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 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():
# 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_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 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))