CI update -> use miniconda v2
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"""
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Tests the dummy atoms utilities.
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"""
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import os |
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import parmed as pmd |
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import paprika.dummy as dummy |
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from paprika.align import zalign |
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def test_extract_dummy(): |
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cb6 = pmd.load_file( |
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os.path.join(os.path.dirname(__file__), "../data/cb6-but/vac.pdb") |
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)
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aligned_cb6 = zalign(cb6, ":CB6", ":BUT") |
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aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM1", z=-6.0) |
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aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM2", z=-9.0) |
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aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM3", z=-11.2, y=2.2) |
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dm_index = [] |
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for atom in aligned_cb6.topology.atoms(): |
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if atom.residue.name in ["DM1", "DM2", "DM3"]: |
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dm_index.append(atom.index) |
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assert len(dm_index) != 0 |
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dummy_dict = dummy.extract_dummy_atoms(aligned_cb6, serial=False) |
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assert all(dummy_dict["DM1"]["pos"] == [0.0, 0.0, -6.0]) |
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assert all(dummy_dict["DM2"]["pos"] == [0.0, 0.0, -9.0]) |
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assert all(dummy_dict["DM3"]["pos"] == [0.0, 2.2, -11.2]) |
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assert dummy_dict["DM1"]["mass"] == 208.0 |
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assert dummy_dict["DM2"]["mass"] == 208.0 |
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assert dummy_dict["DM3"]["mass"] == 208.0 |
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assert dummy_dict["DM1"]["idx"] == dm_index[0] |
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assert dummy_dict["DM2"]["idx"] == dm_index[1] |
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assert dummy_dict["DM3"]["idx"] == dm_index[2] |
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