def test_atom_populate(self):
db_entry = {
"type": "type",
"mass": 1,
"charge": -1,
"sigma": 0.5,
"epsilon": -0.5,
"dipole": 0,
"diameter": 1,
"rotmass": -1
}
atom1 = Atom(**db_entry)
atom2 = Atom(name="name", resname="resname",
resid=1, x=0.5, y=0.5, z=0.5)
atom1.populate(atom2)
self.assertEqual(atom1.name, "name")
self.assertEqual(atom1.type, "type")
self.assertEqual(atom1.resname, "resname")
self.assertEqual(atom1.resid, 1)
self.assertEqual(atom1.x, 0.5)
self.assertEqual(atom1.y, 0.5)
self.assertEqual(atom1.z, 0.5)
self.assertEqual(atom1.diameter, 1)
self.assertEqual(atom1.rotmass, -1)
self.assertEqual(atom1.charge, -1)
self.assertEqual(atom1.mass, 1)
self.assertEqual(atom1.sigma, 0.5)
self.assertEqual(atom1.epsilon, -0.5)
self.assertEqual(atom1.dipole, 0)
def __init__(self, filename):
super(GROReader, self).__init__()
with open(filename) as f:
last_resid = -1
self.comment = f.readline()
natoms = int(f.readline())
for i in range(natoms):
line = f.readline()
self.atoms.append(
Atom(name=line[10:15].strip(),
resname=line[5:10].strip(),
resid=int(line[0:5]),
x=10 * float(line[20:28]),
y=10 * float(line[28:36]),
z=10 * float(line[36:44])))
if self.atoms[-1].resid != last_resid:
self.molecules.append(Molecule(self.atoms[-1].resname, []))
last_resid = self.atoms[-1].resid
self.molecules[-1].atoms.append(int(line[15:20]) - 1)
line = f.readline()
self.cell = [
10 * float(line[0:10]), 10 * float(line[10:20]),
10 * float(line[20:30])
]
def __init__(self, filename):
super(PDBReader, self).__init__()
with open(filename) as f:
last_resid = -1
for line in f:
if line.startswith("ATOM "):
self.atoms.append(
Atom(name=line[13:17].strip(),
resname=line[17:21].strip(),
resid=int(line[22:26]),
x=float(line[30:38]),
y=float(line[38:46]),
z=float(line[46:54])))
if self.atoms[-1].resid != last_resid:
self.molecules.append(
Molecule(self.atoms[-1].resname, []))
last_resid = self.atoms[-1].resid
self.molecules[-1].atoms.append(int(line[6:11]) - 1)
if line.startswith("CRYST1"):
self.cell = [
float(line[6:15]),
float(line[15:24]),
float(line[24:33]),
float(line[33:40]),
float(line[40:47]),
float(line[47:54])
]
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_compare(self):
self.assertEqual(Atom.compare(1, 1), 1)
self.assertEqual(Atom.compare(None, 1), 1)
self.assertEqual(Atom.compare(1, None), 1)
self.assertEqual(Atom.compare(None, None), None)
with self.assertRaises(ValueError):
Atom.compare(1, 2)
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_store_atom(self):
atom = Atom(name="NamE", type="TypE")
self.assertEqual(atom.name, "NamE")
self.assertEqual(atom.type, "TypE")
def test_create_atom(self):
atom = Atom()