def setUp(self):
super(BondTestCase, self).setUp()
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_datastore_v3_stub()
self.testbed.init_memcache_stub()
self.name = "Bob McBob"
self.issued_at_epoch = 1528896868
self.expires_at_epoch = 1529081182
self.fake_access_token = str(uuid.uuid4())
self.user_id = str(uuid.uuid4())
data = {"context": {"user": {"name": self.name}}, 'iat': self.issued_at_epoch}
encoded_jwt = jwt.encode(data, 'secret', 'HS256')
fake_token_dict = {FenceKeys.ACCESS_TOKEN_KEY: self.fake_access_token,
FenceKeys.REFRESH_TOKEN_KEY: str(uuid.uuid4()),
FenceKeys.ID_TOKEN: encoded_jwt,
FenceKeys.EXPIRES_AT_KEY: self.expires_at_epoch}
mock_oauth_adapter = OauthAdapter("foo", "bar", "baz", "qux")
mock_oauth_adapter.exchange_authz_code = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.refresh_access_token = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.revoke_refresh_token = MagicMock()
fence_api = self._mock_fence_api(json.dumps({"private_key_id": "asfasdfasdf"}))
sam_api = self._mock_sam_api(self.user_id, "email")
self.bond = Bond(mock_oauth_adapter, fence_api, sam_api,
FenceTokenVendingMachine(fence_api, sam_api, mock_oauth_adapter, provider_name),
provider_name, "/context/user/name")
def parseBonds(self):
'''
read some bond attributes
'''
bonds = {} # dictionary with bond objects, both orientations
atom_pairs = [] # atom index pairs only, unique
for bond in self.tkmol.iterateBonds():
# start, end, bond_type, stereo = numbers
start = bond.source().index()
end = bond.destination().index()
bond_type = bond.bondOrder() # 1,2,3,4 for single, double, triple, aromatic
stereo = bond.bondStereo()
start_atom = self.atoms[start]
end_atom = self.atoms[end]
bond = Bond(self.options, start_atom, end_atom, bond_type, stereo)
# we store both orientations of the bond, since we don't know yet
# which way it will be used
bonds[(start, end)] = bond
bonds[(end, start)] = bond.invert()
atom_pairs.append((start, end))
return bonds, atom_pairs
def testMakeFromBondsWithSuccess(self):
b1 = bond = Bond(angleTests.a1, angleTests.a2, 2, None)
b2 = bond = Bond(angleTests.a2, angleTests.a3, 2, None)
angle = Angle.makeFromBonds(b1, b2)
self.assertEqual(angle.get_a_1(), angleTests.a1)
self.assertEqual(angle.get_a_2(), angleTests.a2)
self.assertEqual(angle.get_a_3(), angleTests.a3)
def test_bond():
b = Bond(0, 1)
assert b.get_bond_order() == 1
b1 = Bond(1, 0)
assert b == b1
assert b.get_nbr_atom_idx(1) == 0
def authenticate(bond_hub: Bond) -> bool:
try:
bond_hub.getDeviceIds()
return True
except RequestConnectionError:
raise CannotConnect
except JSONDecodeError:
return False
def test_creation():
with pytest.raises(ValueError):
Bond(0, 0)
with pytest.raises(ValueError):
Bond(-1, 0)
with pytest.raises(ValueError):
Bond(0, -1)
def link_atoms(self, x, y):
'''
connect atoms with indexes x and y using a pseudo bond.
Helper for connect_fragments
'''
start_atom = self.atoms[x]
end_atom = self.atoms[y]
bond = Bond(self.options, start_atom, end_atom)
bond.set_link()
self.bonds[(x, y)] = bond
self.bonds[(y, x)] = bond.invert()
start_atom.neighbors.append(y)
end_atom.neighbors.append(x)
def bond_dict_maker(file):
"""
Creates a dictionary of Bond objects by reading from a .csv file.
@type file: str
@rtype: dictionary
"""
bonds = {}
with open(file, "r") as f:
reader = csv.reader(f)
next(reader, None)
for row in reader:
name = row[0]
typ = row[1]
# cleaning up data... needs to be in numerical form, so:
# remove the word "years" from term...
term = float(row[2].strip(" years"))
# ... and remove '%' sign from yield
yld = float(row[3].strip('%'))
new_bond = Bond(name, typ, term, yld)
bonds[name] = new_bond
return bonds
async def async_setup_entry(hass: HomeAssistant, entry: ConfigEntry):
"""Set up Bond from a config entry."""
host = entry.data[CONF_HOST]
token = entry.data[CONF_ACCESS_TOKEN]
bond = Bond(bondIp=host, bondToken=token)
hub = BondHub(bond)
await hass.async_add_executor_job(hub.setup)
hass.data[DOMAIN][entry.entry_id] = hub
device_registry = await dr.async_get_registry(hass)
device_registry.async_get_or_create(
config_entry_id=entry.entry_id,
identifiers={(DOMAIN, hub.bond_id)},
manufacturer="Olibra",
name=hub.bond_id,
model=hub.target,
sw_version=hub.fw_ver,
)
for component in PLATFORMS:
hass.async_create_task(
hass.config_entries.async_forward_entry_setup(entry, component))
return True
def add_bond(self, **bond):
"""
Adding bond interaction information:
Sim = LSimu()
Sim.add_bond(typeb="harmonic",idbond=1,K=60,R0=1.))
Sim.add_bond(typeb="fene",idbond=2,K=80,R0=R0,epsilon=1.2,sigma=1)
"""
self.iBond.append(Bond(**bond))
def __init__(self, args_opt):
super(Simulation, self).__init__()
self.control = controller(args_opt)
self.md_info = md_information(self.control)
self.bond = Bond(self.control, self.md_info)
self.angle = Angle(self.control)
self.dihedral = Dihedral(self.control)
self.nb14 = NON_BOND_14(self.control, self.dihedral,
self.md_info.atom_numbers)
self.nb_info = nb_infomation(self.control, self.md_info.atom_numbers,
self.md_info.box_length)
self.LJ_info = Lennard_Jones_Information(self.control)
self.liujian_info = Langevin_Liujian(self.control,
self.md_info.atom_numbers)
self.pme_method = Particle_Mesh_Ewald(self.control, self.md_info)
self.box_length = Tensor(
np.asarray(self.md_info.box_length, np.float32), mstype.float32)
self.file = None
def test_exchange_authz_code_missing_token(self):
data = {"context": {"user": {"name": self.name}}, 'iat': self.issued_at_epoch}
encoded_jwt = jwt.encode(data, 'secret', 'HS256')
fake_token_dict = {FenceKeys.ACCESS_TOKEN_KEY: self.fake_access_token,
FenceKeys.ID_TOKEN: encoded_jwt,
FenceKeys.EXPIRES_AT_KEY: self.expires_at_epoch}
mock_oauth_adapter = OauthAdapter("foo", "bar", "baz", "qux")
mock_oauth_adapter.exchange_authz_code = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.refresh_access_token = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.revoke_refresh_token = MagicMock()
fence_api = self._mock_fence_api(json.dumps({"private_key_id": "asfasdfasdf"}))
sam_api = self._mock_sam_api(self.user_id, "email")
bond = Bond(mock_oauth_adapter, fence_api, sam_api,
FenceTokenVendingMachine(fence_api, sam_api, mock_oauth_adapter, provider_name),
provider_name, "/context/user/name")
with self.assertRaises(endpoints.BadRequestException):
bond.exchange_authz_code("irrelevantString", "redirect", UserInfo(str(uuid.uuid4()), "", "", 30))
def main():
categories = [
Category("Stocks", Stock.factory()),
Category("Bank deposits", BankDeposit.factory()),
Category("Precious metals", Metal.factory()),
Category("Bonds", Bond.factory())
]
root = Tk()
menu = Menu(root, categories)
menu.mainloop()
def proposeBond(self, source, destination, bondCategory, bondFacet,
sourceDescriptor, destinationDescriptor, oldCodelet):
from bond import Bond
bondFacet.buffer = 100.0
sourceDescriptor.buffer = 100.0
destinationDescriptor.buffer = 100.0
bond = Bond(source, destination, bondCategory, bondFacet,
sourceDescriptor, destinationDescriptor)
urgency = bondCategory.bondDegreeOfAssociation()
self.newCodelet('bond-strength-tester', oldCodelet, urgency, bond)
def process_cross_bonds(self):
'''
if cross bonds have been declared:
1. tag the corresponding bonds within the tree as no-ops
2. create a ghost-bond connection from exit_atom to start atom
3. create a drawn duplicate of the cross bond
4. append 2 and 3 as branch to the exit atom
this is unfortunately all a little hackish.
'''
cross_bonds = self.options['cross_bond']
for start1, end1 in cross_bonds:
start = start1 - 1
end = end1 - 1
# retrieve the matching bond that's in the parse tree
for combo in ((start, end), (end, start)):
if combo in self.seen_bonds:
bond = self.bonds[combo]
break
else: # referenced bond doesn't exist
raise MCFError, "bond %s-%s doesn't exist" % (start1, end1)
# very special case: the bond _might_ already be the very
# last one to be rendered - then we just tag it
if self.exit_bond.descendants and bond is self.exit_bond.descendants[-1]:
bond.set_cross(last=True)
continue
# create a copy of the bond that will be rendered later
bond_copy = bond.clone()
# tag original bond as no-op
bond.set_link()
# modify bond copy
bond_copy.set_cross()
bond_copy.to_phantom = True # don't render atom again
bond_copy.descendants = [] # forget copied descendants
if bond_copy.start_atom is not self.exit_atom: # usual case
# create a pseudo bond from the exit atom to the start atom
# pseudo bond will not be drawn, serves only to "move the pen"
pseudo_bond = Bond(self.options,
self.exit_atom,
bond_copy.start_atom)
pseudo_bond.set_link()
pseudo_bond.to_phantom = True # don't render the atom, either
bond_copy.parent = pseudo_bond
pseudo_bond.descendants.append(bond_copy)
pseudo_bond.parent = self.exit_bond
self.exit_bond.descendants.append(pseudo_bond)
else: # occasionally, the molecule's exit atom may be the starting point
# of the elevated bond
self.exit_bond.descendants.append(bond_copy)
async def validate_input(hass: core.HomeAssistant, data):
"""Validate the user input allows us to connect."""
def authenticate(bond_hub: Bond) -> bool:
try:
bond_hub.getDeviceIds()
return True
except RequestConnectionError:
raise CannotConnect
except JSONDecodeError:
return False
bond = Bond(data[CONF_HOST], data[CONF_ACCESS_TOKEN])
if not await hass.async_add_executor_job(authenticate, bond):
raise InvalidAuth
# Return info that you want to store in the config entry.
return {"title": data[CONF_HOST]}
def __init__(self, obj):
self.damping = 20
if self.name == "Lone Pair":
self.repulsionfactor = 1.25
self.lengthfactor = 10
else:
self.repulsionfactor = 1
self.lengthfactor = 20
self.maxdistance = 100
self.distancefactor = 100
self.strengthfactor = 100
self.totalforce = Vector([0, 0, 0])
##from bond.py
self.bond = Bond(self)
self.molecule = None
if "doubles" in self:
self.charge = self.get_charge()
self.formalCharge = self.get_formal_charge()
def setup(hass, config):
"""Your controller/hub specific code."""
from bond import Bond
# Assign configuration variables.
# The configuration check takes care they are present.
conf = config[DOMAIN]
host = conf[CONF_HOST]
token = conf[CONF_TOKEN]
# Setup connection with devices/cloud
bond = Bond(bondIp=host, bondToken=token)
hass.data[DOMAIN] = {'bond_hub': bond}
hass.helpers.discovery.load_platform('light', DOMAIN, {}, config)
hass.helpers.discovery.load_platform('fan', DOMAIN, {}, config)
return True
def create_provider(provider_name):
client_id = config.get(provider_name, 'CLIENT_ID')
client_secret = config.get(provider_name, 'CLIENT_SECRET')
open_id_config_url = config.get(provider_name,
'OPEN_ID_CONFIG_URL')
fence_base_url = config.get(provider_name, 'FENCE_BASE_URL')
user_name_path_expr = config.get(provider_name,
'USER_NAME_PATH_EXPR')
sam_base_url = config.get('sam', 'BASE_URL')
oauth_adapter = OauthAdapter(client_id, client_secret,
open_id_config_url, provider_name)
fence_api = FenceApi(fence_base_url)
sam_api = SamApi(sam_base_url)
fence_tvm = FenceTokenVendingMachine(fence_api, sam_api,
oauth_adapter, provider_name)
return BondProvider(
fence_tvm,
Bond(oauth_adapter, fence_api, sam_api, fence_tvm,
provider_name, user_name_path_expr))
def __readDataFull(self):
flagAtomsBegan = False
flagVelocitiesBegan = False
flagBondsBegan = False
flagAnglesBegan = False
flagDihedralsBegan = False
flagImpropersBegan = False
flagMassesBegan = False
flagPotentialBegan = False
flagPairCoeffsBegan = False
flagBondCoeffsBegan = False
flagAngleCoeffsBegan = False
flagDihedralCoeffsBegan = False
flagImproperCoeffsBegan = False
potential = None
atoms = []
atomsNumber = 0
atomTypesNumber = 0
bonds = []
bondsNumber = 0
bondTypesNumber = 0
angles = []
anglesNumber = 0
angleTypesNumber = 0
dihedrals = []
dihedralsNumber = 0
dihedralTypesNumber = 0
impropers = []
impropersNumber = 0
improperTypesNumber = 0
comment = None
zRangesLineNumber = None
xlo = None
xhi = None
ylo = None
yhi = None
zlo = None
zhi = None
inclines = True
masses = []
pairCoeffs = []
bondCoeffs = []
angleCoeffs = []
dihedralCoeffs = []
improperCoeffs = []
with open(self['fname'], 'r') as f:
print('ParserLAMMPSData: started reading from file ',
self['fname'])
for lineNumber, line in enumerate(f):
if lineNumber == 0:
comment = line
elif line.endswith(' atoms\n'):
atomsNumber = int(line.split()[0])
atoms = [None for i in range(atomsNumber)]
elif line.endswith(' bonds\n'):
bondsNumber = int(line.split()[0])
bonds = [None for i in range(bondsNumber)]
elif line.endswith(' angles\n'):
anglesNumber = int(line.split()[0])
angles = [None for i in range(anglesNumber)]
elif line.endswith(' dihedrals\n'):
dihedralsNumber = int(line.split()[0])
dihedrals = [None for i in range(dihedralsNumber)]
elif line.endswith(' impropers\n'):
impropersNumber = int(line.split()[0])
impropers = [None for i in range(impropersNumber)]
elif line.endswith('atom types\n'):
atomTypesNumber = int(line.split()[0])
elif line.endswith('bond types\n'):
bondTypesNumber = int(line.split()[0])
elif line.endswith('angle types\n'):
angleTypesNumber = int(line.split()[0])
elif line.endswith('dihedral types\n'):
dihedralTypesNumber = int(line.split()[0])
elif line.endswith('improper types\n'):
improperTypesNumber = int(line.split()[0])
elif line.endswith('xlo xhi\n'):
xlo = float(line.split()[0])
xhi = float(line.split()[1])
elif line.endswith('ylo yhi\n'):
ylo = float(line.split()[0])
yhi = float(line.split()[1])
elif line.endswith('zlo zhi\n'):
zlo = float(line.split()[0])
zhi = float(line.split()[1])
zRangesLineNumber = lineNumber
elif (zRangesLineNumber is not None
and # String with inclines,
lineNumber == zRangesLineNumber): # it may be absent.
if len(line.split()) == 0:
continue
if line.split()[0] != '0':
continue
inclines = False
elif line.startswith('Masses'):
flagMassesBegan = True
elif line.startswith('Pair Coeffs'):
flagPotentialBegan = True
flagPairCoeffsBegan = True
elif line.startswith('Bond Coeffs'):
flagBondCoeffsBegan = True
elif line.startswith('Angle Coeffs'):
flagAngleCoeffsBegan = True
elif line.startswith('Dihedral Coeffs'):
flagDihedralCoeffsBegan = True
elif line.startswith('Improper Coeffs'):
flagImproperCoeffsBegan = True
elif line.startswith('Atoms'):
flagAtomsBegan = True
elif line.startswith('Velocities'):
flagVelocitiesBegan = True
elif line.startswith('Bonds'):
flagBondsBegan = True
flagVelocitiesBegan = True # this is not good
# they really did not begin
elif line.startswith('Angles'):
flagAnglesBegan = True
elif line.startswith('Dihedrals'):
flagDihedralsBegan = True
elif line.startswith('Impropers'):
flagImpropersBegan = True
elif flagMassesBegan and not flagPotentialBegan: # Reading masses
if len(line.split()) == 0:
continue
masses.append(float(line.split()[1]))
elif flagPotentialBegan and not flagAtomsBegan:
if len(line.split()) == 0:
continue
if flagPairCoeffsBegan and not flagBondCoeffsBegan:
pairCoeffs.append(
[float(line.split()[1]),
float(line.split()[2])])
elif flagBondCoeffsBegan and not flagAngleCoeffsBegan:
bondCoeffs.append(
[float(line.split()[1]),
float(line.split()[2])])
elif flagAngleCoeffsBegan and not flagDihedralCoeffsBegan:
angleCoeffs.append(
[float(line.split()[1]),
float(line.split()[2])])
elif flagDihedralCoeffsBegan and not flagImproperCoeffsBegan:
dihedralCoeffs.append([
float(line.split()[1]),
float(line.split()[2]),
float(line.split()[3])
])
elif flagImproperCoeffsBegan:
improperCoeffs.append([
float(line.split()[1]),
float(line.split()[2]),
float(line.split()[3])
])
elif flagAtomsBegan and not flagVelocitiesBegan:
ls = line.split()
if len(ls) < 10:
continue
atomNumber = int(ls[0])
moleculeNumber = int(ls[1])
atomType = int(ls[2])
atomCharge = float(ls[3])
atomX = float(ls[4])
atomY = float(ls[5])
atomZ = float(ls[6])
atomFlagOne = int(ls[7])
atomFlagTwo = int(ls[8])
atomFlagThree = int(ls[9])
if len(ls) > 10:
if len(ls) == 11:
comment = ls[10]
else:
comment = " ".join(*ls[10:-1:1])
else:
comment = None
atoms[atomNumber - 1] = Atom(
lam_id=atomNumber,
x=atomX,
y=atomY,
z=atomZ,
molecule=moleculeNumber,
ff_type=atomType,
ff_charge=atomCharge,
v=None,
flags=[atomFlagOne, atomFlagTwo, atomFlagThree],
comment=comment)
elif flagVelocitiesBegan and not flagBondsBegan:
ls = line.split()
if len(ls) < 4:
continue
atomNumber = int(ls[0]) # Index = number - 1, because
# indices start from 0,
# while numbers - from 1.
atomVx = float(ls[1])
atomVy = float(ls[2])
atomVz = float(ls[3])
# TODO
#atoms[atomNumber - 1].setAtomVx(atomVx=atomVx)
#atoms[atomNumber - 1].setAtomVy(atomVy=atomVy)
#atoms[atomNumber - 1].setAtomVz(atomVz=atomVz)
elif flagBondsBegan and not flagAnglesBegan:
ls = line.split()
if len(ls) < 4:
continue
bondNumber = int(ls[0])
bondType = int(ls[1])
atomOneNumber = int(ls[2])
atomTwoNumber = int(ls[3])
atomOne = atoms[atomOneNumber - 1]
atomTwo = atoms[atomTwoNumber - 1]
# TODO
#neighbors = atomOne.getProperty('neighbors')
#if neighbors is None:
# neighbors = []
#neighbors.append(atomTwo)
#atomOne.updateProperty('neighbors', neighbors)
#neighbors = atomTwo.getProperty('neighbors')
#if neighbors is None:
# neighbors = []
#neighbors.append(atomOne)
#atomTwo.updateProperty('neighbors', neighbors)
bonds[bondNumber - 1] = Bond(lam_id=bondNumber,
ff_type=bondType,
atomOne=atomOne,
atomTwo=atomTwo)
# TODO
#bonds[bondNumber - 1].setBoxBoundaries([xlo, xhi,
# ylo, yhi,
# zlo, zhi])
elif flagAnglesBegan and not flagDihedralsBegan:
ls = line.split()
if len(ls) < 5:
continue
angleNumber = int(ls[0])
angleType = int(ls[1])
atomOneNumber = int(ls[2])
atomTwoNumber = int(ls[3])
atomThreeNumber = int(ls[4])
atomOne = atoms[atomOneNumber - 1]
atomTwo = atoms[atomTwoNumber - 1]
atomThree = atoms[atomThreeNumber - 1]
angles[angleNumber - 1] = Angle(lam_id=angleNumber,
ff_type=angleType,
atomOne=atomOne,
atomTwo=atomTwo,
atomThree=atomThree)
elif flagDihedralsBegan and not flagImpropersBegan:
ls = line.split()
if len(ls) < 6:
continue
dihedralNumber = int(ls[0])
dihedralType = int(ls[1])
atomOneNumber = int(ls[2])
atomTwoNumber = int(ls[3])
atomThreeNumber = int(ls[4])
atomFourNumber = int(ls[5])
atomOne = atoms[atomOneNumber - 1]
atomTwo = atoms[atomTwoNumber - 1]
atomThree = atoms[atomThreeNumber - 1]
atomFour = atoms[atomFourNumber - 1]
dihedrals[dihedralNumber - 1] = Dihedral(
lam_id=dihedralNumber,
ff_type=dihedralType,
atomOne=atomOne,
atomTwo=atomTwo,
atomThree=atomThree,
atomFour=atomFour)
elif flagImpropersBegan:
ls = line.split()
if len(ls) < 6:
continue
improperNumber = int(ls[0])
improperType = int(ls[1])
atomOneNumber = int(ls[2])
atomTwoNumber = int(ls[3])
atomThreeNumber = int(ls[4])
atomFoutNumber = int(ls[5])
atomOne = atoms[atomOneNumber - 1]
atomTwo = atoms[atomTwoNumber - 1]
atomThree = atoms[atomThreeNumber - 1]
atomFour = atoms[atomFourNumber - 1]
impropers[improperNumber - 1] = Improper(
lam_id=improperNumber,
ff_type=improperType,
atomOne=atomOne,
atomTwo=atomTwo,
atomThree=atomThree,
atomFour=atomFour)
else:
if len(line.split()) == 0:
continue
print('This string does not seem to contain data:', line)
self['parsedComment'] = comment
self['parsedPotential'] = potential
self['parsedAtoms'] = atoms
self['parsedBonds'] = bonds
self['parsedAngles'] = angles
self['parsedDihedrals'] = dihedrals
self['parsedImpropers'] = impropers
self['parsedAtomTypesNumber'] = atomTypesNumber
self['parsedBondTypesNumber'] = bondTypesNumber
self['parsedAngleTypesNumber'] = angleTypesNumber
self['parsedDihedralTypesNumber'] = dihedralTypesNumber
self['parsedImproperTypesNumber'] = improperTypesNumber
self['parsedBoundaries'] = [xlo, xhi, ylo, yhi, zlo, zhi]
self['parsedMasses'] = masses
self['parsedInclines'] = inclines
self['parsedPairCoeffs'] = pairCoeffs
self['parsedBondCoeffs'] = bondCoeffs
self['parsedAngleCoeffs'] = angleCoeffs
self['parsedDihedralCoeffs'] = dihedralCoeffs
self['parsedImproperCoeffs'] = improperCoeffs
print('ParserLAMMPSData finished reading')
inventory = Inventory()
print('add cookies')
cookies = Good('cookies', 5)
inventory.add(cookies)
pprint(inventory.goods)
print('add more cookies')
cookies2 = Good('cookies', 5)
inventory.add(cookies2)
pprint(inventory.goods)
print('remove 5 cookies')
inventory.remove(cookies)
pprint(inventory.goods)
inventory.add(PullOption(execution_price=5, underlying='intel'))
pprint(inventory.contracts)
bond1 = Bond(0, num_payments=10, value_payments=1, value_maturity=10)
inventory.add(bond1)
inventory.add(Bond(0, num_payments=100, value_payments=-1,
value_maturity=-100))
pprint(inventory.contracts)
scenario = {
('price', 'cookies'): 1,
('price', 'intel'): 7,
'interestrate': 0.01
}
print('assets')
pprint(inventory.valued_assets(scenario, usgap))
print('liablities')
def generate_interactions_o(self,
interaction_name,
bond="harmonic",
SPB=False,
radius=10,
cutoff=1.15,
reducedv_factor=1,
khun=1.):
if bond == "harmonic":
temp1 = "bond_style harmonic\n"
temp2 = "bond_coeff %i %.2f %.2f"
ene = 350
if bond == "fene":
if SPB:
temp1 = "bond_style hybrid harmonic fene\n"
temp2 = "bond_coeff %i fene %.2f %.2f %.2f %.2f"
else:
temp1 = "bond_style fene\n"
temp2 = "bond_coeff %i %.2f %.2f %.2f %.2f"
ene = 30 * 1
Bond = [temp1]
if bond == "fene":
Bond.append("special_bonds fene\n")
ene_ratio = 1 #.35
#Bond.append("special_bonds 0.0 1.0 1.0\n")
if SPB and False:
#print radius
Pair = [
"pair_style hybrid lj/cut 3.0 gauss/cut %.2f \n" %
(2 * radius) + "pair_modify shift yes\n"
]
else:
Pair = ["pair_style lj/cut 1.4 \n" + "pair_modify shift yes\n"]
Angle = ["angle_style cosine/delta\n"]
Angle = ["angle_style harmonic\n"]
keyl = range(1, len(self.natom) + 1)
for t1 in keyl:
for t2 in keyl:
if t2 >= t1:
if not self.liaison.has_key("%s-%s" % (t1, t2)):
print "Warning liaison between {0} and {1} not defined".format(
t1, t2)
dist, tybe_b = self.liaison["%s-%s" % (t1, t2)]
if cutoff is not None:
cut = dist * cutoff
else:
cut = dist * pow(2., 1 / 6.)
odist = copy.deepcopy(dist)
#dist=1
if bond == "fene":
Bond.append(
temp2 %
(tybe_b, ene_ratio * ene /
(dist * dist), 1.5 * dist, ene_ratio, dist) +
"\n")
else:
Bond.append(temp2 % (tybe_b, ene, dist) + "\n")
dist = odist
precise = ""
if SPB and False:
precise = "lj/cut"
reduced = 1
if t1 == t2 and t1 == 3:
reduced = 1
else:
reduced = reducedv_factor
Pair.append("""pair_coeff %s %s %s %.1f %.2f %.2f\n""" %
(t1, t2, precise, ene_ratio, dist * reduced,
cut * reduced))
if self.angle_def is not None and self.Angle != []:
for t3 in keyl:
if t3 >= t2:
dist, tybe_b = self.angle_def["%s-%s-%s" %
(t1, t2, t3)]
k = khun / 2. * dist # dist = 1 if no ribo involved else 0
Angle.append("angle_coeff %i %.3f 180.0\n" %
(tybe_b, k))
if SPB:
if bond == "fene":
Bond.append("bond_coeff %i harmonic 0 0 \n" %
(self.liaison["spb"][1]))
spbond = "bond_coeff %i harmonic %.1f %.1f\n" % (
self.liaison["spb"][1], 10, microtubule / realsigma)
else:
Bond.append("bond_coeff %i 0 0 \n" % (self.liaison["spb"][1]))
spbond = "bond_coeff %i %.1f %.1f\n" % (
self.liaison["spb"][1], 10, microtubule / realsigma)
n_i = len(diameter) / 2
for t1 in range(len(diameter)):
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n""" %
(t1 + 1, num_particle["spb"], precise, dist, cut))
Pair.append(
"""pair_coeff %i %i %s 0. %.2f %.2f\n""" %
(num_particle["spb"], num_particle["spb"], precise, dist, cut))
g = open(interaction_name, "w")
g.write("".join(Bond) + "\n")
g.write("".join(Pair) + "\n")
if self.Angle != []:
g.write("".join(Angle))
class BondTestCase(unittest.TestCase):
def setUp(self):
super(BondTestCase, self).setUp()
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_datastore_v3_stub()
self.testbed.init_memcache_stub()
self.name = "Bob McBob"
self.issued_at_epoch = 1528896868
self.expires_at_epoch = 1529081182
self.fake_access_token = str(uuid.uuid4())
self.user_id = str(uuid.uuid4())
data = {"context": {"user": {"name": self.name}}, 'iat': self.issued_at_epoch}
encoded_jwt = jwt.encode(data, 'secret', 'HS256')
fake_token_dict = {FenceKeys.ACCESS_TOKEN_KEY: self.fake_access_token,
FenceKeys.REFRESH_TOKEN_KEY: str(uuid.uuid4()),
FenceKeys.ID_TOKEN: encoded_jwt,
FenceKeys.EXPIRES_AT_KEY: self.expires_at_epoch}
mock_oauth_adapter = OauthAdapter("foo", "bar", "baz", "qux")
mock_oauth_adapter.exchange_authz_code = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.refresh_access_token = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.revoke_refresh_token = MagicMock()
fence_api = self._mock_fence_api(json.dumps({"private_key_id": "asfasdfasdf"}))
sam_api = self._mock_sam_api(self.user_id, "email")
self.bond = Bond(mock_oauth_adapter, fence_api, sam_api,
FenceTokenVendingMachine(fence_api, sam_api, mock_oauth_adapter, provider_name),
provider_name, "/context/user/name")
def tearDown(self):
ndb.get_context().clear_cache() # Ensure data is truly flushed from datastore/memcache
self.testbed.deactivate()
def test_exchange_authz_code(self):
issued_at, username = self.bond.exchange_authz_code("irrelevantString", "redirect", UserInfo(str(uuid.uuid4()), "", "", 30))
self.assertEqual(self.name, username)
self.assertEqual(datetime.fromtimestamp(self.issued_at_epoch), issued_at)
def test_exchange_authz_code_missing_token(self):
data = {"context": {"user": {"name": self.name}}, 'iat': self.issued_at_epoch}
encoded_jwt = jwt.encode(data, 'secret', 'HS256')
fake_token_dict = {FenceKeys.ACCESS_TOKEN_KEY: self.fake_access_token,
FenceKeys.ID_TOKEN: encoded_jwt,
FenceKeys.EXPIRES_AT_KEY: self.expires_at_epoch}
mock_oauth_adapter = OauthAdapter("foo", "bar", "baz", "qux")
mock_oauth_adapter.exchange_authz_code = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.refresh_access_token = MagicMock(return_value=fake_token_dict)
mock_oauth_adapter.revoke_refresh_token = MagicMock()
fence_api = self._mock_fence_api(json.dumps({"private_key_id": "asfasdfasdf"}))
sam_api = self._mock_sam_api(self.user_id, "email")
bond = Bond(mock_oauth_adapter, fence_api, sam_api,
FenceTokenVendingMachine(fence_api, sam_api, mock_oauth_adapter, provider_name),
provider_name, "/context/user/name")
with self.assertRaises(endpoints.BadRequestException):
bond.exchange_authz_code("irrelevantString", "redirect", UserInfo(str(uuid.uuid4()), "", "", 30))
def test_generate_access_token(self):
token = str(uuid.uuid4())
TokenStore.save(user_id=self.user_id,
refresh_token_str=token,
issued_at=datetime.fromtimestamp(self.issued_at_epoch),
username=self.name,
provider_name=provider_name)
access_token, expires_at = self.bond.generate_access_token(UserInfo(str(uuid.uuid4()), "", "", 30))
self.assertEqual(self.fake_access_token, access_token)
self.assertEqual(datetime.fromtimestamp(self.expires_at_epoch), expires_at)
def test_generate_access_token_errors_when_missing_token(self):
self.assertRaises(Bond.MissingTokenError, self.bond.generate_access_token, UserInfo(str(uuid.uuid4()), "", "", 30))
def test_revoke_link_exists(self):
token = str(uuid.uuid4())
TokenStore.save(self.user_id, token, datetime.now(), self.name, provider_name)
user_info = UserInfo(str(uuid.uuid4()), "", "", 30)
self.bond.fence_tvm.get_service_account_key_json(user_info)
self.assertIsNotNone(self.bond.fence_tvm._fence_service_account_key(self.user_id).get())
self.bond.unlink_account(user_info)
self.assertIsNone(self.bond.fence_tvm._fence_service_account_key(self.user_id).get())
self.assertIsNone(TokenStore.lookup(self.user_id, provider_name))
self.bond.oauth_adapter.revoke_refresh_token.assert_called_once()
self.bond.fence_api.delete_credentials_google.assert_called_once()
def test_revoke_link_does_not_exists(self):
user_info = UserInfo(str(uuid.uuid4()), "", "", 30)
self.bond.unlink_account(user_info)
def test_link_info_exists(self):
token = str(uuid.uuid4())
TokenStore.save(user_id=self.user_id,
refresh_token_str=token,
issued_at=datetime.fromtimestamp(self.issued_at_epoch),
username=self.name,
provider_name=provider_name)
link_info = self.bond.get_link_info(UserInfo(str(uuid.uuid4()), "", "", 30))
self.assertEqual(token, link_info.token)
def test_link_info_not_exists(self):
link_info = self.bond.get_link_info(UserInfo(str(uuid.uuid4()), "", "", 30))
self.assertIsNone(link_info)
@staticmethod
def _mock_fence_api(service_account_json):
fence_api = FenceApi("")
fence_api.get_credentials_google = MagicMock(return_value=service_account_json)
fence_api.delete_credentials_google = MagicMock()
return fence_api
@staticmethod
def _mock_sam_api(subject_id, email):
sam_api = SamApi("")
sam_api.user_info = MagicMock(return_value={SamKeys.USER_ID_KEY: subject_id, SamKeys.USER_EMAIL_KEY: email})
return sam_api
def group_builder(codelet):
# update strength value of the group
group = codelet.arguments[0]
__showWhichStringObjectIsFrom(group)
equivalent = group.string.equivalentGroup(group)
if equivalent:
logging.info('already exists...activate descriptors & fizzle')
group.activateDescriptions()
equivalent.addDescriptions(group.descriptions)
return
# check to see if all objects are still there
for o in group.objectList:
assert o in workspace.objects
# check to see if bonds are there of the same direction
incompatibleBonds = [] # incompatible bond list
if len(group.objectList) > 1:
previous = group.objectList[0]
for objekt in group.objectList[1:]:
leftBond = objekt.leftBond
if leftBond:
if leftBond.leftObject == previous:
continue
if leftBond.directionCategory == group.directionCategory:
continue
incompatibleBonds += [leftBond]
previous = objekt
next_object = group.objectList[-1]
for objekt in reversed(group.objectList[:-1]):
rightBond = objekt.rightBond
if rightBond:
if rightBond.rightObject == next_object:
continue
if rightBond.directionCategory == group.directionCategory:
continue
incompatibleBonds += [rightBond]
next_object = objekt
# if incompatible bonds exist - fight
group.updateStrength()
assert __fightIncompatibles(incompatibleBonds, group, 'bonds', 1.0, 1.0)
# fight incompatible groups
# fight all groups containing these objects
incompatibleGroups = group.getIncompatibleGroups()
assert __fightIncompatibles(incompatibleGroups, group, 'Groups', 1.0, 1.0)
for incompatible in incompatibleBonds:
incompatible.break_the_structure()
# create new bonds
group.bondList = []
for i in range(1, len(group.objectList)):
object1 = group.objectList[i - 1]
object2 = group.objectList[i]
if not object1.rightBond:
if group.directionCategory == slipnet.right:
source = object1
destination = object2
else:
source = object2
destination = object1
category = group.groupCategory.getRelatedNode(slipnet.bondCategory)
facet = group.facet
newBond = Bond(source, destination, category, facet,
source.getDescriptor(facet),
destination.getDescriptor(facet))
newBond.buildBond()
group.bondList += [object1.rightBond]
for incompatible in incompatibleGroups:
incompatible.break_the_structure()
group.buildGroup()
group.activateDescriptions()
logging.info('building group')
class Simulation(nn.Cell):
"""class simulation"""
def __init__(self, args_opt):
super(Simulation, self).__init__()
self.control = controller(args_opt)
self.md_info = md_information(self.control)
self.bond = Bond(self.control, self.md_info)
self.angle = Angle(self.control)
self.dihedral = Dihedral(self.control)
self.nb14 = NON_BOND_14(self.control, self.dihedral,
self.md_info.atom_numbers)
self.nb_info = nb_infomation(self.control, self.md_info.atom_numbers,
self.md_info.box_length)
self.LJ_info = Lennard_Jones_Information(self.control)
self.liujian_info = Langevin_Liujian(self.control,
self.md_info.atom_numbers)
self.pme_method = Particle_Mesh_Ewald(self.control, self.md_info)
self.box_length = Tensor(
np.asarray(self.md_info.box_length, np.float32), mstype.float32)
self.file = None
def Main_Before_Calculate_Force(self):
"""Main Before Calculate Force"""
_ = self.md_info.MD_Information_Crd_To_Uint_Crd()
self.md_info.uint_crd_with_LJ = (self.md_info.uint_crd,
self.LJ_info.atom_LJ_type,
self.md_info.charge)
return self.md_info.uint_crd, self.md_info.uint_crd_with_LJ
def Initial_Neighbor_List_Update(self, not_first_time):
"""Initial Neighbor List Update"""
res = self.nb_info.NeighborListUpdate(self.md_info.crd,
self.md_info.crd_old,
self.md_info.uint_crd,
self.md_info.crd_to_uint_crd_cof,
self.md_info.uint_dr_to_dr_cof,
self.box_length, not_first_time)
return res
def Main_Calculate_Force(self):
"""main calculate force"""
self.bond.atom_numbers = self.md_info.atom_numbers
md_info = self.md_info
LJ_info = self.LJ_info
nb_info = self.nb_info
pme_method = self.pme_method
bond_frc, _ = self.bond.Bond_Force_With_Atom_Energy(
md_info.uint_crd, md_info.uint_dr_to_dr_cof)
frc_t = bond_frc.asnumpy()
angle_frc, _ = self.angle.Angle_Force_With_Atom_Energy(
md_info.uint_crd, md_info.uint_dr_to_dr_cof)
frc_t += angle_frc.asnumpy()
dihedral_frc, _ = self.dihedral.Dihedral_Force_With_Atom_Energy(
md_info.uint_crd, md_info.uint_dr_to_dr_cof)
frc_t += dihedral_frc.asnumpy()
nb14_frc, _ = self.nb14.Non_Bond_14_LJ_CF_Force_With_Atom_Energy(
md_info.uint_crd_with_LJ, md_info.uint_dr_to_dr_cof, LJ_info.LJ_A,
LJ_info.LJ_B)
frc_t += nb14_frc.asnumpy()
lj_frc = LJ_info.LJ_Force_With_PME_Direct_Force(
md_info.atom_numbers, md_info.uint_crd_with_LJ,
md_info.uint_dr_to_dr_cof, nb_info.nl_atom_numbers,
nb_info.nl_atom_serial, nb_info.cutoff, pme_method.beta)
frc_t += lj_frc.asnumpy()
pme_excluded_frc = pme_method.PME_Excluded_Force(
md_info.uint_crd, md_info.uint_dr_to_dr_cof, md_info.charge,
nb_info.excluded_list_start, nb_info.excluded_list,
nb_info.excluded_numbers)
frc_t += pme_excluded_frc.asnumpy()
pme_reciprocal_frc = pme_method.PME_Reciprocal_Force(
md_info.uint_crd, md_info.charge)
frc_t += pme_reciprocal_frc.asnumpy()
self.md_info.frc = Tensor(frc_t, mstype.float32)
return self.md_info.frc
def Main_Calculate_Energy(self):
"""main calculate energy"""
_ = self.bond.Bond_Energy(self.md_info.uint_crd,
self.md_info.uint_dr_to_dr_cof)
_ = self.angle.Angle_Energy(self.md_info.uint_crd,
self.md_info.uint_dr_to_dr_cof)
_ = self.dihedral.Dihedral_Engergy(self.md_info.uint_crd,
self.md_info.uint_dr_to_dr_cof)
_ = self.nb14.Non_Bond_14_LJ_CF_Energy(self.md_info.uint_crd_with_LJ,
self.md_info.uint_dr_to_dr_cof,
self.LJ_info.LJ_A,
self.LJ_info.LJ_B)
_ = self.LJ_info.LJ_Energy(self.md_info.uint_crd_with_LJ,
self.md_info.uint_dr_to_dr_cof,
self.nb_info.nl_atom_numbers,
self.nb_info.nl_atom_serial,
self.nb_info.cutoff_square)
_ = self.pme_method.PME_Energy(
self.md_info.uint_crd, self.md_info.charge,
self.nb_info.nl_atom_numbers, self.nb_info.nl_atom_serial,
self.md_info.uint_dr_to_dr_cof, self.nb_info.excluded_list_start,
self.nb_info.excluded_list, self.nb_info.excluded_numbers)
_ = self.pme_method.Energy_Device_To_Host()
def Main_After_Calculate_Energy(self):
"""main after calculate energy"""
md_info = self.md_info
LJ_info = self.LJ_info
bond = self.bond
angle = self.angle
dihedral = self.dihedral
nb14 = self.nb14
pme_method = self.pme_method
md_info.total_potential_energy = 0
md_info.total_potential_energy += bond.sigma_of_bond_ene
md_info.total_potential_energy += angle.sigma_of_angle_ene
md_info.total_potential_energy += dihedral.sigma_of_dihedral_ene
md_info.total_potential_energy += nb14.nb14_lj_energy_sum + nb14.nb14_cf_energy_sum
md_info.total_potential_energy += LJ_info.LJ_energy_sum
pme_method.Energy_Device_To_Host()
md_info.total_potential_energy += pme_method.ee_ene
print("md_info.total_potential_energy", md_info.total_potential_energy)
def Main_Iteration_2(self):
"""main iteration2"""
md_info = self.md_info
control = self.control
liujian_info = self.liujian_info
if md_info.mode > 0 and int(control.Command_Set["thermostat"]) == 1:
md_info.vel, md_info.crd, md_info.frc, md_info.acc = liujian_info.MD_Iteration_Leap_Frog(
md_info.d_mass_inverse, md_info.vel, md_info.crd, md_info.frc)
def Main_After_Iteration(self):
"""main after iteration"""
md_info = self.md_info
nb_info = self.nb_info
md_info.Centerize()
_ = nb_info.NeighborListUpdate(md_info.crd,
md_info.crd_old,
md_info.uint_crd,
md_info.crd_to_uint_crd_cof,
md_info.uint_dr_to_dr_cof,
self.box_length,
not_first_time=1)
def Main_Print(self):
"""compute the temperature"""
md_info = self.md_info
temperature = md_info.MD_Information_Temperature()
md_info.h_temperature = temperature
steps = md_info.steps
temperature = temperature.asnumpy()
total_potential_energy = md_info.total_potential_energy.asnumpy()
sigma_of_bond_ene = self.bond.sigma_of_bond_ene.asnumpy()
sigma_of_angle_ene = self.angle.sigma_of_angle_ene.asnumpy()
sigma_of_dihedral_ene = self.dihedral.sigma_of_dihedral_ene.asnumpy()
nb14_lj_energy_sum = self.nb14.nb14_lj_energy_sum.asnumpy()
nb14_cf_energy_sum = self.nb14.nb14_cf_energy_sum.asnumpy()
LJ_energy_sum = self.LJ_info.LJ_energy_sum.asnumpy()
ee_ene = self.pme_method.ee_ene.asnumpy()
print(
"_steps_ _TEMP_ _TOT_POT_ENE_ _BOND_ENE_ "
"_ANGLE_ENE_ _DIHEDRAL_ENE_ _14LJ_ENE_ _14CF_ENE_ _LJ_ENE_ _CF_PME_ENE_"
)
print("{:>7.0f} {:>7.3f} {:>11.3f}".format(
steps, float(temperature), float(total_potential_energy)),
end=" ")
if self.bond.bond_numbers > 0:
print("{:>10.3f}".format(float(sigma_of_bond_ene)), end=" ")
if self.angle.angle_numbers > 0:
print("{:>11.3f}".format(float(sigma_of_angle_ene)), end=" ")
if self.dihedral.dihedral_numbers > 0:
print("{:>14.3f}".format(float(sigma_of_dihedral_ene)), end=" ")
if self.nb14.nb14_numbers > 0:
print("{:>10.3f} {:>10.3f}".format(float(nb14_lj_energy_sum),
float(nb14_cf_energy_sum)),
end=" ")
print("{:>7.3f}".format(float(LJ_energy_sum)), end=" ")
print("{:>12.3f}".format(float(ee_ene)))
if self.file is not None:
self.file.write(
"{:>7.0f} {:>7.3f} {:>11.3f} {:>10.3f} {:>11.3f} {:>14.3f} {:>10.3f} {:>10.3f} {:>7.3f}"
" {:>12.3f}\n".format(steps, float(temperature),
float(total_potential_energy),
float(sigma_of_bond_ene),
float(sigma_of_angle_ene),
float(sigma_of_dihedral_ene),
float(nb14_lj_energy_sum),
float(nb14_cf_energy_sum),
float(LJ_energy_sum), float(ee_ene)))
return temperature
def Main_Initial(self):
"""main initial"""
if self.control.mdout:
self.file = open(self.control.mdout, 'w')
self.file.write(
"_steps_ _TEMP_ _TOT_POT_ENE_ _BOND_ENE_ "
"_ANGLE_ENE_ _DIHEDRAL_ENE_ _14LJ_ENE_ _14CF_ENE_ _LJ_ENE_ _CF_PME_ENE_\n"
)
def Main_Destroy(self):
"""main destroy"""
if self.file is not None:
self.file.close()
print("Save successfully!")
def test_atom_sharing():
b1 = Bond(0, 1)
b2 = Bond(1, 0)
b3 = Bond(2, 1)
b4 = Bond(3, 2)
assert b1.get_bond_order() == 1
assert b1.shares_atom(b2) == -1 # they are equal
# sharing a single atom
assert b2.shares_atom(b3) == b3.shares_atom(b1)
assert b3.shares_atom(b2) == b2.shares_atom(b3)
# no sharing of atoms
assert b4.shares_atom(b1) == -1
def testWrongGetOtherAtom(self):
bond = Bond(bondTests.a1, bondTests.a2, None, None)
self.assertNotEqual(bond.get_other_atom(bondTests.a1), bondTests.a1)
def generate_interactions_o(self,interaction_name,bond="harmonic",SPB=False,radius=10,cutoff=1.15,reducedv_factor=1,khun=1.):
if bond == "harmonic" :
temp1 = "bond_style harmonic\n"
temp2 = "bond_coeff %i %.2f %.2f"
ene = 350
if bond == "fene":
if SPB:
temp1 = "bond_style hybrid harmonic fene\n"
temp2 = "bond_coeff %i fene %.2f %.2f %.2f %.2f"
else:
temp1 = "bond_style fene\n"
temp2 = "bond_coeff %i %.2f %.2f %.2f %.2f"
ene = 30 * 1
Bond = [temp1]
if bond == "fene":
Bond.append("special_bonds fene\n")
ene_ratio=1#.35
#Bond.append("special_bonds 0.0 1.0 1.0\n")
if SPB and False:
#print radius
Pair = ["pair_style hybrid lj/cut 3.0 gauss/cut %.2f \n"%(2*radius) + "pair_modify shift yes\n"]
else:
Pair = ["pair_style lj/cut 1.4 \n" + "pair_modify shift yes\n"]
Angle = ["angle_style cosine/delta\n"]
Angle = ["angle_style harmonic\n"]
keyl = range(1,len(self.natom)+1)
for t1 in keyl:
for t2 in keyl:
if t2 >= t1:
if not self.liaison.has_key("%s-%s"%(t1,t2)):
print "Warning liaison between {0} and {1} not defined".format(t1,t2)
dist,tybe_b = self.liaison["%s-%s"%(t1,t2)]
if cutoff is not None:
cut = dist*cutoff
else:
cut = dist*pow(2.,1/6.)
odist = copy.deepcopy(dist)
#dist=1
if bond == "fene":
Bond.append(temp2 % (tybe_b,ene_ratio * ene/(dist*dist),1.5*dist,ene_ratio,dist) +"\n")
else:
Bond.append(temp2 % (tybe_b, ene,dist) +"\n")
dist = odist
precise =""
if SPB and False:
precise = "lj/cut"
reduced = 1
if t1 == t2 and t1 == 3:
reduced = 1
else:
reduced = reducedv_factor
Pair.append("""pair_coeff %s %s %s %.1f %.2f %.2f\n"""%(t1,t2,precise,ene_ratio,dist*reduced,cut*reduced))
if self.angle_def is not None and self.Angle != []:
for t3 in keyl:
if t3 >= t2:
dist,tybe_b = self.angle_def["%s-%s-%s"%(t1,t2,t3)]
k=khun/2. * dist # dist = 1 if no ribo involved else 0
Angle.append("angle_coeff %i %.3f 180.0\n"%(tybe_b,k))
if SPB:
if bond == "fene":
Bond.append("bond_coeff %i harmonic 0 0 \n"%(self.liaison["spb"][1]))
spbond = "bond_coeff %i harmonic %.1f %.1f\n"%(self.liaison["spb"][1],10,microtubule/realsigma)
else:
Bond.append("bond_coeff %i 0 0 \n"%(self.liaison["spb"][1]))
spbond = "bond_coeff %i %.1f %.1f\n"%(self.liaison["spb"][1],10,microtubule/realsigma)
n_i = len(diameter)/2
for t1 in range(len(diameter) ):
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n"""%(t1+1,num_particle["spb"],precise,dist,cut))
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n"""%(num_particle["spb"],num_particle["spb"],precise,dist,cut))
g = open(interaction_name,"w")
g.write("".join(Bond)+"\n")
g.write("".join(Pair)+"\n")
if self.Angle != []:
g.write("".join(Angle))
from bond import (Bond,Directions)
import time
from pprint import pprint
bond = Bond(bondIp='', bondToken='')
device = bond.getDevice('')
def test_type_checking():
b = Bond(2, 0)
with pytest.raises(TypeError):
value_long = float(
2) # do not test long because it obsolete in python3
b.get_nbr_atom_idx(value_long)
localtime = datetime.datetime(2012,9,19)
# Import our Treasury data
f = io.open('treasuries.csv', 'r')
data = f.read()
bonds = []
i = 0
for line in data.split('\n'):
# import pdb; pdb.set_trace()
i += 1
if (i == 1): continue
entries = line.split(',')
# if (len(entries) != 9): continue
b = Bond()
b.freq = 2
b.cusip = entries[0]
b.desc = entries[1]
b.couponRate = float(entries[2]) / 100.0
b.maturity = datetime.datetime.strptime(entries[3], '%d-%b-%y')
b.bid = float(entries[4]) / 100
b.ask = float(entries[5]) / 100
bonds.append(b)
f.close()
tr = [] # times to maturity
yr = [] # yields
for b in bonds:
print b.maturity
def testNotContainsAtom(self):
bond = Bond(bondTests.a1, bondTests.a2, None, None)
self.assertFalse(bond.contains_atom(bondTests.a3))