def _add_reporter_complex_constraint(self) -> None:
"""Adds reporter complexes to self.constraint
.. code-block:: none
S6 s6
14 2 10
| | ||
<=============--==]
||||||||||||| ||
[=====--=============--==>
| | | | ||
15 19 20 32 |34
33
T* S6* s6*
"""
reporter_strands: List[Tuple[nc.Strand, ...]] = []
for (
_, gate
), reporter_bottom_strand_ in self.reporter_bottom_strands.items():
waste_strand = self.reporter_top_strands[gate]
reporter_strands.append((waste_strand, reporter_bottom_strand_))
reporter_complexes = [
nc.Complex(*strands) for strands in reporter_strands
]
self.constraints.append(
dc_complex_constraint(reporter_complexes,
description="Reporter Complex",
short_description="reporter"))
def _add_reporter_waste_complex_constraint(self) -> None:
"""Adds reporter waste complexes to self.constraint
.. code-block:: none
S5 s5 T S6 s6
21
34 22 |20 19 15 14 2 10
| | || | | | | ||
<=============--==--=====--=============--==]
||||| ||||||||||||| ||
[=====--=============--==>
| | | | ||
35 39 40 52 |54
53
T* S6* s6*
"""
reporter_waste_strands: List[Tuple[nc.Strand, ...]] = []
for (
input_, gate
), reporter_bottom_strand_ in self.reporter_bottom_strands.items():
signal_strand_ = self.signal_strands[(input_, gate)]
reporter_waste_strands.append(
(signal_strand_, reporter_bottom_strand_))
reporter_waste_complexes = [
nc.Complex(*strands) for strands in reporter_waste_strands
]
self.constraints.append(
dc_complex_constraint(reporter_waste_complexes,
description="Reporter Waste Complex",
short_description="reporter waste"))
def _add_threshold_complex_constraint(self) -> None:
"""Adds threshold complexes to self.constraint
.. code-block:: none
S5 s5
14 2 10
| | ||
<=============--==]
||||||||||||| ||
[==--=====--=============--==>
|| | | | | ||
15| 17 21 22 34 |36
16 35
s2* T* S5* s5*
"""
threshold_strands: List[Tuple[nc.Strand, ...]] = []
for (_, gate
), thres_bottom_strand in self.threshold_bottom_strands.items():
waste_strand = self.threshold_top_strands[gate]
threshold_strands.append((waste_strand, thres_bottom_strand))
threshold_complexes = [
nc.Complex(*strands) for strands in threshold_strands
]
self.constraints.append(
dc_complex_constraint(threshold_complexes,
description="Threshold Complex",
short_description="threshold"))
def _add_threshold_waste_complex_constraint(self) -> None:
"""Adds threshold waste complexes to self.constraint
.. code-block:: none
S2 s2 T S5 s5
21
34 22|20 19 15 14 2 10
| | || | | | | ||
<=============-==--=====--=============--==]
|| ||||| ||||||||||||| ||
[==--=====--=============--==>
|| | | | | ||
35| 37 41 42 54 |56
36 55
s2* T* S5* s5*
"""
threshold_waste_strands: List[Tuple[nc.Strand, ...]] = []
for (input_, gate
), thres_bottom_strand in self.threshold_bottom_strands.items():
sig_strand = self.signal_strands[(input_, gate)]
threshold_waste_strands.append((sig_strand, thres_bottom_strand))
threshold_waste_complexes = [
nc.Complex(*strands) for strands in threshold_waste_strands
]
self.constraints.append(
dc_complex_constraint(threshold_waste_complexes,
description="Threshold Waste Complex",
short_description="threshold waste"))
def _add_input_gate_complex_constraint(self) -> None:
"""Adds input:gate complexes to self.constraint
"""
input_gate_strands = []
for (input_, gate), s in self.signal_strands.items():
if gate in self.gate_base_strands:
g = self.gate_base_strands[gate]
input_gate_strands.append((s, g))
input_gate_complexes = [
nc.Complex(*strands) for strands in input_gate_strands
]
self.constraints.append(
input_gate_complex_constraint(input_gate_complexes))
def _add_gate_output_complex_constriant(self) -> None:
"""Adds gate:output complexes to self.constraint
"""
gate_output_strands: List[Tuple[nc.Strand, ...]] = []
for (gate, _), s in self.signal_strands.items():
if gate in self.gate_base_strands:
g = self.gate_base_strands[gate]
gate_output_strands.append((s, g))
gate_output_complexes = [
nc.Complex(*strands) for strands in gate_output_strands
]
self.constraints.append(
gate_output_complex_constraint(gate_output_complexes))
def _add_gate_fuel_complex_constriant(self) -> None:
"""Adds gate:fuel complexes to self.constraint
"""
gate_output_strands: List[Tuple[nc.Strand, ...]] = []
for gate in self.fuel_strands:
if gate in self.fuel_strands:
f = self.fuel_strands[gate]
g = self.gate_base_strands[gate]
gate_output_strands.append((f, g))
gate_output_complexes = [
nc.Complex(*strands) for strands in gate_output_strands
]
# TODO: Make it so that only specific base pairs have lower threshold (such as base index 1)
# which is an A that can bind to any T but it doesn't matter which.
self.constraints.append(
gate_output_complex_constraint(
gate_output_complexes,
base_pair_prob_by_type={nc.BasePairType.UNPAIRED: 0.8},
description='gate:fuel'))
def main() -> None:
args: CLArgs = parse_command_line_arguments()
# dc.logger.setLevel(logging.DEBUG)
nc.logger.setLevel(logging.INFO)
random_seed = 1
# many 4-domain strands with no common domains, 4 domains each, every domain length = 10
# just for testing parallel processing
# num_strands = 3
# num_strands = 5
# num_strands = 10
# num_strands = 50
num_strands = 100
# num_strands = 355
design = nc.Design()
# si wi ni ei
# strand i is [----------|----------|----------|---------->
for i in range(num_strands):
design.add_strand([f's{i}', f'w{i}', f'n{i}', f'e{i}'])
some_fixed = False
# some_fixed = True
if some_fixed:
# fix all domains of strand 0 and one domain of strand 1
for domain in design.strands[0].domains:
domain.set_fixed_sequence('ACGTACGTAC')
design.strands[1].domains[0].set_fixed_sequence('ACGTACGTAC')
parallel = False
# parallel = True
numpy_constraints: List[NumpyConstraint] = [
nc.NearestNeighborEnergyConstraint(-9.3, -9.0, 52.0),
# nc.BaseCountConstraint(base='G', high_count=1),
# nc.BaseEndConstraint(bases=('C', 'G')),
# nc.RunsOfBasesConstraint(['C', 'G'], 4),
# nc.RunsOfBasesConstraint(['A', 'T'], 4),
# nc.BaseEndConstraint(bases=('A', 'T')),
# nc.BaseEndConstraint(bases=('C', 'G'), distance_from_end=1),
# nc.BaseAtPositionConstraint(bases='T', position=3),
# nc.ForbiddenSubstringConstraint(['GGGG', 'CCCC']),
# nc.RestrictBasesConstraint(bases=['A', 'T', 'C']),
]
# def nupack_binding_energy_in_bounds(seq: str) -> bool:
# energy = dv.binding_complement(seq, 52)
# nc.logger.debug(f'nupack complement binding energy = {energy}')
# return -11 < energy < -9
#
# # list of functions:
# sequence_constraints: List[SequenceConstraint] = [
# # nupack_binding_energy_in_bounds,
# ]
replace_with_close_sequences = True
# replace_with_close_sequences = False
domain_pool_10 = nc.DomainPool(
f'length-10_domains',
10,
numpy_constraints=numpy_constraints,
replace_with_close_sequences=replace_with_close_sequences,
)
domain_pool_11 = nc.DomainPool(
f'length-11_domains',
11,
numpy_constraints=numpy_constraints,
replace_with_close_sequences=replace_with_close_sequences,
)
if some_fixed:
for strand in design.strands[
1:]: # skip all domains on strand 0 since all its domains are fixed
for domain in strand.domains[:2]:
if domain.name != 's1': # skip for s1 since that domain is fixed
domain.pool = domain_pool_10
for domain in strand.domains[2:]:
domain.pool = domain_pool_11
else:
for strand in design.strands:
for domain in strand.domains[:2]:
domain.pool = domain_pool_10
for domain in strand.domains[2:]:
domain.pool = domain_pool_11
# have to set nupack_complex_secondary_structure_constraint after DomainPools are set,
# so that we know the domain lengths
strand_complexes = [
nc.Complex(strand) for i, strand in enumerate(design.strands[2:])
]
strand_base_pair_prob_constraint = nc.nupack_complex_base_pair_probability_constraint(
strand_complexes=strand_complexes)
domain_nupack_ss_constraint = nc.nupack_domain_complex_free_energy_constraint(
threshold=-0.0, temperature=52, short_description='DomainSS')
domain_pairs_rna_duplex_constraint = nc.rna_duplex_domain_pairs_constraint(
threshold=-2.0, temperature=52, short_description='DomainPairRNA')
domain_pair_nupack_constraint = nc.nupack_domain_pair_constraint(
threshold=-0.5,
temperature=52,
short_description='DomainPairNUPACK',
parallel=parallel)
strand_pairs_rna_duplex_constraint = nc.rna_duplex_strand_pairs_constraint(
threshold=-1.0,
temperature=52,
short_description='StrandPairRNA',
parallel=parallel)
strand_individual_ss_constraint = nc.nupack_strand_complex_free_energy_constraint(
threshold=-1.0,
temperature=52,
short_description='StrandSS',
parallel=parallel)
strand_individual_ss_constraint2 = nc.nupack_strand_complex_free_energy_constraint(
threshold=-1.0,
temperature=52,
short_description='StrandSS2',
parallel=parallel)
strand_pair_nupack_constraint = nc.nupack_strand_pairs_constraint(
threshold=3.0,
temperature=52,
short_description='StrandPairNUPACK',
parallel=parallel,
weight=0.1)
params = ns.SearchParameters(
constraints=[
# domain_nupack_ss_constraint,
# strand_individual_ss_constraint,
# strand_individual_ss_constraint2,
strand_pairs_rna_duplex_constraint,
# strand_pair_nupack_constraint,
# domain_pair_nupack_constraint,
# domain_pairs_rna_duplex_constraint,
# strand_base_pair_prob_constraint,
# nc.domains_not_substrings_of_each_other_constraint(),
],
out_directory=args.directory,
restart=args.restart,
random_seed=random_seed,
max_iterations=None,
save_sequences_for_all_updates=True,
save_report_for_all_updates=True,
save_design_for_all_updates=True,
force_overwrite=True,
scrolling_output=False,
# report_only_violations=False,
)
ns.search_for_dna_sequences(design, params)
# 35 39 40 52 |54 55 59
# 53
# T* S5* s5* T*
#
# Debugging base pair types:
#
# S5 s5 T S6 / S7 s6 / s7
# DANGLE_5P INTERIOR_TO_STRAND
# | | |
# <=============--==--=====--=============--==]
# ||||||||||||| || |||||
# [=====--=============--==--=====>
# | | |
# INTERIOR_TO_STRAND DANGLE_5P
# T* S5* s5* T*
g_5_s_5_6_complex = nc.Complex(signal_5_6_strand, gate_5_base_strand)
g_5_s_5_7_complex = nc.Complex(signal_5_7_strand, gate_5_base_strand)
g_5_s_5_6_nonimplicit_base_pairs = [(signal_5_6_toehold_addr, gate_5_bound_toehold_3p_addr)]
g_5_s_5_6_complex_constraint = nc.nupack_complex_base_pair_probability_constraint(
strand_complexes=[g_5_s_5_6_complex, g_5_s_5_7_complex],
nonimplicit_base_pairs=g_5_s_5_6_nonimplicit_base_pairs,
# base_pair_probs={
# dc.BasePairType.DANGLE_5P: 0.4
# }
)
# S2 s2 T S5 s5
# 21
# 34 22|20 19 15 14 2 10
# | | || | | | | ||
