def test_get_mw(self):
'''Tests get_mw method.'''
curr_dir = os.path.dirname(os.path.realpath(__file__))
model = read_sbml_model(
os.path.join(curr_dir, '../../../data/models/yeastGEM.xml'))
tests = 0
while tests < 10:
met = random.choice(model.metabolites)
# met = model.metabolites.get_by_id('s_3071__91__lp__93__')
print(met.id, met.name)
# Get existing formula and mw:
formula = met.formula
if formula:
existing_mw = get_molecular_mass(formula, r_mass=2**16)
# Unset formula:
met.formula = None
calc_mw = get_mw(model, met.id)
if calc_mw:
self.assertAlmostEqual(existing_mw, calc_mw, 0)
tests += 1
# Reset formula:
met.formula = formula
def get_mw(model, met_id, parent_reacts=None):
'''Get molecular weight.'''
if parent_reacts is None:
parent_reacts = []
met = model.metabolites.get_by_id(met_id)
target_coeff = float('NaN')
if met.formula:
return get_molecular_mass(met.formula, r_mass=2**16)
for react in met.reactions:
if len(react.metabolites) > 1 and react not in parent_reacts:
mw = 0
for react_met, coeff in react.metabolites.items():
if react_met.id != met.id:
parent_reacts.append(react)
mw += get_mw(model, react_met.id, parent_reacts) * coeff
if np.isnan(mw):
break
else:
target_coeff = -coeff
if not np.isnan(mw):
print('Found:', met.name, mw, react.name)
return mw * target_coeff
print('Unfound:', met.name)
return float('NaN')
def _add_metabolite(model_id, model_ids, current_bigg_ids,
bigg_data):
'''Adds a given metabolite to the collection of metabolites.'''
met_url = 'http://bigg.ucsd.edu/api/v2/models/' + model_id + \
'/metabolites/' + current_bigg_ids[1]
met_data = json.loads(urllib2.urlopen(met_url).read())
bg_dat = {}
bigg_data[met_data['bigg_id']] = bg_dat
bg_dat['name'] = met_data['name']
bg_dat['formula'] = met_data['formula']
bg_dat['database_links'] = dict((key, value[0]['id'])
for key, value
in met_data['database_links']
.iteritems())
bg_dat['models'] = [model['bigg_id']
for model
in met_data['other_models_with_metabolite']
if model['bigg_id'] in model_ids]
bg_dat['models'].append(model_id)
bg_dat['models'] = sorted(set(bg_dat['models']))
try:
bg_dat['mass'] = \
chem_utils.get_molecular_mass(met_data['formula'])
except KeyError, error:
print met_data['bigg_id'] + ': ' + str(error)
def _normalise_mass(properties):
'''Removes ambiguity in mass values by recalculating according to chemical
formula.'''
properties.pop('mass', None)
if 'formula' in properties and properties['formula'] is not None:
mono_mass = chem_utils.get_molecular_mass(properties['formula'])
if not math.isnan(mono_mass):
properties['monoisotopic_mass:float'] = mono_mass
def _normalise_mass(properties):
'''Removes ambiguity in mass values by recalculating according to chemical
formula.'''
properties.pop('mass:float', None)
if 'formula' in properties and properties['formula'] is not None:
mono_mass = chem_utils.get_molecular_mass(properties['formula'])
if not math.isnan(mono_mass):
properties['monoisotopic_mass:float'] = mono_mass
def test_get_molecular_mass(self):
'''Tests get_molecular_mass method.'''
self.assertAlmostEqual(chm_util.get_molecular_mass('H2O'),
18.010564684)
def test_get_molecular_mass(self):
'''Tests get_molecular_mass method.'''
self.assertAlmostEqual(chm_util.get_molecular_mass('H2O'),
18.010564684)
