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 with_strands(N: int = 10):
a1 = np.array([1., 0., 0.])
start = np.array([0., 0., 0.]) + a1 * 0.6
direction = np.array([0., 1., 0.])
strands = generate_helix(
n=N,
start_position=start,
direction=direction,
a1=a1,
initial_rotation=0.0,
)
new_position = start + (N) * 0.39 * direction
new_direction = np.array([0.0, 1.0, 1.0]) / 2**0.5
new_a1 = np.array([0.0, -1.0, 1.0]) / 2**0.5
#print(np.dot(new_a1, new_direction))
rotation = -0.06
#rotation = 0.0
strands += generate_helix(
n=N,
start_position=new_position,
direction=new_direction,
a1=new_a1,
initial_rotation=rotation,
)
strand = Strand(strands[0].nucleotides + strands[1].nucleotides)
return [strand]
def generate_system(box: np.ndarray) -> System:
"""Generate a simple oxDNA system"""
system = System(box)
strand = generate_helix(40, double=False)[0]
new = []
for nt in strand.nucleotides[10:30]:
new.append(nt.make_across())
new = Strand(nucleotides=new[::-1])
system.add_strands([strand, new])
return system
def generate_system(n: int, double_strand_length: int,
single_strand_length: int) -> SystemWithFolder:
"""
Generates an oxDNA system containing a single piece of DNA
which has blocks of equal size of double-stranded portions
and single-stranded portions.
Parameters:
n - number of nucleotides e.g. 100
fraction_ds - fraction of double-strand DNA e.g. 0.5
Returns:
system - oxDNA system
"""
# initialise system to comply with minimum image convention
box = 2. * n * FENE_EPS
print(f'Creating simulation system with box size: {box}')
system = SystemWithFolder(np.array([box, box, box]))
# create a list of strands, our main strand which we will use
# and our complementary strand
strands = generate_helix(n, double=True)
# make a copy of the complementary strand and remove it
# from the main list of strands
second_strand = strands[1].copy()
strands = strands[:1]
# calculate how many portions there should be
portion_size = double_strand_length + single_strand_length
portions = n // portion_size
print(f'Creating {portions} portions of total size: {portion_size}')
# iterate over all portions, adding a new complementary
# strand to the list of strands we will use
for i in range(portions):
# take the nucleotides from each portion and
# create a new strand for each double-stranded part
# of the portion
start = portion_size * i
end = start + double_strand_length
nucleotides = second_strand.nucleotides[start:end]
new_strand = Strand(nucleotides=nucleotides)
strands.append(new_strand)
# finally add the strands to the system and return
# the system
system.add_strands(strands)
return system
def add_strand(self, addition: Strand, index: int = None):
"""
Method to add strand(s) to the system
Parameters:
addition - accepted as Strand objects or a List of Strands
index (default = None) - Strand will append to current system,
otherwise Strand inserted at location given
"""
try:
assert isinstance(addition, Strand)
except TypeError:
raise TypeError(f"addition must be Strand but is {type(addition)}")
try:
if index == None:
self._strands.append(addition.copy())
else:
self._strands.insert(index, addition.copy())
except TypeError:
raise TypeError("Index must an an integer")
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 main(length=16, n_strands=10):
# generate a strand
strands = []
strand = generate_helix(n=length, enforce_180=True)[0]
strands.append(strand.copy())
for i in range(n_strands - 1):
last_nuc = strands[-1].nucleotides[-1]
direction = -last_nuc._a3
a1 = -last_nuc._a1
# ensure the backbone position is FENE_LENGTH away from
# the backbone position of the previous nucleotide
start = last_nuc.pos_back + (FENE_LENGTH - POS_BACK) * a1
# generate strand above that's going in opposite direction
strand = generate_helix(
n=length,
start_position=start,
direction=direction,
a1=a1,
enforce_180=True,
)[0]
strands.append(strand)
# using the two previously created strands create a new strand that
# we will add to the system
nucleotides = []
for strand in strands:
nucleotides += strand.nucleotides
strand = Strand(nucleotides=nucleotides)
# create system and add the final completed strand
system = System(np.array([50., 50., 50.]))
system.add_strand(strand)
system.write_oxDNA('turns_18nt')
return system
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