def test_prepare_amber_explicit(verbose=False):
store_directory = tempfile.mkdtemp()
examples_path = utils.get_data_filename("../examples/benzene-toluene-explicit/setup/") # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
command = 'yank prepare binding amber --setupdir=%(examples_path)s --ligname=BEN --store=%(store_directory)s --iterations=1 --nbmethod=CutoffPeriodic --temperature=300*kelvin --pressure=1*atmospheres' % vars()
if verbose: command += ' --verbose'
argv = command.split()
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import prepare
prepare.dispatch(args)
def test_prepare_gromacs_explicit(verbose=False):
store_directory = tempfile.mkdtemp()
examples_path = utils.get_data_filename("../examples/p-xylene-gromacs-example/setup/")
command = 'yank prepare binding gromacs --setupdir=%(examples_path)s --store=%(store_directory)s --iterations=1 --nbmethod=CutoffPeriodic --temperature=300*kelvin --pressure=1*atmospheres --cutoff=1*nanometer' % vars()
if verbose: command += ' --verbose'
argv = command.split()
argv.append('--ligand=resname MOL') # if included in the command string it is split in two
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import prepare
prepare.dispatch(args)
def test_prepare_amber_implicit(verbose=False):
store_directory = tempfile.mkdtemp()
examples_path = utils.get_data_filename("../examples/benzene-toluene-implicit/setup/") # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
command = 'yank prepare binding amber --setupdir=%(examples_path)s --store=%(store_directory)s --iterations=1 --restraints=harmonic --gbsa=OBC2 --temperature=300*kelvin' % vars()
if verbose: command += ' --verbose'
argv = command.split()
argv.append('--ligand=resname BEN') # if included in the command string it is split in two
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import prepare
prepare.dispatch(args)
def test_prepare_gromacs_explicit(verbose=False):
store_directory = tempfile.mkdtemp()
examples_path = utils.get_data_filename("../examples/p-xylene-gromacs-example/setup/")
command = 'yank prepare binding gromacs --setupdir=%(examples_path)s --store=%(store_directory)s --iterations=1 --nbmethod=CutoffPeriodic --temperature=300*kelvin --pressure=1*atmospheres --cutoff=1*nanometer' % vars()
if verbose: command += ' --verbose'
argv = command.split()
argv.append("--ligand=resname 'p-xylene'") # if included in the command string it is split in two
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import prepare
prepare.dispatch(args)
def test_prepare_amber_explicit(verbose=False):
store_directory = tempfile.mkdtemp()
examples_path = utils.get_data_filename("../examples/benzene-toluene-explicit/setup/") # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
command = 'yank prepare binding amber --setupdir=%(examples_path)s --store=%(store_directory)s --iterations=1 --nbmethod=CutoffPeriodic --temperature=300*kelvin --pressure=1*atmospheres' % vars()
if verbose: command += ' --verbose'
argv = command.split()
argv.append('--ligand=resname TOL') # if included in the command string it is split in two
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import prepare
prepare.dispatch(args)
