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Remove explicit hydrogens from smarts
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Brian Kelley
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Feb 23, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| from rd_filters import rd_filters | ||
| import pkg_resources | ||
|
|
||
| # these just stop on the first filter | ||
| test_lint = [ | ||
| ('C1N=C1', 'aziridine-like N in 3-membered ring > 0'), | ||
| ('NN=N', 'acyclic N-,=N and not N bound to carbonyl or sulfone > 0'), | ||
| ] | ||
|
|
||
| test_inpharmatica = [ | ||
| ('CN=C', 'OK'), | ||
| ('CN=CC', 'Filter39_imine > 0'), | ||
| ('CN=C(C)', 'Filter39_imine > 0'), | ||
| ('CN=NC', 'Filter5_azo > 0'), | ||
| ('CN=N', 'Filter5_azo > 0'), | ||
| ('N=N', 'Filter5_azo > 0'), | ||
| ('[Fe]C', 'Filter9_metal > 0'), | ||
| ('[FeH]', 'Filter9_metal > 0'), | ||
| ('[Fe]', 'OK'), | ||
| ('CN=O', 'Filter12_nitroso > 0'), | ||
| ('N=O', 'Filter12_nitroso > 0'), | ||
| ('S=P', 'Filter13_PS_double_bond > 0'), | ||
| ('S=PC', 'Filter13_PS_double_bond > 0'), | ||
| ('CC(=O)SC', 'Filter29_thioester > 0'), | ||
| ('CC(=S)SC', 'Filter29_thioester > 0'), | ||
| ('CC(=N)SC', 'Filter29_thioester > 0'), | ||
| ('CC(=O)S', 'Filter29_thioester > 0'), | ||
| ('CC(=S)S', 'Filter29_thioester > 0'), | ||
| ('CC(=N)S', 'Filter29_thioester > 0'), | ||
| ('CC(=O)CCBr', 'Filter26_alkyl_halide > 0'), | ||
| ('CC(=O)CCI', 'Filter26_alkyl_halide > 0'), | ||
| ('C(=O)CCI', 'Filter26_alkyl_halide > 0'), | ||
| ('NC(=O)CCI', 'Filter26_alkyl_halide > 0'), | ||
| ('CC=NOS(=O)N', 'Filter18_oxime_ester > 0'), | ||
| ('NC=NOP(=O)N', 'Filter89_hydroxylamine > 0'), | ||
| ('C=NOP(=O)N', 'Filter18_oxime_ester > 0'), | ||
| ('SO', 'Filter31_so_bond > 0'), | ||
| ('SOC', 'Filter31_so_bond > 0'), | ||
| ('c1csocc1', 'OK'), | ||
| ('OO', 'Filter32_oo_bond > 0'), | ||
| ('COO', 'Filter32_oo_bond > 0'), | ||
| ('c1coocc1', 'OK'), | ||
| ('CC(=O)C=C', 'Filter44_michael_acceptor2 > 0'), | ||
| ('C(=O)C=C', 'Filter38_aldehyde > 0'), | ||
| ('OC(=O)C=C', 'Filter44_michael_acceptor2 > 0'), | ||
| ('C1(=O)C=CC(=O)C=C1', 'Filter53_para_quinones > 0'), | ||
| ('CIC', 'Filter49_halogen > 0'), | ||
| ('CI(C)C', 'Filter49_halogen > 0'), | ||
| ('CC=NOS(=O)N', 'Filter18_oxime_ester > 0'), | ||
| ('NC=NO', 'Filter89_hydroxylamine > 0'), | ||
| ('C(=O)NOS', 'Filter31_so_bond > 0'), | ||
| ] | ||
|
|
||
| def test_hydrogen_suppression(): | ||
| alert_file_name = pkg_resources.resource_filename('rd_filters', | ||
| "data/alert_collection.csv") | ||
| for rule_list, tests in [(["Inpharmatica"], test_inpharmatica), | ||
| (["LINT"], test_lint)]: | ||
| rf = rd_filters.RDFilters(alert_file_name) | ||
| rf.build_rule_list(rule_list) | ||
| for smi, res in tests: | ||
| result = rf.evaluate((smi,smi)) | ||
| assert result[2] == res, repr((result[:3], res)) | ||
|
|