Mercurial > repos > galaxy-australia > alphafold2
view docker/alphafold/alphafold/common/residue_constants_test.py @ 1:6c92e000d684 draft
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
| author | galaxy-australia |
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| date | Tue, 01 Mar 2022 02:53:05 +0000 |
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# Copyright 2021 DeepMind Technologies Limited # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """Test that residue_constants generates correct values.""" from absl.testing import absltest from absl.testing import parameterized from alphafold.common import residue_constants import numpy as np class ResidueConstantsTest(parameterized.TestCase): @parameterized.parameters( ('ALA', 0), ('CYS', 1), ('HIS', 2), ('MET', 3), ('LYS', 4), ('ARG', 4), ) def testChiAnglesAtoms(self, residue_name, chi_num): chi_angles_atoms = residue_constants.chi_angles_atoms[residue_name] self.assertLen(chi_angles_atoms, chi_num) for chi_angle_atoms in chi_angles_atoms: self.assertLen(chi_angle_atoms, 4) def testChiGroupsForAtom(self): for k, chi_groups in residue_constants.chi_groups_for_atom.items(): res_name, atom_name = k for chi_group_i, atom_i in chi_groups: self.assertEqual( atom_name, residue_constants.chi_angles_atoms[res_name][chi_group_i][atom_i]) @parameterized.parameters( ('ALA', 5), ('ARG', 11), ('ASN', 8), ('ASP', 8), ('CYS', 6), ('GLN', 9), ('GLU', 9), ('GLY', 4), ('HIS', 10), ('ILE', 8), ('LEU', 8), ('LYS', 9), ('MET', 8), ('PHE', 11), ('PRO', 7), ('SER', 6), ('THR', 7), ('TRP', 14), ('TYR', 12), ('VAL', 7) ) def testResidueAtoms(self, atom_name, num_residue_atoms): residue_atoms = residue_constants.residue_atoms[atom_name] self.assertLen(residue_atoms, num_residue_atoms) def testStandardAtomMask(self): with self.subTest('Check shape'): self.assertEqual(residue_constants.STANDARD_ATOM_MASK.shape, (21, 37,)) with self.subTest('Check values'): str_to_row = lambda s: [c == '1' for c in s] # More clear/concise. np.testing.assert_array_equal( residue_constants.STANDARD_ATOM_MASK, np.array([ # NB This was defined by c+p but looks sane. str_to_row('11111 '), # ALA str_to_row('111111 1 1 11 1 '), # ARG str_to_row('111111 11 '), # ASP str_to_row('111111 11 '), # ASN str_to_row('11111 1 '), # CYS str_to_row('111111 1 11 '), # GLU str_to_row('111111 1 11 '), # GLN str_to_row('111 1 '), # GLY str_to_row('111111 11 1 1 '), # HIS str_to_row('11111 11 1 '), # ILE str_to_row('111111 11 '), # LEU str_to_row('111111 1 1 1 '), # LYS str_to_row('111111 11 '), # MET str_to_row('111111 11 11 1 '), # PHE str_to_row('111111 1 '), # PRO str_to_row('11111 1 '), # SER str_to_row('11111 1 1 '), # THR str_to_row('111111 11 11 1 1 11 '), # TRP str_to_row('111111 11 11 11 '), # TYR str_to_row('11111 11 '), # VAL str_to_row(' '), # UNK ])) with self.subTest('Check row totals'): # Check each row has the right number of atoms. for row, restype in enumerate(residue_constants.restypes): # A, R, ... long_restype = residue_constants.restype_1to3[restype] # ALA, ARG, ... atoms_names = residue_constants.residue_atoms[ long_restype] # ['C', 'CA', 'CB', 'N', 'O'], ... self.assertLen(atoms_names, residue_constants.STANDARD_ATOM_MASK[row, :].sum(), long_restype) def testAtomTypes(self): self.assertEqual(residue_constants.atom_type_num, 37) self.assertEqual(residue_constants.atom_types[0], 'N') self.assertEqual(residue_constants.atom_types[1], 'CA') self.assertEqual(residue_constants.atom_types[2], 'C') self.assertEqual(residue_constants.atom_types[3], 'CB') self.assertEqual(residue_constants.atom_types[4], 'O') self.assertEqual(residue_constants.atom_order['N'], 0) self.assertEqual(residue_constants.atom_order['CA'], 1) self.assertEqual(residue_constants.atom_order['C'], 2) self.assertEqual(residue_constants.atom_order['CB'], 3) self.assertEqual(residue_constants.atom_order['O'], 4) self.assertEqual(residue_constants.atom_type_num, 37) def testRestypes(self): three_letter_restypes = [ residue_constants.restype_1to3[r] for r in residue_constants.restypes] for restype, exp_restype in zip( three_letter_restypes, sorted(residue_constants.restype_1to3.values())): self.assertEqual(restype, exp_restype) self.assertEqual(residue_constants.restype_num, 20) def testSequenceToOneHotHHBlits(self): one_hot = residue_constants.sequence_to_onehot( 'ABCDEFGHIJKLMNOPQRSTUVWXYZ-', residue_constants.HHBLITS_AA_TO_ID) exp_one_hot = np.array( [[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]) np.testing.assert_array_equal(one_hot, exp_one_hot) def testSequenceToOneHotStandard(self): one_hot = residue_constants.sequence_to_onehot( 'ARNDCQEGHILKMFPSTWYV', residue_constants.restype_order) np.testing.assert_array_equal(one_hot, np.eye(20)) def testSequenceToOneHotUnknownMapping(self): seq = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' expected_out = np.zeros([26, 21]) for row, position in enumerate( [0, 20, 4, 3, 6, 13, 7, 8, 9, 20, 11, 10, 12, 2, 20, 14, 5, 1, 15, 16, 20, 19, 17, 20, 18, 20]): expected_out[row, position] = 1 aa_types = residue_constants.sequence_to_onehot( sequence=seq, mapping=residue_constants.restype_order_with_x, map_unknown_to_x=True) self.assertTrue((aa_types == expected_out).all()) @parameterized.named_parameters( ('lowercase', 'aaa'), # Insertions in A3M. ('gaps', '---'), # Gaps in A3M. ('dots', '...'), # Gaps in A3M. ('metadata', '>TEST'), # FASTA metadata line. ) def testSequenceToOneHotUnknownMappingError(self, seq): with self.assertRaises(ValueError): residue_constants.sequence_to_onehot( sequence=seq, mapping=residue_constants.restype_order_with_x, map_unknown_to_x=True) if __name__ == '__main__': absltest.main()