def test_include_file(self):
elba = Parser("data/mol-elba.json")
self.assertTrue("version" in elba)
self.assertTrue("lipids" in elba.version)
molecules = Parser("data/mol-elba.json", section="molecules")
self.assertTrue("DOPC" in molecules)
self.assertTrue("DOPE" in molecules)
def __init__(self, filename=None):
"""
Create a new AtomDatabase object
Args:
filename: Name of atom database file to open.
"""
if filename is None:
filename = os.path.join(os.path.dirname(os.path.dirname(__file__)),
os.path.join("data", "atoms.json"))
db = Parser(filename)
self.atoms = {}
self._lj_table_eps = defaultdict(dict)
# Read atom types
for name, data in db.atoms.items():
if "rotmass" not in data:
data.rotmass = data.mass
self.atoms[name] = Atom(type=name, **data)
for name1, atom1 in self.atoms.items():
for name2, atom2 in self.atoms.items():
try:
h = db.h_values[name1][name2]
except KeyError:
try:
h = db.h_values[name2][name1]
except KeyError:
h = 1.
self._lj_table_eps[name1][name2] = h * sqrt(atom1.epsilon * atom2.epsilon)
def test_json_section(self):
bonds = Parser("data/bonds.json", "bonds")
self.assertTrue("length" in bonds)
self.assertTrue("test" in bonds.length)
self.assertEqual(["test", "100", "1.000"],
bonds.length["test"].split())
def test_json_read(self):
parser = Parser("data/bonds.json")
self.assertTrue("bonds" in parser)
self.assertTrue("length" in parser.bonds)
self.assertTrue("test" in parser.bonds.length)
self.assertEqual(["test", "100", "1.000"],
parser.bonds.length["test"].split())
def __init__(self, filename=None):
if filename is None:
filename = os.path.join(os.path.dirname(os.path.dirname(__file__)),
os.path.join("data", "bonds.json"))
db = Parser(filename)
Param = namedtuple("Param", ["style", "params"])
for tipe in ["length", "angle", "dihedral", "improper"]:
setattr(self, tipe, dict())
for name, bond in db.bonds[tipe].items():
style, *params = bond.split()
getattr(self, tipe)[name] = Param(style, " ".join(params))
def __init__(self, filename=None):
"""
Create a new MolDatabase object
Args:
filename: Name of molecule database file to open.
"""
if filename is None:
filename = os.path.join(os.path.dirname(os.path.dirname(__file__)),
os.path.join("data", "mol-elba.json"))
db = Parser(filename)
try:
self.version = db.version
except KeyError:
self.version = None
self.molecules = {}
for name, data in db.molecules.items():
try:
# Pop this because we want to add it separately
atoms = data.pop("atoms")
except KeyError:
atoms = []
self.molecules[name] = Molecule(**data)
for atom in atoms:
self.molecules[name].atoms[atom.name] = Atom(**atom)
# Allow molecules to be based on templates
# Allow nested templates, but ignore duplicates
for mol in self.molecules.values():
used_templates = set()
while mol.templates:
template = mol.templates.pop()
if template not in used_templates:
mol.extend(self.molecules[template])
used_templates.add(template)
def test_missing_section(self):
with self.assertRaises(KeyError):
Parser("data/bonds.json", "potato")