def setUp(self): set_io_objects(D=MyDomain) self.SKIP = False try: import matplotlib.pyplot except ImportError: self.SKIP = True
def read_pil_line(*args, **kwargs): set_io_objects(D=PepperDomain, S=PepperStrand, C=PepperComplex, R=PepperReaction, M=PepperMacrostate) out = dsd_read_pil_line(*args, **kwargs) clear_io_objects() return out
def load_pil(data, is_file=False): """ Parses a string or file written in PIL notation! """ # We only assign reactions in a postprocessing step, # because there are no macrostates in nuskell. set_io_objects(D=NuskellDomain, C=NuskellComplex) out = dsd_read_pil(data, is_file) clear_io_objects() cxs = {k: v for k, v in out['complexes'].items()} rms = {k: v for k, v in out['macrostates'].items()} det = set(list(out['det_reactions'])) con = set(list(out['con_reactions'])) [o.clear() for o in out.values()] out.clear() return cxs, rms, det, con
def read_pil(data, is_file=False, ignore=None): set_io_objects(D=PepperDomain, S=PepperStrand, C=PepperComplex, R=PepperReaction, M=PepperMacrostate) out = dsd_read_pil(data, is_file, ignore) clear_io_objects() if len(out['con_reactions']): log.warning('Ignoring condensed reaction input.') if len(out['macrostates']): log.warning('Ignoring complex macrostate input.') # Make sure that strands are not within initial complexes! for strand in out['strands'].values(): strand.concentration = ('constant', 0, 'M') out['complexes'][('s', strand.name)] = strand out['domains'].clear() return out['complexes'], out['det_reactions']
def setUp(self): set_io_objects()
def setUp(self): set_io_objects(D=MyDomain)