def get_in_frame(self,position):
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+self.name+'.cml'
from molmod.io.cml import load_cml
molecules = load_cml(filename)
molecule = molecules[0] #we only look at first molecule in the list
#load 'universe' from file trough cml load filter (stolen from models.py > file_open)
load_filter = context.application.plugins.get_load_filter('cml')
#create frame
Frame = context.application.plugins.get_node("Frame")
self.fragment_frame = Frame(name=self.name)
#fill frame with molecule
load_filter.load_molecule(self.fragment_frame,molecule)
#rotate frame?
rotation = numpy.array([[1,2,0],
[0,0,0],
[0,0,0]])
# self.fragment_frame.transformation.r[:] = rotation
print self.fragment_frame.transformation.r
#apply transformation to frame
self.fragment_frame.transformation.t[:] = position
return self.fragment_frame
def run(self, minimize, involved_frames, update_interval, update_steps,
num_springs):
self.la_num_iter.set_text("0")
self.la_rms_error.set_text(express_measure(0.0, "Length"))
self.progress_bar.set_fraction(0.0)
self.progress_bar.set_text("0%")
self.minimize = minimize
self.involved_frames = [
frame for frame in involved_frames if frame is not None
]
self.update_interval = update_interval
self.update_steps = update_steps
self.num_springs = num_springs
self.last_time = time.time()
self.last_step = 0
self.status = None
result = ChildProcessDialog.run(
self, [context.get_share_filename("helpers/iterative")],
self.minimize,
pickle=True)
# just to avoid confusion
del self.minimize
del self.involved_frames
del self.update_interval
del self.update_steps
del self.last_time
del self.last_step
del self.num_springs
del self.status
return result
def addToModel(self,position=[0,0,0],parent=None):
if parent is None:
parent = context.application.model.universe
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+self.name+'.cml'
from molmod.io.cml import load_cml
molecules = load_cml(filename)
molecule = molecules[0] #we only look at first molecule in the list
#load 'universe' from file trough cml load filter (stolen from models.py > file_open)
load_filter = context.application.plugins.get_load_filter('cml')
#create frame
Frame = context.application.plugins.get_node("Frame")
self.fragment_frame = Frame(name=self.name)
#fill frame with molecule
load_filter.load_molecule(self.fragment_frame,molecule)
#rotate frame?
rotation = numpy.array([[1,2,0],
[0,0,0],
[0,0,0]])
# self.fragment_frame.transformation.r[:] = rotation
print self.fragment_frame.transformation.r
#apply transformation to frame
self.fragment_frame.transformation.t[:] = position
#add to model (note: should add to parent frame, not universe)
primitive.Add(self.fragment_frame, parent)
def run(self, minimize, auto_close, involved_frames, update_interval, update_steps, num_springs):
self.la_num_iter.set_text("0")
self.la_rms_error.set_text(express_measure(0.0, "Length"))
self.progress_bar.set_fraction(0.0)
self.progress_bar.set_text("0%")
self.minimize = minimize
self.involved_frames = [frame for frame in involved_frames if frame is not None]
self.update_interval = update_interval
self.update_steps = update_steps
self.num_springs = num_springs
self.last_time = time.time()
self.last_step = 0
self.status = None
result = ChildProcessDialog.run(self,
[context.get_share_filename("helpers/iterative")],
self.minimize, auto_close, pickle=True
)
# just to avoid confusion
del self.minimize
del self.involved_frames
del self.update_interval
del self.update_steps
del self.last_time
del self.last_step
del self.num_springs
del self.status
return result
def load_image(filename, size=None):
filename = context.get_share_filename(filename)
if os.path.isfile(filename):
if size is None:
return gtk.gdk.pixbuf_new_from_file(filename)
else:
return gtk.gdk.pixbuf_new_from_file_at_size(
filename, size[0], size[1])
def load_image(filename, size=None):
filename = context.get_share_filename(filename)
if os.path.isfile(filename):
if size is None:
return gtk.gdk.pixbuf_new_from_file(filename)
else:
return gtk.gdk.pixbuf_new_from_file_at_size(
filename, size[0], size[1]
)
def run(self, inp):
self.clear_gui()
self.connections = []
response = ChildProcessDialog.run(
self, [context.get_share_filename("helpers/conscan")],
inp,
pickle=True)
if response == gtk.RESPONSE_OK:
result = self.connections
del self.connections
return result
def run(self, inp):
self.clear_gui()
self.connections = []
response = ChildProcessDialog.run(self,
[context.get_share_filename("helpers/conscan")],
inp, pickle=True
)
if response == gtk.RESPONSE_OK:
result = self.connections
del self.connections
return result
def get_fragment(self, fragmentname):
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+fragmentname+'.cml'
molecules = load_cml(filename)
molecule = molecules[0]
Frame = context.application.plugins.get_node("Frame")
fragment_frame = Frame(name=fragmentname)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(fragment_frame,molecule)
return fragment_frame
def __init__(self, glade_file, widget_name, widget_dict_name=None):
"This method loads the widget from the glade XML file"
# widget_dict_name is the name of the attribute to which the widget
# will be assigned. if left to none the widget name will be used
# load the glade file
self.widgets = gtk.glade.XML(context.get_share_filename(glade_file), widget_name)
if self.widgets is None:
raise GladeWrapperError("Could not find glade file %s in any of the share directories %s." % (glade_file, context.share_dirs))
# load the requested widget as widget_dict_name
if widget_dict_name is None:
widget_dict_name = widget_name
widget = self.widgets.get_widget(widget_name)
if widget is None:
raise GladeWrapperError, "The widget '%s' passed to the constructor does not exist." % widget_name
else:
self.__dict__[widget_dict_name] = widget
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 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 __init__(self, glade_file, widget_name, widget_dict_name=None):
"This method loads the widget from the glade XML file"
# widget_dict_name is the name of the attribute to which the widget
# will be assigned. if left to none the widget name will be used
# load the glade file
self.widgets = gtk.glade.XML(context.get_share_filename(glade_file), widget_name)
if self.widgets is None:
raise GladeWrapperError("Could not find glade file %s in the share directory %s." % (glade_file, context.share_dir))
# load the requested widget as widget_dict_name
if widget_dict_name is None:
widget_dict_name = widget_name
widget = self.widgets.get_widget(widget_name)
if widget is None:
raise GladeWrapperError, "The widget '%s' passed to the constructor does not exist." % widget_name
else:
self.__dict__[widget_dict_name] = widget
# In case of a dialog in a test application, connect to a signal to
# close immedeately.
if widget_dict_name == "dialog":
widget.connect("show", self.on_dialog_show)
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)
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)