def __init__(self,
abort_event,
primers, #all primers (generally degenerate) that may be present in the system
min_amplicon, #minimum amplicon length
max_amplicon, #maximum amplicon length
with_exonuclease=False, #if polymerase does have have 3' exonuclease activity, products of primers with 3'-mismatches will also be icluded
include_side_annealings=False, #if True, include annealings which do not give any products into equilibrium system as side reactions
):
AbortableBase.__init__(self, abort_event)
self._primers = primers
self._min_amplicon = min_amplicon
self._max_amplicon = max_amplicon
self._with_exonuclease = with_exonuclease
self._include_side_annealings = include_side_annealings
def __init__(self, abort_event, reactions, concentrations, precision):
EquilibriumBase.__init__(self, reactions, concentrations, precision)
AbortableBase.__init__(self, abort_event)
#indexed reactants and concentrations
self._concentrations = [concentrations[r] for r in self._reactants_ids] #list of reactants' concentrations
self._min_C = min(self._concentrations)
#indexed reactions
self._reaction_ids = reactions.keys() #reaction index to ID
self._reactions = [self._indexed_reaction(reactions[rid])
for rid in self._reaction_ids] #list of reactions
self._Ri_reactions = [[] for _n in self._concentrations]
for ri, R in enumerate(self._reactions): #partition reactions by reactants
self._Ri_reactions[R[1]].append((ri, R))
if R[2] is not None:
self._Ri_reactions[R[2]].append((ri, R))
def __init__(
self,
abort_event,
primers, #all primers (generally degenerate) that may be present in the system
min_amplicon, #minimum amplicon length
max_amplicon, #maximum amplicon length
with_exonuclease=False, #if polymerase does have have 3' exonuclease activity, products of primers with 3'-mismatches will also be icluded
include_side_annealings=False, #if True, include annealings which do not give any products into equilibrium system as side reactions
):
AbortableBase.__init__(self, abort_event)
self._primers = primers
self._min_amplicon = min_amplicon
self._max_amplicon = max_amplicon
self._with_exonuclease = with_exonuclease
self._include_side_annealings = include_side_annealings
def __init__(self, abort_event, reactions, concentrations, precision):
EquilibriumBase.__init__(self, reactions, concentrations, precision)
AbortableBase.__init__(self, abort_event)
#indexed reactants and concentrations
self._concentrations = [
concentrations[r] for r in self._reactants_ids
] #list of reactants' concentrations
self._min_C = min(self._concentrations)
#indexed reactions
self._reaction_ids = reactions.keys() #reaction index to ID
self._reactions = [
self._indexed_reaction(reactions[rid])
for rid in self._reaction_ids
] #list of reactions
self._Ri_reactions = [[] for _n in self._concentrations]
for ri, R in enumerate(
self._reactions): #partition reactions by reactants
self._Ri_reactions[R[1]].append((ri, R))
if R[2] is not None:
self._Ri_reactions[R[2]].append((ri, R))
def __init__(self, abort_event):
AbortableBase.__init__(self, abort_event)
self._newline_last = False
def __init__(self, abort_event):
AbortableBase.__init__(self, abort_event)
self._tasks = []
def __init__(self, abort_event):
AbortableBase.__init__(self, abort_event)
self._tasks = []
def __init__(self, abort_event):
AbortableBase.__init__(self, abort_event)
self._newline_last = False
