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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. | |
| """Tests for relax.cleanup.""" | |
| import io | |
| from absl.testing import absltest | |
| from alphafold.relax import cleanup | |
| from simtk.openmm.app.internal import pdbstructure | |
| def _pdb_to_structure(pdb_str): | |
| handle = io.StringIO(pdb_str) | |
| return pdbstructure.PdbStructure(handle) | |
| def _lines_to_structure(pdb_lines): | |
| return _pdb_to_structure('\n'.join(pdb_lines)) | |
| class CleanupTest(absltest.TestCase): | |
| def test_missing_residues(self): | |
| pdb_lines = ['SEQRES 1 C 3 CYS GLY LEU', | |
| 'ATOM 1 N CYS C 1 -12.262 20.115 60.959 1.00 ' | |
| '19.08 N', | |
| 'ATOM 2 CA CYS C 1 -11.065 20.934 60.773 1.00 ' | |
| '17.23 C', | |
| 'ATOM 3 C CYS C 1 -10.002 20.742 61.844 1.00 ' | |
| '15.38 C', | |
| 'ATOM 4 O CYS C 1 -10.284 20.225 62.929 1.00 ' | |
| '16.04 O', | |
| 'ATOM 5 N LEU C 3 -7.688 18.700 62.045 1.00 ' | |
| '14.75 N', | |
| 'ATOM 6 CA LEU C 3 -7.256 17.320 62.234 1.00 ' | |
| '16.81 C', | |
| 'ATOM 7 C LEU C 3 -6.380 16.864 61.070 1.00 ' | |
| '16.95 C', | |
| 'ATOM 8 O LEU C 3 -6.551 17.332 59.947 1.00 ' | |
| '16.97 O'] | |
| input_handle = io.StringIO('\n'.join(pdb_lines)) | |
| alterations = {} | |
| result = cleanup.fix_pdb(input_handle, alterations) | |
| structure = _pdb_to_structure(result) | |
| residue_names = [r.get_name() for r in structure.iter_residues()] | |
| self.assertCountEqual(residue_names, ['CYS', 'GLY', 'LEU']) | |
| self.assertCountEqual(alterations['missing_residues'].values(), [['GLY']]) | |
| def test_missing_atoms(self): | |
| pdb_lines = ['SEQRES 1 A 1 PRO', | |
| 'ATOM 1 CA PRO A 1 1.000 1.000 1.000 1.00 ' | |
| ' 0.00 C'] | |
| input_handle = io.StringIO('\n'.join(pdb_lines)) | |
| alterations = {} | |
| result = cleanup.fix_pdb(input_handle, alterations) | |
| structure = _pdb_to_structure(result) | |
| atom_names = [a.get_name() for a in structure.iter_atoms()] | |
| self.assertCountEqual(atom_names, ['N', 'CD', 'HD2', 'HD3', 'CG', 'HG2', | |
| 'HG3', 'CB', 'HB2', 'HB3', 'CA', 'HA', | |
| 'C', 'O', 'H2', 'H3', 'OXT']) | |
| missing_atoms_by_residue = list(alterations['missing_heavy_atoms'].values()) | |
| self.assertLen(missing_atoms_by_residue, 1) | |
| atoms_added = [a.name for a in missing_atoms_by_residue[0]] | |
| self.assertCountEqual(atoms_added, ['N', 'CD', 'CG', 'CB', 'C', 'O']) | |
| missing_terminals_by_residue = alterations['missing_terminals'] | |
| self.assertLen(missing_terminals_by_residue, 1) | |
| has_missing_terminal = [r.name for r in missing_terminals_by_residue.keys()] | |
| self.assertCountEqual(has_missing_terminal, ['PRO']) | |
| self.assertCountEqual([t for t in missing_terminals_by_residue.values()], | |
| [['OXT']]) | |
| def test_remove_heterogens(self): | |
| pdb_lines = ['SEQRES 1 A 1 GLY', | |
| 'ATOM 1 CA GLY A 1 0.000 0.000 0.000 1.00 ' | |
| ' 0.00 C', | |
| 'ATOM 2 O HOH A 2 0.000 0.000 0.000 1.00 ' | |
| ' 0.00 O'] | |
| input_handle = io.StringIO('\n'.join(pdb_lines)) | |
| alterations = {} | |
| result = cleanup.fix_pdb(input_handle, alterations) | |
| structure = _pdb_to_structure(result) | |
| self.assertCountEqual([res.get_name() for res in structure.iter_residues()], | |
| ['GLY']) | |
| self.assertEqual(alterations['removed_heterogens'], set(['HOH'])) | |
| def test_fix_nonstandard_residues(self): | |
| pdb_lines = ['SEQRES 1 A 1 DAL', | |
| 'ATOM 1 CA DAL A 1 0.000 0.000 0.000 1.00 ' | |
| ' 0.00 C'] | |
| input_handle = io.StringIO('\n'.join(pdb_lines)) | |
| alterations = {} | |
| result = cleanup.fix_pdb(input_handle, alterations) | |
| structure = _pdb_to_structure(result) | |
| residue_names = [res.get_name() for res in structure.iter_residues()] | |
| self.assertCountEqual(residue_names, ['ALA']) | |
| self.assertLen(alterations['nonstandard_residues'], 1) | |
| original_res, new_name = alterations['nonstandard_residues'][0] | |
| self.assertEqual(original_res.id, '1') | |
| self.assertEqual(new_name, 'ALA') | |
| def test_replace_met_se(self): | |
| pdb_lines = ['SEQRES 1 A 1 MET', | |
| 'ATOM 1 SD MET A 1 0.000 0.000 0.000 1.00 ' | |
| ' 0.00 Se'] | |
| structure = _lines_to_structure(pdb_lines) | |
| alterations = {} | |
| cleanup._replace_met_se(structure, alterations) | |
| sd = [a for a in structure.iter_atoms() if a.get_name() == 'SD'] | |
| self.assertLen(sd, 1) | |
| self.assertEqual(sd[0].element_symbol, 'S') | |
| self.assertCountEqual(alterations['Se_in_MET'], [sd[0].residue_number]) | |
| def test_remove_chains_of_length_one(self): | |
| pdb_lines = ['SEQRES 1 A 1 GLY', | |
| 'ATOM 1 CA GLY A 1 0.000 0.000 0.000 1.00 ' | |
| ' 0.00 C'] | |
| structure = _lines_to_structure(pdb_lines) | |
| alterations = {} | |
| cleanup._remove_chains_of_length_one(structure, alterations) | |
| chains = list(structure.iter_chains()) | |
| self.assertEmpty(chains) | |
| self.assertCountEqual(alterations['removed_chains'].values(), [['A']]) | |
| if __name__ == '__main__': | |
| absltest.main() | |