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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
121 lines
4.4 KiB
Python
121 lines
4.4 KiB
Python
# Copyright 2018 by Francesco Gastaldello. All rights reserved.
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#
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# Converted by Francesco Gastaldello from an older unit test copyright 2002
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# by Thomas Hamelryck.
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#
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# Merged related test files into one, by Joao Rodrigues (2020)
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#
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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.ResidueDepth module."""
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import subprocess
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import unittest
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import warnings
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from Bio.PDB import MMCIFParser
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from Bio.PDB import PDBParser
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from Bio.PDB import ResidueDepth
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from Bio.PDB.PDBExceptions import PDBConstructionWarning
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from Bio.PDB.ResidueDepth import _get_atom_radius
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class MSMS_tests(unittest.TestCase):
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"""Test calling MSMS via Bio.PDB.ResidueDepth."""
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@classmethod
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def setUpClass(cls):
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# Check if MSMS is installed
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try:
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v = subprocess.check_output(
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["msms", "-h"], text=True, stderr=subprocess.STDOUT
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)
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except OSError:
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raise unittest.SkipTest(
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"Install MSMS if you want to use it from Biopython."
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)
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cls.pdbparser = PDBParser()
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cls.cifparser = MMCIFParser()
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def check_msms(self, prot_file, first_100_residues):
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"""Wrap calls to MSMS and the respective tests."""
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", PDBConstructionWarning)
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s = self.pdbparser.get_structure("X", prot_file)
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model = s[0]
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rd = ResidueDepth(model)
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residues = []
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for item in rd.property_list[:100]:
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residues.append(item[0].get_resname())
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self.assertEqual("".join(residues), first_100_residues)
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# def test_ResidueDepth_2XHE(self):
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# self.check_msms(
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# "PDB/2XHE.pdb",
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# "HISMETSERLEULYSSERALAVALLYSTHRVALLEUTHRASNSERLEUARGSERVALALAASPGLYGLYASPTR"
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# "PLYSVALLEUVALVALASPLYSPROALALEUARGMETILESERGLUCYSALAARGMETSERGLUILELEUASPL"
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# "EUGLYVALTHRVALVALGLUASPVALSERLYSGLNARGLYSVALLEUPROGLNPHEHISGLYVALTYRPHEILE"
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# "GLUPROTHRGLUGLUASNLEUASPTYRVALILEARGASPPHEALAASPARGTHRPROTHRTYRGLUALAALAHI"
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# "SLEU",
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# )
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def test_ResidueDepth_2BEG(self):
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self.check_msms(
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"PDB/2BEG.pdb",
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"LEUVALPHEPHEALAGLUASPVALGLYSERASNLYSGLYALAILEILEGLYLEUMETVALGLYGLYVALVALIL"
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"EALALEUVALPHEPHEALAGLUASPVALGLYSERASNLYSGLYALAILEILEGLYLEUMETVALGLYGLYVALV"
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"ALILEALALEUVALPHEPHEALAGLUASPVALGLYSERASNLYSGLYALAILEILEGLYLEUMETVALGLYGLY"
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"VALVALILEALALEUVALPHEPHEALAGLUASPVALGLYSERASNLYSGLYALAILEILEGLYLEUMETVALGL"
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"YGLY",
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)
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def test_ResidueDepth_1LCD(self):
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self.check_msms(
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"PDB/1LCD.pdb",
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"METLYSPROVALTHRLEUTYRASPVALALAGLUTYRALAGLYVALSERTYRGLNTHRVALSERARGVALVALAS"
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"NGLNALASERHISVALSERALALYSTHRARGGLULYSVALGLUALAALAMETALAGLULEUASNTYRILEPROA"
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"SNARG",
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)
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def test_ResidueDepth_1A8O(self):
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self.check_msms(
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"PDB/1A8O.pdb",
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"MSEASPILEARGGLNGLYPROLYSGLUPROPHEARGASPTYRVALASPARGPHETYRLYSTHRLEUARGALAGL"
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"UGLNALASERGLNGLUVALLYSASNTRPMSETHRGLUTHRLEULEUVALGLNASNALAASNPROASPCYSLYST"
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"HRILELEULYSALALEUGLYPROGLYALATHRLEUGLUGLUMSEMSETHRALACYSGLNGLY",
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)
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class ResidueDepth_tests(unittest.TestCase):
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"""Tests for Bio.PDB.ResidueDepth, except for running MSMS itself."""
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def test_pdb_to_xyzr(self):
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"""Test generation of xyzr (atomic radii) file."""
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", PDBConstructionWarning)
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p = PDBParser(PERMISSIVE=1)
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structure = p.get_structure("example", "PDB/1A8O.pdb")
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# Read radii produced with original shell script
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with open("PDB/1A8O.xyzr") as handle:
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msms_radii = []
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for line in handle:
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fields = line.split()
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radius = float(fields[3])
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msms_radii.append(radius)
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model = structure[0]
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biopy_radii = []
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for atom in model.get_atoms():
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biopy_radii.append(_get_atom_radius(atom, rtype="united"))
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self.assertEqual(msms_radii, biopy_radii)
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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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