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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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cif_names = [ |
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9
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'cubic', |
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10
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'T2_experimental', |
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11
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] |
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12
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return {name: os.path.join(root_dir, f'{name}.cif') for name in cif_names} |
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13
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14
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def test_CifReader_ase(cif_paths, reference_data): |
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for name in cif_paths: |
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references = reference_data[name] |
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read_in = list(amd.CifReader(cif_paths[name])) |
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19
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
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21
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22
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for s, s_ in zip(read_in, references): |
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if not s == s_['PeriodicSet']: |
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pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
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26
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27
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View Code Duplication |
def test_CifReader_pymatgen(cif_paths, reference_data): |
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28
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for name in cif_paths: |
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references = reference_data[name] |
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try: |
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read_in = list(amd.CifReader(cif_paths[name], reader='pymatgen')) |
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except ImportError as _: |
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pytest.skip('Skipping pymatgen reader test as pymatgen is not installed.') |
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34
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35
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
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38
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for s, s_ in zip(read_in, references): |
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if not s == s_['PeriodicSet']: |
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pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
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41
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42
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43
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View Code Duplication |
def test_CifReader_gemmi(cif_paths, reference_data): |
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for name in cif_paths: |
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references = reference_data[name] |
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try: |
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read_in = list(amd.CifReader(cif_paths[name], reader='gemmi')) |
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except ImportError as _: |
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pytest.skip('Skipping gemmi reader test as gemmi is not installed.') |
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51
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
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53
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54
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for s, s_ in zip(read_in, references): |
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55
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if not s == s_['PeriodicSet']: |
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56
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pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
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57
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58
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59
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View Code Duplication |
def test_CifReader_ccdc(cif_paths, reference_data): |
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60
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for name in cif_paths: |
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references = reference_data[name] |
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try: |
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63
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read_in = list(amd.CifReader(cif_paths[name], reader='ccdc')) |
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64
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except ImportError as _: |
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pytest.skip('Skipping ccdc reader test as ccdc is not installed.') |
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66
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67
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if (not len(references) == len(read_in)) or len(read_in) == 0: |
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68
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pytest.fail(f'There are {len(references)} references, but {len(read_in)} structures were read.') |
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69
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70
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for s, s_ in zip(read_in, references): |
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71
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if not s == s_['PeriodicSet']: |
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72
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pytest.fail(f'Structure {s.name} read with CifReader disagrees with reference.') |
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73
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74
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75
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@pytest.fixture(scope='module') |
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76
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def asym_unit_test_cif_path(root_dir): |
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77
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return os.path.join(root_dir, 'OJIGOG.cif') |
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78
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79
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def test_CifReader_equiv_structs(asym_unit_test_cif_path): |
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80
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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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81
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if amd.emd(pdds[0], pdds[1]) > 0: |
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82
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pytest.fail(f'Asymmetric structure was read differently than identical expanded version.') |
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83
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84
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85
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@pytest.fixture(scope='module') |
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86
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def equiv_sites_cif_path(root_dir): |
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87
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return os.path.join(root_dir, 'BABMUQ.cif') |
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88
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89
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def test_equiv_sites(equiv_sites_cif_path): |
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90
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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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91
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if amd.PDD_pdist(pdds): |
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pytest.fail(f'Equivalent structures by symmetry differ by PDD.') |
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93
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94
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95
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@pytest.fixture(scope='module') |
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96
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def T2_alpha_cif_path(root_dir): |
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97
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return os.path.join(root_dir, 'T2-alpha-solvent.cif') |
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98
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99
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def test_heaviest_component(T2_alpha_cif_path, ccdc_enabled): |
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100
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101
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if not ccdc_enabled: |
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102
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pytest.skip('Skipping test_CSDReader as csd-python-api is not installed.') |
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103
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104
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s = amd.CifReader( |
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105
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T2_alpha_cif_path, |
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106
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reader='ccdc', |
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107
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disorder='all_sites', |
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108
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heaviest_component=True |
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109
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).read() |
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110
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111
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if not s.asymmetric_unit.shape[0] == 26: |
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112
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pytest.fail(f'Heaviest component test failed.') |
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113
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dwiddo /
average-minimum-distance
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