fix for building ua bead when customised_axes False and UA trans axes when customised_axes True

Author: ioanaapapa

CodeEntropy/levels/axes.py

@@ -225,7 +225,7 @@ def get_UA_axes(self, data_container, index: int, res_position):
                 # only the one residue => use principal axes
                 residue = data_container
                 trans_center = data_container.atoms.center_of_mass(unwrap=True)
-                trans_axes = data_container.atoms.principal_axes
+                trans_axes = data_container.atoms.principal_axes()
             else:
                 # residue of interest has at least one neighbour
                 if res_position == -1:

CodeEntropy/levels/nodes/covariance.py

@@ -223,6 +223,7 @@ def _process_united_atom(
             else:
                 # only one residue
                 res_position = None
+                residue_group = res
             bead_key = (mol_id, "united_atom", local_res_i)
             bead_idx_list = beads.get(bead_key, [])
             if not bead_idx_list:
@@ -475,9 +476,12 @@ def _build_ua_vectors(
                 if res_position == -1:
                     # first residue in group
                     residue = residue_group.residues[0]
-                else:
+                elif res_position == 0 or res_position == 1:
                     # middle or last residue => second in group
                     residue = residue_group.residues[1]
+                else:
+                    # res_position is None bc there is only one residue
+                    residue = residue_group
                 trans_axes = residue.atoms.principal_axes()
                 rot_axes, moi = axes_manager.get_vanilla_axes(bead)
                 center = bead.center_of_mass(unwrap=True)