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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, PDBParser, ResidueDepth
from Bio import MissingExternalDependencyError
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"], universal_newlines=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.assertListEqual(msms_radii, biopy_radii)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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