike_length, self.spike_length, self.spike_length]]))
class Arrow(Vector, ColorMixin):
info = ModelObjectInfo("plugins/basic/arrow.svg")
authors = [authors.toon_verstraelen]
#
# Properties
#
def set_radius(self, radius, init=False):
self.radius = radius
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_quality(self, quality, init=False):
self.quality = quality
if not init:
self.invalidate_draw_list()
def set_arrow_length(self, arrow_length, init=False):
self.arrow_length = arrow_length
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_arrow_radius(self, arrow_radius, init=False):
self.arrow_radius = arrow_radius
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_arrow_position(self, arrow_position, init=False):
self.arrow_position = arrow_position
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("radius", 0.15, lambda self: self.radius, set_radius),
Property("quality", 15, lambda self: self.quality, set_quality),
Property("arrow_length", 0.6, lambda self: self.arrow_length,
set_arrow_length),
Property("arrow_radius", 0.3, lambda self: self.arrow_radius,
set_arrow_radius),
Property("arrow_position", 0.5, lambda self: self.arrow_position,
set_arrow_position)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 2),
fields.faulty.Length(
label_text="Radius",
attribute_name="radius",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo(
"Geometry", (2, 3),
fields.faulty.Length(
label_text="Arrow length",
attribute_name="arrow_length",
low=0.0,
)),
DialogFieldInfo(
"Geometry", (2, 4),
fields.faulty.Length(
label_text="Arrow radius",
attribute_name="arrow_radius",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo(
"Geometry", (2, 5),
fields.faulty.Float(
label_text="Arrow position",
attribute_name="arrow_position",
low=0.0,
high=1.0,
)),
DialogFieldInfo(
"Markup", (1, 3),
fields.faulty.Int(
label_text="Quality",
attribute_name="quality",
minimum=3,
)),
])
#
# Draw
#
def draw(self):
Vector.draw(self)
ColorMixin.draw(self)
vb = context.application.vis_backend
if self.length == 0.0: return
# usefull variable
if self.arrow_radius <= 0:
arrowtop_length = self.arrow_length
else:
arrowtop_length = self.arrow_length / self.arrow_radius * self.radius
# stick and bottom
if (self.length - arrowtop_length > 0) and (self.radius > 0):
vb.draw_cylinder(self.radius, self.length - arrowtop_length,
self.quality)
vb.set_quadric_inside()
vb.draw_disk(self.radius, self.quality)
# arrowtop
if (self.radius > 0):
if (arrowtop_length > 0):
vb.push_matrix()
vb.translate(0.0, 0.0, self.length - arrowtop_length)
vb.set_quadric_outside()
vb.draw_cone(self.radius, 0, arrowtop_length, self.quality)
vb.pop_matrix()
else:
vb.push_matrix()
vb.translate(0.0, 0.0, self.length)
vb.set_quadric_outside()
vb.draw_disk(self.radius, self.quality)
vb.pop_matrix()
# arrow
if (self.arrow_radius - self.radius >
0) and (self.arrow_length - arrowtop_length) > 0:
vb.push_matrix()
vb.translate(0.0, 0.0, (self.length - self.arrow_length) *
(self.arrow_position))
vb.set_quadric_outside()
vb.draw_cone(self.arrow_radius, self.radius,
self.arrow_length - arrowtop_length, self.quality)
vb.set_quadric_inside()
vb.draw_disk(self.arrow_radius, self.quality)
vb.pop_matrix()
vb.set_quadric_outside()
#
# Revalidation
#
def revalidate_bounding_box(self):
Vector.revalidate_bounding_box(self)
if self.length > 0.0:
self.bounding_box.extend_with_corners(
numpy.array([[0.0, 0.0, 0.0], [0.0, 0.0, self.length]]))
temp = {
True: self.radius,
False: self.arrow_radius
}[self.radius > self.arrow_radius]
self.bounding_box.extend_with_corners(
numpy.array([[-temp, -temp, 0.0], [temp, temp, 0.0]]))
class Plane(GLReferentBase, ColorMixin):
info = ModelObjectInfo("plugins/basic/plane.svg")
authors = [authors.toon_verstraelen]
#
# State
#
def set_targets(self, targets, init=False):
self.set_children([SpatialReference("Point") for target in targets])
GLReferentBase.set_targets(self, targets, init)
#
# Properties
#
def set_margin(self, margin, init=False):
self.margin = margin
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("margin", 1.0, lambda self: self.margin, set_margin),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 10),
fields.faulty.Length(
label_text="Margin",
attribute_name="margin",
low=0.0,
low_inclusive=True,
)),
])
#
# Draw
#
def update_normal(self):
self.points = numpy.array([
child.target.get_frame_relative_to(self.parent).t
for child in self.children if child.target is not None
], float)
self.center = sum(self.points) / len(self.points)
tmp = self.points - self.center
tensor = (tmp.ravel()**2).sum() * numpy.identity(3) - numpy.dot(
tmp.transpose(), tmp)
evals, evecs = numpy.linalg.eigh(tensor)
indices = evals.argsort()
self.x = evecs[:, indices[0]]
self.y = evecs[:, indices[1]]
if numpy.linalg.det(evecs) < 0:
self.normal = evecs[:, indices[2]]
else:
self.normal = -evecs[:, indices[2]]
px = numpy.dot(tmp, self.x)
py = numpy.dot(tmp, self.y)
px_low = px.min() - self.margin
px_high = px.max() + self.margin
py_low = py.min() - self.margin
py_high = py.max() + self.margin
self.l_l = self.x * px_low + self.y * py_low + self.center
self.l_h = self.x * px_low + self.y * py_high + self.center
self.h_l = self.x * px_high + self.y * py_low + self.center
self.h_h = self.x * px_high + self.y * py_high + self.center
def draw(self):
GLReferentBase.draw(self)
ColorMixin.draw(self)
self.update_normal()
vb = context.application.vis_backend
vb.draw_quads((
self.normal,
[
self.l_l + 0.001 * self.normal,
self.l_h + 0.001 * self.normal,
self.h_h + 0.001 * self.normal,
self.h_l + 0.001 * self.normal,
],
), (
-self.normal,
[
self.h_l - 0.001 * self.normal,
self.h_h - 0.001 * self.normal,
self.l_h - 0.001 * self.normal,
self.l_l - 0.001 * self.normal,
],
))
#
# Revalidation
#
def revalidate_bounding_box(self):
GLReferentBase.revalidate_bounding_box(self)
self.update_normal()
self.bounding_box.extend_with_point(self.l_l)
self.bounding_box.extend_with_point(self.l_h)
self.bounding_box.extend_with_point(self.h_l)
self.bounding_box.extend_with_point(self.h_h)
#
# Vector
#
def define_target(self, reference, new_target):
GLReferentBase.define_target(self, reference, new_target)
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
def target_moved(self, reference, target):
GLReferentBase.target_moved(self, reference, target)
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
class Box(GLGeometricBase, ColorMixin):
info = ModelObjectInfo("plugins/basic/box.svg")
authors = [authors.toon_verstraelen]
def initnonstate(self):
GLGeometricBase.initnonstate(self, Complete)
#
# Properties
#
def set_size(self, size, init=False):
self.size = size
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("size", numpy.array([1.0, 1.0, 1.0]), lambda self: self.size,
set_size),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 6),
fields.composed.ComposedArray(
FieldClass=fields.faulty.Length,
array_name="%s",
suffices=["Width", "Height", "Depth"],
label_text="Box size",
attribute_name="size",
))
])
#
# Draw
#
def draw(self):
GLGeometricBase.draw(self)
ColorMixin.draw(self)
vb = context.application.vis_backend
x, y, z = numpy.identity(3)
sides = numpy.array([(x, y, z, z), (x, y, -z, -z), (y, z, x, x),
(y, z, -x, -x), (z, x, y, y), (z, x, -y, -y)],
float)
sides[:, :3] *= 0.5 * self.size
vb.draw_quads(*[(normal, [
a + b + c,
a - b + c,
-a - b + c,
-a + b + c,
]) for a, b, c, normal in sides])
#
# Revalidation
#
def revalidate_bounding_box(self):
GLGeometricBase.revalidate_bounding_box(self)
self.bounding_box.extend_with_corners(
numpy.array([-0.5 * self.size, 0.5 * self.size]))
class Universe(GLPeriodicContainer, FrameAxes):
info = ModelObjectInfo("plugins/basic/universe.svg")
authors = [authors.toon_verstraelen]
clip_margin = 0.1
#
# State
#
def initnonstate(self):
GLPeriodicContainer.initnonstate(self)
self.model_center = Translation.identity()
def update_center(self):
self.model_center = Translation(
0.5 *
numpy.dot(self.cell.matrix, self.repetitions * self.cell.active))
#
# Properties
#
def set_cell(self, cell, init=False):
GLPeriodicContainer.set_cell(self, cell, init)
if not init:
self.update_clip_planes()
self.update_center()
self.invalidate_total_list()
self.invalidate_box_list()
def set_repetitions(self, repetitions, init=False):
self.repetitions = repetitions
if not init:
self.update_clip_planes()
self.update_center()
self.invalidate_box_list()
self.invalidate_total_list()
def set_box_visible(self, box_visible, init=False):
self.box_visible = box_visible
if not init:
self.invalidate_total_list()
def set_clipping(self, clipping, init=False):
self.clipping = clipping
if not init:
self.invalidate_total_list()
self.invalidate_box_list()
self.update_clip_planes()
properties = [
Property("repetitions", numpy.array([1, 1, 1], int),
lambda self: self.repetitions, set_repetitions),
Property("box_visible", True, lambda self: self.box_visible,
set_box_visible),
Property("clipping", False, lambda self: self.clipping, set_clipping),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Unit cell", (5, 2),
fields.composed.Repetitions(
label_text="Repetitions",
attribute_name="repetitions",
)),
DialogFieldInfo(
"Markup", (1, 5),
fields.edit.CheckButton(
label_text="Show periodic box (if active)",
attribute_name="box_visible",
)),
DialogFieldInfo(
"Markup", (1, 6),
fields.edit.CheckButton(
label_text="Clip the unit cell contents.",
attribute_name="clipping",
)),
])
#
# Tree
#
@classmethod
def check_add(Class, ModelObjectClass):
if not GLPeriodicContainer.check_add(ModelObjectClass): return False
if issubclass(ModelObjectClass, Universe): return False
return True
#
# OpenGL
#
def initialize_gl(self):
vb = context.application.vis_backend
self.set_clip_planes()
self.update_center()
self.box_list = vb.create_list()
##print "Created box list (%i): %s" % (self.box_list, self.get_name())
self.box_list_valid = True
GLPeriodicContainer.initialize_gl(self)
def cleanup_gl(self):
vb = context.application.vis_backend
GLPeriodicContainer.cleanup_gl(self)
##print "Deleting box list (%i): %s" % (self.box_list, self.get_name())
vb.delete_list(self.box_list)
del self.box_list
del self.box_list_valid
self.unset_clip_planes()
#
# Clipping
#
def update_clip_planes(self):
if self.gl_active > 0:
self.unset_clip_planes()
self.set_clip_planes()
def set_clip_planes(self):
if not self.clipping:
return
clip_planes = context.application.scene.clip_planes
assert len(clip_planes) == 0
active, inactive = self.cell.active_inactive
for index in active:
axis = self.cell.matrix[:, index]
ortho = self.cell.reciprocal[index] / numpy.linalg.norm(
self.cell.reciprocal[index])
length = abs(numpy.dot(ortho, axis))
repetitions = self.repetitions[index]
clip_planes.append(numpy.array(list(ortho) + [self.clip_margin]))
clip_planes.append(
numpy.array(
list(-ortho) + [repetitions * length + self.clip_margin]))
context.application.main.drawing_area.queue_draw()
def unset_clip_planes(self):
context.application.scene.clip_planes = []
context.application.main.drawing_area.queue_draw()
def shortest_vector(self, delta):
return self.cell.shortest_vector(delta)
#
# Invalidation
#
def invalidate_box_list(self):
if self.gl_active > 0 and self.box_list_valid:
self.box_list_valid = False
context.application.main.drawing_area.queue_draw()
context.application.scene.add_revalidation(
self.revalidate_box_list)
##print "EMIT %s: on-box-list-invalidated" % self.get_name()
def invalidate_all_lists(self):
self.invalidate_box_list()
GLPeriodicContainer.invalidate_all_lists(self)
#
# Draw
#
def draw_box(self):
vb = context.application.vis_backend
vb.set_line_width(2)
vb.set_specular(False)
col = {True: 4.0, False: 2.5}[self.selected]
sat = {True: 0.0, False: 0.5}[self.selected]
gray = {True: 4.0, False: 2.5}[self.selected]
def draw_three(origin):
if self.cell.active[0]:
vb.set_color(col, sat, sat)
vb.draw_line(origin, origin + self.cell.matrix[:, 0])
if self.cell.active[1]:
vb.set_color(sat, col, sat)
vb.draw_line(origin, origin + self.cell.matrix[:, 1])
if self.cell.active[2]:
vb.set_color(sat, sat, col)
vb.draw_line(origin, origin + self.cell.matrix[:, 2])
def draw_gray(origin, axis1, axis2, n1, n2, delta, nd):
c = context.application.configuration.periodic_box_color
vb.set_color(gray * c[0], gray * c[1], gray * c[2], c[3])
if n1 == 0 and n2 == 0:
return
for i1 in xrange(n1 + 1):
if i1 == 0:
b2 = 1
vb.draw_line(origin + delta, origin + nd * delta)
else:
b2 = 0
for i2 in xrange(b2, n2 + 1):
vb.draw_line(origin + i1 * axis1 + i2 * axis2,
origin + i1 * axis1 + i2 * axis2 + nd * delta)
def draw_ortho(origin, axis1, axis2, n1, n2, delta):
c = context.application.configuration.periodic_box_color
vb.set_color(gray * c[0], gray * c[1], gray * c[2], c[3])
if n1 == 0 and n2 == 0:
return
for i1 in xrange(n1 + 1):
for i2 in xrange(n2 + 1):
vb.draw_line(
origin + i1 * axis1 + i2 * axis2 - 0.5 * delta,
origin + i1 * axis1 + i2 * axis2 + 0.5 * delta)
origin = numpy.zeros(3, float)
draw_three(origin)
repetitions = self.repetitions * self.cell.active
if self.cell.active[2]:
draw_gray(origin, self.cell.matrix[:, 0], self.cell.matrix[:, 1],
repetitions[0], repetitions[1], self.cell.matrix[:, 2],
repetitions[2])
else:
draw_ortho(origin, self.cell.matrix[:, 0], self.cell.matrix[:, 1],
repetitions[0], repetitions[1], self.cell.matrix[:, 2])
if self.cell.active[0]:
draw_gray(origin, self.cell.matrix[:, 1], self.cell.matrix[:, 2],
repetitions[1], repetitions[2], self.cell.matrix[:, 0],
repetitions[0])
else:
draw_ortho(origin, self.cell.matrix[:, 1], self.cell.matrix[:, 2],
repetitions[1], repetitions[2], self.cell.matrix[:, 0])
if self.cell.active[1]:
draw_gray(origin, self.cell.matrix[:, 2], self.cell.matrix[:, 0],
repetitions[2], repetitions[0], self.cell.matrix[:, 1],
repetitions[1])
else:
draw_ortho(origin, self.cell.matrix[:, 2], self.cell.matrix[:, 0],
repetitions[2], repetitions[0], self.cell.matrix[:, 1])
vb.set_specular(True)
def draw(self):
FrameAxes.draw(self, self.selected)
GLPeriodicContainer.draw(self)
#
# Revalidation
#
def revalidate_box_list(self):
if self.gl_active > 0:
##print "Compiling box list (%i): %s" % (self.box_list, self.get_name())
vb = context.application.vis_backend
vb.begin_list(self.box_list)
if sum(self.cell.active) > 0:
self.draw_box()
vb.end_list()
self.box_list_valid = True
def revalidate_total_list(self):
if self.gl_active > 0:
##print "Compiling total list (%i): %s" % (self.total_list, self.get_name())
vb = context.application.vis_backend
vb.begin_list(self.total_list)
if self.visible:
vb.push_name(self.draw_list)
if sum(self.cell.active) == 0:
if self.selected:
vb.call_list(self.boundingbox_list)
else:
if self.selected:
vb.set_bright(True)
else:
vb.set_bright(False)
if self.box_visible: vb.call_list(self.box_list)
# repeat the draw list for all the unit cell images.
if self.clipping:
repetitions = (self.repetitions +
2) * self.cell.active + 1 - self.cell.active
else:
repetitions = self.repetitions * self.cell.active + 1 - self.cell.active
for position in iter_all_positions(repetitions):
vb.push_matrix()
t = numpy.dot(
self.cell.matrix,
numpy.array(position) -
self.cell.active * self.clipping)
vb.translate(*t)
vb.call_list(self.draw_list)
vb.pop_matrix()
vb.pop_name()
vb.end_list()
self.total_list_valid = True
def revalidate_bounding_box(self):
GLPeriodicContainer.revalidate_bounding_box(self)
FrameAxes.extend_bounding_box(self, self.bounding_box)
#
# Signal handlers
#
def on_select_chaged(self, selected):
GLPeriodicContainer.on_select_chaged(self, selected)
self.invalidate_box_list()
class Sphere(GLGeometricBase, ColorMixin):
info = ModelObjectInfo("plugins/basic/sphere.svg")
authors = [authors.toon_verstraelen]
def initnonstate(self):
GLGeometricBase.initnonstate(self, Translation)
#
# Properties
#
def set_radius(self, radius, init=False):
self.radius = radius
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_quality(self, quality, init=False):
self.quality = quality
if not init:
self.invalidate_draw_list()
properties = [
Property("radius", 0.5, lambda self: self.radius, set_radius),
Property("quality", 15, lambda self: self.quality, set_quality),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo("Geometry", (2, 2), fields.faulty.Length(
label_text="Radius",
attribute_name="radius",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo("Markup", (1, 3), fields.faulty.Int(
label_text="Quality",
attribute_name="quality",
minimum=3,
))
])
#
# Draw
#
def draw(self):
GLGeometricBase.draw(self)
ColorMixin.draw(self)
vb = context.application.vis_backend
vb.draw_sphere(self.radius, self.quality)
#
# Revalidation
#
def revalidate_bounding_box(self):
GLGeometricBase.revalidate_bounding_box(self)
self.bounding_box.extend_with_corners(numpy.array([
[-self.radius, -self.radius, -self.radius],
[ self.radius, self.radius, self.radius]
]))
class Bond(Vector):
info = ModelObjectInfo("plugins/molecular/bond.svg")
authors = [authors.toon_verstraelen]
#
# State
#
def initnonstate(self):
Vector.initnonstate(self)
self.handlers = {}
#
# Properties
#
def set_quality(self, quality, init=False):
self.quality = quality
if not init:
self.invalidate_draw_list()
def set_bond_type(self, bond_type, init=False):
self.bond_type = bond_type
if not init:
self.invalidate_draw_list()
properties = [
Property("quality", 15, lambda self: self.quality, set_quality),
Property("bond_type", BOND_SINGLE, lambda self: self.bond_type, set_bond_type)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo("Markup", (1, 3), fields.faulty.Int(
label_text="Quality",
attribute_name="quality",
minimum=3,
)),
DialogFieldInfo("Molecular", (6, 1), fields.edit.ComboBox(
choices=[
(BOND_SINGLE, "Single bond"),
(BOND_DOUBLE, "Double bond"),
(BOND_TRIPLE, "Triple bond"),
(BOND_HYBRID, "Hybrid bond"),
(BOND_HYDROGEN, "Hydrogen bond"),
],
label_text="Bond type",
attribute_name="bond_type",
)),
])
#
# References
#
def define_target(self, reference, new_target):
Vector.define_target(self, reference, new_target)
self.handlers[new_target] = [
new_target.connect("on_number_changed", self.atom_property_changed),
new_target.connect("on_user_radius_changed", self.atom_property_changed),
new_target.connect("on_user_color_changed", self.atom_property_changed),
]
def undefine_target(self, reference, old_target):
Vector.undefine_target(self, reference, old_target)
for handler in self.handlers[old_target]:
old_target.disconnect(handler)
def check_target(self, reference, target):
return isinstance(target, context.application.plugins.get_node("Atom"))
def atom_property_changed(self, atom):
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
#
# Draw
#
def draw(self):
Vector.draw(self)
if self.length <= 0: return
half_length = 0.5 * (self.end_position - self.begin_position)
if half_length <= 0: return
half_radius = 0.5 * (self.begin_radius + self.end_radius)
begin = self.children[0].target
end = self.children[1].target
vb = context.application.vis_backend
vb.set_color(*begin.get_color())
vb.translate(0.0, 0.0, self.begin_position)
vb.draw_cone(self.begin_radius, half_radius, half_length, self.quality)
vb.translate(0.0, 0.0, half_length)
vb.set_color(*end.get_color())
vb.draw_cone(half_radius, self.end_radius, half_length, self.quality)
#
# Revalidation
#
def revalidate_bounding_box(self):
Vector.revalidate_bounding_box(self)
if self.length > 0:
temp = {True: self.begin_radius, False: self.end_radius}[self.begin_radius > self.end_radius]
self.bounding_box.extend_with_point(numpy.array([-temp, -temp, self.begin_position]))
self.bounding_box.extend_with_point(numpy.array([temp, temp, self.end_position]))
def calc_vector_dimensions(self):
Vector.calc_vector_dimensions(self)
begin = self.children[0].target
end = self.children[1].target
if self.length <= 0.0: return
c = (begin.get_radius() - end.get_radius()) / self.length
if abs(c) > 1:
self.begin_radius = 0
self.end_radius = 0
self.begin_position = 0
self.end_position = 0
else:
scale = 0.4
s = numpy.sqrt(1 - c**2)
self.begin_radius = scale * begin.get_radius() * s
self.end_radius = scale * end.get_radius() * s
self.begin_position = scale * c * begin.get_radius()
self.end_position = self.length + scale * c * end.get_radius()
class ModelObject(Node):
info = ModelObjectInfo(default_action_name="EditProperties")
#
# State
#
def __init__(self, **initstate):
# some debugging code
#Node.count += 1
#print " PLUS => Initializing " + str(self.__class__) + " (" + str(Node.count) + ") " + hex(id(self))
Node.__init__(self)
# initialisation of non state variables
self.initnonstate()
# further initialize the state (the properties)
self.initstate(**initstate)
def __del__(self):
pass
# some debugging code
#Node.count -= 1
#print " MIN => Deleting " + str(self.__class__) + " (" + str(Node.count) + ") " + hex(id(self))
def __getstate__(self):
result = {}
for p in self.properties:
value = p.get(self)
equal = (value == p.default(self))
if isinstance(equal, numpy.ndarray):
equal = equal.all()
if not equal:
result[p.name] = value
return result
def initstate(self, **initstate):
for p in self.properties:
if p.name in initstate:
p.set(self, initstate[p.name], init=True)
else:
p.set(self, p.default(self), init=True)
def initnonstate(self):
self.references = []
#
# Properties
#
@classmethod
def class_name(cls):
temp = str(cls)
return temp[temp.rfind(".")+1:-2]
def default_name(self):
return self.class_name()
def get_name(self):
return self.name
def set_name(self, name, init=False):
self.name = name
def set_extra(self, extra, init=False):
self.extra = extra
properties = [
Property("name", default_name, get_name, set_name),
Property("extra", {}, (lambda self: self.extra), set_extra),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo("Basic", (0, 0), fields.faulty.Name(
label_text="Name",
attribute_name="name",
)),
])
#
# Tree
#
def delete_referents(self):
while len(self.references) > 0:
primitive.Delete(self.references[0].parent)
#for reference in copy.copy(self.references):
# if reference.model is not None:
# #print "Deleting Referent %s(%i)" % (reference.parent.get_name(), id(reference.parent))
# primitive.Delete(reference.parent)
def move(self, new_parent, index=-1):
if (index > 0) and (self.parent == new_parent) and index > self.get_index():
index -= 1
self.parent.remove(self)
new_parent.add(self, index)
self.emit("on-move")
#print "EMIT: on-move"
#
# Flags
#
def get_fixed(self):
return (self.model is not None) and (self.parent is None)
class GLMixin(gobject.GObject):
__metaclass__ = NodeClass
double_sided = False
#
# State
#
def initnonstate(self):
self.gl_active = False
self.connect("on-selected", self.on_select_changed)
self.connect("on-deselected", self.on_select_changed)
#
# Properties
#
def set_visible(self, visible, init=False):
if init:
self.visible = visible
elif self.visible != visible:
self.visible = visible
self.invalidate_total_list()
properties = [
Property("visible", True, lambda self: self.visible, set_visible)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Markup", (1, 2),
fields.edit.CheckButton(
label_text="Visible (also hides children)",
attribute_name="visible",
)),
DialogFieldInfo(
"Basic", (0, 3),
fields.read.BBox(
label_text="Bounding box",
attribute_name="bounding_box",
)),
])
#
# OpenGL
#
def initialize_gl(self):
assert not self.gl_active
vb = context.application.vis_backend
self.gl_active = True
self.bounding_box = BoundingBox()
self.draw_list = vb.create_list(self)
self.boundingbox_list = vb.create_list()
self.total_list = vb.create_list()
##print "Created lists (%i, %i, %i): %s" % (self.draw_list, self.boundingbox_list, self.total_list, self.get_name())
self.draw_list_valid = True
self.boundingbox_list_valid = True
self.total_list_valid = True
self.invalidate_all_lists()
if isinstance(self.parent, GLMixin):
self.parent.invalidate_all_lists()
def cleanup_gl(self):
assert self.gl_active
self.gl_active = False
vb = context.application.vis_backend
##print "Deleting lists (%i, %i, %i): %s" % (self.draw_list, self.boundingbox_list, self.total_list, self.get_name())
vb.delete_list(self.draw_list)
vb.delete_list(self.boundingbox_list)
vb.delete_list(self.total_list)
del self.bounding_box
del self.draw_list
del self.boundingbox_list
del self.total_list
del self.draw_list_valid
del self.boundingbox_list_valid
del self.total_list_valid
if isinstance(self.parent, GLMixin):
self.parent.invalidate_all_lists()
#
# Invalidation
#
def invalidate_draw_list(self):
if self.gl_active and self.draw_list_valid:
self.draw_list_valid = False
context.application.main.drawing_area.queue_draw()
context.application.scene.add_revalidation(
self.revalidate_draw_list)
self.emit("on-draw-list-invalidated")
##print "EMIT %s: on-draw-list-invalidated" % self.get_name()
if isinstance(self.parent, GLMixin):
self.parent.invalidate_boundingbox_list()
def invalidate_boundingbox_list(self):
##print "TRY: %s: on-boundingbox-list-invalidated" % self.get_name()
if self.gl_active and self.boundingbox_list_valid:
self.boundingbox_list_valid = False
context.application.main.drawing_area.queue_draw()
context.application.scene.add_revalidation(
self.revalidate_boundingbox_list)
self.emit("on-boundingbox-list-invalidated")
##print "EMIT %s: on-boundingbox-list-invalidated" % self.get_name()
if isinstance(self.parent, GLMixin):
self.parent.invalidate_boundingbox_list()
def invalidate_total_list(self):
if self.gl_active and self.total_list_valid:
self.total_list_valid = False
context.application.main.drawing_area.queue_draw()
context.application.scene.add_revalidation(
self.revalidate_total_list)
self.emit("on-total-list-invalidated")
##print "EMIT %s: on-total-list-invalidated" % self.get_name()
if isinstance(self.parent, GLMixin):
self.parent.invalidate_boundingbox_list()
def invalidate_all_lists(self):
self.invalidate_total_list()
self.invalidate_boundingbox_list()
self.invalidate_draw_list()
#
# Revalidation
#
def revalidate_draw_list(self):
if self.gl_active:
vb = context.application.vis_backend
##print "Compiling draw list (%i): %s" % (self.draw_list, self.get_name())
vb.begin_list(self.draw_list)
self.prepare_draw()
self.draw()
self.finish_draw()
vb.end_list()
self.draw_list_valid = True
def revalidate_boundingbox_list(self):
if self.gl_active:
vb = context.application.vis_backend
##print "Compiling selection list (%i): %s" % (self.boundingbox_list, self.get_name())
vb.begin_list(self.boundingbox_list)
self.revalidate_bounding_box()
self.bounding_box.draw()
vb.end_list()
self.boundingbox_list_valid = True
def revalidate_bounding_box(self):
self.bounding_box.clear()
def revalidate_total_list(self):
if self.gl_active:
vb = context.application.vis_backend
##print "Compiling total list (%i): %s" % (self.total_list, self.get_name())
vb.begin_list(self.total_list)
if self.visible:
vb.push_name(self.draw_list)
self.draw_selection()
vb.call_list(self.draw_list)
vb.pop_name()
vb.end_list()
self.total_list_valid = True
#
# Draw
#
def draw_selection(self):
vb = context.application.vis_backend
if self.selected:
vb.set_bright(True)
else:
vb.set_bright(False)
def call_list(self):
##print "Executing total list (%i): %s" % (self.total_list, self.get_name())
context.application.vis_backend.call_list(self.total_list)
def prepare_draw(self):
pass
def draw(self):
pass
def finish_draw(self):
pass
#
# Frame
#
def get_bounding_box_in_parent_frame(self):
return self.bounding_box
def get_absolute_frame(self):
return self.get_absolute_parentframe()
def get_absolute_parentframe(self):
if not isinstance(self.parent, GLMixin):
return Complete.identity()
else:
return self.parent.get_absolute_frame()
def get_frame_up_to(self, upper_parent):
if (upper_parent == self) or (self.parent == upper_parent):
return Complete.identity()
else:
return self.get_parentframe_up_to(upper_parent)
def get_parentframe_up_to(self, upper_parent):
if not isinstance(self.parent, GLMixin):
assert upper_parent is None, "upper_parent must be (an indirect) parent of self."
return Complete.identity()
elif self.parent == upper_parent:
return Complete.identity()
else:
return self.parent.get_frame_up_to(upper_parent)
def get_frame_relative_to(self, other):
common = common_parent([self, other])
return other.get_frame_up_to(common).inv * self.get_frame_up_to(common)
#
# Signal handlers
#
def on_select_changed(self, foo):
self.invalidate_total_list()
class Spring(Vector, ColorMixin):
info = ModelObjectInfo("plugins/builder/spring.svg")
authors = [authors.toon_verstraelen]
#
# Properties
#
def set_radius(self, radius, init=False):
self.radius = radius
if not init:
self.invalidate_draw_list()
def set_quality(self, quality, init=False):
self.quality = quality
if not init:
self.invalidate_draw_list()
def set_rest_length(self, rest_length, init=False):
self.rest_length = rest_length
if not init:
self.invalidate_draw_list()
properties = [
Property("radius", 0.5, lambda self: self.radius, set_radius),
Property("quality", 15, lambda self: self.quality, set_quality),
Property("rest_length", 0.0, lambda self: self.rest_length,
set_rest_length),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 2),
fields.faulty.Length(
label_text="Radius",
attribute_name="radius",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo(
"Markup", (1, 3),
fields.faulty.Int(
label_text="Quality",
attribute_name="quality",
minimum=3,
)),
DialogFieldInfo(
"Basic", (0, 8),
fields.faulty.Length(
label_text="Rest length",
attribute_name="rest_length",
low=0.0,
low_inclusive=True,
)),
])
#
# Draw
#
def draw(self):
Vector.draw(self)
ColorMixin.draw(self)
vb = context.application.vis_backend
if self.length > self.rest_length:
l_cyl = self.rest_length
l_cone = 0.5 * (self.length - l_cyl)
if l_cone > 0:
vb.draw_cone(self.radius, 0.0, l_cone, self.quality)
vb.translate(0.0, 0.0, l_cone)
if l_cyl > 0:
vb.draw_cone(0.5 * self.radius, 0.5 * self.radius, l_cyl,
self.quality)
vb.translate(0.0, 0.0, l_cyl)
if l_cone > 0:
vb.draw_cone(0.0, self.radius, l_cone, self.quality)
else:
l_cyl = self.length
l_cone = 0.5 * (self.rest_length - self.length)
if l_cone > 0:
vb.translate(0.0, 0.0, -l_cone)
vb.draw_cone(0.0, self.radius, l_cone, self.quality)
vb.translate(0.0, 0.0, l_cone)
if l_cyl > 0:
vb.draw_cylinder(0.5 * self.radius, l_cyl, self.quality)
vb.translate(0.0, 0.0, l_cyl)
if l_cone > 0:
vb.draw_cone(self.radius, 0.0, l_cone, self.quality)
#
# Revalidation
#
def revalidate_bounding_box(self):
Vector.revalidate_bounding_box(self)
if self.length > 0:
self.bounding_box.extend_with_point(
numpy.array([-self.radius, -self.radius, 0]))
self.bounding_box.extend_with_point(
numpy.array([self.radius, self.radius, self.length]))
class FrameAxes(object):
__metaclass__ = NodeClass
#
# Properties
#
def set_axis_thickness(self, axis_thickness, init=False):
self.axis_thickness = axis_thickness
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_axis_length(self, axis_length, init=False):
self.axis_length = axis_length
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_axes_visible(self, axes_visible, init=False):
self.axes_visible = axes_visible
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("axis_thickness", 0.1 * angstrom,
lambda self: self.axis_thickness, set_axis_thickness),
Property("axis_length", 1.0 * angstrom, lambda self: self.axis_length,
set_axis_length),
Property("axes_visible", True, lambda self: self.axes_visible,
set_axes_visible)
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 0),
fields.faulty.Length(
label_text="Axis thickness",
attribute_name="axis_thickness",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo(
"Geometry", (2, 1),
fields.faulty.Length(
label_text="Axes length",
attribute_name="axis_length",
low=0.0,
low_inclusive=False,
)),
DialogFieldInfo(
"Markup", (1, 4),
fields.edit.CheckButton(
label_text="Show frame axes",
attribute_name="axes_visible",
)),
])
#
# Draw
#
def draw(self, light):
if self.axes_visible:
col = {True: 2.0, False: 1.2}[light]
sat = {True: 0.2, False: 0.1}[light]
vb = context.application.vis_backend
vb.push_matrix()
# x-axis
vb.set_color(col, sat, sat)
draw_axis_spike(self.axis_thickness, self.axis_length)
# y-axis
vb.rotate(120, 1.0, 1.0, 1.0)
vb.set_color(sat, col, sat)
draw_axis_spike(self.axis_thickness, self.axis_length)
# z-axis
vb.rotate(120, 1.0, 1.0, 1.0)
vb.set_color(sat, sat, col)
draw_axis_spike(self.axis_thickness, self.axis_length)
vb.pop_matrix()
#
# Revalidation
#
def extend_bounding_box(self, bounding_box):
bounding_box.extend_with_corners(
numpy.array([[
-self.axis_thickness, -self.axis_thickness,
-self.axis_thickness
], [self.axis_length, self.axis_length, self.axis_length]]))
class Atom(GLGeometricBase, UserColorMixin):
info = ModelObjectInfo("plugins/molecular/atom.svg")
authors = [authors.toon_verstraelen]
#
# State
#
def initnonstate(self):
GLGeometricBase.initnonstate(self, Translation)
#
# Properties
#
def set_user_radius(self, user_radius, init=False):
self.user_radius = user_radius
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
def set_quality(self, quality, init=False):
self.quality = quality
if not init:
self.invalidate_draw_list()
def set_number(self, number, init=False):
self.number = number
atom_info = periodic[number]
if atom_info.vdw_radius is not None:
self.default_radius = atom_info.vdw_radius * 0.2
else:
self.default_radius = 1.0
color = [atom_info.red, atom_info.green, atom_info.blue, 1.0]
if None in color:
self.default_color = numpy.array([0.7, 0.7, 0.7, 1.0], float)
else:
self.default_color = numpy.array(color, float)
if not init:
self.invalidate_draw_list()
self.invalidate_boundingbox_list()
properties = [
Property("user_radius",
Undefined(0.5),
lambda self: self.user_radius,
set_user_radius,
signal=True),
Property("quality", 15, lambda self: self.quality, set_quality),
Property("number",
6,
lambda self: self.number,
set_number,
signal=True),
]
#
# Dialog fields (see action EditProperties)
#
dialog_fields = set([
DialogFieldInfo(
"Geometry", (2, 9),
fields.optional.CheckOptional(
fields.faulty.Length(
label_text="User defined radius",
attribute_name="user_radius",
low=0.0,
low_inclusive=False,
))),
DialogFieldInfo(
"Markup", (1, 3),
fields.faulty.Int(
label_text="Quality",
attribute_name="quality",
minimum=3,
)),
DialogFieldInfo(
"Molecular", (6, 0),
fields.edit.Element(
attribute_name="number",
show_popup=False,
)),
])
#
# Draw
#
def get_radius(self):
if isinstance(self.user_radius, Undefined):
return self.default_radius
else:
return self.user_radius
def draw(self):
GLGeometricBase.draw(self)
UserColorMixin.draw(self)
vb = context.application.vis_backend
vb.draw_sphere(self.get_radius(), self.quality)
#
# Revalidation
#
def revalidate_bounding_box(self):
GLGeometricBase.revalidate_bounding_box(self)
radius = self.get_radius()
self.bounding_box.extend_with_corners(
numpy.array([[-radius, -radius, -radius], [radius, radius,
radius]]))
#
# Tools
#
def num_bonds(self):
Bond = context.application.plugins.get_node("Bond")
return sum(
isinstance(reference.parent, Bond)
for reference in self.references)
def iter_bonds(self):
Bond = context.application.plugins.get_node("Bond")
for reference in self.references:
referent = reference.parent
if isinstance(referent, Bond):
yield referent
def iter_neighbors(self):
for bond in self.iter_bonds():
first = bond.children[0].target
if first == self:
neighbor = bond.children[1].target
else:
neighbor = first
if isinstance(neighbor, Atom):
yield neighbor