| import shutil |
| import tempfile |
| import gzip |
| from pathlib import Path |
|
|
| import pytest |
|
|
| from haddock.libs.libontology import Format, PDBFile, Persistent |
| from haddock.modules.refinement.flexref import ( |
| DEFAULT_CONFIG as DEFAULT_FLEXREF_CONFIG, |
| ) |
| from haddock.modules.refinement.flexref import HaddockModule as FlexrefModule |
|
|
| from integration_tests import GOLDEN_DATA |
|
|
|
|
| @pytest.fixture |
| def flexref_module(): |
| with tempfile.TemporaryDirectory() as tmpdir: |
| flexref = FlexrefModule( |
| order=0, path=Path(tmpdir), initial_params=DEFAULT_FLEXREF_CONFIG |
| ) |
| yield flexref |
|
|
|
|
| class MockPreviousIO: |
| def __init__(self, path): |
| self.path = path |
|
|
| def retrieve_models(self, crossdock: bool = False): |
| shutil.copy( |
| Path(GOLDEN_DATA, "2oob.pdb"), |
| Path(self.path, "2oob.pdb"), |
| ) |
| shutil.copy( |
| Path(GOLDEN_DATA, "2oob_A.psf"), |
| Path(self.path, "2oob_A.psf"), |
| ) |
|
|
| shutil.copy( |
| Path(GOLDEN_DATA, "2oob_B.psf"), |
| Path(self.path, "2oob_B.psf"), |
| ) |
|
|
| model = PDBFile( |
| file_name="2oob.pdb", |
| path=self.path, |
| topology=( |
| Persistent( |
| file_name="2oob_A.psf", |
| path=self.path, |
| file_type=Format.TOPOLOGY, |
| ), |
| Persistent( |
| file_name="2oob_B.psf", |
| path=self.path, |
| file_type=Format.TOPOLOGY, |
| ), |
| ), |
| ) |
|
|
| model.seed = 42 |
|
|
| return [model] |
|
|
| def output(self): |
| return None |
|
|
|
|
| def test_flexref_defaults(flexref_module, calc_fnat): |
|
|
| flexref_module.previous_io = MockPreviousIO(path=flexref_module.path) |
|
|
| flexref_module.run() |
|
|
| assert Path(flexref_module.path, "flexref_1.pdb").exists() |
|
|
| fnat = calc_fnat( |
| model=Path(flexref_module.path, "flexref_1.pdb"), |
| native=Path(GOLDEN_DATA, "2oob.pdb"), |
| ) |
|
|
| assert fnat == pytest.approx(0.9, abs=0.1) |
|
|
|
|
| def test_flexref_fle(flexref_module, calc_fnat): |
|
|
| flexref_module.previous_io = MockPreviousIO(path=flexref_module.path) |
|
|
| flexref_module.params["nfle "] = 1 |
|
|
| flexref_module.params["fle_sta_1 "] = 66 |
| flexref_module.params["fle_end_1 "] = 77 |
| flexref_module.params["fle_seg_1 "] = "B" |
| flexref_module.params["log_level"] = "verbose" |
| flexref_module.params["debug"] = True |
|
|
| flexref_module.run() |
|
|
| assert Path(flexref_module.path, "flexref_1.pdb").exists() |
| assert Path(flexref_module.path, "flexref_1.out.gz").exists() |
| file_content = gzip.open(Path(flexref_module.path, "flexref_1.out.gz"), 'rt').read() |
| assert '$SAPROTOCOL.TADFACTOR set to 4.00000' in file_content |
|
|
| fnat = calc_fnat( |
| model=Path(flexref_module.path, "flexref_1.pdb"), |
| native=Path(GOLDEN_DATA, "2oob.pdb"), |
| ) |
|
|
| assert fnat == pytest.approx(0.9, abs=0.1) |
|
|
|
|
| def test_flexref_mutliple_fle(flexref_module, calc_fnat): |
|
|
| flexref_module.previous_io = MockPreviousIO(path=flexref_module.path) |
|
|
| flexref_module.params["nfle "] = 2 |
|
|
| flexref_module.params["fle_sta_1 "] = 66 |
| flexref_module.params["fle_end_1 "] = 77 |
| flexref_module.params["fle_seg_1 "] = "B" |
|
|
| flexref_module.params["fle_sta_2 "] = 41 |
| flexref_module.params["fle_end_2 "] = 47 |
| flexref_module.params["fle_seg_2 "] = "B" |
|
|
| flexref_module.params["debug"] = True |
|
|
| flexref_module.run() |
|
|
| assert Path(flexref_module.path, "flexref_1.pdb").exists() |
| assert Path(flexref_module.path, "flexref_1.out.gz").exists() |
|
|
| fnat = calc_fnat( |
| model=Path(flexref_module.path, "flexref_1.pdb"), |
| native=Path(GOLDEN_DATA, "2oob.pdb"), |
| ) |
|
|
| assert fnat == pytest.approx(0.9, abs=0.1) |
|
|
