python_packaging/test/test_fr09.py

   1 #
   2 # This file is part of the GROMACS molecular simulation package.
   3 #
   4 # Copyright (c) 2019, by the GROMACS development team, led by
   5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 # and including many others, as listed in the AUTHORS file in the
   7 # top-level source directory and at http://www.gromacs.org.
   8 #
   9 # GROMACS is free software; you can redistribute it and/or
  10 # modify it under the terms of the GNU Lesser General Public License
  11 # as published by the Free Software Foundation; either version 2.1
  12 # of the License, or (at your option) any later version.
  13 #
  14 # GROMACS is distributed in the hope that it will be useful,
  15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17 # Lesser General Public License for more details.
  18 #
  19 # You should have received a copy of the GNU Lesser General Public
  20 # License along with GROMACS; if not, see
  21 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23 #
  24 # If you want to redistribute modifications to GROMACS, please
  25 # consider that scientific software is very special. Version
  26 # control is crucial - bugs must be traceable. We will be happy to
  27 # consider code for inclusion in the official distribution, but
  28 # derived work must not be called official GROMACS. Details are found
  29 # in the README & COPYING files - if they are missing, get the
  30 # official version at http://www.gromacs.org.
  31 #
  32 # To help us fund GROMACS development, we humbly ask that you cite
  33 # the research papers on the package. Check out http://www.gromacs.org.
  34
  35 """Test gmxapi functionality described in roadmap.rst."""
  36
  37 import pytest
  38
  39 import gmxapi as gmx
  40 from gmxapi.version import has_feature
  41
  42 @pytest.mark.skipif(not has_feature('fr9'),
  43                    reason="Feature level not met.")
  44 def test_fr9():
  45     """FR9: *gmx.mdrun supports interface for binding MD plugins*
  46
  47     (requires interaction with library development)
  48     """
  49     import sample_restraint
  50
  51     starting_structure = 'input_conf.gro'
  52     topology_file = 'input.top'
  53     run_parameters = 'params.mdp'
  54
  55     initial_tpr = gmx.commandline_operation(
  56         'gmx',
  57         'grompp',
  58         input={
  59             '-f': run_parameters,
  60             '-c': starting_structure,
  61             '-p': topology_file
  62         },
  63         output={'-o': gmx.OutputFile('.tpr')})
  64
  65     simulation_input = gmx.read_tpr(initial_tpr.output.file['-o'])
  66
  67     # Prepare a simple harmonic restraint between atoms 1 and 4
  68     restraint_params = {'sites': [1, 4],
  69                         'R0': 2.0,
  70                         'k': 10000.0}
  71
  72     restraint = sample_restraint.harmonic_restraint(input=restraint_params)
  73
  74     md = gmx.mdrun(input=simulation_input, potential=sample_restraint)
  75
  76     #md.run()