Lines Matching refs:atomgroup
850 atomgroup = self.atoms
854 x = atomgroup.pack_into_box(inplace=False)
856 x = atomgroup.positions
888 atomgroup = self.atoms.unique
892 x = atomgroup.pack_into_box(inplace=False)
893 centroid = atomgroup.center_of_geometry(pbc=True)
895 x = atomgroup.positions
896 centroid = atomgroup.center_of_geometry(pbc=False)
965 atomgroup = self.atoms.unique
968 atomgroup.universe.trajectory.ts.positions[atomgroup.indices] += vector
1009 atomgroup = self.atoms.unique
1012 atomgroup.translate(-point)
1013 x = atomgroup.universe.trajectory.ts.positions
1014 idx = atomgroup.indices
1017 atomgroup.translate(point)
1184 atomgroup = self.atoms.unique
1186 return atomgroup.pack_into_box(box=box)
1189 objects = [atomgroup.atoms]
1191 objects = atomgroup.residues
1193 objects = atomgroup.segments
1195 objects = atomgroup.fragments
1212 box = atomgroup.dimensions