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Strands.py
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from helpers import *
""" Strand-based components """
class StrandComponent():
def __hash__(self):
return hash(self.rxn_name)
def __repr__(self):
return self.__str__()
class SignalStrand(StrandComponent):
"""
Strands like
3' left domain - T - right domain 5'
"""
fuel_domain = "f"
def __init__(self, left_domain, right_domain, rel_amount = 1.0):
self.left_domain = str(left_domain)
self.right_domain = str(right_domain)
self.rel_amount = rel_amount
self.rxn_name = "%s_T_%s" % \
(format_domain_rxn(self.left_domain), format_domain_rxn(self.right_domain))
# 3' -> 5' description
def __str__(self):
return "%s\tT\t%s" % \
(format_domain(self.left_domain), format_domain(self.right_domain))
# this is 3' -> 5'
class GateStrand(StrandComponent):
"""
Strands like
5' T* - main_domain* - T* 3'
"""
def __init__(self, main_domain, rel_amount = 1.0):
self.main_domain = str(main_domain)
self.rel_amount = rel_amount
self.right_partners = []
self.left_partners = []
self.rxn_name = "Tc_%s_Tc" % format_domain_rxn(self.main_domain)
# 5' -> 3' description
def __str__(self):
return "T*\t%s*\tT*" % format_domain(self.main_domain)
# this is 5' -> 3'
class GO(StrandComponent):
"""
Complexes like
3' |-------Si--------|--T---|-------Sk--------| 5'
5' |--T*--|-------Si*-------|--T*--| 3'
"""
def __init__(self, main_domain, out_domain, rel_amount = 1.0):
self.main_domain = main_domain
self.out_domain = out_domain
self.gate = GateStrand(main_domain)
self.out_signal = SignalStrand(main_domain, out_domain)
self.rel_amount = rel_amount
self.rxn_name = rxn_name_components(self.out_signal, self.gate)
def __str__(self):
return "\t%s\n%s" % \
(str(self.out_signal), str(self.gate))
class DynamicGate(StrandComponent):
"""
Complexes like
3' |-------Si--------|-------Sj--------| 5'
5' |--T*--|-------Si*-------|-------Sj*-------|--T*--| 3'
"""
def __init__(self, left_domain, right_domain, rel_amount = 1.0):
self.left_domain = left_domain
self.right_domain = right_domain
self.rel_amount = rel_amount
self.right_partners = []
self.left_partners = []
self.rxn_name = "%s_%s-Tc_%sc_%sc_Tc" % \
(format_domain_rxn(self.left_domain), format_domain_rxn(self.right_domain),
format_domain_rxn(self.left_domain), format_domain_rxn(self.right_domain))
def __str__(self):
return "\t%s\t%s\nT*\t%s\t%s\tT*" % \
(format_domain(self.left_domain), format_domain(self.right_domain),
format_domain(self.left_domain), format_domain(self.right_domain))
class Th(StrandComponent):
def __init__(self, in_toehold_domain, in_domain, rel_amount = 1.0):
self.in_toehold_domain = in_toehold_domain
self.in_domain = in_domain
self.rel_amount = rel_amount
self.rxn_name = "%s-%s_Tc_%sc" % \
(format_domain_rxn(self.in_domain),
format_domain_rxn(self.in_toehold_domain).lower(),
format_domain_rxn(self.in_domain))
def rxn_products(self, in_signal):
return [ "%s-%s_Tc_%sc" % \
(in_signal.rxn_name,
format_domain_rxn(self.in_toehold_domain).lower(),
format_domain_rxn(self.in_domain)),
format_domain_rxn(self.in_domain) ]
def __str__(self):
return "\t\t%s\n%s\tT*\t%s*" % \
(format_domain(self.in_domain),
format_domain(self.in_toehold_domain).lower(),
format_domain(self.in_domain))
class Reporter(StrandComponent):
def __init__(self, main_domain, rel_amount = 1.0):
self.main_domain = main_domain
self.rel_amount = 1.0
self.rxn_name = "%sQ-Tc_%scF" % \
(format_domain_rxn(self.main_domain),
format_domain_rxn(self.main_domain))
def rxn_products(self, in_signal):
return [ "%s-Tc_%scF" % \
(in_signal.rxn_name,
format_domain_rxn(self.main_domain)),
format_domain_rxn(self.main_domain + "Q") ]
def __str__(self):
return "\t%s\tQ\nTc_%sc\tF" % \
(format_domain_rxn(self.main_domain),
format_domain_rxn(self.main_domain))