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import pytest |
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2
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import os |
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3
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import amd |
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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 cif_paths(root_dir): |
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8
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9
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cif_names = [ |
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10
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'cubic', |
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11
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'T2_experimental', |
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12
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] |
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13
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14
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return {name: os.path.join(root_dir, f'{name}.cif') for name in cif_names} |
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15
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16
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17
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def test_CifReader(cif_paths, reference_data): |
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18
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19
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for name in cif_paths: |
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references = reference_data[name] |
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21
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read_in = list(amd.CifReader(cif_paths[name], show_warnings=True)) |
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22
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23
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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24
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pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
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26
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for s, s_ in zip(read_in, references): |
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if not s == s_: |
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28
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pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
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29
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30
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31
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@pytest.fixture(scope='module') |
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32
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def asym_unit_test_cif_path(root_dir): |
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33
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return os.path.join(root_dir, 'OJIGOG.cif') |
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34
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35
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def test_CifReader_equiv_structs(asym_unit_test_cif_path): |
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36
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37
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pdds = [amd.PDD(struct, 100) for struct in amd.CifReader(asym_unit_test_cif_path, show_warnings=False)] |
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38
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39
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if amd.emd(pdds[0], pdds[1]) > 0: |
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40
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pytest.fail(f'Asymmetric structure was read differently than identical expanded version.') |
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41
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42
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43
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@pytest.fixture(scope='module') |
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44
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def equiv_sites_cif_path(root_dir): |
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45
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return os.path.join(root_dir, 'BABMUQ.cif') |
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46
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47
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def test_equiv_sites(equiv_sites_cif_path): |
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48
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49
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pdds = [amd.PDD(s, 100) for s in amd.CifReader(equiv_sites_cif_path, show_warnings=False)] |
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50
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51
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if amd.PDD_pdist(pdds): |
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52
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pytest.fail(f'Equivalent structures by symmetry differ by PDD.') |
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53
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54
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55
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@pytest.fixture(scope='module') |
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56
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def T2_alpha_cif_path(root_dir): |
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57
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return os.path.join(root_dir, 'T2-alpha-solvent.cif') |
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58
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59
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def test_heaviest_component(T2_alpha_cif_path): |
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60
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61
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if not amd.io._CSD_PYTHON_API_ENABLED: |
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62
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pytest.skip(f'Skipping test_heaviest_component as csd-python-api is not installed.') |
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63
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64
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s = amd.CifReader(T2_alpha_cif_path, |
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65
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reader='ccdc', |
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66
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disorder='all_sites', |
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67
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heaviest_component=True).read_one() |
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68
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69
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if not s.asymmetric_unit.shape[0] == 26: |
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70
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pytest.fail(f'Heaviest component test failed.') |
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71
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dwiddo /
average-minimum-distance
