def test_system():
system = System(np.array([50., 50., 50.]))
system.add_strands(generate_helix(10, double=True))
print(system.lammps)
print(system.bonds)
return system
def main(strands: bool = True, edges: bool = False):
system = System(np.array([30., 30., 30.]))
if strands:
system.add_strands(with_strands())
if edges:
system.add_strands(with_edges())
system.write_oxDNA('connect')
return
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 main():
strand = long_strand()
print(f"Strand:\n {strand}")
print(f" Length between bases of the end nucleotides: {strand_length(strand)}")
route = long_route()
print(f"\nSingle-Edge Route:\n {route}")
print(f" Length between bases of the end nucleotides: {strand_length(route)}")
multi = multi_route()
print(f"\nDouble-Edge Route:\n {multi}")
print(f" Length between bases of the end nucleotides: {strand_length(multi)}")
system = System(np.array([50., 50., 50.]))
system.add_strands([strand, route, multi])
system.write_oxDNA('route')
return
def generate_system(length=16, n_strands=10, stapled=5):
# generate a strand
strands = []
doubles = []
strand, double = generate_helix(n=length, double=True)
strands.append(strand.copy())
doubles.append(double.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, double = generate_helix(
n=length,
start_position=start,
direction=direction,
a1=a1,
double=True,
)
strands.append(strand)
doubles.append(double)
# using the two previously created strands create a new strand that is added to the system
nucleotides = []
for strand in strands:
nucleotides += strand.nucleotides
strand = Strand(nucleotides=nucleotides)
# create system and add the final completed strand
main_system = System(np.array([80.0, 80.0, 80.0]))
main_system.add_strand(strand)
actual_doubles = []
for strand in doubles:
nucleotides = strand.nucleotides[:stapled]
actual_doubles.append(Strand(nucleotides=nucleotides))
main_system.add_strands(actual_doubles)
#main_system.write_oxDNA('turns')
return main_system
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