def test_w_just_one_fragment_by_user(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.interface([self.traj, self.traj_reverse],
self.geom,
output_dir=tmpdir,
fragments=["0-5"],
flareplot=False,
no_disk=self.no_disk
)
def test_interface_wo_frag_idxs_groups(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
input_values = (val for val in ["0-1", "2,3"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
cli.interface([self.traj, self.traj_reverse],
self.geom,
output_dir=tmpdir,
flareplot=False,
no_disk=self.no_disk
)
def test_no_top(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.interface([self.traj, self.traj_reverse],
frag_idxs_group_1=[0],
frag_idxs_group_2=[1],
output_dir=tmpdir,
flareplot=False,
plot_timedep=False,
no_disk = self.no_disk
)
def test_w_just_two_fragments_by_user(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.interface([self.traj, self.traj_reverse],
self.geom,
frag_idxs_group_1=[0],
frag_idxs_group_2=[1],
output_dir=tmpdir,
fragments=["0-5",
"6-10"],
flareplot=False,
no_disk=self.no_disk
)
def test_w_nomenclature_CGN_BW_fragments_are_consensus_and_flareplot(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
input_values = (val for val in ["TM6", "*H5"])
shutil.copy(test_filenames.CGN_3SN6, tmpdir)
shutil.copy(test_filenames.pdb_3SN6, tmpdir)
shutil.copy(test_filenames.adrb2_human_xlsx, tmpdir)
with remember_cwd():
os.chdir(tmpdir)
with mock.patch('builtins.input', lambda *x: next(input_values)):
cli.interface([self.traj, self.traj_reverse],
self.geom,
output_dir=tmpdir,
fragments=["consensus"],
CGN_PDB="3SN6",
BW_uniprot="adrb2_human",
accept_guess=True,
#no_disk=self.no_disk
)
def test_w_nomenclature_CGN_BW(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
shutil.copy(test_filenames.CGN_3SN6, tmpdir)
shutil.copy(test_filenames.pdb_3SN6, tmpdir)
shutil.copy(test_filenames.adrb2_human_xlsx, tmpdir)
with remember_cwd():
os.chdir(tmpdir)
cli.interface([self.traj, self.traj_reverse],
self.geom,
output_dir=tmpdir,
fragments=["967-1001", # TM6
"328-353"], # a5
CGN_PDB="3SN6",
BW_uniprot="adrb2_human",
accept_guess=True,
flareplot=False,
no_disk=self.no_disk
)
# mdciao is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (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.cli import interface
from mdciao.parsers import parser_for_interface
parser = parser_for_interface()
a = parser.parse_args()
#from mdciao.command_line_tools import _inform_of_parser
#_inform_of_parser(parser)
if not a.fragmentify:
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", "fragmentify"]:
b.pop(key)
neighborhood = interface(a.trajectories,**b)