def to_Peppercorn(*args, **kargs):
"""Converts DNAObjects objects to Peppercorn objects.
The following objects will be recognized in the key list and converted:
- domains
- complexes
- reactions
Other supplied objects are ignored.
The output is in the form of a dictionary mapping the keys
'domains', 'complexes', and 'reactions' to a list of tuples
of the form (object, converted_object). This may be iterated through
directly or converted into a dict for object lookup.
"""
## Clear previously created Peppercorn objects from memory
## to prevent duplication errors.
enumobj.clear_memory()
## Extract all objects to be converted
reactions = set(kargs.get('reactions', []))
complexes = set(
sum([list(r.reactants + r.products)
for r in reactions], []) + kargs.get('complexes', []))
domains = set(
[d for c in complexes for d_list in c.base_domains() for d in d_list] +
sum([d.base_domains() for d in kargs.get('domains', [])], []))
## Convert domains, strands, complexes, and reactions
enum_domains = {}
for d in set(sum([d.base_domains() for d in domains], [])):
enum_domains[d] = to_Peppercorn_domain(d)
enum_complexes = {}
for complex in set(complexes):
enum_complexes[complex] = to_Peppercorn_complex(complex, enum_domains)
enum_reactions = {}
for reaction in set(reactions):
enum_reactions[reaction] = to_Peppercorn_reaction(
reaction, enum_complexes)
## Return in a dict
results = dict()
results['domains'] = enum_domains.items()
results['complexes'] = enum_complexes.items()
results['reactions'] = enum_reactions.items()
return results
def tearDown(self):
clear_memory()
def tearDown(self):
objects.clear_memory()
def main():
logdata = True
if not os.path.exists('tmp'):
raise SystemExit('Please make a directory called "tmp" to store temorary results')
fig = plt.figure()
ax1 = fig.add_subplot(111)
mycolors = list('bgrcmyk')
mymarker = list('o*^.vph+D')
(mc,mm) = (0,0)
allresults = []
for data in paperdata:
results = []
for e, pilstring in enumerate(map(data['piltemplate'], data['pilparams'])):
clear_memory()
tmpname = 'tmp/'+data['name'] + '_' + str(e)
print tmpname
enumOBJ, crn = peppercorn(pilstring, name=tmpname, **data['pepperargs'])
if 'rates' in data:
if len(enumOBJ.condensed_reactions) == 1:
rxn = enumOBJ.condensed_reactions[0]
er = data['exp_results'][e]
results.append([er, rxn.rate])
else :
if 'reactants' in data['rates']:
for rxn in enumOBJ.condensed_reactions:
if sorted([rs.name for rs in rxn.reactants]) == sorted(data['rates']['reactants']):
er = data['exp_results'][e]
results.append([er, rxn.rate])
break
else:
raise NotImplementedError('multiple condensed reactions')
if 'simulation' in data:
for i, command in enumerate(data['simulation']):
nxy = simulate_crn(crn, tmpname, command)
rep = data['reporter']
(et, ec) = data['exp_results'][e+i]
time = get_simulated_time(nxy, rep, ec)
#print e+i, rep, et, ec, time
results.append([et, time])
#assert len(results) == len(data['exp_results'])
xs = []
ys = []
for e, (x,y) in enumerate(results):
if x is None or y is None:
print 'WARNING: Skipping data points {}'.format(e)
continue
if logdata:
xs.append(log(x,10))
ys.append(log(y,10))
else:
xs.append(x)
ys.append(y)
print xs
print ys
ax1.scatter(xs, ys, color=mycolors[mc], marker=mymarker[mm], label=data['name'])
mc += 1
if mc >= mcmax[mm]:
mc = 0
mm += 1
plt.title('Peppercorn vs. experiment');
if logdata:
ax1.set_xlabel('Experimental system speed [$\log_{10}(s)$]', fontsize=16)
ax1.set_ylabel('Simulated system speed [$\log_{10}(s)$]', fontsize=16)
(mi,ma)=(0, 6)
(mi,ma)=(-3, 7)
#plt.xlim(mi, ma)
#plt.ylim(mi, ma)
plt.plot([mi, ma], [mi, ma], color='black')
else:
ax1.set_xlabel('Experimental system speed [s]', fontsize=16)
ax1.set_ylabel('Simulated system speed [s]', fontsize=16)
(mi,ma) = (-10, 600)
plt.xlim(mi, ma)
plt.ylim(mi, ma)
plt.plot([mi, ma], [mi, ma], color='black')
lgd = plt.legend(bbox_to_anchor=(1.40, 1.0), loc='upper right', borderaxespad=0.)
#plt.legend(loc='lower right');
#plt.legend(loc='lower right');
#pfile = 'zhang2009_condensed_log.png'
#plt.savefig(pfile, bbox_extra_artists=(lgd,), bbox_inches='tight')
plt.savefig('test.pdf', bbox_extra_artists=(lgd,), bbox_inches='tight')
return