def fn():
context.application.model.file_open("test/input/tpa.xyz")
Atom = context.application.plugins.get_node("Atom")
for child in context.application.model.universe.children[::-1]:
if isinstance(child, Atom) and child.number == 1:
context.application.model.universe.children.remove(child)
context.application.main.select_nodes([context.application.model.universe])
AutoConnectPhysical = context.application.plugins.get_action("AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
parameters = Parameters()
parameters.num_hydrogens = 2
parameters.valence_angle = 1.9093
context.application.main.select_nodes([context.application.model.universe.children[1]])
SaturateHydrogensManual = context.application.plugins.get_action("SaturateHydrogensManual")
assert SaturateHydrogensManual.analyze_selection(parameters)
SaturateHydrogensManual(parameters)
def fn():
context.application.model.file_open("test/input/tpa.xyz")
Atom = context.application.plugins.get_node("Atom")
for child in context.application.model.universe.children[::-1]:
if isinstance(child, Atom) and child.number == 1:
context.application.model.universe.children.remove(child)
context.application.main.select_nodes(
[context.application.model.universe])
AutoConnectPhysical = context.application.plugins.get_action(
"AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
parameters = Parameters()
parameters.num_hydrogens = 2
parameters.valence_angle = 1.9093
context.application.main.select_nodes(
[context.application.model.universe.children[1]])
SaturateHydrogensManual = context.application.plugins.get_action(
"SaturateHydrogensManual")
assert SaturateHydrogensManual.analyze_selection(parameters)
SaturateHydrogensManual(parameters)
def default_parameters(cls):
result = Parameters()
result.num_hydrogens = 2
result.valence_angle = 109.4 * deg
return result
def default_parameters(cls):
result = Parameters()
result.num_hydrogens = 2
result.valence_angle = 109.4*deg
return result
