def setUp(self): self.nrigid = 10 self.topology = RBTopology() self.topology.add_sites( [create_tetrahedron() for _ in range(self.nrigid)]) self.topology.finalize_setup() self.measure = MeasureAngleAxisCluster(self.topology)
def get_mindist(self, **kwargs): from pele.angleaxis import MinPermDistAACluster from pele.angleaxis import TransformAngleAxisCluster, MeasureAngleAxisCluster transform = TransformAngleAxisCluster(self.aatopology) measure = MeasureAngleAxisCluster(self.aatopology, transform=transform, permlist=[]) return MinPermDistAACluster(self.aasystem, measure=measure, transform=transform, accuracy=0.1, **kwargs)