def _make_rigid_group_constants()

in src/analysis/residue_constants.py [0:0]

• 47 lines of code
• 10 McCabe index (conditional complexity)

def _make_rigid_group_constants():
  """Fill the arrays above."""
  for restype, restype_letter in enumerate(restypes):
    resname = restype_1to3[restype_letter]
    for atomname, group_idx, atom_position in rigid_group_atom_positions[
        resname]:
      atomtype = atom_order[atomname]
      restype_atom37_to_rigid_group[restype, atomtype] = group_idx
      restype_atom37_mask[restype, atomtype] = 1
      restype_atom37_rigid_group_positions[restype, atomtype, :] = atom_position

      atom14idx = restype_name_to_atom14_names[resname].index(atomname)
      restype_atom14_to_rigid_group[restype, atom14idx] = group_idx
      restype_atom14_mask[restype, atom14idx] = 1
      restype_atom14_rigid_group_positions[restype,
                                           atom14idx, :] = atom_position

  for restype, restype_letter in enumerate(restypes):
    resname = restype_1to3[restype_letter]
    atom_positions = {name: np.array(pos) for name, _, pos
                      in rigid_group_atom_positions[resname]}

    # backbone to backbone is the identity transform
    restype_rigid_group_default_frame[restype, 0, :, :] = np.eye(4)

    # pre-omega-frame to backbone (currently dummy identity matrix)
    restype_rigid_group_default_frame[restype, 1, :, :] = np.eye(4)

    # phi-frame to backbone
    mat = _make_rigid_transformation_4x4(
        ex=atom_positions['N'] - atom_positions['CA'],
        ey=np.array([1., 0., 0.]),
        translation=atom_positions['N'])
    restype_rigid_group_default_frame[restype, 2, :, :] = mat

    # psi-frame to backbone
    mat = _make_rigid_transformation_4x4(
        ex=atom_positions['C'] - atom_positions['CA'],
        ey=atom_positions['CA'] - atom_positions['N'],
        translation=atom_positions['C'])
    restype_rigid_group_default_frame[restype, 3, :, :] = mat

    # chi1-frame to backbone
    if chi_angles_mask[restype][0]:
      base_atom_names = chi_angles_atoms[resname][0]
      base_atom_positions = [atom_positions[name] for name in base_atom_names]
      mat = _make_rigid_transformation_4x4(
          ex=base_atom_positions[2] - base_atom_positions[1],
          ey=base_atom_positions[0] - base_atom_positions[1],
          translation=base_atom_positions[2])
      restype_rigid_group_default_frame[restype, 4, :, :] = mat

    # chi2-frame to chi1-frame
    # chi3-frame to chi2-frame
    # chi4-frame to chi3-frame
    # luckily all rotation axes for the next frame start at (0,0,0) of the
    # previous frame
    for chi_idx in range(1, 4):
      if chi_angles_mask[restype][chi_idx]:
        axis_end_atom_name = chi_angles_atoms[resname][chi_idx][2]
        axis_end_atom_position = atom_positions[axis_end_atom_name]
        mat = _make_rigid_transformation_4x4(
            ex=axis_end_atom_position,
            ey=np.array([-1., 0., 0.]),
            translation=axis_end_atom_position)
        restype_rigid_group_default_frame[restype, 4 + chi_idx, :, :] = mat