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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
61 lines
2.1 KiB
Python
61 lines
2.1 KiB
Python
# Copyright 2019 by Sergio Valqui. All rights reserved.
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Unit tests for the Bio.PDB.Dice Module."""
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import os
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import tempfile
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import unittest
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from Bio.PDB import Dice
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from Bio.PDB import PDBParser
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class DiceTests(unittest.TestCase):
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"""Tests for PDB.Dice module."""
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def test_dice(self):
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"""Self test for PDB.Dice module."""
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# Load and dice 2BEG.pdb
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parser = PDBParser()
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pdb_file = "PDB/2BEG.pdb"
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structure = parser.get_structure("scr", pdb_file)
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file_number, file_pdb_diced = tempfile.mkstemp()
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os.close(file_number)
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# dice 2BEG.pdb, chain "B" from residue 18 to 20"
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Dice.extract(structure, "B", 18, 20, file_pdb_diced)
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try:
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# Load the diced file
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diced_str = parser.get_structure("2beg_diced", file_pdb_diced)
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l_diced_cha = list(diced_str.get_chains())
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l_diced_res = list(diced_str.get_residues())
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l_diced_ato = list(diced_str.get_atoms())
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# Chain checks
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self.assertEqual(len(l_diced_cha), 1)
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self.assertEqual(l_diced_cha[0].id, "B")
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# Residue Checks
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self.assertEqual(len(l_diced_res), 3)
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self.assertEqual(l_diced_res[0].id[1], 18)
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self.assertEqual(l_diced_res[2].id[1], 20)
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# Atom checks
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self.assertEqual(len(l_diced_ato), 29)
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self.assertEqual(l_diced_ato[0].name, "N")
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self.assertEqual(l_diced_ato[0].parent.resname, "VAL")
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self.assertEqual(l_diced_ato[0].parent.parent.id, "B")
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self.assertEqual(l_diced_ato[28].name, "CZ")
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self.assertEqual(l_diced_ato[28].parent.resname, "PHE")
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self.assertEqual(l_diced_ato[28].parent.parent.id, "B")
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finally:
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os.remove(file_pdb_diced)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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