def do(self):
edit_config = FieldsDialogSimple(
"Zeobuilder configuration",
context.application.configuration.create_main_field(),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
class Settings(object):
pass
settings = Settings()
settings.__dict__ = context.application.configuration.settings
edit_config.run(settings)
context.application.configuration.settings = settings.__dict__
def do(self):
edit_config = FieldsDialogSimple(
"Zeobuilder configuration",
context.application.configuration.create_main_field(),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL),
(gtk.STOCK_OK, gtk.RESPONSE_OK)))
class Settings(object):
pass
settings = Settings()
settings.__dict__ = context.application.configuration.settings
edit_config.run(settings)
context.application.configuration.settings = settings.__dict__
def on_set_parameters(self, menu, cell):
from zeobuilder.gui.fields_dialogs import FieldsDialogSimple
dialog = FieldsDialogSimple(
"Set the cell parameters",
CellParameters(
attribute_name="cell",
show_popup=False,
),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK)),
)
parameters = Parameters()
parameters.cell = cell
if dialog.run(parameters) == gtk.RESPONSE_OK:
self.field.write_to_widget(self.field.convert_to_representation(parameters.cell))
def run(self, max_shell_size, rows, graph):
self.graph = graph
self.max_shell_size = max_shell_size
self.list_store = gtk.ListStore(int, int, *([str]*(max_shell_size+2)))
for index, row in enumerate(rows):
row += [""]*(max_shell_size-(len(row)-4))
self.list_store.append(row)
response = FieldsDialogSimple.run(self, self)
self.list_view.set_model(None)
for column in self.list_view.get_columns():
self.list_view.remove_column(column)
del self.graph
del self.max_shell_size
return response
def on_set_parameters(self, menu, cell):
from zeobuilder.gui.fields_dialogs import FieldsDialogSimple
dialog = FieldsDialogSimple(
"Set the cell parameters",
CellParameters(
attribute_name="cell",
show_popup=False,
),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL),
(gtk.STOCK_OK, gtk.RESPONSE_OK)),
)
parameters = Parameters()
parameters.cell = cell
if dialog.run(parameters) == gtk.RESPONSE_OK:
self.field.write_to_widget(
self.field.convert_to_representation(parameters.cell))
def run(self, max_shell_size, rows, graph):
self.graph = graph
self.max_shell_size = max_shell_size
self.list_store = gtk.ListStore(int, int,
*([str] * (max_shell_size + 2)))
for index, row in enumerate(rows):
row += [""] * (max_shell_size - (len(row) - 4))
self.list_store.append(row)
response = FieldsDialogSimple.run(self, self)
self.list_view.set_model(None)
for column in self.list_view.get_columns():
self.list_view.remove_column(column)
del self.graph
del self.max_shell_size
return response
class SketchOptions(GladeWrapper):
edit_erase_filter = FieldsDialogSimple(
"Edit the Erase filter",
fields.faulty.Expression(
label_text="Erase filter expression",
attribute_name="erase_filter",
show_popup=True,
history_name="filter",
), ((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL),
(gtk.STOCK_OK, gtk.RESPONSE_OK)))
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade", "wi_sketch",
"window")
self.window.hide()
self.init_callbacks(self.__class__)
self.init_proxies([
"cb_object", "cb_vector", "cb_erase_filter",
"bu_edit_erase_filter", "la_current", "bu_set_atom", "cb_bondtype",
"hbox_atoms", "hbox_quickpicks", "hbox_fragments", "la_fragment",
"cb_fragment"
])
self.erase_filter = Expression("True")
#Initialize atom number - this can be changed anytime with the edit_atom_number dialog
self.atom_number = 6
# Initialize the GUI
# 1) common parts of the comboboxes
def render_icon(column, cell, model, iter):
if model.get_value(iter, 0) == "Fragment":
cell.set_property(
"pixbuf",
context.application.plugins.get_node("Atom").icon)
else:
cell.set_property(
"pixbuf",
context.application.plugins.get_node(
model.get_value(iter, 0)).icon)
# 2) fill the objects combo box
self.object_store = gtk.ListStore(str)
self.object_store.append(["Atom"])
self.object_store.append(["Fragment"])
self.object_store.append(["Point"])
self.object_store.append(["Sphere"])
self.object_store.append(["Box"])
self.cb_object.set_model(self.object_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_object.pack_start(renderer_pixbuf, expand=False)
self.cb_object.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_object.pack_start(renderer_text, expand=True)
self.cb_object.add_attribute(renderer_text, "text", 0)
self.cb_object.set_active(0)
# 3) fill the vector combo box
self.vector_store = gtk.ListStore(str)
self.vector_store.append(["Bond"])
self.vector_store.append(["Arrow"])
self.vector_store.append(["Spring"])
self.cb_vector.set_model(self.vector_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_vector.pack_start(renderer_pixbuf, expand=False)
self.cb_vector.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_vector.pack_start(renderer_text, expand=True)
self.cb_vector.add_attribute(renderer_text, "text", 0)
self.cb_vector.set_active(0)
# 4) fill the bond type combo box
self.bondtype_store = gtk.ListStore(str, int)
self.bondtype_store.append(["Single bond", BOND_SINGLE])
self.bondtype_store.append(["Double bond", BOND_DOUBLE])
self.bondtype_store.append(["Triple bond", BOND_TRIPLE])
self.bondtype_store.append(["Hybrid bond", BOND_HYBRID])
self.bondtype_store.append(["Hydrogen bond", BOND_HYDROGEN])
self.cb_bondtype.set_model(self.bondtype_store)
#no icons like the others, just text here
renderer_text = gtk.CellRendererText()
self.cb_bondtype.pack_start(renderer_text, expand=True)
self.cb_bondtype.add_attribute(renderer_text, "text", 0)
self.cb_bondtype.set_active(0)
# register quick pick config setting
config = context.application.configuration
config.register_setting(
"sketch_quickpicks",
[6, 7, 8, 9, 10, 11],
DialogFieldInfo(
"Sketch tool", (0, 2),
fields.faulty.IntegerList(
label_text="Quick pick atoms (applies after restart)",
attribute_name="sketch_quickpicks",
)),
)
# 5)create the "quick pick" atom buttons
for index in xrange(len(config.sketch_quickpicks)):
atomnumber = config.sketch_quickpicks[index]
bu_element = gtk.Button("")
bu_element.set_label("%s" % periodic[atomnumber].symbol)
bu_element.connect("clicked", self.on_bu_element_clicked, index)
# add to hbox
self.hbox_quickpicks.pack_start(bu_element)
bu_element.show()
# 6)fill the fragment combo box with filenames from share/fragments
fragment_dir = context.get_share_filename('fragments')
self.fragment_store = gtk.ListStore(str)
for filename in sorted(os.listdir(fragment_dir)):
# Ignore subfolders and files with extension other than cml
if os.path.isdir(os.path.join(fragment_dir,
filename)) or filename[-3:] != 'cml':
continue
self.fragment_store.append([filename[:-4]])
self.cb_fragment.set_model(self.fragment_store)
renderer_text = gtk.CellRendererText()
self.cb_fragment.pack_start(renderer_text, expand=True)
self.cb_fragment.add_attribute(renderer_text, "text", 0)
self.cb_fragment.set_active(0)
@property
def current_object(self):
return self.object_store.get_value(self.cb_object.get_active_iter(), 0)
@property
def current_fragment(self):
return self.fragment_store.get_value(
self.cb_fragment.get_active_iter(), 0)
def on_window_delete_event(self, window, event):
self.window.hide()
return True
def on_bu_edit_erase_filter_clicked(self, button):
self.edit_erase_filter.run(self)
def on_bu_set_atom_clicked(self, button):
self.edit_atom_number = FieldsDialogSimple(
"Select atom number",
fields.edit.Element(attribute_name="atom_number"),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL),
(gtk.STOCK_OK, gtk.RESPONSE_OK)))
self.edit_atom_number.run(self)
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s " % str(atom_symbol))
def on_cb_object_changed(self, combo):
self.hbox_atoms.hide()
self.la_current.hide()
self.hbox_fragments.hide()
if (self.current_object == "Atom"):
self.hbox_atoms.show()
self.la_current.show()
if (self.current_object == "Fragment"):
self.cb_fragment.show()
self.hbox_fragments.show()
def on_bu_element_clicked(self, widget, index):
self.atom_number = context.application.configuration.sketch_quickpicks[
index]
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s" % str(atom_symbol))
def on_cb_vector_changed(self, combo):
# When the selected object is an atom, show the extra button.
if (self.vector_store.get_value(self.cb_vector.get_active_iter(),
0) == "Bond"):
self.cb_bondtype.show()
else:
self.cb_bondtype.hide()
def get_new(self, position):
if self.current_object == "Fragment":
filename = context.get_share_filename('fragments/%s.cml' %
self.current_fragment)
molecule = load_cml(filename)[0]
Frame = context.application.plugins.get_node("Frame")
new = Frame(name=self.current_fragment)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(new, molecule)
else:
NewClass = context.application.plugins.get_node(
self.current_object)
new = NewClass()
if self.current_object == "Atom":
new.set_number(self.atom_number)
new.set_name(periodic[self.atom_number].symbol)
translation = Translation(position)
primitive.Transform(new, translation)
return new
def add_new(self, position, parent):
new = self.get_new(position)
if self.current_object == "Fragment":
result = new.children[1]
primitive.Add(new, parent)
UnframeAbsolute = context.application.plugins.get_action(
"UnframeAbsolute")
UnframeAbsolute([new])
#return result
else:
primitive.Add(new, parent)
return new
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if (self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if (self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(
gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(
new.children[1].number,
bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1 / old_length *
(new_length - old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if (self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action(
"UnframeAbsolute")
UnframeAbsolute([new])
def connect(self, gl_object1, gl_object2):
try:
new = context.application.plugins.get_node(
self.vector_store.get_value(
self.cb_vector.get_active_iter(),
0))(targets=[gl_object1, gl_object2])
except TargetError:
return
if (self.vector_store.get_value(self.cb_vector.get_active_iter(),
0) == "Bond"):
new.set_bond_type(
self.bondtype_store.get_value(
self.cb_bondtype.get_active_iter(), 1))
primitive.Add(new,
common_parent([gl_object1.parent, gl_object2.parent]))
def erase_at(self, p, parent):
for node in context.application.main.drawing_area.iter_hits(
(p[0] - 2, p[1] - 2, p[0] + 2, p[1] + 2)):
try:
match = (node is not None and node != parent
and node.is_indirect_child_of(parent)
and node.model == context.application.model
and (not self.cb_erase_filter.get_active()
or self.erase_filter(node)))
except Exception:
raise UserError(
"An exception occured while evaluating the erase filter expression."
)
if match:
primitive.Delete(node)
def tool_draw(self, p1, p2):
drawing_area = context.application.main.drawing_area
r1 = drawing_area.screen_to_camera(p1)
r2 = drawing_area.screen_to_camera(p2)
context.application.vis_backend.tool("line", r1, r2)
def tool_special(self, p1, p2):
pass
def move_special(self, gl_object1, gl_object2, p1, p2):
pass
def click_special(self, gl_object):
pass
class SketchOptions(GladeWrapper):
edit_erase_filter = FieldsDialogSimple(
"Edit the Erase filter",
fields.faulty.Expression(
label_text="Erase filter expression",
attribute_name="erase_filter",
show_popup=True,
history_name="filter",
),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade", "wi_sketch", "window")
self.window.hide()
self.init_callbacks(self.__class__)
self.init_proxies([
"cb_object",
"cb_vector",
"cb_erase_filter",
"bu_edit_erase_filter",
"la_current",
"bu_set_atom",
"cb_bondtype",
"hbox_atoms",
"hbox_quickpicks",
"hbox_fragments",
"la_fragment",
"cb_fragment"
])
self.erase_filter = Expression("True")
#Initialize atom number - this can be changed anytime with the edit_atom_number dialog
self.atom_number = 6;
# Initialize the GUI
# 1) common parts of the comboboxes
def render_icon(column, cell, model, iter):
if model.get_value(iter, 0) == "Fragment":
cell.set_property(
"pixbuf",
context.application.plugins.get_node("Atom").icon
)
else:
cell.set_property(
"pixbuf",
context.application.plugins.get_node(model.get_value(iter, 0)).icon
)
# 2) fill the objects combo box
self.object_store = gtk.ListStore(str)
self.object_store.append(["Atom"])
self.object_store.append(["Fragment"])
self.object_store.append(["Point"])
self.object_store.append(["Sphere"])
self.object_store.append(["Box"])
self.cb_object.set_model(self.object_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_object.pack_start(renderer_pixbuf, expand=False)
self.cb_object.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_object.pack_start(renderer_text, expand=True)
self.cb_object.add_attribute(renderer_text, "text", 0)
self.cb_object.set_active(0)
# 3) fill the vector combo box
self.vector_store = gtk.ListStore(str)
self.vector_store.append(["Bond"])
self.vector_store.append(["Arrow"])
self.vector_store.append(["Spring"])
self.cb_vector.set_model(self.vector_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_vector.pack_start(renderer_pixbuf, expand=False)
self.cb_vector.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_vector.pack_start(renderer_text, expand=True)
self.cb_vector.add_attribute(renderer_text, "text", 0)
self.cb_vector.set_active(0)
# 4) fill the bond type combo box
self.bondtype_store = gtk.ListStore(str,int)
self.bondtype_store.append(["Single bond",BOND_SINGLE])
self.bondtype_store.append(["Double bond",BOND_DOUBLE])
self.bondtype_store.append(["Triple bond",BOND_TRIPLE])
self.bondtype_store.append(["Hybrid bond",BOND_HYBRID])
self.bondtype_store.append(["Hydrogen bond",BOND_HYDROGEN])
self.cb_bondtype.set_model(self.bondtype_store)
#no icons like the others, just text here
renderer_text = gtk.CellRendererText()
self.cb_bondtype.pack_start(renderer_text, expand=True)
self.cb_bondtype.add_attribute(renderer_text, "text", 0)
self.cb_bondtype.set_active(0)
# register quick pick config setting
config = context.application.configuration
config.register_setting(
"sketch_quickpicks",
[6,7,8,9,10,11],
DialogFieldInfo("Sketch tool", (0,2), fields.faulty.IntegerList(
label_text="Quick pick atoms (applies after restart)",
attribute_name="sketch_quickpicks",
)),
)
# 5)create the "quick pick" atom buttons
for index in xrange(len(config.sketch_quickpicks)):
atomnumber = config.sketch_quickpicks[index]
bu_element = gtk.Button("")
bu_element.set_label("%s" % periodic[atomnumber].symbol)
bu_element.connect("clicked", self.on_bu_element_clicked, index)
# add to hbox
self.hbox_quickpicks.pack_start(bu_element)
bu_element.show()
# 6)fill the fragment combo box with filenames from share/fragments
fragment_dir = context.get_share_filename('fragments')
self.fragment_store = gtk.ListStore(str)
for filename in sorted(os.listdir(fragment_dir)):
# Ignore subfolders and files with extension other than cml
if os.path.isdir (os.path.join (fragment_dir, filename)) or filename[-3:] != 'cml':
continue
self.fragment_store.append([filename[:-4]])
self.cb_fragment.set_model(self.fragment_store)
renderer_text = gtk.CellRendererText()
self.cb_fragment.pack_start(renderer_text, expand=True)
self.cb_fragment.add_attribute(renderer_text, "text", 0)
self.cb_fragment.set_active(0)
@property
def current_object(self):
return self.object_store.get_value(self.cb_object.get_active_iter(),0)
@property
def current_fragment(self):
return self.fragment_store.get_value(self.cb_fragment.get_active_iter(), 0)
def on_window_delete_event(self, window, event):
self.window.hide()
return True
def on_bu_edit_erase_filter_clicked(self, button):
self.edit_erase_filter.run(self)
def on_bu_set_atom_clicked(self, button):
self.edit_atom_number = FieldsDialogSimple(
"Select atom number",
fields.edit.Element(attribute_name="atom_number"),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
self.edit_atom_number.run(self)
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s " % str(atom_symbol))
def on_cb_object_changed(self, combo):
self.hbox_atoms.hide()
self.la_current.hide()
self.hbox_fragments.hide()
if(self.current_object=="Atom"):
self.hbox_atoms.show()
self.la_current.show()
if(self.current_object=="Fragment"):
self.cb_fragment.show()
self.hbox_fragments.show()
def on_bu_element_clicked(self, widget, index):
self.atom_number = context.application.configuration.sketch_quickpicks[index]
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s" % str(atom_symbol))
def on_cb_vector_changed(self, combo):
# When the selected object is an atom, show the extra button.
if (self.vector_store.get_value(self.cb_vector.get_active_iter(),0)=="Bond"):
self.cb_bondtype.show()
else:
self.cb_bondtype.hide()
def get_new(self, position):
if self.current_object == "Fragment":
filename = context.get_share_filename('fragments/%s.cml' % self.current_fragment)
molecule = load_cml(filename)[0]
Frame = context.application.plugins.get_node("Frame")
new = Frame(name=self.current_fragment)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(new, molecule)
else:
NewClass = context.application.plugins.get_node(self.current_object)
new = NewClass()
if self.current_object == "Atom":
new.set_number(self.atom_number)
new.set_name(periodic[self.atom_number].symbol)
translation = Translation(position)
primitive.Transform(new, translation)
return new
def add_new(self, position, parent):
new = self.get_new(position)
if self.current_object == "Fragment":
result = new.children[1]
primitive.Add(new, parent)
UnframeAbsolute = context.application.plugins.get_action("UnframeAbsolute")
UnframeAbsolute([new])
#return result
else:
primitive.Add(new, parent)
return new
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if(self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if(self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(new.children[1].number, bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1/old_length*(new_length-old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if(self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action("UnframeAbsolute")
UnframeAbsolute([new])
def connect(self, gl_object1, gl_object2):
try:
new = context.application.plugins.get_node(
self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)
)(targets=[gl_object1, gl_object2])
except TargetError:
return
if(self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)=="Bond"):
new.set_bond_type(self.bondtype_store.get_value(self.cb_bondtype.get_active_iter(),1))
primitive.Add(new, common_parent([gl_object1.parent, gl_object2.parent]))
def erase_at(self, p, parent):
for node in context.application.main.drawing_area.iter_hits((p[0]-2, p[1]-2, p[0]+2, p[1]+2)):
try:
match = (
node is not None and node != parent and
node.is_indirect_child_of(parent) and
node.model == context.application.model and (
not self.cb_erase_filter.get_active() or
self.erase_filter(node)
)
)
except Exception:
raise UserError("An exception occured while evaluating the erase filter expression.")
if match:
primitive.Delete(node)
def tool_draw(self, p1, p2):
drawing_area = context.application.main.drawing_area
r1 = drawing_area.screen_to_camera(p1)
r2 = drawing_area.screen_to_camera(p2)
context.application.vis_backend.tool("line", r1, r2)
def tool_special(self, p1, p2):
pass
def move_special(self, gl_object1, gl_object2, p1, p2):
pass
def click_special(self, gl_object):
pass
class SketchOptions(GladeWrapper):
edit_erase_filter = FieldsDialogSimple(
"Edit the Erase filter",
fields.faulty.Expression(
label_text="Erase filter expression",
attribute_name="erase_filter",
show_popup=True,
history_name="filter",
),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade", "wi_sketch", "window")
self.window.hide()
self.init_callbacks(self.__class__)
self.init_proxies([
"cb_object",
"cb_vector",
"cb_erase_filter",
"bu_edit_erase_filter",
"la_current",
"bu_set_atom",
"cb_bondtype",
"hbox_atoms",
"hbox_quickpicks",
"hbox_fragments",
"la_fragment",
"cb_fragment"
])
self.erase_filter = Expression("True")
#Initialize atom number - this can be changed anytime with the edit_atom_number dialog
self.atom_number = 6;
# Initialize the GUI
# 1) common parts of the comboboxes
def render_icon(column, cell, model, iter):
cell.set_property(
"pixbuf",
context.application.plugins.get_node(model.get_value(iter, 0)).icon
)
# 2) fill the objects combo box
self.object_store = gtk.ListStore(str)
self.object_store.append(["Atom"])
self.object_store.append(["Fragment"])
self.object_store.append(["Point"])
self.object_store.append(["Sphere"])
self.object_store.append(["Box"])
self.cb_object.set_model(self.object_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_object.pack_start(renderer_pixbuf, expand=False)
self.cb_object.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_object.pack_start(renderer_text, expand=True)
self.cb_object.add_attribute(renderer_text, "text", 0)
self.cb_object.set_active(0)
# 3) fill the vector combo box
self.vector_store = gtk.ListStore(str)
self.vector_store.append(["Bond"])
self.vector_store.append(["Arrow"])
self.vector_store.append(["Spring"])
self.cb_vector.set_model(self.vector_store)
renderer_pixbuf = gtk.CellRendererPixbuf()
self.cb_vector.pack_start(renderer_pixbuf, expand=False)
self.cb_vector.set_cell_data_func(renderer_pixbuf, render_icon)
renderer_text = gtk.CellRendererText()
self.cb_vector.pack_start(renderer_text, expand=True)
self.cb_vector.add_attribute(renderer_text, "text", 0)
self.cb_vector.set_active(0)
# 4) fill the bond type combo box
self.bondtype_store = gtk.ListStore(str,int)
self.bondtype_store.append(["Single bond",BOND_SINGLE])
self.bondtype_store.append(["Double bond",BOND_DOUBLE])
self.bondtype_store.append(["Triple bond",BOND_TRIPLE])
self.bondtype_store.append(["Hybrid bond",BOND_HYBRID])
self.bondtype_store.append(["Hydrogen bond",BOND_HYDROGEN])
self.cb_bondtype.set_model(self.bondtype_store)
#no icons like the others, just text here
renderer_text = gtk.CellRendererText()
self.cb_bondtype.pack_start(renderer_text, expand=True)
self.cb_bondtype.add_attribute(renderer_text, "text", 0)
self.cb_bondtype.set_active(0)
# register quick pick config setting
config = context.application.configuration
config.register_setting(
"sketch_quickpicks",
[6,7,8,9,10,11],
)
#WOUTER I messed up this setting and now Zeobuilder keeps crashing cause it was set to empty
config.sketch_quickpicks = [6,7,8,9,10,11]
# 5)create the "quick pick" atom buttons
for index in xrange(len(config.sketch_quickpicks)):
atomnumber = config.sketch_quickpicks[index]
bu_element = gtk.Button("")
bu_element.set_label("%s" % periodic[atomnumber].symbol)
bu_element.connect("clicked", self.on_bu_element_clicked, index)
# add to hbox
self.hbox_quickpicks.pack_start(bu_element)
bu_element.show()
# 6)fill the fragment combo box with filenames from share/fragments
fragmentdir = context.get_share_filename('fragments')
self.fragment_store = gtk.ListStore(str)
for filename in os.listdir (fragmentdir):
# Ignore subfolders and files with extension other than cml
if os.path.isdir (os.path.join (fragmentdir, filename)) or filename[-3:] != 'cml':
continue
self.fragment_store.append([filename[:-4]])
self.cb_fragment.set_model(self.fragment_store)
renderer_text = gtk.CellRendererText()
self.cb_fragment.pack_start(renderer_text, expand=True)
self.cb_fragment.add_attribute(renderer_text, "text", 0)
self.cb_fragment.set_active(0)
self.doing_fragment = False #at init we do atoms :)
def on_window_delete_event(self, window, event):
return True
def on_bu_edit_erase_filter_clicked(self, button):
self.edit_erase_filter.run(self)
def on_bu_set_atom_clicked(self, button):
self.edit_atom_number = FieldsDialogSimple(
"Select atom number",
fields.edit.Element(attribute_name="atom_number"),
((gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL), (gtk.STOCK_OK, gtk.RESPONSE_OK))
)
self.edit_atom_number.run(self)
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s " % str(atom_symbol))
def on_cb_object_changed(self, combo):
# When the selected object is an atom, show the extra button.
self.hbox_atoms.hide()
self.la_current.hide()
self.hbox_fragments.hide()
self.doing_fragment = False
if(self.object_store.get_value(self.cb_object.get_active_iter(),0)=="Atom"):
self.hbox_atoms.show()
self.la_current.show()
if(self.object_store.get_value(self.cb_object.get_active_iter(),0)=="Fragment"):
self.doing_fragment = True
self.cb_fragment.show()
#self.la_fragment.show()
self.hbox_fragments.show()
def on_bu_element_clicked(self, widget, index):
self.atom_number = context.application.configuration.sketch_quickpicks[index]
atom_symbol = periodic[self.atom_number].symbol
self.la_current.set_label("Current: %s" % str(atom_symbol))
def on_cb_vector_changed(self, combo):
# When the selected object is an atom, show the extra button.
if (self.vector_store.get_value(self.cb_vector.get_active_iter(),0)=="Bond"):
self.cb_bondtype.show()
else:
self.cb_bondtype.hide()
def get_new(self,position):
object_type = self.object_store.get_value(self.cb_object.get_active_iter(), 0)
print object_type
if object_type == "Fragment": #if it's a 'Fragment', set fragment name to current item in combo box
fragment = context.application.plugins.get_node("Fragment")(self.fragment_store.get_value(self.cb_fragment.get_active_iter(),0))
fragment.set_name(self.fragment_store.get_value(self.cb_fragment.get_active_iter(),0))
new = fragment.get_in_frame(position)
else:
new = context.application.plugins.get_node(object_type)()
if object_type == "Atom": #if it's an 'Atom', set the atom number to the current atom number?
new.set_number(self.atom_number)
new.set_name(periodic[self.atom_number].symbol)
new.transformation.t[:] = position
return new
def add_new(self, position, parent):
print "position:"
print position
new = self.get_new(position)
print new
primitive.Add(new, parent)
def replace(self, gl_object):
print gl_object
if not gl_object.get_fixed():
if self.doing_fragment:
print "replacing atom with fragment"
position = gl_object.transformation.t
parent = gl_object.parent
new = self.get_new(position)
new.addToModel(position,parent)
primitive.Delete(gl_object)
else:
new = self.get_new(gl_object.transformation.t)
# old way: new.transformation.t[:] =
for reference in gl_object.references[::-1]:
if not reference.check_target(new):
return
parent = gl_object.parent
primitive.Add(new, parent)
for reference in gl_object.references[::-1]:
reference.set_target(new)
primitive.Delete(gl_object)
def connect(self, gl_object1, gl_object2):
print "connecting:"
print gl_object1,gl_object2
try:
new = context.application.plugins.get_node(
self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)
)(targets=[gl_object1, gl_object2])
except TargetError:
return
if(self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)=="Bond"):
new.set_bond_type(self.bondtype_store.get_value(self.cb_bondtype.get_active_iter(),1))
primitive.Add(new, common_parent([gl_object1.parent, gl_object2.parent]))
def erase_at(self, p, parent):
for node in context.application.main.drawing_area.yield_hits((p[0]-2, p[1]-2, p[0]+2, p[1]+2)):
try:
match = (
node is not None and node != parent and
node.is_indirect_child_of(parent) and
node.model == context.application.model and (
not self.cb_erase_filter.get_active() or
self.erase_filter(node)
)
)
except Exception:
raise UserError("An exception occured while evaluating the erase filter expression.")
if match:
primitive.Delete(node)
def tool_draw(self, p1, p2):
drawing_area = context.application.main.drawing_area
r1 = drawing_area.screen_to_camera(p1)
r2 = drawing_area.screen_to_camera(p2)
context.application.vis_backend.tool("line", r1, r2)
def tool_special(self, p1, p2):
pass
def move_special(self, gl_object1, gl_object2, p1, p2):
pass
def click_special(self, gl_object):
pass
