# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
"""Test gmxapi functionality described in roadmap.rst."""
import os
import shutil
import stat
import tempfile
import gmxapi as gmx
import pytest
from gmxapi.version import has_feature
@pytest.mark.skipif(not has_feature('fr3'),
reason="Feature level not met.")
def test_fr3():
"""FR3: Output proxy can be used as input."""
with tempfile.TemporaryDirectory() as directory:
file1 = os.path.join(directory, 'input')
file2 = os.path.join(directory, 'output')
# Make a shell script that acts like the type of tool we are wrapping.
scriptname = os.path.join(directory, 'clicommand.sh')
with open(scriptname, 'w') as fh:
fh.write('\n'.join(['#!' + shutil.which('bash'),
'# Concatenate an input file and a string argument to an output file.',
'# Mock a utility with the tested syntax.',
'# clicommand.sh "some words" -i inputfile -o outputfile',
'echo $1 | cat $3 - > $5\n']))
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
"""Test gmxapi functionality described in roadmap.rst."""
import pytest
import gmxapi as gmx
from gmxapi.version import has_feature
@pytest.mark.skipif(not has_feature('fr15'), reason="Feature level not met.")
def test_fr15():
"""FR15: Simulation input modification.
* *gmx.modify_input produces new (tpr) simulation input in data flow operation*
(requires interaction with library development)
* gmx.make_input dispatches appropriate preprocessing for file or in-memory simulation input.
"""
initial_input = gmx.read_tpr([tpr_filename for _ in range(10)])
tau_t = list([i / 10. for i in range(10)])
param_sweep = gmx.modify_input(input=initial_input,
parameters={'tau_t': tau_t})
md = gmx.mdrun(param_sweep)
for tau_expected, tau_actual in zip(tau_t,
md.output.params['tau_t'].extract()):
assert tau_expected == tau_actual
#
# If you want to redistribute modifications to GROMACS, please
# consider that scientific software is very special. Version
# control is crucial - bugs must be traceable. We will be happy to
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
"""Test gmxapi functionality described in roadmap.rst."""
import pytest
import gmxapi as gmx
from gmxapi.version import has_feature
@pytest.mark.skipif(not has_feature('fr20'),
reason="Feature level not met.")
def test_fr20():
"""FR20: Python bindings use C++ API for expressing user interface
gmx.tool operations are migrated to updated Options infrastructure
(requires interaction with library development)
"""
analysis = gmx.rmsf(trajectory=md.output.trajectory,
topology=initial_input)
file_list = gmx.fileio.write_xvg(analysis.output).result()
