def __init__(self, abort_event, *args, **kwargs): MixtureFactory.__init__(self, abort_event, *args, **kwargs) MultiprocessingBase.__init__(self, abort_event) self._searcher = SearchEngine(self._abort_event) self._p_weights = [p.num_components for p in self._primers] self._pw_sum = sum(self._p_weights) self._num_p = len(self._primers)
def __init__(self, abort_event, *args, **kwargs): MixtureFactory.__init__(self, abort_event, *args, **kwargs) MultiprocessingBase.__init__(self, abort_event) self._searcher = SearchEngine(self._abort_event) self._p_weights = [p.num_components for p in self._primers] self._pw_sum = sum(self._p_weights) self._num_p = len(self._primers)
def __init__(self, abort_event, reactions, concentrations, precision = 1e-10): MultiprocessingBase.__init__(self, abort_event) EquilibriumBase.__init__(self, reactions, concentrations, precision) #input parameters self.reactions = reactions self.concentrations = concentrations #group reactions by their connected graph components self._reactions_groups = self._group_reactions()
def __init__(self, abort_event, polymerase, with_exonuclease, num_cycles, ): MultiprocessingBase.__init__(self, abort_event) self._polymerase = polymerase self._with_exonuclease = with_exonuclease self._num_cycles = num_cycles self._PCR_P = deepcopy(tdf.PCR_P)
def __init__( self, abort_event, polymerase, with_exonuclease, num_cycles, ): MultiprocessingBase.__init__(self, abort_event) self._polymerase = polymerase self._with_exonuclease = with_exonuclease self._num_cycles = num_cycles self._PCR_P = deepcopy(tdf.PCR_P)
def __init__(self, abort_event, reactions, concentrations, precision=1e-10): MultiprocessingBase.__init__(self, abort_event) EquilibriumBase.__init__(self, reactions, concentrations, precision) #input parameters self.reactions = reactions self.concentrations = concentrations #group reactions by their connected graph components self._reactions_groups = self._group_reactions()
def __init__(self, abort_event, *args, **kwargs): iPCR_Interface.__init__(self, abort_event, *args, **kwargs) MultiprocessingBase.__init__(self, abort_event) self._blast_results = None self._bounds = None self._query = None #PCR parameters self._PCR_Simulations = dict() #query_id use hash of primers instead of all-config hash as in job_id self._primers_hash = (hash(tuple(self._primers)) & 0xFFFFFFF) self._query_id = re.split('_[0-9]+\Z', self._job_id)[0] self._query_id += '_%s' % str(self._primers_hash) #results self._results_filename = self._query_id+'-blast.xml' self._query_filename = self._query_id+'-blast.cfg' #reports self._hits_report_filename = '%s-%s-hits.txt' % (self._job_id, self._PCR_report_suffix.rstrip('-PCR')) #flags self._have_blast_results = False self._have_saved_results = False
def __init__(self, abort_event, job_id, primers): #initial check try: if len(primers) == 0: raise ValueError('AllSecStructures: no primers given.') except TypeError: raise TypeError(('AllSecStructures: primers should be an iterable. ' 'Given %s instead') % str(primers)) ReporterInterface.__init__(self) MultiprocessingBase.__init__(self, abort_event) #all primers list and concentrations dict self._primers = primers self._all_primers = [] self._concentrations = dict() self._reactions = dict() self._self = [] self._cross = [] self._all_structures = dict() self._equilibrium_concentrations = None #reports self._job_id = job_id self._short_structs_filename = job_id+'-structures-short.txt' self._full_structs_filename = job_id+'-structures-full.txt'
def __init__(self, abort_event, job_id, primers): #initial check try: if len(primers) == 0: raise ValueError('AllSecStructures: no primers given.') except TypeError: raise TypeError( ('AllSecStructures: primers should be an iterable. ' 'Given %s instead') % str(primers)) ReporterInterface.__init__(self) MultiprocessingBase.__init__(self, abort_event) #all primers list and concentrations dict self._primers = primers self._all_primers = [] self._concentrations = dict() self._reactions = dict() self._self = [] self._cross = [] self._all_structures = dict() self._equilibrium_concentrations = None #reports self._job_id = job_id self._short_structs_filename = job_id + '-structures-short.txt' self._full_structs_filename = job_id + '-structures-full.txt'
def __init__(self, abort_event): MultiprocessingBase.__init__(self, abort_event) self._a = 5
def __init__(self, abort_event): MultiprocessingBase.__init__(self, abort_event) self._a = 5