def preprocess_forcefield_files(forcefield_files=None, backend="gmso"):
"""Pre-process foyer Forcefield XML files."""
if forcefield_files is None:
return None
tmp_processed_files = list()
if backend == "gmso":
# Run through the forcefield XML conversion
from gmso.external.convert_foyer_xml import from_foyer_xml
for idx, file in enumerate(forcefield_files):
_, suffix = os.path.split(file)
tempfile = NamedTemporaryFile(suffix=suffix, delete=False)
try:
Validator(ff_file_name=file, debug=False)
from_foyer_xml(
foyer_xml=str(file),
gmso_xml=str(tempfile.name),
overwrite=True,
)
except:
warnings.warn(f"Could not convert {str(file)} as a foyer XML,"
f"attempt to read in as a GMSO XML.")
shutil.copyfile(file, tempfile.name)
tmp_processed_files.append(tempfile.name)
else:
raise FoyerError("Backend not supported." 'Supports backend: "gmso".')
return tmp_processed_files
def test_from_foyer_validate_foyer(self, ff):
from_foyer_xml(
get_fn(ff),
f"{ff}-gmso-converted.xml",
overwrite=True,
validate_foyer=True,
)
def foyer_periodic(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("oplsaa-periodic.xml"), overwrite=True)
gmso_ff = ForceField("oplsaa-periodic_gmso.xml")
return gmso_ff
def foyer_fullerene(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("fullerene.xml"), overwrite=True)
gmso_ff = ForceField("fullerene_gmso.xml")
return gmso_ff
def foyer_urey_bradley(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("charmm36_cooh.xml"), overwrite=True)
gmso_ff = ForceField("charmm36_cooh_gmso.xml")
return gmso_ff
def foyer_rb_torsion(self):
if has_foyer:
import foyer
from foyer.tests.utils import get_fn
from_foyer_xml(get_fn("refs-multi.xml"),
overwrite=True,
validate_foyer=True)
gmso_ff = ForceField("refs-multi_gmso.xml")
return gmso_ff
def test_foyer_file_not_found(self):
file_path = "dummy_name.xml"
with pytest.raises(FileNotFoundError):
from_foyer_xml(file_path, overwrite=True)
def test_foyer_pathlib(self, ff):
file_path = Path(get_fn(ff))
from_foyer_xml(file_path, overwrite=True)
def test_from_foyer_different_name(self, ff):
from_foyer_xml(get_fn(ff), f"{ff}-gmso-converted.xml", overwrite=True)
def test_from_foyer_overwrite_false(self, ff):
from_foyer_xml(get_fn(ff), overwrite=False)
with pytest.raises(FileExistsError):
from_foyer_xml(get_fn(ff), overwrite=False)
def test_from_foyer(self, ff):
from_foyer_xml(get_fn(ff), overwrite=True)
def test_empty_foyer_atomtype(self):
with pytest.raises(ForceFieldParseError):
from_foyer_xml(get_path("empty_foyer.xml"))
