[NumPy] Remove references to deprecated NumPy type aliases.

This change replaces references to a number of deprecated NumPy type aliases (np.bool, np.int, np.float, np.complex, np.object, np.str) with their recommended replacement (bool, int, float, complex, object, str).

NumPy 1.24 drops the deprecated aliases, so we must remove uses before updating NumPy.

PiperOrigin-RevId: 496396651
Change-Id: Ifbf86edb8c7ba3bf1a427c1b5276e8eb33041ab9

alphafold/common/residue_constants.py

@@ -772,10 +772,10 @@ def _make_rigid_transformation_4x4(ex, ey, translation):
 # and an array with (restype, atomtype, coord) for the atom positions
 # and compute affine transformation matrices (4,4) from one rigid group to the
 # previous group
-restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int)
+restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=int)
 restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
 restype_atom37_rigid_group_positions = np.zeros([21, 37, 3], dtype=np.float32)
-restype_atom14_to_rigid_group = np.zeros([21, 14], dtype=np.int)
+restype_atom14_to_rigid_group = np.zeros([21, 14], dtype=int)
 restype_atom14_mask = np.zeros([21, 14], dtype=np.float32)
 restype_atom14_rigid_group_positions = np.zeros([21, 14, 3], dtype=np.float32)
 restype_rigid_group_default_frame = np.zeros([21, 8, 4, 4], dtype=np.float32)

alphafold/relax/utils.py

@@ -63,7 +63,7 @@ def assert_equal_nonterminal_atom_types(
   """Checks that pre- and post-minimized proteins have same atom set."""
   # Ignore any terminal OXT atoms which may have been added by minimization.
   oxt = residue_constants.atom_order['OXT']
-  no_oxt_mask = np.ones(shape=atom_mask.shape, dtype=np.bool)
+  no_oxt_mask = np.ones(shape=atom_mask.shape, dtype=bool)
   no_oxt_mask[..., oxt] = False
   np.testing.assert_almost_equal(ref_atom_mask[no_oxt_mask],
                                  atom_mask[no_oxt_mask])