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