def test_script_yaml():
"""Check that yank script --yamlscript command works."""
setup_dir = utils.get_data_filename(os.path.join("..", "examples", "p-xylene-implicit", "setup"))
pxylene_path = os.path.join(setup_dir, "ligand.tripos.mol2")
lysozyme_path = os.path.join(setup_dir, "receptor.pdbfixer.pdb")
with utils.temporary_directory() as tmp_dir:
yaml_content = """
---
options:
number_of_iterations: 1
output_dir: '.'
molecules:
T4lysozyme:
filepath: {}
parameters: oldff/leaprc.ff99SBildn
p-xylene:
filepath: {}
parameters: antechamber
solvents:
vacuum:
nonbonded_method: NoCutoff
experiments:
components:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
""".format(
lysozyme_path, pxylene_path
)
yaml_file_path = os.path.join(tmp_dir, "yank.yaml")
with open(yaml_file_path, "w") as f:
f.write(textwrap.dedent(yaml_content))
run_cli("script --yaml={}".format(yaml_file_path))
def notest_prepare_binding():
dirname = 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/
with omt.utils.temporary_directory() as store_dir:
run_cli(
'prepare binding amber --setupdir=%(dirname)s --ligand="resname TOL" --store %(store_dir)s --gbsa OBC1'
% vars())
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_script_yaml():
"""Check that yank script --yaml command works."""
setup_dir = utils.get_data_filename(
os.path.join('tests', 'data', 'p-xylene-implicit'))
pxylene_path = os.path.join(setup_dir, 'p-xylene.mol2')
lysozyme_path = os.path.join(setup_dir, '181L-pdbfixer.pdb')
yaml_content = """
---
options:
number_of_iterations: 0
output_dir: '.'
resume_setup: yes
resume_simulation: no
minimize: no
molecules:
T4lysozyme:
filepath: {}
p-xylene:
filepath: {}
antechamber:
charge_method: bcc
solvents:
vacuum:
nonbonded_method: NoCutoff
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.0, 0.5, 0.0]
lambda_sterics: [1.0, 0.5, 0.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 0.5, 0.0]
lambda_sterics: [1.0, 0.5, 0.0]
systems:
system:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
leap:
parameters: [leaprc.gaff, oldff/leaprc.ff14SB]
experiments:
system: system
protocol: absolute-binding
restraint:
type: FlatBottom
""".format(lysozyme_path, pxylene_path)
with omt.utils.temporary_directory() as tmp_dir:
yaml_file_path = os.path.join(tmp_dir, 'yank.yaml')
with open(yaml_file_path, 'w') as f:
f.write(textwrap.dedent(yaml_content))
run_cli('script --yaml={}'.format(yaml_file_path))
# Test option overriding.
run_cli('script --yaml={} -o options:resume_simulation:yes'.format(
yaml_file_path))
def test_prepare_binding():
# NOTE: switched to yank p-xylene from openmmtools T4-lysozyme because of yank bugs.
dirname = utils.get_data_filename(
"../examples/p-xylene-implicit/setup/"
) # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
with utils.temporary_directory() as store_dir:
run_cli(
'prepare binding amber --setupdir=%(dirname)s --ligand="resname MOL" --store %(store_dir)s --gbsa OBC1'
% vars())
def test_prepare_binding():
dirname = 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/
with omt.utils.temporary_directory() as store_dir:
run_cli(
'prepare binding amber --setupdir=%(dirname)s --ligand="resname TOL" --store %(store_dir)s --gbsa OBC1'
% vars()
)
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_binding():
# NOTE: switched to yank p-xylene from openmmtools T4-lysozyme because of yank bugs.
dirname = utils.get_data_filename(
"../examples/p-xylene-implicit/setup/"
) # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
with utils.temporary_directory() as store_dir:
run_cli(
'prepare binding amber --setupdir=%(dirname)s --ligand="resname MOL" --store %(store_dir)s --gbsa OBC1'
% vars()
)
def test_setup_binding():
# NOTE: switched to yank p-xylene from openmmtools T4-lysozyme because of yank bugs.
#dirname = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit")
dirname = utils.get_data_filename(
"../examples/p-xylene-implicit/setup/"
) # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
storedir = tempfile.mkdtemp()
run_cli(
'setup binding amber --setupdir=%(dirname)s --ligname MOL --store %(storedir)s'
% vars())
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_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)
def test_script_yaml():
"""Check that yank script --yaml command works."""
setup_dir = utils.get_data_filename(os.path.join('tests', 'data', 'p-xylene-implicit'))
pxylene_path = os.path.join(setup_dir, 'p-xylene.mol2')
lysozyme_path = os.path.join(setup_dir, '181L-pdbfixer.pdb')
yaml_content = """
---
options:
default_number_of_iterations: 0
output_dir: '.'
resume_setup: yes
resume_simulation: no
minimize: no
molecules:
T4lysozyme:
filepath: {}
p-xylene:
filepath: {}
antechamber:
charge_method: bcc
solvents:
vacuum:
nonbonded_method: NoCutoff
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.0, 0.5, 0.0]
lambda_sterics: [1.0, 0.5, 0.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 0.5, 0.0]
lambda_sterics: [1.0, 0.5, 0.0]
systems:
system:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
leap:
parameters: [leaprc.gaff, oldff/leaprc.ff14SB]
experiments:
system: system
protocol: absolute-binding
restraint:
type: FlatBottom
""".format(lysozyme_path, pxylene_path)
with mmtools.utils.temporary_directory() as tmp_dir:
yaml_file_path = os.path.join(tmp_dir, 'yank.yaml')
with open(yaml_file_path, 'w') as f:
f.write(textwrap.dedent(yaml_content))
run_cli('script --yaml={}'.format(yaml_file_path))
# Test option overriding.
run_cli('script --yaml={} -o options:resume_simulation:yes'.format(yaml_file_path))
def test_setup_amber_implicit(verbose=False):
"""
Test 'yank setup binding amber' for implicit solvent system.
"""
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 setup binding amber --setupdir=%(examples_path)s --ligname=BEN --store=%(store_directory)s --iterations=1 --restraints=harmonic --gbsa=OBC2 --temperature=300*kelvin' % vars()
if verbose: command += ' --verbose'
argv = command.split()
args = docopt(usage, version=version.version, argv=argv[1:])
from yank.commands import setup
setup.dispatch(args)
def test_script_yaml():
"""Check that yank script --yaml command works."""
setup_dir = utils.get_data_filename(os.path.join("..", "examples", "p-xylene-implicit", "input"))
pxylene_path = os.path.join(setup_dir, "p-xylene.mol2")
lysozyme_path = os.path.join(setup_dir, "181L-pdbfixer.pdb")
with omt.utils.temporary_directory() as tmp_dir:
yaml_content = """
---
options:
number_of_iterations: 1
output_dir: '.'
molecules:
T4lysozyme:
filepath: {}
p-xylene:
filepath: {}
antechamber:
charge_method: bcc
solvents:
vacuum:
nonbonded_method: NoCutoff
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
lambda_sterics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 0.8, 0.6, 0.3, 0.0]
lambda_sterics: [1.0, 0.8, 0.6, 0.3, 0.0]
systems:
system:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
leap:
parameters: [leaprc.gaff, leaprc.ff14SB]
experiments:
system: system
protocol: absolute-binding
""".format(
lysozyme_path, pxylene_path
)
yaml_file_path = os.path.join(tmp_dir, "yank.yaml")
with open(yaml_file_path, "w") as f:
f.write(textwrap.dedent(yaml_content))
run_cli("script --yaml={}".format(yaml_file_path))
def test_setup_amber_explicit(verbose=False):
"""
Test 'yank setup binding amber' for explicit solvent system.
"""
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 setup 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 setup
setup.dispatch(args)
def test_script_yaml():
"""Check that yank script --yaml command works."""
setup_dir = utils.get_data_filename(os.path.join('..', 'examples', 'p-xylene-implicit', 'input'))
pxylene_path = os.path.join(setup_dir, 'p-xylene.mol2')
lysozyme_path = os.path.join(setup_dir, '181L-pdbfixer.pdb')
with omt.utils.temporary_directory() as tmp_dir:
yaml_content = """
---
options:
number_of_iterations: 1
output_dir: '.'
molecules:
T4lysozyme:
filepath: {}
p-xylene:
filepath: {}
antechamber:
charge_method: bcc
solvents:
vacuum:
nonbonded_method: NoCutoff
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
lambda_sterics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 0.8, 0.6, 0.3, 0.0]
lambda_sterics: [1.0, 0.8, 0.6, 0.3, 0.0]
systems:
system:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
leap:
parameters: [leaprc.gaff, leaprc.ff14SB]
experiments:
system: system
protocol: absolute-binding
""".format(lysozyme_path, pxylene_path)
yaml_file_path = os.path.join(tmp_dir, 'yank.yaml')
with open(yaml_file_path, 'w') as f:
f.write(textwrap.dedent(yaml_content))
run_cli('script --yaml={}'.format(yaml_file_path))
def general_restraint_run(options):
"""
Generalized restraint simulation run to test free energy = standard state correction.
options : Dict. A dictionary of substitutions for restraint_test_yaml
"""
with mmtools.utils.temporary_directory() as output_directory:
# TODO refactor this to use AlchemicalPhase API rather than a YAML script.
options['input_directory'] = get_data_filename(
os.path.join('tests', 'data'))
options['output_directory'] = output_directory
# run both setup and experiment
yaml_builder = experiment.ExperimentBuilder(restraint_test_yaml %
options)
yaml_builder.run_experiments()
# Estimate Free Energies
ncfile_path = os.path.join(output_directory, 'experiments',
'complex.nc')
reporter = multistate.MultiStateReporter(ncfile_path, open_mode='r')
#analyzer = multistate.MultiStateSamplerAnalyzer(reporter)
analyzer = YankMultiStateSamplerAnalyzer(reporter)
Deltaf_ij, dDeltaf_ij = analyzer.get_free_energy()
# Correct the sign for the fact that we are adding vs removing the restraints
DeltaF_simulated = Deltaf_ij[-1, 0]
dDeltaF_simulated = dDeltaf_ij[-1, 0]
print('Standard state correction:')
#ncfile = netcdf.Dataset(ncfile_path, 'r')
#print(ncfile.groups['metadata'].variables['standard_state_correction'][:])
#print(float(ncfile.groups['metadata'].variables['standard_state_correction'][:]))
#ncfile.close()
DeltaF_restraints = analyzer.get_standard_state_correction()
# Check if they are close
msg = ''
msg += 'Computed: %8.3f kT\n' % (DeltaF_restraints)
msg += 'Actual: %8.3f +- %8.3f kT\n' % (DeltaF_simulated,
dDeltaF_simulated)
msg += 'ERROR: %8.3f +- %8.3f kT\n' % (
DeltaF_restraints - DeltaF_simulated, dDeltaF_simulated)
# DEBUG
print(msg)
assert np.allclose(
DeltaF_restraints, DeltaF_simulated, rtol=2 *
dDeltaF_simulated), 'Standard state correction is inaccurate.\n' + msg
def test_script_yaml():
"""Check that yank script --yamlscript command works."""
setup_dir = utils.get_data_filename(os.path.join('..', 'examples', 'p-xylene-implicit', 'setup'))
pxylene_path = os.path.join(setup_dir, 'ligand.tripos.mol2')
lysozyme_path = os.path.join(setup_dir, 'receptor.pdbfixer.pdb')
with utils.temporary_directory() as tmp_dir:
yaml_content = """
---
options:
number_of_iterations: 1
output_dir: '.'
molecules:
T4lysozyme:
filepath: {}
parameters: oldff/leaprc.ff99SBildn
p-xylene:
filepath: {}
parameters: antechamber
solvents:
vacuum:
nonbonded_method: NoCutoff
protocols:
absolute-binding:
phases:
complex:
alchemical_path:
lambda_electrostatics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
lambda_sterics: [1.0, 0.9, 0.8, 0.6, 0.4, 0.2, 0.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 0.8, 0.6, 0.3, 0.0]
lambda_sterics: [1.0, 0.8, 0.6, 0.3, 0.0]
experiments:
components:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
protocol: absolute-binding
""".format(lysozyme_path, pxylene_path)
yaml_file_path = os.path.join(tmp_dir, 'yank.yaml')
with open(yaml_file_path, 'w') as f:
f.write(textwrap.dedent(yaml_content))
run_cli('script --yaml={}'.format(yaml_file_path))
def general_restraint_run(options):
"""
Generalized restraint simulation run to test free energy = standard state correction.
options : Dict. A dictionary of substitutions for restraint_test_yaml
"""
with mmtools.utils.temporary_directory() as output_directory:
# TODO refactor this to use AlchemicalPhase API rather than a YAML script.
options['input_directory'] = get_data_filename(os.path.join('tests', 'data'))
options['output_directory'] = output_directory
# run both setup and experiment
yaml_builder = experiment.ExperimentBuilder(restraint_test_yaml % options)
yaml_builder.run_experiments()
# Estimate Free Energies
ncfile_path = os.path.join(output_directory, 'experiments', 'complex.nc')
reporter = multistate.MultiStateReporter(ncfile_path, open_mode='r')
#analyzer = multistate.MultiStateSamplerAnalyzer(reporter)
analyzer = YankMultiStateSamplerAnalyzer(reporter)
Deltaf_ij, dDeltaf_ij = analyzer.get_free_energy()
# Correct the sign for the fact that we are adding vs removing the restraints
DeltaF_simulated = Deltaf_ij[-1, 0]
dDeltaF_simulated = dDeltaf_ij[-1, 0]
print('Standard state correction:')
#ncfile = netcdf.Dataset(ncfile_path, 'r')
#print(ncfile.groups['metadata'].variables['standard_state_correction'][:])
#print(float(ncfile.groups['metadata'].variables['standard_state_correction'][:]))
#ncfile.close()
DeltaF_restraints = analyzer.get_standard_state_correction()
# Check if they are close
msg = ''
msg += 'Computed: %8.3f kT\n' % (DeltaF_restraints)
msg += 'Actual: %8.3f +- %8.3f kT\n' % (DeltaF_simulated, dDeltaF_simulated)
msg += 'ERROR: %8.3f +- %8.3f kT\n' % (DeltaF_restraints - DeltaF_simulated, dDeltaF_simulated)
# DEBUG
print(msg)
assert np.allclose(DeltaF_restraints, DeltaF_simulated, rtol=2*dDeltaF_simulated), 'Standard state correction is inaccurate.\n' + msg
def test_setup_binding():
# NOTE: switched to yank p-xylene from openmmtools T4-lysozyme because of yank bugs.
#dirname = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit")
dirname = utils.get_data_filename("../examples/p-xylene-implicit/setup/") # Could only figure out how to install things like yank.egg/examples/, rather than yank.egg/yank/examples/
storedir = tempfile.mkdtemp()
run_cli('setup binding amber --setupdir=%(dirname)s --ligname MOL --store %(storedir)s' % vars())
def test_protein_ligand_restraints():
"""Test the restraints in a protein:ligand system.
"""
from yank.yamlbuild import YamlBuilder
from yank.utils import get_data_filename
yaml_script = """
---
options:
minimize: no
verbose: no
output_dir: %(output_directory)s
number_of_iterations: 2
nsteps_per_iteration: 10
temperature: 300*kelvin
molecules:
T4lysozyme:
filepath: %(receptor_filepath)s
p-xylene:
filepath: %(ligand_filepath)s
antechamber:
charge_method: bcc
solvents:
vacuum:
nonbonded_method: NoCutoff
systems:
lys-pxyl:
receptor: T4lysozyme
ligand: p-xylene
solvent: vacuum
leap:
parameters: [oldff/leaprc.ff14SB, leaprc.gaff]
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_restraints: [0.0, 0.5, 1.0]
lambda_electrostatics: [1.0, 1.0, 1.0]
lambda_sterics: [1.0, 1.0, 1.0]
solvent:
alchemical_path:
lambda_electrostatics: [1.0, 1.0, 1.0]
lambda_sterics: [1.0, 1.0, 1.0]
experiments:
system: lys-pxyl
protocol: absolute-binding
restraint:
type: %(restraint_type)s
"""
# Test all possible restraint types.
available_restraint_types = yank.restraints.available_restraint_types()
for restraint_type in available_restraint_types:
print('***********************************')
print('Testing %s restraints...' % restraint_type)
print('***********************************')
output_directory = tempfile.mkdtemp()
data = {
'output_directory':
output_directory,
'restraint_type':
restraint_type,
'receptor_filepath':
get_data_filename(
'tests/data/p-xylene-implicit/181L-pdbfixer.pdb'),
'ligand_filepath':
get_data_filename('tests/data/p-xylene-implicit/p-xylene.mol2'),
}
# run both setup and experiment
yaml_builder = YamlBuilder(yaml_script % data)
yaml_builder.build_experiments()
# Clean up
shutil.rmtree(output_directory)
