def test_sites_distro(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.sites([test_filenames.tip_json],
[self.traj, self.traj_reverse],
self.geom,
distro=True,
output_dir=tmpdir)
def test_sites_no_distk(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.sites([test_filenames.tip_json],[self.traj, self.traj_reverse], self.geom,
no_disk=True)
def test_w_table_dat(self):
with TemporaryDirectory(suffix='_test_mdciao') as tmpdir:
cli.sites([test_filenames.tip_json], [self.traj, self.traj_reverse],self.geom,
output_dir=tmpdir,
scheme="COM",
table_ext=".dat")
# 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 sites
from mdciao.parsers import parser_for_sites
# Get and instantiate parser
parser = parser_for_sites()
a = parser.parse_args()
#_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", "site_files", "fragmentify"]:
b.pop(key)
sites(a.site_files, a.trajectories, **b)