def test_input_options(self, tmpdir):
u = mda.Universe(PDB_HOLE)
cog = u.select_atoms('protein').center_of_geometry()
with tmpdir.as_cwd():
hole2.hole(self.filename,
random_seed=self.random_seed,
infile='hole.inp',
cpoint=cog,
ignore_residues=[])
infile = str(tmpdir.join('hole.inp'))
with open(infile, 'r') as f:
contents = f.read()
hole_input = textwrap.dedent("""
RADIUS simple2.rad
SPHPDB hole.sph
SAMPLE 0.200000
ENDRAD 22.000000
IGNORE
SHORTO 0
RASEED 31415
CPOINT -0.0180961507 -0.0122730583 4.1497999943
""")
# don't check filenames
assert contents.endswith(hole_input)
def test_keep_files(self, tmpdir):
with tmpdir.as_cwd():
hole2.hole(self.filename,
random_seed=self.random_seed,
infile='hole.inp',
keep_files=False)
sphpdbs = tmpdir.join('*.sph')
assert len(glob.glob(str(sphpdbs))) == 0
outfiles = tmpdir.join('*.out')
assert len(glob.glob(str(outfiles))) == 0
vdwradii = tmpdir.join('simple2.rad')
assert len(glob.glob(str(vdwradii))) == 0
pdbfiles = tmpdir.join('*.pdb')
assert len(glob.glob(str(pdbfiles))) == 0
oldfiles = tmpdir.join('*.old')
assert len(glob.glob(str(oldfiles))) == 0
def test_output_level(self, tmpdir):
with tmpdir.as_cwd():
with pytest.warns(UserWarning, match="needs to be < 3"):
profiles = hole2.hole(self.filename,
random_seed=self.random_seed,
output_level=100)
assert len(profiles) == 0
def test_output_level(self, tmpdir):
with tmpdir.as_cwd():
with pytest.warns(UserWarning) as rec:
profiles = hole2.hole(self.filename,
random_seed=self.random_seed,
output_level=100)
assert len(rec) == 1
assert 'needs to be < 3' in rec[0].message.args[0]
# no profiles
assert len(profiles) == 0
def test_correct_input(self, tmpdir):
with tmpdir.as_cwd():
hole2.hole(self.filename,
random_seed=self.random_seed,
infile='hole.inp')
infile = str(tmpdir.join('hole.inp'))
with open(infile, 'r') as f:
contents = f.read()
hole_input = textwrap.dedent("""
RADIUS simple2.rad
SPHPDB hole.sph
SAMPLE 0.200000
ENDRAD 22.000000
IGNORE SOL WAT TIP HOH K NA CL
SHORTO 0
RASEED 31415
""")
# don't check filenames
assert contents.endswith(hole_input)
def test_correct_profile_values(self, tmpdir):
with tmpdir.as_cwd():
profiles = hole2.hole(self.filename, random_seed=self.random_seed)
values = list(profiles.values())
assert_equal(len(values), 1, err_msg='Should only have 1 HOLE profile')
profile = values[0]
assert_equal(len(profile),
self.profile_length,
err_msg='Wrong number of points in HOLE profile')
assert_almost_equal(profile.rxn_coord.mean(),
self.rxn_coord_mean,
err_msg='Wrong mean HOLE rxn_coord')
assert_almost_equal(profile.radius.min(),
self.radius_min,
err_msg='Wrong minimum HOLE radius')
def test_application_error(self, tmpdir):
with tmpdir.as_cwd():
with pytest.raises(ApplicationError):
hole2.hole(self.filename, dcd=DCD)