def test_Nucleotide_across():
nucleotide = Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 1.0]),
)
# memory address of each object is stored
# in the Nucleotide._across attribute
new = nucleotide.make_across()
assert id(new._across) == id(nucleotide)
assert id(nucleotide._across) == id(new)
# Should correctly raise some warnings and pass the
# following assertions
new_2 = nucleotide.make_across()
assert id(new._across) != id(nucleotide)
assert id(nucleotide._across) != id(new)
assert id(new_2._across) == id(nucleotide)
assert id(nucleotide._across) == id(new_2)
# check the actual setting of indices works
nucleotide.index = 0
new_2.index = 1
assert nucleotide.across == new_2.index
assert new_2.across == nucleotide.index
def main(number: int = 10, double: bool = False):
# Add Strand 1 - ssDNA
n = number
nucleotides = []
print("Creating a nucleotide:")
nucleotides.append(
Nucleotide(random.choice(['A', 'T', 'C', 'G']),
np.array([0., -10., 0.]),
a1=np.array([1., 0., 0.]),
a3=np.array([0., 1., 0.])))
print(f"Nucleotide #0: {nucleotides[0]}")
print("Creating more nucleotides...\n")
for i in range(n):
nucleotides.append(
get_5p(nucleotides[-1], base=random.choice(['A', 'T', 'C', 'G'])))
strand = Strand(nucleotides=nucleotides)
print(f"Strand: {strand}")
system = System(np.array([20., 20., 20.]))
system.add_strand(strand)
# Add Strand 2 - complementary ssDNA -> dsDNA
if double:
nucleotides = []
for nucleotide in strand.nucleotides[::-1]:
nucleotides.append(get_across(nucleotide))
# for i in range(10):
# nucleotides.append(get_5p(nucleotides[-1]))
strand = Strand(nucleotides=nucleotides)
print(f"Adding double: {strand}")
system.add_strand(strand)
system.write_oxDNA('local')
return
def get_across(nuc: Nucleotide) -> Nucleotide:
"""
Returns Nucleotide o
"""
a1 = -nuc._a1
a3 = -nuc._a3
pos_com = nuc.pos_com - a1 * 2 * (POS_BASE + BASE_BASE)
return Nucleotide(ACROSS[nuc._base], pos_com, a1, a3)
def test_nucleotide():
print(
Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 1.0]),
).lammps)
return
def get_5p(nuc: Nucleotide, base: str = 'T') -> Nucleotide:
# shift round in a1 direction
angle = (np.pi / 180.0) * 35.9
rotation_matrix = get_rotation_matrix(nuc._a3, angle)
a1 = np.dot(
rotation_matrix,
nuc._a1,
)
# shift up in a3 direction
new_base = nuc.pos_base + 0.39 * nuc._a3
new_pos = new_base - a1 * (POS_BASE) - 0.105 * np.cross(nuc._a3, a1)
return Nucleotide(base, new_pos, a1, nuc._a3.copy())
def test_Nucleotide():
nucleotide = Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 1.0]),
)
assert len(nucleotide.series) == 10
assert (nucleotide.pos_back == [0.6, 0.0, 0.0]).all()
assert (nucleotide.pos_back_rel == [-0.4, 0.0, 0.0]).all()
assert (nucleotide.pos_base == [1.4, 0.0, 0.0]).all()
assert (nucleotide.pos_stack == [1.34, 0.0, 0.0]).all()
assert (nucleotide._a2 == [0.0, 1.0, 0.0]).all()
print(nucleotide)
print(nucleotide.series)
nucleotide.make_5p('A')
nucleotide.make_across()
nucleotide.copy()
return
def test_strand():
strand = Strand([
Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([2.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([3.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([4.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([5.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([6.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
])
print(strand.lammps)
return
def generate_helix(
n: int = None,
sequence: str = None,
start_position: np.ndarray = np.array([0., 0., 0.]),
direction: np.ndarray = np.array([0., 1., 0.]),
a1: np.ndarray = np.array([1., 0., 0.]),
initial_rotation: float = None,
double: bool = False,
enforce_180: bool = False,
bp_per_turn: float = 10.45,
) -> List[Strand]:
# handle sequence/n arguments
if sequence and n:
if len(sequence) != n:
difference = len(sequence) - n
# sequence longer than n
if difference > 0:
sequence = sequence[:n]
# n longer than sequence
else:
sequence += ''.join([
random.choice(['A', 'T', 'C', 'G'])
for i in range(-difference)
])
elif sequence:
n = len(sequence)
elif n:
sequence = ''.join(
[random.choice(['A', 'T', 'C', 'G']) for i in range(n)])
else:
raise TypeError(
'Please provide either the number of base-pairs or a sequence')
# handle a1/angle arguments
if initial_rotation:
a1 = get_rotation_matrix(direction, initial_rotation)
if enforce_180:
half_turns = round_to_multiple(n / bp_per_turn, 0.5, 1)
angle = np.radians(360 * half_turns / (n - 1))
else:
angle = 0.626
# initialise strand list
strands = []
# create main strand
strand = Strand()
strand.add_nucleotide(
Nucleotide(sequence[0], start_position, a1=a1, a3=direction))
for base in sequence[1:]:
strand.add_nucleotide(strand.nucleotides[-1].make_5p(base, angle))
# add to strand list which will be returned
strands.append(strand.copy())
# create across strand
if double:
strand = Strand()
# iterate over nucleotides from original strand but in reverse
for nucleotide in strands[0].nucleotides[::-1]:
strand.add_nucleotide(nucleotide.make_across())
strands.append(strand.copy())
return strands
def test_System():
system = System(np.array([50.0, 50.0, 50.0]))
strand_1 = Strand(
[
Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([2.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([3.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([4.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([5.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"A",
np.array([6.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
]
)
strand_2 = Strand(
[
Nucleotide(
"T",
np.array([1.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"T",
np.array([2.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"T",
np.array([3.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"T",
np.array([4.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"T",
np.array([5.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
Nucleotide(
"T",
np.array([6.0, 2.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0, 0.0, 1.0]),
),
]
)
system.add_strands([strand_1, strand_2])
assert isinstance(system, System)
assert system.E_tot == 0.0
assert len(system.dataframe.count()) == 10
assert len(system.configuration.count()) == 5
assert len(system.topology.count()) == 4
assert len(system.strands) == 2
assert len(system.nucleotides) == 12
system.strands[0].sequence = "AGAGAG"
system.add_strand(system.strands[0].copy())
system.strands[0].sequence = "TATATA"
assert len(system.strands) == 3
assert len(system.nucleotides) == 18
assert system.strands[0].sequence == "TATATA"
assert system.strands[2].sequence == "AGAGAG"
strand_3 = system.strands[1].copy()
strand_3.sequence = "CCCGGG"
strand_4 = strand_3.copy()
strand_4.sequence = "AAATTT"
system.add_strands({
0 : strand_3,
1 : strand_4
})
assert len(system.strands) == 5
assert len(system.nucleotides) == 30
print(system.strands)
assert system.strands[0].sequence == "CCCGGG"
assert system.strands[1].sequence == "AAATTT"
assert system.strands[2].sequence == "TATATA"
print(system)
print(system.dataframe)
# system.write_oxDNA()
return
def test_Nucleotide_transform():
nucleotide = Nucleotide(
"A",
np.array([1.0, 0.0, 0.0]),
np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 1.0]),
)
nucleotide.translate(np.array([10., 0., 0.]))
assert all(nucleotide.pos_com == [11., 0., 0.])
nucleotide.rotate([0., 0., 0., 1.])
nucleotide.rotate([0., 0., 0.])
nucleotide.rotate(np.array([
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 0.],
]))
nucleotide.transform(
np.array([
[1., 0., 0., 0.],
[0., 1., 0., 0.],
[0., 0., 1., 0.],
]))
return