def test_excel(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("395",
[self.traj, self.traj_reverse],
self.geom,
table_ext=".xlsx",
output_dir=tmpdir)
def test_AAs(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("395",
[self.traj, self.traj_reverse],
self.geom,
short_AA_names=True,
output_dir=tmpdir,
no_disk=self.no_disk)
def test_no_top(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
input_values = (val for val in ["1.0"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
cli.residue_neighborhoods("200,395",
self.geom,
output_dir=tmpdir,
no_disk=self.no_disk)
def test_no_bonds_fail(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
top = self.geom[0]
top.top._bonds = []
with pytest.raises(ValueError):
cli.residue_neighborhoods("R131",
[self.traj, self.traj_reverse],
top,
output_dir=tmpdir)
def test_wrong_input_resSeq_idxs(self):
with pytest.raises(ValueError):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("AX*",
[self.traj, self.traj_reverse],
self.geom,
distro=True,
output_dir=tmpdir,
no_disk=self.no_disk)
def test_precomputed_raises(self):
with pytest.raises(ValueError):
cli.residue_neighborhoods([1043],
[self.traj, self.traj_reverse],
self.geom,
res_idxs=True,
no_disk=False,
figures=False,
pre_computed_contact_matrix=_np.zeros((self.geom.n_residues,
self.geom.n_residues + 1)))
def test_some_CG_have_no_contacts(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("0-3",
[self.traj, self.traj_reverse],
self.geom,
ctc_cutoff_Ang=3.2,
res_idxs=True,
output_dir=tmpdir,
no_disk=self.no_disk
)
def test_nomenclature_BW(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("R131",
[self.traj, self.traj_reverse],
self.geom,
BW_uniprot=test_filenames.adrb2_human_xlsx,
output_dir=tmpdir,
accept_guess=True,
no_disk=self.no_disk
)
def test_res_idxs(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.residue_neighborhoods("1043",
[self.traj, self.traj_reverse],
self.geom,
fragment_colors=True,
allow_same_fragment_ctcs=False,
short_AA_names=True,
res_idxs=True,
output_dir=tmpdir,
no_disk=self.no_disk)
def test_neighborhoods_no_disk_works(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
with remember_cwd():
os.chdir(tmpdir)
input_values = (val for val in ["1.0"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
cli.residue_neighborhoods("200,395",
self.traj,
self.geom,
no_disk=True
)
assert len(os.listdir(".")) == 0
def test_nomenclature_CGN(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
shutil.copy(test_filenames.CGN_3SN6, tmpdir)
shutil.copy(test_filenames.pdb_3SN6, tmpdir)
with remember_cwd():
os.chdir(tmpdir)
cli.residue_neighborhoods("R131",
[self.traj, self.traj_reverse],
self.geom,
CGN_PDB="3SN6",
output_dir=tmpdir,
accept_guess=True,
no_disk=self.no_disk
)
def test_precomputed(self):
CG1 = list(cli.residue_neighborhoods([1043],
[self.traj, self.traj_reverse],
self.geom,
res_idxs=True,
no_disk=True,
figures=False)["neighborhoods"].values())[0]
CG2 = list(cli.residue_neighborhoods([1043],
[self.traj, self.traj_reverse],
self.geom,
res_idxs=True,
no_disk=True,
figures=False,
pre_computed_contact_matrix=_np.zeros((self.geom.n_residues,
self.geom.n_residues)))[
"neighborhoods"].values())[0]
_np.testing.assert_array_equal(CG1.frequency_per_contact(3.5), CG2.frequency_per_contact(3.5))
def test_no_residues_returns_None(self):
# This is more of an argparse fail
# TODO consider throwing exception
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
assert None == cli.residue_neighborhoods(None,
[self.traj, self.traj_reverse],
self.geom,
None,
distro=True,
output_dir=tmpdir,
no_disk=self.no_disk)
# (at your option) any later version.
#
# mdciao is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with mdciao. If not, see <https://www.gnu.org/licenses/>.
##############################################################################
from mdciao.parsers import parser_for_rn, _inform_of_parser
from mdciao.cli import residue_neighborhoods
# Get and instantiate parser
parser = parser_for_rn()
a = parser.parse_args()
if not a.fragmentify:
a.fragments=["None"]
a.fragment_names="None"
# Make a dictionary out ot of it and pop the positional keywords
b = {key:getattr(a,key) for key in dir(a) if not key.startswith("_")}
for key in ["trajectories","residues", "fragmentify"]:
b.pop(key)
# Call the method
out_dict = residue_neighborhoods(a.residues, a.trajectories, **b)
def test_no_contacts_at_allp(self):
cli.residue_neighborhoods("R131",
[self.traj, self.traj_reverse],
self.geom,
ctc_cutoff_Ang=.1,
)
