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BUG: Investigate potential PLAMS-related failures #258

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BvB93 opened this issue Sep 1, 2022 · 0 comments
Open

BUG: Investigate potential PLAMS-related failures #258

BvB93 opened this issue Sep 1, 2022 · 0 comments
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bug Something isn't working
Milestone
CAT 1.1.1

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@BvB93
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BvB93 commented Sep 1, 2022

As of de99e15 (e.g. https://github.com/nlesc-nano/CAT/runs/8132805178?check_suite_focus=true) the pre-release tests show coordinate-related failures, presumably related to some change in the dev version of PLAMS.

CI output 
============================= test session starts ==============================
platform linux -- Python 3.10.6, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/runner/work/CAT/CAT, configfile: setup.cfg, testpaths: CAT, tests
plugins: cov-3.0.0, mock-3.8.2
collected 201 items / 1 deselected / 200 selected

CAT/recipes.py .                                                         [  0%]
CAT/utils.py .                                                           [  1%]
CAT/attachment/as_array.py .                                             [  1%]
CAT/attachment/distribution.py .                                         [  2%]
CAT/attachment/distribution_utils.py .                                   [  2%]
CAT/attachment/mol_split_cm.py .                                         [  3%]
CAT/attachment/remove_atoms_cm.py .                                      [  3%]
CAT/data_handling/mol_import.py .                                        [  4%]
CAT/data_handling/validate_mol.py .                                      [  4%]
CAT/workflows/workflow.py ..                                             [  5%]
tests/test_CAT.py .                                                      [  6%]
tests/test_distribution.py .                                             [  6%]
tests/test_distribution_brute.py .                                       [  7%]
tests/test_edge_dist.py ...                                              [  8%]
tests/test_entry_points.py .xFxFFFFFxFxFFFFFFFF                          [ 18%]
tests/test_frozen_settings.py ....                                       [ 20%]
tests/test_gen_job_manager.py ..                                         [ 21%]
tests/test_indices.py F                                                  [ 22%]
tests/test_ligand_anchoring.py ....FFFFFF.F............................. [ 42%]
........................                                                 [ 54%]
tests/test_ligand_attach.py ..FFFF.F.F.F.F.                              [ 62%]
tests/test_ligand_opt.py .                                               [ 62%]
tests/test_logger.py .                                                   [ 63%]
tests/test_mol_import.py .........F                                      [ 68%]
tests/test_mol_str_parser.py ........................                    [ 80%]
tests/test_mol_to_file.py .                                              [ 80%]
tests/test_mol_utils.py .......F.                                        [ 85%]
tests/test_multi_ligand.py x                                             [ 85%]
tests/test_perp_surface.py .                                             [ 86%]
tests/test_schemas.py ..........                                         [ 91%]
tests/test_settings_dataframe.py .                                       [ 91%]
tests/test_sphinx.py .                                                   [ 92%]
tests/test_thermo_chem.py ..                                             [ 93%]
tests/test_thread_safe.py .                                              [ 93%]
tests/test_utils.py .......                                              [ 97%]
tests/test_validate_input.py ..                                          [ 98%]
tests/test_validate_mol.py ....                                          [100%]

=================================== FAILURES ===================================
___________________ TestMain.test_mol[CCCCCCCCPCCCCCCCC@P17] ___________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 52 (0%)
E   Mismatched atoms:              50 / 52 (96%)
E   Mismatched atomic symbols:     15 / 52 (29%)
E   Atoms max absolute difference: 0.3118937474148371
E   Atoms max relative difference: 1.0
E    actual: array([[ 3.98 , -2.056, -2.91 ],
E          [ 3.984,  2.709,  2.265],
E          [ 4.657, -3.314, -3.434],...
E    desired: array([[ 3.983, -2.185, -2.789],
E          [ 3.971,  2.846,  2.078],
E          [ 4.668, -3.487, -3.213],...
_____________ TestMain.test_mol[CCCCCCCCCC[N+][C][C]CCCCCCCCCC@N1] _____________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 71 (0%)
E   Mismatched atoms:              70 / 71 (99%)
E   Mismatched atomic symbols:     23 / 71 (32%)
E   Atoms max absolute difference: 1.4658656167658575
E   Atoms max relative difference: 83.65651864559885
E    actual: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 5.9100e-01, -2.0000e-03, -1.3780e+00],
E          [ 7.7600e-01, -8.6700e-01,  9.5500e-01],...
E    desired: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 7.7600e-01,  3.1300e-01, -1.2520e+00],
E          [ 5.9200e-01, -1.1470e+00,  7.6400e-01],...
________________ TestMain.test_mol[CCCCCCCCC[CCCCCC]C[=O]O@O17] ________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 50 (0%)
E   Mismatched atoms:              50 / 50 (100%)
E   Mismatched atomic symbols:     18 / 50 (36%)
E   Atoms max absolute difference: 1.9054727118818675
E   Atoms max relative difference: 57.82825215885746
E    actual: array([[ 2.323,  0.648, -0.703],
E          [ 2.906,  0.569,  0.727],
E          [ 2.567, -0.645, -1.529],...
E    desired: array([[ 2.478,  0.273,  0.279],
E          [ 3.405,  0.111, -0.95 ],
E          [ 3.061,  1.223,  1.363],...
___________________ TestMain.test_mol[CCCCCCCCNCCCCCCCC@N17] ___________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 52 (0%)
E   Mismatched atoms:              52 / 52 (100%)
E   Mismatched atomic symbols:     17 / 52 (33%)
E   Atoms max absolute difference: 0.03831557434947497
E   Atoms max relative difference: 1.0
E    actual: array([[ 3.361,  3.737,  0.018],
E          [ 3.635, -3.377, -0.796],
E          [ 4.132,  4.726,  0.898],...
E    desired: array([[ 3.36 ,  3.637,  0.857],
E          [ 3.635, -3.111, -1.535],
E          [ 4.132,  4.403,  1.938],...
_______________________ TestMain.test_mol[CCCCCCCCO@O9] ________________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 27 (0%)
E   Mismatched atoms:              5 / 27 (19%)
E   Mismatched atomic symbols:     2 / 27 (7%)
E   Atoms max absolute difference: 0.013943408383097267
E   Atoms max relative difference: 1.0
E    actual: array([[ 4.911, -0.041, -0.474],
E          [ 6.244,  0.151,  0.259],
E          [ 3.725,  0.151,  0.479],...
E    desired: array([[ 4.911, -0.098, -0.465],
E          [ 6.244,  0.181,  0.239],
E          [ 3.725,  0.208,  0.458],...
_______________________ TestMain.test_mol[CCCCCCCCN@N9] ________________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 28 (0%)
E   Mismatched atoms:              28 / 28 (100%)
E   Mismatched atomic symbols:     9 / 28 (32%)
E   Atoms max absolute difference: 0.7988422625040431
E   Atoms max relative difference: 433.6202146821628
E    actual: array([[ 4.986,  0.411,  0.031],
E          [ 6.309, -0.361, -0.027],
E          [ 3.788, -0.544, -0.04 ],...
E    desired: array([[ 4.953,  0.479,  0.188],
E          [ 6.297, -0.162, -0.179],
E          [ 3.781, -0.402, -0.261],...
___________________ TestMain.test_mol[CCCCCCCCOCCCCCCCC@O17] ___________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 51 (0%)
E   Mismatched atoms:              51 / 51 (100%)
E   Mismatched atomic symbols:     17 / 51 (33%)
E   Atoms max absolute difference: 10.619717625139197
E   Atoms max relative difference: 18.252201013628
E    actual: array([[ 2.201,  2.905,  3.339],
E          [ 1.521, -3.803, -2.731],
E          [ 2.38 ,  4.348,  3.827],...
E    desired: array([[ 1.521,  3.398, -3.221],
E          [ 2.199, -3.828,  2.224],
E          [ 2.453,  4.595, -3.447],...
___________________ TestMain.test_mol[CCCCCCCCC[=O][O-]@O11] ___________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 28 (0%)
E   Mismatched atoms:              28 / 28 (100%)
E   Mismatched atomic symbols:     11 / 28 (39%)
E   Atoms max absolute difference: 0.587513165061302
E   Atoms max relative difference: 2.876356200754237
E    actual: array([[ 5.619, -0.466, -0.299],
E          [ 6.967, -0.354,  0.423],
E          [ 4.538,  0.344,  0.426],...
E    desired: array([[ 5.6190e+00,  5.5300e-01,  4.0000e-03],
E          [ 6.9670e+00,  7.3000e-02, -5.4700e-01],
E          [ 4.5380e+00, -5.1900e-01, -1.7600e-01],...
_______________________ TestMain.test_mol[CCCCCCCCS@S9] ________________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 27 (0%)
E   Mismatched atoms:              18 / 27 (67%)
E   Mismatched atomic symbols:     6 / 27 (22%)
E   Atoms max absolute difference: 0.035392630152596964
E   Atoms max relative difference: 1.7266079468597542
E    actual: array([[ 5.259, -0.288, -0.374],
E          [ 6.619,  0.267,  0.067],
E          [ 4.11 ,  0.464,  0.31 ],...
E    desired: array([[ 5.259, -0.166, -0.441],
E          [ 6.619,  0.236,  0.142],
E          [ 4.11 ,  0.353,  0.432],...
_____________ TestMain.test_mol[cis-CCCCCCCCC=CCCCCCCCC[=O]O@O19] ______________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 54 (0%)
E   Mismatched atoms:              53 / 54 (98%)
E   Mismatched atomic symbols:     20 / 54 (37%)
E   Atoms max absolute difference: 2.4421088146280545
E   Atoms max relative difference: 952.6685533634258
E    actual: array([[ 1.6038e+01,  3.7300e-01, -1.0930e+00],
E          [ 1.6670e+01,  1.7320e+00, -1.4160e+00],
E          [ 5.5990e+00, -8.8700e-01,  6.0200e-01],...
E    desired: array([[ 1.6038e+01,  8.1700e-01, -8.1700e-01],
E          [ 1.6670e+01,  5.0700e-01, -2.1790e+00],
E          [ 5.5990e+00, -1.4900e-01,  1.0610e+00],...
________________ TestMain.test_mol[CCCCCCC[CCCCC]CCCC[=O]O@O17] ________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 50 (0%)
E   Mismatched atoms:              50 / 50 (100%)
E   Mismatched atomic symbols:     18 / 50 (36%)
E   Atoms max absolute difference: 2.594354081674596
E   Atoms max relative difference: 28.02485986668024
E    actual: array([[ 5.784, -0.236,  0.075],
E          [ 7.   , -1.201,  0.095],
E          [ 5.652,  0.515,  1.435],...
E    desired: array([[ 5.709, -0.312,  0.028],
E          [ 6.885, -1.114, -0.584],
E          [ 6.111,  0.323,  1.397],...
___________________ TestMain.test_mol[CCCCCCCCSCCCCCCCC@S17] ___________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 51 (0%)
E   Mismatched atoms:              51 / 51 (100%)
E   Mismatched atomic symbols:     17 / 51 (33%)
E   Atoms max absolute difference: 1.2238138857338379
E   Atoms max relative difference: 117.03113510631259
E    actual: array([[ 3.684,  2.057,  3.173],
E          [ 4.014, -2.649, -2.228],
E          [ 4.643,  3.217,  3.465],...
E    desired: array([[ 4.014,  0.722,  3.385],
E          [ 3.684, -1.834, -3.307],
E          [ 4.619,  1.577,  4.506],...
_______________________ TestMain.test_mol[CCCCCCCCP@P9] ________________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 28 (0%)
E   Mismatched atoms:              26 / 28 (93%)
E   Mismatched atomic symbols:     8 / 28 (29%)
E   Atoms max absolute difference: 0.1396562958185361
E   Atoms max relative difference: 2.707397040483221
E    actual: array([[ 5.2750e+00,  3.9300e-01, -6.0000e-03],
E          [ 6.6100e+00, -3.8400e-01,  3.4000e-02],
E          [ 4.0810e+00, -5.4400e-01, -2.1000e-02],...
E    desired: array([[ 5.273,  0.363,  0.101],
E          [ 6.597, -0.367, -0.098],
E          [ 4.085, -0.523, -0.19 ],...
_____________________ TestMain.test_mol[O=C[O]c1ccccc1@O8] _____________________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 15 (0%)
E   Mismatched atoms:              15 / 15 (100%)
E   Mismatched atomic symbols:     9 / 15 (60%)
E   Atoms max absolute difference: 3.206923323132984
E   Atoms max relative difference: 29.48696648245082
E    actual: array([[ 2.485, -0.165,  0.053],
E          [ 2.619,  1.169, -0.373],
E          [ 3.646, -0.924,  0.295],...
E    desired: array([[ 2.485,  0.04 ,  0.169],
E          [ 3.646,  0.221,  0.944],
E          [ 2.619, -0.279, -1.195],...
____________ TestMain.test_mol[trans-CCCCCCCCC=CCCCCCCCC[=O]O@O19] _____________
tests/test_entry_points.py:90: in test_mol
    assert_mol_allclose(mol, mol_ref, rtol=0, atol=10**-2)
E   AssertionError: 
E   Not equal to tolerance rtol=0, atol=0.01
E   
E   Mismatched lattice:            False
E   Mismatched bonds:              0 / 54 (0%)
E   Mismatched atoms:              54 / 54 (100%)
E   Mismatched atomic symbols:     20 / 54 (37%)
E   Atoms max absolute difference: 0.18246937996604368
E   Atoms max relative difference: 3.958486001605863
E    actual: array([[ 1.6878e+01, -5.1400e-01, -9.2900e-01],
E          [ 1.8059e+01,  4.5000e-02, -1.7310e+00],
E          [ 5.6810e+00,  3.5100e-01,  3.1400e-01],...
E    desired: array([[ 1.6878e+01,  4.8000e-02, -1.0600e+00],
E          [ 1.8059e+01,  9.4500e-01, -1.4520e+00],
E          [ 5.6810e+00,  1.3500e-01,  4.5100e-01],...
___________________________________ test_cat ___________________________________
tests/test_indices.py:32: in test_cat
    assertion.eq(set(ligand_df.index), ref)
E   AssertionError: output = eq(a, b); assert output
E   
E   exception: AssertionError = 'None'
E   
E   output: bool = False
E   a: set = {('CCCCCCC(=O)O', 'O8'), ('CCCNCCC(=O)O', 'C5'), ('CCCOCCC(=O)O', 'C5')}
E   b: set = {('CCCCCCC(=O)[O-]', 'O8'), ('CCCNCCC(=O)O', 'C5'), ('CCCOCCC(=O)O', 'C5')}
------------------------------ Captured log call -------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCCCCCC[=O]O@O8 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCCCCCC[=O]O@O8 optimization is successful
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCCOCCC[=O]O@C5 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCCOCCC[=O]O@C5 optimization is successful
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCCNCCC[=O]O@C5 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCCNCCC[=O]O@C5 optimization is successful
INFO     CAT:base.py:132 Total elapsed time: 1.6784 sec
__________________ TestFindSubstructure.test_options[remove] ___________________
tests/test_ligand_anchoring.py:183: in test_options
    np.testing.assert_allclose(coords, coords_ref, atol=10e-3)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0.01
E   
E   Mismatched elements: 53 / 60 (88.3%)
E   Max absolute difference: 0.52868769
E   Max relative difference: 4.65620726
E    x: array([[-3.132869,  0.576224, -0.400106],
E          [-1.650983,  0.806733, -0.434622],
E          [-0.857199, -0.396575,  0.067837],...
E    y: array([[-3.116677,  0.60374 , -0.326707],
E          [-1.635916,  0.841603, -0.414185],
E          [-0.838439, -0.394686,  0.011993],...
________________ TestFindSubstructure.test_options[kind_first] _________________
tests/test_ligand_anchoring.py:183: in test_options
    np.testing.assert_allclose(coords, coords_ref, atol=10e-3)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0.01
E   
E   Mismatched elements: 53 / 60 (88.3%)
E   Max absolute difference: 0.52868769
E   Max relative difference: 4.65620726
E    x: array([[-3.132869,  0.576224, -0.400106],
E          [-1.650983,  0.806733, -0.434622],
E          [-0.857199, -0.396575,  0.067837],...
E    y: array([[-3.116677,  0.60374 , -0.326707],
E          [-1.635916,  0.841603, -0.414185],
E          [-0.838439, -0.394686,  0.011993],...
_________________ TestFindSubstructure.test_options[kind_mean] _________________
tests/test_ligand_anchoring.py:183: in test_options
    np.testing.assert_allclose(coords, coords_ref, atol=10e-3)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0.01
E   
E   Mismatched elements: 53 / 60 (88.3%)
E   Max absolute difference: 0.52868769
E   Max relative difference: 4.65620726
E    x: array([[-3.132869,  0.576224, -0.400106],
E          [-1.650983,  0.806733, -0.434622],
E          [-0.857199, -0.396575,  0.067837],...
E    y: array([[-3.116677,  0.60374 , -0.326707],
E          [-1.635916,  0.841603, -0.414185],
E          [-0.838439, -0.394686,  0.011993],...
____________ TestFindSubstructure.test_options[kind_mean_translate] ____________
tests/test_ligand_anchoring.py:183: in test_options
    np.testing.assert_allclose(coords, coords_ref, atol=10e-3)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0.01
E   
E   Mismatched elements: 53 / 60 (88.3%)
E   Max absolute difference: 0.52868769
E   Max relative difference: 4.65620726
E    x: array([[-3.132869,  0.576224, -0.400106],
E          [-1.650983,  0.806733, -0.434622],
E          [-0.857199, -0.396575,  0.067837],...
E    y: array([[-3.116677,  0.60374 , -0.326707],
E          [-1.635916,  0.841603, -0.414185],
E          [-0.838439, -0.394686,  0.011993],...
___________________ TestFindSubstructure.test_options[angle] ___________________
tests/test_ligand_anchoring.py:183: in test_options
    np.testing.assert_allclose(coords, coords_ref, atol=10e-3)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0.01
E   
E   Mismatched elements: 53 / 60 (88.3%)
E   Max absolute difference: 0.52868769
E   Max relative difference: 4.65620726
E    x: array([[-3.132869,  0.576224, -0.400106],
E          [-1.650983,  0.806733, -0.434622],
E          [-0.857199, -0.396575,  0.067837],...
E    y: array([[-3.116677,  0.60374 , -0.326707],
E          [-1.635916,  0.841603, -0.414185],
E          [-0.838439, -0.394686,  0.011993],...
_______________________ TestFindSubstructure.test_split ________________________
tests/test_ligand_anchoring.py:200: in test_split
    assertion.eq(mol1.properties.smiles, '[NH-]C(O)C(=O)O')
E   AssertionError: output = eq(a, b); assert output
E   
E   exception: AssertionError = 'None'
E   
E   output: bool = False
E   a: str = 'NC(O)C(=O)O'
E   b: str = '[NH-]C(O)C(=O)O'
__________________________ test_init_ligand_anchoring __________________________
tests/test_ligand_anchoring.py:245: in test_init_ligand_anchoring
    assertion.eq(df.index.tolist(), idx)
E   AssertionError: output = eq(a, b); assert output
E   
E   exception: AssertionError = 'None'
E   
E   output: bool = False
E   a: list = [('CO', 'O2'), ('CCO', 'O3')]
E   b: list = [('C[O-]', 'O2'), ('CC[O-]', 'O3')]
------------------------------ Captured log call -------------------------------
INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
______________________ TestDihedral.test_atoms[dihed_45] _______________________
tests/test_ligand_attach.py:132: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 135 / 915 (14.8%)
E   Max absolute difference: 0.002
E   Max relative difference: 0.00035286
E    x: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
E    y: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CC[=O]O@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CC[=O]O@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.7664 sec
____________________ TestDihedral.test_atoms[dihed_45_deg] _____________________
tests/test_ligand_attach.py:132: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 135 / 915 (14.8%)
E   Max absolute difference: 0.002
E   Max relative difference: 0.00035286
E    x: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
E    y: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CC[=O]O@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CC[=O]O@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.7804 sec
______________________ TestDihedral.test_atoms[dihed_180] ______________________
tests/test_ligand_attach.py:132: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 151 / 915 (16.5%)
E   Max absolute difference: 0.001
E   Max relative difference: 0.0003095
E    x: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
E    y: array([[12.318, 13.562, 10.963],
E          [12.417, 10.883, 14.27 ],
E          [10.032, 14.341, 14.385],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CC[=O]O@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CC[=O]O@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.7596 sec
______________________ TestAllignment.test_atoms[sphere] _______________________
tests/test_ligand_attach.py:174: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.atoms_ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 418 / 645 (64.8%)
E   Max absolute difference: 0.316
E   Max relative difference: 8.35294118
E    x: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 1.0000e+00,  0.0000e+00,  0.0000e+00],
E          [-1.0000e+00,  0.0000e+00,  0.0000e+00],...
E    y: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 1.0000e+00,  0.0000e+00,  0.0000e+00],
E          [-1.0000e+00,  0.0000e+00,  0.0000e+00],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCO@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCO@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.5938 sec
______________________ TestAllignment.test_atoms[surface] ______________________
tests/test_ligand_attach.py:174: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.atoms_ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 457 / 645 (70.9%)
E   Max absolute difference: 0.005
E   Max relative difference: 0.05
E    x: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 1.0000e+00,  0.0000e+00,  0.0000e+00],
E          [-1.0000e+00,  0.0000e+00,  0.0000e+00],...
E    y: array([[ 0.0000e+00,  0.0000e+00,  0.0000e+00],
E          [ 1.0000e+00,  0.0000e+00,  0.0000e+00],
E          [-1.0000e+00,  0.0000e+00,  0.0000e+00],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCO@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCO@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.5983 sec
___________________ TestAllignment.test_atoms[sphere_invert] ___________________
tests/test_ligand_attach.py:174: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.atoms_ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 430 / 645 (66.7%)
E   Max absolute difference: 3.068
E   Max relative difference: 12.16157205
E    x: array([[ 0.000e+00,  0.000e+00,  0.000e+00],
E          [ 1.000e+00,  0.000e+00,  0.000e+00],
E          [-1.000e+00,  0.000e+00,  0.000e+00],...
E    y: array([[ 0.000e+00,  0.000e+00,  0.000e+00],
E          [ 1.000e+00,  0.000e+00,  0.000e+00],
E          [-1.000e+00,  0.000e+00,  0.000e+00],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCO@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCO@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.6097 sec
__________________ TestAllignment.test_atoms[surface_invert] ___________________
tests/test_ligand_attach.py:174: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.atoms_ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 432 / 645 (67%)
E   Max absolute difference: 0.005
E   Max relative difference: 0.25
E    x: array([[ 0.000e+00,  0.000e+00,  0.000e+00],
E          [ 1.000e+00,  0.000e+00,  0.000e+00],
E          [-1.000e+00,  0.000e+00,  0.000e+00],...
E    y: array([[ 0.000e+00,  0.000e+00,  0.000e+00],
E          [ 1.000e+00,  0.000e+00,  0.000e+00],
E          [-1.000e+00,  0.000e+00,  0.000e+00],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCO@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCO@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.6109 sec
________________________ TestCoreAnchor.test_atoms[HCl] ________________________
tests/test_ligand_attach.py:233: in test_atoms
    np.testing.assert_allclose(atoms.coords, output.atoms_ref.coords)
E   AssertionError: 
E   Not equal to tolerance rtol=1e-07, atol=0
E   
E   Mismatched elements: 69 / 543 (12.7%)
E   Max absolute difference: 0.005
E   Max relative difference: 3.
E    x: array([[-2.2890e+00, -1.4400e+00,  4.4400e+00],
E          [-3.1800e-01,  2.3290e+00,  4.3260e+00],
E          [-3.9990e+00,  1.7730e+00,  2.3770e+00],...
E    y: array([[-2.2890e+00, -1.4400e+00,  4.4400e+00],
E          [-3.1800e-01,  2.3290e+00,  4.3260e+00],
E          [-3.9990e+00,  1.7730e+00,  2.3770e+00],...
------------------------------ Captured log setup ------------------------------
INFO     CAT:base.py:101 Starting CAT (version: 1.0.1.dev0)
INFO     CAT:base.py:103 The optional Nano-CAT package was successfully found (version: 0.7.2.dev0)
INFO     CAT:base.py:110 The optional Data-CAT package was successfully found (version: 0.7.3.dev0)

INFO     CAT:create_database.py:72 ligand_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating ligand database
INFO     CAT:create_database.py:72 qd_database.csv not found in /home/runner/work/CAT/CAT/tests/test_files/database, creating qd database
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'core_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'ligand_no_opt'
INFO     CAT:create_database.py:251 Updating h5py Dataset to data-CAT >= 0.4 style: 'qd_no_opt'
INFO     CAT:workflow.py:396 Starting ligand geometry optimization
INFO     CAT:ligand_opt.py:162 UFFGetMoleculeForceField: CCO@O3 optimization has started
INFO     CAT:ligand_opt.py:172 UFFGetMoleculeForceField: CCO@O3 optimization is successful
INFO     CAT:workflow.py:396 Starting quantum dot construction
INFO     CAT:workflow.py:422 Finishing quantum dot construction

INFO     CAT:base.py:132 Total elapsed time: 1.7396 sec
______________________________ test_set_mol_prop _______________________________
tests/test_mol_import.py:160: in test_set_mol_prop
    assertion.eq(at.properties, ref1)
E   AssertionError: output = eq(a, b); assert output
E   
E   exception: AssertionError = 'None'
E   
E   output: bool = False
E   a: Settings =
E       Settings(
E           rdkit:
E               stereo:    Settings()
E           pdb_info:
E               ResidueName:    'LIG'
E               Occupancy:    1.0000
E               TempFactor:    0.0000e+00
E               ResidueNumber:    1
E               ...
E           charge:    0
E       )
E   b: Settings =
E       Settings(
E           stereo:    Settings()
E           charge:    0
E           pdb_info:
E               ResidueName:    'LIG'
E               Occupancy:    1.0000
E               TempFactor:    0.0000e+00
E               ResidueNumber:    1
E               ...
E       )
______________________________ test_fix_carboxyl _______________________________
tests/test_mol_utils.py:115: in test_fix_carboxyl
    assertion.eq(round(angle), 120)
E   AssertionError: output = eq(a, b); assert output
E   
E   exception: AssertionError = 'None'
E   
E   output: bool = False
E   a: int = 9
E   b: int = 120
=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/FOX/armc/package_manager.py:38
  /opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/FOX/armc/package_manager.py:38: QMFlowsDeprecationWarning: `qmflows.packages.cp2k_package` is a deprecated alias for `qmflows.packages`
    from qmflows.packages.cp2k_package import CP2K, CP2K_Result

../../../../../opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nanoCAT/cdft.py:8
  /opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nanoCAT/cdft.py:8: QMFlowsDeprecationWarning: `qmflows.packages.SCM` is a deprecated alias for `qmflows.packages`
    from qmflows.packages.SCM import ADF_Result

../../../../../opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nanoCAT/recipes/multi_lig_job.py:38
  /opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nanoCAT/recipes/multi_lig_job.py:38: QMFlowsDeprecationWarning: `qmflows.packages.cp2k_mm` is a deprecated alias for `qmflows.packages`
    from qmflows.packages.cp2k_mm import CP2KMM_Result

tests/test_entry_points.py: 1 warning
tests/test_indices.py: 1 warning
tests/test_ligand_attach.py: 16 warnings
tests/test_thread_safe.py: 2 warnings
  /opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/dataCAT/database.py:384: FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)`
    db.update(hdf5_series, overwrite=True)
@BvB93 BvB93 added the bug Something isn't working label Sep 1, 2022
@BvB93 BvB93 added this to the 1.1 milestone Sep 15, 2022
@BvB93 BvB93 modified the milestones: 1.1, CAT 1.1.1 Sep 29, 2022
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