def setup(self):
self.tmpdir = td.TempDir()
self.old_path = os.getcwd()
self.resources = os.path.join(self.old_path, 'mdpow', 'tests',
'testing_resources')
m = pybol.Manifest(os.path.join(self.resources, 'manifest.yml'))
m.assemble('base', self.tmpdir.name)
def setup(self):
self.tmpdir = td.TempDir()
self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml'))
self.m.assemble('example_FEP', self.tmpdir.name)
self.ens = Ensemble(dirname=self.tmpdir.name, solvents=['water'])
self.solute = self.ens.select_atoms('not resname SOL')
self.solvent = self.ens.select_atoms('resname SOL and name OW')
def setup(self):
self.tmpdir = td.TempDir()
self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml'))
self.m.assemble('md_npt', self.tmpdir.name)
simulation_filename = os.path.join(self.tmpdir.name, 'benzene',
'water.simulation')
self.S = equil.Simulation(filename=simulation_filename)
self.S.make_paths_relative(prefix=os.path.join(
self.tmpdir.name, 'benzene', 'Equilibrium', 'water'))
self.S.dirs.includes = os.path.join(self.tmpdir.name, 'top')
self.S.save()
def setup(self):
self.tmpdir = td.TempDir()
self.old_path = os.getcwd()
self.resources = RESOURCES
self.m = pybol.Manifest(str(self.resources / 'manifest.yml'))
self.m.assemble('md_npt', self.tmpdir.name)
S = Simulation(filename=os.path.join(self.tmpdir.name, 'benzene',
'water.simulation'))
S.make_paths_relative(prefix=os.path.join(self.tmpdir.name, 'benzene',
'Equilibrium', 'water'))
S.dirs.includes = os.path.join(self.tmpdir.name, 'top')
S.save()
def setup(self):
self.tmpdir = td.TempDir()
self.old_path = os.getcwd()
self.resources = os.path.join(self.old_path, 'mdpow', 'tests',
'testing_resources')
self.m = pybol.Manifest(os.path.join(self.resources, 'manifest.yml'))
self.m.assemble('md_npt', self.tmpdir.name)
simulation_filename = os.path.join(self.tmpdir.name, 'benzene',
'water.simulation')
self.S = mdpow.equil.Simulation(filename=simulation_filename)
self.S.make_paths_relative(prefix=os.path.join(
self.tmpdir.name, 'benzene', 'Equilibrium', 'water'))
self.S.dirs.includes = os.path.join(self.tmpdir.name, 'top')
self.S.save()
def setup(self):
self.tmpdir = td.TempDir()
self.m = pybol.Manifest(str(RESOURCES / 'manifest.yml'))
self.m.assemble('example_FEP', self.tmpdir.name)
def setup(self):
self.tmpdir = td.TempDir()
self.old_path = os.getcwd()
self.resources = RESOURCES
m = pybol.Manifest(str(self.resources / 'manifest.yml'))
m.assemble('base', self.tmpdir.name)
def fep_benzene_directory(tmpdir_factory):
topdir = tmpdir_factory.mktemp('analysis')
m = pybol.Manifest(fix_manifest(topdir).strpath)
m.assemble('FEP', topdir.strpath)
return topdir.join("benzene")