def threshold_bottom_strand(input_: int, gate: int) -> nc.Strand:
"""Returns a threshold bottom strand for seesaw gate labeled `gate` that
thresholds `input`
.. code-block:: none
s{input}* T* ss{gate}* s{gate}*
| | | |
[==--=====--=============--==>
:param input_: Name of input that is being thresholded
:type input_: int
:param gate: Name of gate
:type gate: int
:return: Threshold bottom strand
:rtype: dc.Strand
"""
# Note, this assumes that this input signal domain has already been built
d_input_sub = recognition_domains_and_subdomains[f's{input_}']
d_gate = get_signal_domain(gate)
s: nc.Strand = nc.Strand(domains=[d_input_sub, TOEHOLD_DOMAIN, d_gate],
starred_domain_indices=[0, 1, 2],
name=f'threshold_bottom_{input_}_{gate}')
return s
def signal_strand(gate3p: Union[int, str], gate5p: Union[int,
str]) -> nc.Strand:
"""Returns a signal strand with recognition domains
gate3p and gate5p on the 3' and 5' respectively
.. code-block:: none
S{g3p} S{g5p}
ss{g3p} s{g3p} T ss{g5p} s{g5p}
| | | | |
<=============--==--=====--=============--==]
:param gate3p: Gate to be identified by the recognition domain on the 3'
end
:type gate3p: Union[int, str]
:param gate5p: Gate to be identified by the recognition domain on the 5'
end
:type gate5p: Union[int, str]
:return: Strand
:rtype: dc.Strand
"""
d3p = get_signal_domain(gate3p)
d5p = get_signal_domain(gate5p)
name = f'signal_{gate3p}_{gate5p}'
return nc.Strand(domains=[d5p, TOEHOLD_DOMAIN, d3p],
starred_domain_indices=[],
name=name)
def main():
domain_length = 15
# energy_constraint = dc.NearestNeighborEnergyConstraint(low_energy=-9.2, high_energy=-7)
numpy_constraints = [ # energy_constraint,
nc.RunsOfBasesConstraint(['C', 'G'], 4),
nc.RunsOfBasesConstraint(['A', 'T'], 4)
]
domain_pool = nc.DomainPool(f'length-{domain_length} domains', domain_length,
numpy_constraints=numpy_constraints, replace_with_close_sequences=True)
random_seed = 0
strands = [nc.Strand([f'{i}' for i in range(1, 50)])]
for strand in strands:
for domain in strand.domains:
domain.pool = domain_pool
params = ns.SearchParameters(
constraints=[nc.nupack_strand_complex_free_energy_constraint(
threshold=-1.5, temperature=52, short_description='StrandSS', parallel=False)],
out_directory='output/hamming_dist_test',
# weigh_violations_equally=True
report_only_violations=False,
random_seed=random_seed,
max_iterations=None)
params.force_overwrite = True # directly deletes output folder contents w/o user input
# params.report_delay = 0.0
design = nc.Design(strands)
ns.search_for_dna_sequences(design, params)
def reporter_bottom_strand(gate) -> nc.Strand:
"""Returns a reporter bottom strand for seesaw gate labeled `gate`
.. code-block:: none
T* ss{gate}* s{gate}*
| | |
[=====--=============--==>
:param gate: Name of gate
:type gate: [type]
:return: Reporter bottom strand
:rtype: dc.Strand
"""
s: nc.Strand = nc.Strand(domains=[TOEHOLD_DOMAIN,
get_signal_domain(gate)],
starred_domain_indices=[0, 1],
name=f'reporter_bottom_{gate}')
return s
def reporter_top_strand(gate: int) -> nc.Strand:
"""Returns a waste strand for a reporting reaction involving
the seesaw gate labeled `gate`
.. code-block:: none
ss{gate} s{gate}
| |
<=============--==]
:param gate: Name of gate
:type gate: int
:return: Waste strand
:rtype: dc.Strand
"""
s: nc.Strand = nc.Strand(domains=[get_signal_domain(gate)],
starred_domain_indices=[],
name=f'reporter_top_{gate}')
return s
def gate_base_strand(gate: int) -> nc.Strand:
"""Returns a gate base strand with recognition domain `gate`.
.. code-block:: none
S{gate}*
T* ss{gate}* s{gate}* T*
| | | |
[=====--=============--==--=====>
:param gate: Gate to be identified by the recognition domain
:type gate: int
:return: Gate base strand
:rtype: dc.Strand
"""
d = get_signal_domain(gate)
s: nc.Strand = nc.Strand(domains=[TOEHOLD_DOMAIN, d, TOEHOLD_DOMAIN],
starred_domain_indices=[0, 1, 2],
name=f'gate_base_{gate}')
return s
def fuel_strand(gate: int) -> nc.Strand:
"""Returns a fuel strand with recognition domain `gate`.
.. code-block:: none
ss{gate} s{gate} T ssf sf
| | | | |
<=============--==--=====--=============--==]
:param gate: The name of the gate that this fuel strand will fuel.
:type gate: int
:return: Fuel strand
:rtype: dc.Strand
"""
d3p = get_signal_domain(gate)
fuel = FUEL_DOMAIN
name = f'fuel_{gate}'
return nc.Strand(domains=[fuel, TOEHOLD_DOMAIN, d3p],
starred_domain_indices=[],
name=name)