def test_write_refs_multiple(self, requests_mock):
import mbuild as mb
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/ja9621760/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JA962170,
)
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/jp0484579/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JP0484579,
)
mol2 = mb.load(get_fn("ethane.mol2"))
oplsaa = Forcefield(forcefield_files=get_fn("refs-multi.xml"))
ethane = oplsaa.apply(mol2, references_file="ethane-multi.bib")
assert os.path.isfile("ethane-multi.bib")
with open(get_fn("ethane-multi.bib")) as file1:
with open("ethane-multi.bib") as file2:
diff = list(
difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
def test_write_bad_ref(requests_mock):
import mbuild as mb
register_mock_request(mocker=requests_mock,
url='http://api.crossref.org/',
path='works/10.1021/garbage_bad_44444444jjjj/transform/application/x-bibtex',
headers={'accept': 'application/x-bibtex'},
status_code=404)
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(forcefield_files=get_fn('refs-bad.xml'))
with pytest.warns(UserWarning):
ethane = oplsaa.apply(mol2, references_file='ethane.bib')
def test_write_bad_ref(self, requests_mock):
import mbuild as mb
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path=
"works/10.1021/garbage_bad_44444444jjjj/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
status_code=404,
)
mol2 = mb.load(get_fn("ethane.mol2"))
oplsaa = Forcefield(forcefield_files=get_fn("refs-bad.xml"))
with pytest.warns(UserWarning):
ethane = oplsaa.apply(mol2, references_file="ethane.bib")
def test_write_refs(requests_mock):
import mbuild as mb
register_mock_request(mocker=requests_mock,
url='http://api.crossref.org/',
path='works/10.1021/ja9621760/transform/application/x-bibtex',
headers={'accept': 'application/x-bibtex'},
text=RESPONSE_BIB_ETHANE_JA962170)
mol2 = mb.load(get_fn('ethane.mol2'))
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2, references_file='ethane.bib')
assert os.path.isfile('ethane.bib')
with open(get_fn('ethane.bib')) as file1:
with open('ethane.bib') as file2:
diff = list(difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
def test_write_refs(self, requests_mock, oplsaa):
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/ja9621760/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JA962170,
)
mol2 = mb.load(get_fn("ethane.mol2"), backend="parmed")
ethane = oplsaa.apply(mol2,
references_file="ethane.bib",
assert_improper_params=False)
assert os.path.isfile("ethane.bib")
with open(get_fn("ethane.bib")) as file1:
with open("ethane.bib") as file2:
diff = list(
difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
