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 = []