class SeparateFrame(Immediate):
description = "Separate the selected frame"
menu_info = MenuInfo("default/_Object:tools/A_rrange:single",
"_Separate frame",
order=(0, 4, 1, 1, 2, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating & initializing
node = context.application.cache.node
Frame = context.application.plugins.get_node("Frame")
if not Frame.check_add(node.__class__): return False
if node.get_fixed(): return False
if not isinstance(node, GLTransformationMixin): return False
if not node.parent.check_add(Frame): return False
# C) passed all tests:
return True
def do(self):
victim = context.application.cache.node
Frame = context.application.plugins.get_node("Frame")
frame = Frame(name="Frame of " + victim.name)
primitive.Add(frame, victim.parent, index=victim.get_index())
primitive.Transform(frame, victim.transformation)
primitive.Move(victim, frame)
primitive.SetProperty(victim, "transformation",
victim.Transformation())
class MoldenLabels(Immediate):
description = "Label the atoms in molden style."
menu_info = MenuInfo("default/_Object:tools/_Molecular:rearrange",
"_Molden labels",
order=(0, 4, 1, 5, 0, 2))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
cache = context.application.cache
if cache.node is None: return False
contains_atoms = False
for cls in cache.child_classes:
if issubclass(cls, Atom):
contains_atoms = True
break
if not contains_atoms: return False
# C) passed all tests
return True
def do(self):
counter = 1
for node in context.application.cache.children:
if isinstance(node, Atom):
primitive.SetProperty(
node, "name", periodic[node.number].symbol + str(counter))
counter += 1
class SelectBondedNeighbors(Immediate):
description = "Select bonded neighbors"
menu_info = MenuInfo("default/_Select:default",
"_Bonded neighbors",
ord("n"),
False,
order=(0, 3, 0, 5))
authors = [authors.bartek_szyja]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
if len(context.application.cache.nodes) == 0: return False
# C) passed all tests:
return True
def do(self):
Atom = context.application.plugins.get_node("Atom")
to_select = []
for node in context.application.cache.nodes:
if isinstance(node, Atom):
to_select.append(node)
for bond in node.iter_bonds():
if bond.children[
0].target not in context.application.cache.nodes:
to_select.append(bond.children[0].target)
if bond.children[
1].target not in context.application.cache.nodes:
to_select.append(bond.children[1].target)
context.application.main.select_nodes(to_select)
class EditSelectionFilter(Immediate):
description = "Edit selection filter"
menu_info = MenuInfo("default/_Select:preferences", "_Selection filter", order=(0, 3, 2, 0))
authors = [authors.toon_verstraelen]
selection_filter = FieldsDialogSimple(
"Selection filter",
fields.group.Table(fields=[
fields.edit.CheckButton(
label_text="Filter active",
attribute_name="filter_active",
show_popup=False,
),
fields.faulty.Expression(
label_text="Filter expression",
attribute_name="filter_expression",
show_popup=True,
history_name="filter",
)
]),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# C) passed all tests:
return True
def do(self):
self.selection_filter.run(context.application.main)
class AddPlane(Immediate):
description = "Add plane"
menu_info = MenuInfo("default/_Object:tools/_Add:3d",
"_Plane",
image_name="plugins/basic/plane.svg",
order=(0, 4, 1, 0, 0, 5))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
cache = context.application.cache
if len(cache.nodes) < 3: return False
if len(cache.translations) < 3: return False
if cache.common_parent is None: return False
# C) passed all tests:
return True
def do(self):
cache = context.application.cache
nodes = cache.nodes
primitive.Add(Plane(targets=nodes),
cache.common_parent,
index=cache.highest_index + 1)
class About(Immediate):
description = "Show the about box"
menu_info = MenuInfo("help/_Help:default", "_About", image_name=gtk.STOCK_ABOUT, order=(1, 0, 0, 0))
authors = [authors.toon_verstraelen]
def do(self):
about.run()
class FileImport(Immediate):
description = "Import a file in the current model"
menu_info = MenuInfo("default/_File:impexp", "_Import", order=(0, 0, 1, 0))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
def file_import(filename):
tmp_model = Model()
tmp_model.file_open(filename)
if len(tmp_model.universe.children) > 0:
Frame = context.application.plugins.get_node("Frame")
root_frame = Frame(name=os.path.basename(filename))
tmp = list(tmp_model.universe.children)
while len(tmp_model.universe.children) > 0:
tmp_model.universe.remove(tmp_model.universe.children[0])
for node in tmp:
root_frame.add(node)
del tmp
context.application.model.universe.add(root_frame)
if len(tmp_model.folder.children) > 0:
Folder = context.application.plugins.get_node("Folder")
root_folder = Folder(name=os.path.basename(filename))
tmp = list(tmp_model.folder.children)
while len(tmp_model.folder.children) > 0:
tmp_model.universe.remove(tmp_model.folder.children[0])
for node in tmp:
root_folder.add(node)
del tmp
context.application.model.folder.add(root_folder)
tmp_model.file_close()
run_file_dialog(context.application.file_import_dialog, file_import)
class Cut(Immediate):
description = "Cut the selection to the clipboard"
menu_info = MenuInfo("default/_Edit:clipboard",
"Cu_t",
accel_key=ord("x"),
image_name=gtk.STOCK_CUT,
order=(0, 1, 1, 0))
repeatable = False
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
cache = context.application.cache
if len(cache.nodes) == 0: return False
if cache.some_nodes_without_children_fixed: return False
# C) passed all tests:
return True
def do(self):
source = list(context.application.cache.nodes_without_children)
copy_to_clipboard(source)
delete(source)
class WrapCellContents(Immediate):
description = "Wrap the unit cell contents"
menu_info = MenuInfo("default/_Object:tools/_Unit Cell:default",
"_Wrap cell contents",
ord("w"),
order=(0, 4, 1, 4, 0, 3))
repeatable = False
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
universe = context.application.model.universe
if sum(universe.cell.active) == 0: return False
if len(universe.children) == 0: return False
# C) passed all tests:
return True
def do(self):
universe = context.application.model.universe
for child in universe.children:
if isinstance(child, GLTransformationMixin) and isinstance(
child.transformation, Translation):
cell_index = universe.cell.to_fractional(
child.transformation.t)
cell_index = numpy.floor(cell_index)
if cell_index.any():
t = child.transformation.t - universe.cell.to_cartesian(
cell_index)
new_transformation = child.transformation.copy_with(t=t)
primitive.SetProperty(child, "transformation",
new_transformation)
class AutoConnectPhysical(AutoConnectMixin, Immediate):
description = "Add bonds (database)"
menu_info = MenuInfo("default/_Object:tools/_Molecular:add", "_Add bonds (database)", ord("b"), order=(0, 4, 1, 5, 1, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not AutoConnectMixin.analyze_selection(): return False
if not Immediate.analyze_selection(): return False
# C) passed all tests:
return True
def allow_node(self, node):
return isinstance(node, context.application.plugins.get_node("Atom"))
def get_vector(self, atom0, atom1, distance):
if atom0 in atom1.iter_neighbors():
return None
bond_type = bonds.bonded(atom0.number, atom1.number, distance)
if bond_type is None:
return None
else:
return Bond(bond_type=bond_type, targets=[atom0, atom1])
def do(self):
AutoConnectMixin.do(self, bonds.max_length)
class Duplicate(Immediate):
description = "Duplicate nodes"
menu_info = MenuInfo("default/_Edit:deldup",
"_Duplicate",
ord("d"),
order=(0, 1, 2, 1))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
cache = context.application.cache
if cache.some_nodes_fixed: return False
if not isinstance(cache.parent, ContainerMixin): return False
# D) passed all tests:
return True
def do(self):
cache = context.application.cache
originals = cache.nodes
parent = cache.parent
highest_index = cache.highest_index
serialized = StringIO.StringIO()
dump_to_file(serialized, originals)
serialized.seek(0)
duplicates = load_from_file(serialized)
for duplicate in duplicates:
highest_index += 1
primitive.Add(duplicate, parent, index=highest_index)
class Align(CenterAlignBase):
description = "Align to parent"
menu_info = MenuInfo("default/_Object:tools/_Transform:align",
"_Align",
order=(0, 4, 1, 2, 3, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not CenterAlignBase.analyze_selection(): return False
# B) validating
cache = context.application.cache
node = cache.node
if not isinstance(node, GLTransformationMixin): return False
if not isinstance(node.transformation, Rotation): return False
if cache.some_neighbors_fixed: return False
# C) passed all tests:
return True
def do(self):
cache = context.application.cache
rotation = Rotation(cache.node.transformation.r)
CenterAlignBase.do(self, cache.parent, cache.transformed_neighbors,
rotation)
class AutoConnectSprings(AutoConnectMixin, Immediate):
description = "Connect overlapping atoms with springs"
menu_info = MenuInfo("default/_Object:tools/_Builder:spring",
"_Connect overlapping atoms with springs",
order=(0, 4, 1, 6, 0, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not AutoConnectMixin.analyze_selection(): return False
if not Immediate.analyze_selection(): return False
# C) passed all tests:
return True
def allow_node(self, node):
return isinstance(node, context.application.plugins.get_node("Atom"))
def get_vector(self, atom1, atom2, distance):
for reference in atom2.references:
referent = reference.parent
if isinstance(referent, Spring):
if (referent.children[0].target == atom1) or \
(referent.children[1].target == atom1):
return None
if 0.5 * (periodic[atom1.number].covalent_radius +
periodic[atom2.number].covalent_radius) >= distance:
return Spring(targets=[atom1, atom2])
else:
return None
def do(self):
AutoConnectMixin.do(self, 2 * periodic.max_radius)
class FileSave(Immediate):
description = "Save the current file"
menu_info = MenuInfo("default/_File:default", "_Save", ord("s"), image_name=gtk.STOCK_SAVE, order=(0, 0, 0, 2))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
context.application.main.file_save()
class FileOpen(Immediate):
description = "Open a file"
menu_info = MenuInfo("default/_File:default", "_Open", ord("o"), image_name=gtk.STOCK_OPEN, order=(0, 0, 0, 1))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
context.application.main.file_open()
class FileQuit(Immediate):
description = "Quit zeobuilder"
menu_info = MenuInfo("default/_File:quit", "_Quit", ord("q"), image_name=gtk.STOCK_QUIT, order=(0, 0, 2, 0))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
context.application.main.file_quit()
class FileSaveAs(Immediate):
description = "Save the current file under a new name"
menu_info = MenuInfo("default/_File:default", "Save _as", ord("s"), True, True, image_name=gtk.STOCK_SAVE_AS, order=(0, 0, 0, 3))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
context.application.main.file_save_as()
class ViewPlugins(Immediate):
description = "Plugins"
menu_info = MenuInfo("help/_Help:default", "_Plugins", order=(1, 0, 0, 1))
plugins_dialog = PluginsDialog()
authors = [authors.toon_verstraelen]
def do(self):
self.plugins_dialog.run()
class ConnectArrow(ConnectBase):
description = "Connect with arrow"
menu_info = MenuInfo("default/_Object:tools/_Connect:pair",
"_Arrow",
image_name="plugins/basic/arrow.svg",
order=(0, 4, 1, 3, 0, 0))
authors = [authors.toon_verstraelen]
def new_connector(self, begin, end):
return Arrow(targets=[begin, end])
class ConnectSpring(ConnectBase):
description = "Connect with spring"
menu_info = MenuInfo("default/_Object:tools/_Connect:pair",
"_Spring",
image_name="plugins/builder/spring.svg",
order=(0, 4, 1, 3, 0, 4))
authors = [authors.toon_verstraelen]
def new_connector(self, begin, end):
return Spring(targets=[begin, end])
class AddNotes(AddBase):
description = "Add notes"
menu_info = MenuInfo("default/_Object:tools/_Add:non3d", "_Notes", image_name="plugins/basic/notes.svg", order=(0, 4, 1, 0, 1, 1))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
return AddBase.analyze_selection(Notes)
def do(self):
AddBase.do(self, Notes)
class AddSphere(AddBase):
description = "Add sphere"
menu_info = MenuInfo("default/_Object:tools/_Add:3d", "_Sphere", image_name="plugins/basic/sphere.svg", order=(0, 4, 1, 0, 0, 1))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
return AddBase.analyze_selection(Sphere)
def do(self):
AddBase.do(self, Sphere)
class FileNew(Immediate):
description = "Create a new file"
menu_info = MenuInfo("default/_File:default", "_New", ord("n"), image_name=gtk.STOCK_NEW, order=(0, 0, 0, 0))
repeatable = False
authors = [authors.toon_verstraelen]
def do(self):
Universe = context.application.plugins.get_node("Universe")
universe = Universe(axes_visible=False)
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
context.application.main.file_new(universe, folder)
class AddFolder(AddBase):
description = "Add folder"
menu_info = MenuInfo("default/_Object:tools/_Add:non3d",
"_Folder",
image_name="plugins/basic/folder.svg",
order=(0, 4, 1, 0, 1, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
return AddBase.analyze_selection(Folder)
def do(self):
AddBase.do(self, Folder)
class AddPoint(AddBase):
description = "Add point"
menu_info = MenuInfo("default/_Object:tools/_Add:3d",
"_Point",
image_name="plugins/basic/point.svg",
order=(0, 4, 1, 0, 0, 2))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
return AddBase.analyze_selection(Point)
def do(self):
AddBase.do(self, Point)
class TetraCoordination(Immediate):
description = "T-atom coordination"
menu_info = MenuInfo("default/_Object:tools/_Molecular:info",
"_T-atom coordination",
order=(0, 4, 1, 5, 2, 1))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# B) validating
if len(context.application.cache.nodes) == 0: return False
# C) passed all tests:
return True
def do(self):
Atom = context.application.plugins.get_node("Atom")
def iter_all_tetra(nodes):
for node in nodes:
if isinstance(node, Atom) and node.number > 12:
yield node
elif isinstance(node, ContainerMixin):
for tetra in iter_all_tetra(node.children):
yield tetra
coordinated_tetra = [[] for i in xrange(5)]
for tetra in iter_all_tetra(
context.application.cache.nodes_without_children):
coordination = 0
for bridging in tetra.iter_neighbors():
if bridging.number > 6:
num_t = len([
t for t in bridging.iter_neighbors() if t.number > 12
])
if num_t > 2:
raise UserError("Invalid zeolite structure.")
if num_t == 2:
coordination += 1
if coordination > 4:
raise UserError("Invalid zeolite structure.")
coordinated_tetra[coordination].append(tetra)
result_dialog = CoordinationDialog(coordinated_tetra)
response = result_dialog.run()
if response != gtk.RESPONSE_CLOSE:
main = context.application.main
main.select_nodes(coordinated_tetra[response])
class TranslateDialog(ImmediateWithMemory):
description = "Apply translation"
menu_info = MenuInfo("default/_Object:tools/_Transform:dialogs",
"_Translate",
order=(0, 4, 1, 2, 1, 2))
authors = [authors.toon_verstraelen]
parameters_dialog = FieldsDialogSimple(
"Translation",
fields.composed.Translation(
label_text="Translate with vector t",
attribute_name="translation",
), ((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL),
(gtk.STOCK_OK, gtk.RESPONSE_OK)))
@staticmethod
def analyze_selection(parameters=None):
# A) calling ancestor
if not ImmediateWithMemory.analyze_selection(parameters): return False
# B) validating
cache = context.application.cache
if len(cache.translated_nodes) == 0: return False
if cache.parent_of_translated_nodes is None: return False
if cache.some_nodes_fixed: return False
# C) passed all tests:
return True
@classmethod
def default_parameters(cls):
result = Parameters()
result.translation = Translation.identity()
return result
def ask_parameters(self):
cache = context.application.cache
last = cache.last
parent = cache.parent_of_translated_nodes
if isinstance(last, Vector):
b = last.children[0].translation_relative_to(parent)
e = last.children[1].translation_relative_to(parent)
if (b is not None) and (e is not None):
self.parameters.translation = Translation(e - b)
else:
self.parameters = self.last_parameters()
if self.parameters_dialog.run(self.parameters) != gtk.RESPONSE_OK:
self.parameters.clear()
def do(self):
for victim in context.application.cache.translated_nodes:
primitive.Transform(victim, self.parameters.translation)
class SelectNone(Immediate):
description = "Select none"
menu_info = MenuInfo("default/_Select:default", "_None", order=(0, 3, 0, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
# A) calling ancestor
if not Immediate.analyze_selection(): return False
# C) passed all tests:
return True
def do(self):
context.application.main.tree_selection.unselect_all()
class AddBox(AddBase):
description = "Add box"
menu_info = MenuInfo("default/_Object:tools/_Add:3d",
"_Box",
image_name="plugins/basic/box.svg",
order=(0, 4, 1, 0, 0, 0))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
return AddBase.analyze_selection(Box)
def do(self):
AddBase.do(self, Box)
class CloneOrder(Immediate):
description = "Apply the order of the first selection to all the other."
menu_info = MenuInfo("default/_Object:tools/_Molecular:rearrange",
"_Clone order",
order=(0, 4, 1, 5, 0, 3))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
if not Immediate.analyze_selection(): return False
cache = context.application.cache
if len(cache.nodes) < 2: return False
Frame = context.application.plugins.get_node("Frame")
for cls in cache.classes:
if not issubclass(cls, Frame): return False
return True
def do(self):
frame_ref = context.application.cache.nodes[0]
graph_ref = create_molecular_graph([frame_ref])
try:
match_generator = GraphSearch(EqualPattern(graph_ref))
except GraphError, e:
raise UserError(
"Could not setup a graph match definition to clone the order.")
some_failed = False
all_failed = True
for frame_other in context.application.cache.nodes[1:]:
graph_other = create_molecular_graph([frame_other])
try:
match = match_generator(graph_other).next()
all_failed = False
except (StopIteration, GraphError):
some_failed = True
continue
moves = [(index1, graph_other.molecule.atoms[index2])
for index1, index2 in match.forward.iteritems()]
moves.sort()
for new_index, atom2 in moves:
primitive.Move(atom2, frame_other, new_index)
if all_failed:
raise UserError("None of the atom orders could be cloned.")
elif some_failed:
ok_error(
"Some molecules/frames did not match the first frame, so they are not reordered."
)
