def testDeltaG(self):
# Create a test compound.
species = [models.Specie(number_of_hydrogens=12, net_charge=0,
formation_energy=-10.5),
models.Specie(number_of_hydrogens=11, net_charge=-1,
formation_energy=-12.1),
models.Specie(number_of_hydrogens=10, net_charge=-2,
formation_energy=-13.4)]
species_group = models.SpeciesGroup()
species_group._all_species = species
compound = models.Compound(kegg_id='fake compound')
compound._species_group_to_use = species_group
# Format: ph, ionic strength, dG.
test_data = ((6.5, 0.1, 361.094),
(7.0, 0.1, 389.619),
(7.5, 0.1, 418.143),
(7.0, 0.0001, 386.118),
(7.0, 0.001, 386.473),
(7.0, 0.2, 390.505))
for ph, i_s, expected_dg in test_data:
actual_dg = compound.DeltaG(pH=ph, ionic_strength=i_s)
self.assertAlmostEqual(expected_dg, actual_dg, 3,
'ph: %f, i_s: %f, expected dG: %f, actual dG: %f' %
(ph, i_s, expected_dg, actual_dg))
def testTransform(self):
specie = models.Specie(number_of_hydrogens=2, number_of_mgs=0,
net_charge=-1, formation_energy=-10.0)
# Test some hand-calculated numbers: (ph, ionic strength, result)
test_data = (
# Move pH, keep ionic strength constant.
(6.0, 0.1, 59.071),
(6.5, 0.1, 64.776),
(7.0, 0.1, 70.481),
(7.5, 0.1, 76.186),
(8.0, 0.1, 81.891),
# Move ionic strength, keep pH constant.
(7.0, 0.0001, 69.898),
(7.0, 0.001, 69.957),
(7.0, 0.01, 70.121),
(7.0, 0.05, 70.349),
(7.0, 0.11, 70.501),
(7.0, 0.15, 70.566),
(7.0, 0.2, 70.629),
# Move both.
(6.0, 0.0001, 58.488),
(6.5, 0.001, 64.252),
(8.0, 0.0001, 81.308),
(7.5, 0.15, 76.271),
)
for ph, ionic_strength, expected_transform in test_data:
actual_transform = specie.Transform(pH=ph, ionic_strength=ionic_strength)
self.assertAlmostEqual(expected_transform, actual_transform, 3)
def MakeSpeciesGroup(pmap, source, compound):
logging.debug('Writing data from source %s', source.name)
if 'priority' not in pmap or 'species' not in pmap:
logging.error('Malformed pmap field for %s', compound.kegg_id)
return None
sg = models.SpeciesGroup(kegg_id=compound.kegg_id,
priority=pmap['priority'],
formation_energy_source=source)
sg.save()
for sdict in pmap['species']:
specie = models.Specie(kegg_id=compound.kegg_id,
number_of_hydrogens=sdict['nH'],
number_of_mgs=sdict['nMg'],
net_charge=sdict['z'],
formation_energy=sdict['dG0_f'])
specie.save()
sg.species.add(specie)
sg.save()
return sg