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)