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 main(length=17, n_strands=10, output_format='oxdna'):
# generate a strand
strands = []
staples = []
strand, staple = generate_helix(n=length, double=True)
staples.append(staple.copy())
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, staple = generate_helix(n=length,
start_position=start,
direction=direction,
a1=a1,
double=True)
strands.append(strand.copy())
staples.append(staple.copy())
print(staples)
# 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)
# create staples from staple list
# iterate over every 2 staples in reverse
# and append the last onto the first, and add to the system
staples = staples[::-1]
completed_staples = []
for i, staple in enumerate(staples):
if i % 2 != 0:
continue
try:
new_nucleotides = []
new_nucleotides += staples[i + 1].nucleotides
new_nucleotides += staple.nucleotides
new_staple = Strand(nucleotides=new_nucleotides)
system.add_strand(new_staple.copy())
except IndexError:
pass
if output_format.lower() == 'oxdna':
system.write_oxDNA('stapled_turns')
elif output_format.lower() == 'lammps':
system.write_lammps_data('stapled_turns')
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 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 test_route():
nodes = [
LatticeNode(np.array([0., 10., 0.])),
LatticeNode(np.array([0., 30., 0.])),
LatticeNode(np.array([30., 30., 0.])),
LatticeNode(np.array([30., 10., 0.])),
]
route = LatticeRoute(nodes)
assert len(route.edges) == 3
system = System(np.array([50., 50., 50.]))
system.add_strand(route)
assert len(system.strands) == 1
system = route.system(box=np.array([50., 50., 50.]))
assert len(system.strands) == 1
system.write_oxDNA(root=ROOT)
return route
def main(length=16, n_strands=10):
# 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
# 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([20., 20., 20.]))
system.add_strand(strand)
actual_doubles = []
for strand in doubles:
nucleotides = strand.nucleotides[:5]
actual_doubles.append(Strand(nucleotides=nucleotides))
system.add_strands(actual_doubles)
system.write_oxDNA('turns')
.format(file_path),
shell=True)
#Delete all previously generated .turns.top and .turns.conf files out of /sim folder:
#shutil.move(file_path + '/' + './oxdna.turns.top','./oxdna.turns.top')
#shutil.move(file_path + '/' + './oxdna.turns.conf', './oxdna.turns.conf')
#shutil.move(file_path + '/' + './oxdna.turns.conf.pdb', './oxdna.turns.conf.pdb')
os.remove(file_path + '/' + './oxdna.turns.top')
os.remove(file_path + '/' + './oxdna.turns.conf')
os.remove(file_path + '/' + './oxdna.turns.conf.pdb')
#remove sim_path folder before running the final simulation of mother_system
shutil.rmtree(sim_path)
#write mother_system to oxDNA input (.conf and .top)
mother_system.write_oxDNA('mother_turns')
#move oxDNA files to simulation folder
shutil.move('./oxdna.mother_turns.top',
file_path + '/' + './oxdna.mother_turns.top')
shutil.move('./oxdna.mother_turns.conf',
file_path + '/' + './oxdna.mother_turns.conf')
#Convert oxDNA output files to .pdb input file format
subprocess.call(
"bash -c \"source ~/.bashrc && module load CUDA && cd {} && python3 /home/fiona/tacoxDNA-python3/src/oxDNA_PDB.py oxdna.mother_turns.top oxdna.mother_turns.conf 35\""
.format(file_path),
shell=True)
#Running mrdna simulation with the .pdb input file from the MOTHER_SYSTEM
subprocess.call(
def test_square():
route = square_route()
system = System(np.array([50.0, 50.0, 50.0]))
system.add_strand(route)
system.write_oxDNA(root=ROOT)