def on_bu_apply_opt_clicked(self, button):
action = CustomAction("Apply connection and optimize springs")
old_selection = list(context.application.cache.nodes)
self.apply_normal()
self.optimize()
context.application.main.select_nodes(old_selection)
action.finish()
def on_bu_apply_opt_clicked(self, button):
action = CustomAction("Apply connection and optimize springs")
old_selection = list(context.application.cache.nodes)
self.apply_normal()
self.optimize()
context.application.main.select_nodes(old_selection)
action.finish()
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes(context.application.model.universe.children)
ScanForConnections = context.application.plugins.get_action("ScanForConnections")
parameters = ScanForConnections.default_parameters()
parameters.connect_description1 = (
Expression("isinstance(node, Atom) and node.number == 8 and node.num_bonds() == 1"),
Expression("node.get_radius()"),
)
parameters.repulse_description1 = (
Expression("isinstance(node, Atom) and (node.number == 8 or node.number == 14)"),
Expression("node.get_radius()*1.5"),
)
parameters.action_radius = 4*angstrom
parameters.hit_tolerance = 0.1*angstrom
parameters.allow_inversions = True
parameters.minimum_triangle_size = 0.1*angstrom
parameters.rotation2 = Undefined()
assert ScanForConnections.analyze_selection(parameters)
ScanForConnections(parameters)
# Try to save the result to file an open it again.
context.application.model.file_save("test/output/tmp.zml")
FileNew = context.application.plugins.get_action("FileNew")
FileNew()
context.application.model.file_open("test/output/tmp.zml")
# Do some consistency tests on the connection scanner results:
scan_results = context.application.model.folder.children[0]
for quality, transformation, pairs, inverse_pairs in scan_results.get_connections():
assert len(pairs) >= 3
if len(inverse_pairs) > 0:
assert len(pairs) == len(inverse_pairs)
# Test for the first case that the indicated atom pairs are indeed
# overlapping.
context.application.main.select_nodes([scan_results])
ShowConscanResultsWindow = context.application.plugins.get_action("ShowConscanResultsWindow")
assert ShowConscanResultsWindow.analyze_selection()
ShowConscanResultsWindow()
csrw = ShowConscanResultsWindow.conscan_results_window
csrw.tree_selection.select_path(0)
action = CustomAction("Apply connection")
csrw.apply_normal()
action.finish()
quality, transformation, pairs, inverse_pairs = scan_results.connections[0]
for atom1, atom2 in pairs:
f1 = atom1().get_absolute_frame()
f2 = atom2().get_absolute_frame()
d = numpy.linalg.norm(f1.t - f2.t)
assert d < 1e-5
csrw.window.hide()
def on_bu_apply_clicked(self, button):
action = CustomAction("Apply connection")
self.apply_normal()
action.finish()
def auto_apply(self):
if self.cb_auto_apply.get_active() and \
self.tree_selection.get_selected()[1] is not None:
action = CustomAction("Auto apply connection")
self.apply_normal()
action.finish()
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes(
context.application.model.universe.children)
ScanForConnections = context.application.plugins.get_action(
"ScanForConnections")
parameters = ScanForConnections.default_parameters()
parameters.connect_description1 = (
Expression(
"isinstance(node, Atom) and node.number == 8 and node.num_bonds() == 1"
),
Expression("node.get_radius()"),
)
parameters.repulse_description1 = (
Expression(
"isinstance(node, Atom) and (node.number == 8 or node.number == 14)"
),
Expression("node.get_radius()*1.5"),
)
parameters.action_radius = 4 * angstrom
parameters.hit_tolerance = 0.1 * angstrom
parameters.allow_inversions = True
parameters.minimum_triangle_size = 0.1 * angstrom
parameters.rotation2 = Undefined()
assert ScanForConnections.analyze_selection(parameters)
ScanForConnections(parameters)
# Try to save the result to file an open it again.
context.application.model.file_save("test/output/tmp.zml")
FileNew = context.application.plugins.get_action("FileNew")
FileNew()
context.application.model.file_open("test/output/tmp.zml")
# Do some consistency tests on the connection scanner results:
scan_results = context.application.model.folder.children[0]
for quality, transformation, pairs, inverse_pairs in scan_results.get_connections(
):
assert len(pairs) >= 3
if len(inverse_pairs) > 0:
assert len(pairs) == len(inverse_pairs)
# Test for the first case that the indicated atom pairs are indeed
# overlapping.
context.application.main.select_nodes([scan_results])
ShowConscanResultsWindow = context.application.plugins.get_action(
"ShowConscanResultsWindow")
assert ShowConscanResultsWindow.analyze_selection()
ShowConscanResultsWindow()
csrw = ShowConscanResultsWindow.conscan_results_window
csrw.tree_selection.select_path(0)
action = CustomAction("Apply connection")
csrw.apply_normal()
action.finish()
quality, transformation, pairs, inverse_pairs = scan_results.connections[
0]
for atom1, atom2 in pairs:
f1 = atom1().get_absolute_frame()
f2 = atom2().get_absolute_frame()
d = numpy.linalg.norm(f1.t - f2.t)
assert d < 1e-5
csrw.window.hide()
def on_bu_apply_clicked(self, button):
action = CustomAction("Apply connection")
self.apply_normal()
action.finish()
def auto_apply(self):
if self.cb_auto_apply.get_active() and \
self.tree_selection.get_selected()[1] is not None:
action = CustomAction("Auto apply connection")
self.apply_normal()
action.finish()
