def test_constrain_on_polymer_end():
end = Point(index=19,position=[0.2,0.2,0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0,0,0],[20,20,20])
coords,bonds,type_beads,ids = one_polymer(N=20,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[end],gconstrain=[box],max_trial=1000)
print norm(coords[-2]-np.array([0.2,0.2,0.2]))
assert(norm(coords[-2]-np.array([0.2,0.2,0.2])) < 3)
def test_create_mixture_angle_start_angle_start_id():
coords,bonds,type_beads,ids = one_polymer(N=3,type_bead=[0,1,0],
liaison={"0-0":[1.0,0],"0-1":[2.0,1]},
angle_bond=True,start_angle=10,
angle_def={"0-0-0":[1.,0],"0-0-1":[1.,1],"0-1-1":[1.,2],"1-1-1":[1.,3]},
ptolerance=0,type_polymer="linear",start_id=20)
assert (bonds[0] == [[0,1,20,21],[1,1,21,22]])
assert (bonds[1] == [[10,1,20,21,22]])
def test_startid():
coords, bonds, type_beads, ids = one_polymer(N=2,
type_bead=0,
liaison={"0-0": [1.0, 0]},
ptolerance=0,
type_polymer="linear",
start_id=1)
assert (bonds[0] == [[0, 0, 1, 2]])
def test_one_particule():
coords, bonds, type_beads, ids = one_polymer(N=1,
type_bead=0,
liaison={"0-0": [1.0, 0]},
ptolerance=0,
type_polymer="linear",
start_id=1)
assert (bonds[0] == [])
def test_bond_size_angle():
box = Box([-100,-100,-100],[400,400,400])
coords,bonds,type_beads,ids = one_polymer(N=400,type_bead=1,liaison={"1-1":[1.5,1]},ptolerance=0,
type_polymer="linear",start_id=0,lconstrain=[],
gconstrain=[box],max_trial=500000,rc=1,virtual_lp=4,rigid_constrain=False,flexible_lp=True)
bonds = np.mean(np.sqrt(np.sum((coords[1:]-coords[:-1])**2,axis=1)))
assert(abs(bonds-1.5)< 0.1)
def testerror1(self):
self.assertRaises(
SomeCoolException,
one_polymer(N=3,
type_bead=[0, 1],
liaison={"0-0": [1.0, 0]},
ptolerance=0,
type_polymer="linear",
start_id=0))
def test_constrain_box_on_polymer():
box = Box([0, 0, 0], [10, 10, 10])
coords, bonds, type_beads, ids = one_polymer(N=200,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
gconstrain=[box])
for p in coords:
assert (box.is_inside(p))
def test_angle():
coords, bonds, type_beads, ids = one_polymer(N=2,
type_bead=0,
liaison={"0-0": [1.0, 0]},
ptolerance=0,
type_polymer="linear",
start_id=1,
start_bond=1,
angle_bond=True)
assert (bonds[1] == [])
def test_create():
coords, bonds, type_beads, ids = one_polymer(N=2,
type_bead=0,
liaison={"0-0": [1.0, 0]},
ptolerance=0,
type_polymer="linear",
start_id=0)
assert (bonds[0] == [[0, 0, 0, 1]])
assert (round(norm(coords[0] - coords[1]), 3) == 1.00)
assert (type_beads == [0, 0])
def test_constrain_on_polymer_start():
start = Point(index=0, position=[0.2, 0.2, 0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0, 0, 0], [10, 10, 10])
coords, bonds, type_beads, ids = one_polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[start],
gconstrain=[box])
assert (norm(coords[0] - np.array([0.2, 0.2, 0.2])) < 0.01)
def test_crash():
PS = [0.2,0.2,0.2]
PM = [10,10.2,0.2]
PE = [0.2,199,19]
start = Point(index=0,position=PS)
middle = Point(index=39,position=PM)
end = Point(index=399,position=PE)
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([-10,-10,-10],[400,400,400])
coords_lp,bonds,type_beads,ids = one_polymer(N=400,type_bead=1,liaison={"1-1":[1.0,1]},ptolerance=0,
type_polymer="linear",start_id=0,lconstrain=[start,middle,end],
gconstrain=[box],max_trial=500000,rc=0.5,virtual_lp=3,rigid_constrain=True)
def test_create_mixture():
coords, bonds, type_beads, ids = one_polymer(N=3,
type_bead=[0, 1, 0],
liaison={
"0-0": [1.0, 0],
"0-1": [2.0, 1]
},
ptolerance=0,
type_polymer="linear",
start_id=0)
assert (bonds[0] == [[0, 1, 0, 1], [1, 1, 1, 2]])
assert (round(norm(coords[0] - coords[1]), 3) == 2.00)
assert (round(norm(coords[1] - coords[2]), 3) == 2.00)
def test_constrain_on_polymer_end():
end = Point(index=19, position=[0.2, 0.2, 0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0, 0, 0], [20, 20, 20])
coords, bonds, type_beads, ids = one_polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[end],
gconstrain=[box],
max_trial=1000)
print norm(coords[-2] - np.array([0.2, 0.2, 0.2]))
assert (norm(coords[-2] - np.array([0.2, 0.2, 0.2])) < 3)
def test_bond_size():
box = Box([-100, -100, -100], [400, 400, 400])
coords, bonds, type_beads, ids = one_polymer(N=400,
type_bead=1,
liaison={"1-1": [2.0, 1]},
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[],
gconstrain=[box],
max_trial=300000,
rc=0.5,
virtual_lp=None,
rigid_constrain=True)
bonds = np.mean(np.sqrt(np.sum((coords[1:] - coords[:-1])**2, axis=1)))
assert (abs(bonds - 2) < 0.1)
def test_create_mixture_angle():
coords, bonds, type_beads, ids = one_polymer(N=3,
type_bead=[0, 1, 0],
liaison={
"0-0": [1.0, 0],
"0-1": [2.0, 1]
},
angle_bond=True,
angle_def={
"0-0-0": [1., 0],
"0-0-1": [1., 1],
"0-1-1": [1., 2],
"1-1-1": [1., 3]
},
ptolerance=0,
type_polymer="linear",
start_id=0)
assert (bonds[0] == [[0, 1, 0, 1], [1, 1, 1, 2]])
assert (bonds[1] == [[0, 1, 0, 1, 2]])
def __init__(self, **kwargs):
coords, bonds, type_beads, ids = one_polymer(**kwargs)
#Getting liaison and angle information
self.liaison = kwargs.get("liaison", None)
self.angle_def = kwargs.get("angle_def", None)
a = inspect.getargspec(one_polymer)
for arg, value in zip(a.args[-len(a.defaults):], a.defaults):
#print arg
if self.liaison is None and arg == "liaison":
self.liaison = value
if self.angle_def is None and arg == "angle_def":
self.angle_def = value
self.coords = coords
self.bond = bonds[0]
self.angle = bonds[1]
self.types_beads = type_beads
self.ids = ids
self.extrabond = []
def __init__(self,**kwargs):
coords,bonds,type_beads,ids = one_polymer(**kwargs)
#Getting liaison and angle information
self.liaison = kwargs.get("liaison",None)
self.angle_def = kwargs.get("angle_def",None)
a = inspect.getargspec(one_polymer)
for arg,value in zip(a.args[-len(a.defaults):],a.defaults):
#print arg
if self.liaison is None and arg == "liaison":
self.liaison =value
if self.angle_def is None and arg == "angle_def":
self.angle_def = value
self.coords = coords
self.bond = bonds[0]
self.angle = bonds[1]
self.types_beads = type_beads
self.ids = ids
self.extrabond = []
def test_crash():
PS = [0.2, 0.2, 0.2]
PM = [10, 10.2, 0.2]
PE = [0.2, 199, 19]
start = Point(index=0, position=PS)
middle = Point(index=39, position=PM)
end = Point(index=399, position=PE)
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([-10, -10, -10], [400, 400, 400])
coords_lp, bonds, type_beads, ids = one_polymer(
N=400,
type_bead=1,
liaison={"1-1": [1.0, 1]},
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[start, middle, end],
gconstrain=[box],
max_trial=500000,
rc=0.5,
virtual_lp=3,
rigid_constrain=True)
def test_constrain_on_polymer_start():
start = Point(index=0,position=[0.2,0.2,0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0,0,0],[10,10,10])
coords,bonds,type_beads,ids = one_polymer(N=20,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[start],gconstrain=[box])
assert(norm(coords[0]-np.array([0.2,0.2,0.2])) < 0.01)
def test_create():
coords,bonds,type_beads,ids = one_polymer(N=2,type_bead=0,liaison={"0-0":[1.0,0]},ptolerance=0,type_polymer="linear",start_id=0)
assert (bonds[0] == [[0,0,0,1]])
assert (round(norm(coords[0]-coords[1]),3) == 1.00)
assert(type_beads == [0,0])
def testerror1(self):
self.assertRaises(SomeCoolException, one_polymer(N=3,type_bead=[0,1],liaison={"0-0":[1.0,0]},ptolerance=0,type_polymer="linear",start_id=0))
def test_create_mixture():
coords,bonds,type_beads,ids = one_polymer(N=3,type_bead=[0,1,0],liaison={"0-0":[1.0,0],"0-1":[2.0,1]},ptolerance=0,type_polymer="linear",start_id=0)
assert (bonds[0] == [[0,1,0,1],[1,1,1,2]])
assert (round(norm(coords[0]-coords[1]),3) == 2.00)
assert (round(norm(coords[1]-coords[2]),3)== 2.00)
def test_one_particule():
coords,bonds,type_beads,ids = one_polymer(N=1,type_bead=0,liaison={"0-0":[1.0,0]},ptolerance=0,type_polymer="linear",start_id=1)
assert (bonds[0] == [])
def test_startbond():
coords,bonds,type_beads,ids = one_polymer(N=2,type_bead=0,liaison={"0-0":[1.0,0]},ptolerance=0,type_polymer="linear",start_id=1,start_bond=1)
assert (bonds[0] == [[1,0,1,2]])
def test_angle():
coords,bonds,type_beads,ids = one_polymer(N=2,type_bead=0,liaison={"0-0":[1.0,0]},ptolerance=0,type_polymer="linear",start_id=1,start_bond=1,angle_bond=True)
assert (bonds[1] == [])
def test_constrain_box_on_polymer():
box = Box([0,0,0],[10,10,10])
coords,bonds,type_beads,ids = one_polymer(N=200,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,gconstrain=[box])
for p in coords:
assert(box.is_inside(p))
