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import pytest |
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2
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import amd |
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3
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import warnings |
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4
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5
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6
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@pytest.fixture(scope="module") |
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7
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def data_cif_paths(data_dir): |
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8
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cif_names = ["cubic", "T2_experimental"] |
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9
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return {name: str(data_dir / f"{name}.cif") for name in cif_names} |
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10
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11
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12
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@pytest.mark.parametrize("reader", ["gemmi", "ccdc"]) |
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def test_CifReader(reader, data_cif_paths, reference_data): |
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for name in data_cif_paths: |
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try: |
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read_in = list(amd.CifReader(data_cif_paths[name], reader=reader)) |
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except ImportError: |
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18
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pytest.skip( |
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f"Skipping test_CifReader[{reader}] as {reader} failed to " "import." |
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) |
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22
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references = reference_data[name] |
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail( |
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f"There are {len(references)} references, but {len(read_in)}" |
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f"structures were read from {name}." |
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) |
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29
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30
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for s, s_ in zip(read_in, references): |
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31
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if not s._equal_cell_and_motif(s_["PeriodicSet"]): |
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32
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pytest.fail( |
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f"Structure {name}:{s.name} read with CifReader disagrees " |
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"with reference." |
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) |
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37
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38
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def test_CifReader_equiv_structs(data_dir): |
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structs = list(amd.CifReader(data_dir / "eq_sites_test.cif", show_warnings=False)) |
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40
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pdds = [amd.PDD(struct, 100) for struct in structs] |
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41
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42
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if amd.EMD(pdds[0], pdds[1]) > 1e-10: # change |
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pytest.fail( |
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"Asymmetric structure was read differently than identical " |
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"expanded version." |
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) |
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47
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48
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49
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def test_heaviest_component(data_dir, ccdc_enabled): |
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50
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if not ccdc_enabled: |
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pytest.skip("Skipping test_CSDReader as csd-python-api failed to import.") |
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52
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53
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s = amd.CifReader( |
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data_dir / "T2-alpha-solvent.cif", |
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reader="ccdc", |
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heaviest_component=True, |
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57
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).read() |
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58
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59
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if not s.asym_unit.shape[0] == 26: |
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60
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pytest.fail("Heaviest component test failed.") |
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61
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dwiddo /
average-minimum-distance
