def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade", "wi_ring_distribution", "window")
self.window.hide()
self.init_callbacks(RingDistributionWindow)
self.init_proxies(["al_image", "cb_filter", "tv_rings"])
import zeobuilder.mplwrap as mplwrap
import pylab
self.figure = pylab.figure(figsize=(4, 4), dpi=100)
self.mpl_widget = mplwrap.FigureCanvas(self.figure)
self.mpl_widget.set_size_request(400, 400)
#self.mpl_widget.set_border_width(6) TODO
self.al_image.add(self.mpl_widget)
self.filter_store = gtk.ListStore(str, int)
self.cb_filter.set_model(self.filter_store)
cell_renderer = gtk.CellRendererText()
self.cb_filter.pack_start(cell_renderer)
self.cb_filter.add_attribute(cell_renderer, "text", 0)
self.cb_filter.connect("changed", self.on_filter_changed)
self.ring_store = gtk.ListStore(int, str, str, str, object)
self.tv_rings.set_model(self.ring_store)
self.tv_rings.append_column(gtk.TreeViewColumn("Size", gtk.CellRendererText(), text=0))
self.tv_rings.append_column(gtk.TreeViewColumn("Av. diameter", gtk.CellRendererText(), text=1))
self.tv_rings.append_column(gtk.TreeViewColumn("Min. diameter", gtk.CellRendererText(), text=2))
self.tv_rings.append_column(gtk.TreeViewColumn("Label", gtk.CellRendererText(), text=3))
self.tv_rings.get_selection().connect("changed", self.on_ring_selection_changed)
context.application.action_manager.connect("model-changed", self.on_model_changed)
def __init__(self):
GladeWrapper.__init__(self, "plugins/builder/gui.glade", "di_optimize",
"dialog")
ChildProcessDialog.__init__(self, self.dialog,
self.dialog.action_area.get_children())
self.init_callbacks(OptimizationReportDialog)
self.init_proxies(["la_num_iter", "la_rms_error", "progress_bar"])
self.state_indices = None
def __init__(self):
GladeWrapper.__init__(self, "plugins/basic/gui.glade", "di_plugin_info", "dialog")
self.dialog.hide()
self.init_proxies([
"la_category", "la_required_modules", "la_failed_modules",
"la_file", "la_status", "vb_authors", "tv_authors",
"bu_information", "sw_extra", "tv_extra",
])
self.author_store = authors.init_widgets(self.tv_authors, self.bu_information)
def __init__(self):
GladeWrapper.__init__(self, "plugins/basic/gui.glade", "di_plugin_info", "dialog")
self.dialog.hide()
self.init_proxies([
"la_category", "la_required_modules", "la_failed_modules",
"la_file", "la_status", "vb_authors", "tv_authors",
"bu_information", "sw_extra", "tv_extra",
])
self.author_store = authors.init_widgets(self.tv_authors, self.bu_information)
def __init__(self):
GladeWrapper.__init__(self, "plugins/basic/gui.glade", "wi_measurements", "window")
self.window.hide()
self.init_callbacks(self.__class__)
labels_chain2 = ["distances",
"label_12", "distance_12"
]
labels_chain3 = ["angles", "distances_to_line",
"label_23", "distance_23",
"label_123", "angle_123",
"label_1_23", "distance_1_23",
]
labels_chain_only3 = [
"label_12_3", "distance_12_3",
]
labels_chain4 = [
"dihedral_angles", "out_of_plane_angles",
"distances_to_plane", "distances_between_lines",
"label_34", "distance_34",
"label_234", "angle_234",
"label_123_234", "angle_123_234",
"label_12_234", "angle_12_234",
"label_123_34", "angle_123_34",
"label_1_234", "distance_1_234",
"label_123_4", "distance_123_4",
"label_23_4", "distance_23_4",
"label_12_34", "distance_12_34",
]
labels_chain_closed = [
"label_31", "distance_31",
"label_231", "angle_231",
"label_312", "angle_312",
"label_31_2", "distance_31_2",
]
self.init_proxies(
labels_chain2 + labels_chain3 + labels_chain_only3 + labels_chain4 +
labels_chain_closed
)
self.labels_chain2 = [self.__dict__[label] for label in labels_chain2]
self.labels_chain3 = [self.__dict__[label] for label in labels_chain3]
self.labels_chain_only3 = [self.__dict__[label] for label in labels_chain_only3]
self.labels_chain4 = [self.__dict__[label] for label in labels_chain4]
self.labels_chain_closed = [self.__dict__[label] for label in labels_chain_closed]
context.application.action_manager.connect("action-started", self.on_action_started)
context.application.action_manager.connect("action-ends", self.on_action_ended)
context.application.action_manager.connect("action-cancels", self.on_action_ended)
self.model_objects = []
self.points = []
self.vectors = []
glutInit([])
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade", "di_distribution", "dialog")
self.dialog.hide()
self.init_callbacks(DistributionDialog)
self.init_proxies(["fa_image"])
import zeobuilder.mplwrap as mplwrap
import pylab
figure = pylab.figure(0, figsize=(8, 4), dpi=100)
self.mpl_widget = mplwrap.FigureCanvas(figure)
self.mpl_widget.set_size_request(800, 400)
self.fa_image.add(self.mpl_widget)
def __init__(self):
self.frame1 = None
self.frame2 = None
GladeWrapper.__init__(self, "plugins/builder/gui.glade",
"wi_conscan_results", "window")
self.init_callbacks(ConscanResultsWindow)
self.init_proxies([
"tv_results",
"cb_auto_apply",
"bu_apply",
"bu_apply_opt",
"cb_inverse",
])
self.window.hide()
self.list_store = gtk.ListStore(float, int, str, object)
column = gtk.TreeViewColumn("")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
def cell_data_func(column, cell, model, iter):
cell.set_property("text", model.get_path(iter)[0])
column.set_cell_data_func(renderer_text, cell_data_func)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("Quality")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 0)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("#")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 1)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("Invertible")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 2)
self.tv_results.append_column(column)
self.tv_results.set_model(self.list_store)
self.tree_selection = self.tv_results.get_selection()
self.tree_selection.connect("changed", self.on_selection_changed)
context.application.cache.connect("cache-invalidated",
self.on_cache_invalidated)
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade",
"di_distribution", "dialog")
self.dialog.hide()
self.init_callbacks(DistributionDialog)
self.init_proxies(["fa_image"])
import zeobuilder.mplwrap as mplwrap
import pylab
figure = pylab.figure(0, figsize=(8, 4), dpi=100)
self.mpl_widget = mplwrap.FigureCanvas(figure)
self.mpl_widget.set_size_request(800, 400)
self.fa_image.add(self.mpl_widget)
def __init__(self):
model = context.application.model
model.connect("file-new", self.on_filename_changed)
model.connect("file-opened", self.on_filename_changed)
model.connect("file-saved", self.on_filename_changed)
context.application.action_manager.connect("model-changed", self.on_model_changed)
GladeWrapper.__init__(self, "zeobuilder.glade", "wi_main", "window")
self.init_callbacks(self.__class__)
self.init_proxies(["sw_nodes", "hp_main", "vb_main", "menubar"])
# add model gui:
self.init_tree_view()
self.init_drawing_area()
def __init__(self):
model = context.application.model
model.connect("file-new", self.on_filename_changed)
model.connect("file-opened", self.on_filename_changed)
model.connect("file-saved", self.on_filename_changed)
context.application.action_manager.connect("model-changed",
self.on_model_changed)
GladeWrapper.__init__(self, "zeobuilder.glade", "wi_main", "window")
self.init_callbacks(self.__class__)
self.init_proxies(["sw_nodes", "hp_main", "vb_main", "menubar"])
# add model gui:
self.init_tree_view()
self.init_drawing_area()
def __init__(self):
self.frame1 = None
self.frame2 = None
GladeWrapper.__init__(self, "plugins/builder/gui.glade", "wi_conscan_results", "window")
self.init_callbacks(ConscanResultsWindow)
self.init_proxies([
"tv_results", "cb_auto_apply", "bu_apply", "bu_apply_opt",
"cb_inverse",
])
self.window.hide()
self.list_store = gtk.ListStore(float, int, str, object)
column = gtk.TreeViewColumn("")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
def cell_data_func(column, cell, model, iter):
cell.set_property("text", model.get_path(iter)[0])
column.set_cell_data_func(renderer_text, cell_data_func)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("Quality")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 0)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("#")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 1)
self.tv_results.append_column(column)
column = gtk.TreeViewColumn("Invertible")
renderer_text = gtk.CellRendererText()
column.pack_start(renderer_text, expand=False)
column.add_attribute(renderer_text, "text", 2)
self.tv_results.append_column(column)
self.tv_results.set_model(self.list_store)
self.tree_selection = self.tv_results.get_selection()
self.tree_selection.connect("changed", self.on_selection_changed)
context.application.cache.connect("cache-invalidated", self.on_cache_invalidated)
def __init__(self):
GladeWrapper.__init__(self, "plugins/molecular/gui.glade",
"wi_ring_distribution", "window")
self.window.hide()
self.init_callbacks(RingDistributionWindow)
self.init_proxies(["al_image", "cb_filter", "tv_rings"])
import zeobuilder.mplwrap as mplwrap
import pylab
self.figure = pylab.figure(figsize=(4, 4), dpi=100)
self.mpl_widget = mplwrap.FigureCanvas(self.figure)
self.mpl_widget.set_size_request(400, 400)
#self.mpl_widget.set_border_width(6) TODO
self.al_image.add(self.mpl_widget)
self.filter_store = gtk.ListStore(str, int)
self.cb_filter.set_model(self.filter_store)
cell_renderer = gtk.CellRendererText()
self.cb_filter.pack_start(cell_renderer)
self.cb_filter.add_attribute(cell_renderer, "text", 0)
self.cb_filter.connect("changed", self.on_filter_changed)
self.ring_store = gtk.ListStore(int, str, str, str, object)
self.tv_rings.set_model(self.ring_store)
self.tv_rings.append_column(
gtk.TreeViewColumn("Size", gtk.CellRendererText(), text=0))
self.tv_rings.append_column(
gtk.TreeViewColumn("Av. diameter", gtk.CellRendererText(), text=1))
self.tv_rings.append_column(
gtk.TreeViewColumn("Min. diameter", gtk.CellRendererText(),
text=2))
self.tv_rings.append_column(
gtk.TreeViewColumn("Label", gtk.CellRendererText(), text=3))
self.tv_rings.get_selection().connect("changed",
self.on_ring_selection_changed)
context.application.action_manager.connect("model-changed",
self.on_model_changed)
def __init__(self):
GladeWrapper.__init__(self, "plugins/builder/gui.glade", "di_optimize", "dialog")
ChildProcessDialog.__init__(self, self.dialog, self.dialog.action_area.get_children())
self.init_callbacks(OptimizationReportDialog)
self.init_proxies(["la_num_iter", "la_rms_error", "progress_bar"])
self.state_indices = None
def __init__(self):
GladeWrapper.__init__(self, "zeobuilder.glade", "di_author", "dialog")
self.init_proxies(["la_author", "la_affiliation"])
self.dialog.hide()
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, dialog_name):
GladeWrapper.__init__(self, "plugins/basic/gui.glade", dialog_name, "dialog")
self.dialog.hide()
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/basic/gui.glade",
"wi_measurements", "window")
self.window.hide()
self.init_callbacks(self.__class__)
labels_chain2 = ["distances", "label_12", "distance_12"]
labels_chain3 = [
"angles",
"distances_to_line",
"label_23",
"distance_23",
"label_123",
"angle_123",
"label_1_23",
"distance_1_23",
]
labels_chain_only3 = [
"label_12_3",
"distance_12_3",
]
labels_chain4 = [
"dihedral_angles",
"out_of_plane_angles",
"distances_to_plane",
"distances_between_lines",
"label_34",
"distance_34",
"label_234",
"angle_234",
"label_123_234",
"angle_123_234",
"label_12_234",
"angle_12_234",
"label_123_34",
"angle_123_34",
"label_1_234",
"distance_1_234",
"label_123_4",
"distance_123_4",
"label_23_4",
"distance_23_4",
"label_12_34",
"distance_12_34",
]
labels_chain_closed = [
"label_31",
"distance_31",
"label_231",
"angle_231",
"label_312",
"angle_312",
"label_31_2",
"distance_31_2",
]
self.init_proxies(labels_chain2 + labels_chain3 + labels_chain_only3 +
labels_chain4 + labels_chain_closed)
self.labels_chain2 = [self.__dict__[label] for label in labels_chain2]
self.labels_chain3 = [self.__dict__[label] for label in labels_chain3]
self.labels_chain_only3 = [
self.__dict__[label] for label in labels_chain_only3
]
self.labels_chain4 = [self.__dict__[label] for label in labels_chain4]
self.labels_chain_closed = [
self.__dict__[label] for label in labels_chain_closed
]
context.application.action_manager.connect("action-started",
self.on_action_started)
context.application.action_manager.connect("action-ends",
self.on_action_ended)
context.application.action_manager.connect("action-cancels",
self.on_action_ended)
self.model_objects = []
self.points = []
self.vectors = []
glutInit([])
def __init__(self, dialog_name):
GladeWrapper.__init__(self, "plugins/basic/gui.glade", dialog_name, "dialog")
self.dialog.hide()
def __init__(self):
GladeWrapper.__init__(self, "zeobuilder.glade", "di_author", "dialog")
self.init_proxies(["la_author", "la_affiliation"])
self.dialog.hide()
