def make_atom14_dists_bounds()

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

• 38 lines of code
• 13 McCabe index (conditional complexity)

def make_atom14_dists_bounds(overlap_tolerance=1.5,
                             bond_length_tolerance_factor=15):
  """compute upper and lower bounds for bonds to assess violations."""
  restype_atom14_bond_lower_bound = np.zeros([21, 14, 14], np.float32)
  restype_atom14_bond_upper_bound = np.zeros([21, 14, 14], np.float32)
  restype_atom14_bond_stddev = np.zeros([21, 14, 14], np.float32)
  residue_bonds, residue_virtual_bonds, _ = load_stereo_chemical_props()
  for restype, restype_letter in enumerate(restypes):
    resname = restype_1to3[restype_letter]
    atom_list = restype_name_to_atom14_names[resname]

    # create lower and upper bounds for clashes
    for atom1_idx, atom1_name in enumerate(atom_list):
      if not atom1_name:
        continue
      atom1_radius = van_der_waals_radius[atom1_name[0]]
      for atom2_idx, atom2_name in enumerate(atom_list):
        if (not atom2_name) or atom1_idx == atom2_idx:
          continue
        atom2_radius = van_der_waals_radius[atom2_name[0]]
        lower = atom1_radius + atom2_radius - overlap_tolerance
        upper = 1e10
        restype_atom14_bond_lower_bound[restype, atom1_idx, atom2_idx] = lower
        restype_atom14_bond_lower_bound[restype, atom2_idx, atom1_idx] = lower
        restype_atom14_bond_upper_bound[restype, atom1_idx, atom2_idx] = upper
        restype_atom14_bond_upper_bound[restype, atom2_idx, atom1_idx] = upper

    # overwrite lower and upper bounds for bonds and angles
    for b in residue_bonds[resname] + residue_virtual_bonds[resname]:
      atom1_idx = atom_list.index(b.atom1_name)
      atom2_idx = atom_list.index(b.atom2_name)
      lower = b.length - bond_length_tolerance_factor * b.stddev
      upper = b.length + bond_length_tolerance_factor * b.stddev
      restype_atom14_bond_lower_bound[restype, atom1_idx, atom2_idx] = lower
      restype_atom14_bond_lower_bound[restype, atom2_idx, atom1_idx] = lower
      restype_atom14_bond_upper_bound[restype, atom1_idx, atom2_idx] = upper
      restype_atom14_bond_upper_bound[restype, atom2_idx, atom1_idx] = upper
      restype_atom14_bond_stddev[restype, atom1_idx, atom2_idx] = b.stddev
      restype_atom14_bond_stddev[restype, atom2_idx, atom1_idx] = b.stddev
  return {'lower_bound': restype_atom14_bond_lower_bound,  # shape (21,14,14)
          'upper_bound': restype_atom14_bond_upper_bound,  # shape (21,14,14)
          'stddev': restype_atom14_bond_stddev,  # shape (21,14,14)
         }