def LoadKeggCompounds(kegg_json_filename=COMPOUND_FILE, draw_thumbnails=True):
parsed_json = json.load(gzip.open(kegg_json_filename, 'r'))
for cd in parsed_json:
try:
cid = cd['CID']
logging.debug('Handling compound %s', cid)
formula = cd.get('formula')
mass = cd.get('mass')
if mass is not None:
mass = float(mass)
inchi = cd.get('InChI')
num_electrons = cd.get('num_electrons')
group_vector = cd.get('group_vector')
name = models.CommonName.GetOrCreate(cd['name'])
"""
if formula is None:
raise KeyError('Missing formula for CID %s' % cid)
if mass is None:
raise KeyError('Missing mass for CID %s' % cid)
if inchi is None:
raise KeyError('Missing inchi for CID %s' % cid)
"""
c = models.Compound(kegg_id=cid,
formula=formula,
inchi=inchi,
mass=mass,
name=name,
group_vector=group_vector)
if num_electrons is not None:
c.num_electrons = int(num_electrons)
if draw_thumbnails:
c.WriteStructureThumbnail()
c.save()
# Add the thermodynamic data.
pmaps = cd.get('pmaps')
if not pmaps:
error = cd.get('error')
if error:
c.no_dg_explanation = error
else:
for pmap in pmaps:
AddPmapToCompound(pmap, c)
# Add the common names.
names = GetOrCreateNames(cd['names'])
for n in names:
c.common_names.add(n)
c.save()
except Exception, e:
logging.error(e)
continue
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 testHasData(self):
compound = models.Compound(kegg_id='fake compound')
self.assertFalse(compound.HasData())
compound.formula = 'C12H22O11'
self.assertFalse(compound.HasData())
compound.mass = 0.0
self.assertFalse(compound.HasData())
compound.mass = 14.5
self.assertTrue(compound.HasData())
def testGetAtomBag(self):
compound = models.Compound(kegg_id='fake compound')
self.assertEqual(None, compound.GetAtomBag())
compound.formula = 'C12H22O11'
expected_atom_bag = {'C': 12, 'H': 22, 'O': 11}
self.assertEqual(expected_atom_bag, compound.GetAtomBag())
compound.formula = 'C10H16N5O12P3S'
expected_atom_bag = {'C': 10, 'H': 16, 'N': 5,
'O': 12, 'P': 3, 'S': 1}
self.assertEqual(expected_atom_bag, compound.GetAtomBag())
# Contains an R group.
compound.formula = 'C10R11H16N5O12P3S'
self.assertEqual(None, compound.GetAtomBag())
def testHashableReactionString(self):
"""Ensure that hashable strings for different reactions are different."""
compound_a = models.Compound(kegg_id='C00010')
compound_b = models.Compound(kegg_id='C00009')
compound_c = models.Compound(kegg_id='C00021')
compound_d = models.Compound(kegg_id='C00032')
compound_e = models.Compound(kegg_id='C00190')
hydrogen = models.Compound(kegg_id='C00080')
# 1 a + 1 b = 1 c + 1 d
reactants_a = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
products_a = [models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=1, compound=compound_d)]
hashable_a = models.StoredReaction.HashableReactionString(reactants_a,
products_a)
# 1 a + 1 b = 1 c + 2 d
reactants_b = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
products_b = [models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=2, compound=compound_d)]
hashable_b = models.StoredReaction.HashableReactionString(reactants_b,
products_b)
# 1 a + 1 b = 1 c + 1 e
reactants_c = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
products_c = [models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=1, compound=compound_e)]
hashable_c = models.StoredReaction.HashableReactionString(reactants_c,
products_c)
# 3 a + 1 b = 2 c
reactants_d = [models.Reactant(coeff=3, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
products_d = [models.Reactant(coeff=2, compound=compound_c)]
hashable_d = models.StoredReaction.HashableReactionString(reactants_d,
products_d)
all_hashables = (hashable_a, hashable_b, hashable_c, hashable_d)
for a, b in itertools.combinations(all_hashables, 2):
self.assertNotEqual(a, b)
# 1 a + 1 b = 1 d + 1 c
reactants_a2 = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
products_a2 = [models.Reactant(coeff=1, compound=compound_d),
models.Reactant(coeff=1, compound=compound_c)]
hashable_a2 = models.StoredReaction.HashableReactionString(reactants_a2,
products_a2)
self.assertEqual(hashable_a2, hashable_a)
# 1 d + 1 c = 1 a + 1 b
products_a3 = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b)]
reactants_a3 = [models.Reactant(coeff=1, compound=compound_d),
models.Reactant(coeff=1, compound=compound_c)]
hashable_a3 = models.StoredReaction.HashableReactionString(reactants_a3,
products_a3)
self.assertEqual(hashable_a3, hashable_a)
# 1 b + 3 a = 2 c
reactants_d2 = [models.Reactant(coeff=1, compound=compound_b),
models.Reactant(coeff=3, compound=compound_a)]
products_d2 = [models.Reactant(coeff=2, compound=compound_c)]
hashable_d2 = models.StoredReaction.HashableReactionString(reactants_d2,
products_d2)
self.assertEqual(hashable_d2, hashable_d)
# 2 c = 1 b + 3 a
products_d3 = [models.Reactant(coeff=1, compound=compound_b),
models.Reactant(coeff=3, compound=compound_a)]
reactants_d3 = [models.Reactant(coeff=2, compound=compound_c)]
hashable_d3 = models.StoredReaction.HashableReactionString(reactants_d3,
products_d3)
self.assertEqual(hashable_d3, hashable_d)
# 1 b + 3 a = 2 c + 2 h+
reactants_d4 = [models.Reactant(coeff=1, compound=compound_b),
models.Reactant(coeff=3, compound=compound_a)]
products_d4 = [models.Reactant(coeff=2, compound=compound_c),
models.Reactant(coeff=2, compound=hydrogen)]
hashable_d4 = models.StoredReaction.HashableReactionString(reactants_d4,
products_d4)
self.assertEqual(hashable_d4, hashable_d)
def setUp(self):
self.compound = models.Compound(kegg_id='fake compound',
formula='C10H16N5O12P3S')
def testHashableReactionString(self):
"""
Ensure that hashable strings for different reactions are different
and the same for equivalent reactions.
"""
compound_a = models.Compound(kegg_id='C00010')
compound_b = models.Compound(kegg_id='C00009')
compound_c = models.Compound(kegg_id='C00021')
compound_d = models.Compound(kegg_id='C00032')
compound_e = models.Compound(kegg_id='C00190')
# 1 a + 1 b = 1 c + 1 d
reactants_a = [models.Reactant(coeff=-1, compound=compound_a),
models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=1, compound=compound_d)]
sr_a = models.StoredReaction.HashableReactionString(reactants_a)
# 1 a + 1 b = 1 c + 2 d
reactants_b = [models.Reactant(coeff=-1, compound=compound_a),
models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=2, compound=compound_d)]
sr_b = models.StoredReaction.HashableReactionString(reactants_b)
# 1 a + 1 b = 1 c + 1 e
reactants_c = [models.Reactant(coeff=-1, compound=compound_a),
models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=1, compound=compound_c),
models.Reactant(coeff=1, compound=compound_e)]
sr_c = models.StoredReaction.HashableReactionString(reactants_c)
# 3 a + 1 b = 2 c
reactants_d = [models.Reactant(coeff=-3, compound=compound_a),
models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=2, compound=compound_c)]
sr_d = models.StoredReaction.HashableReactionString(reactants_d)
# 1 a + 1 b = 1 d + 1 c
reactants_a2 = [models.Reactant(coeff=-1, compound=compound_a),
models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=1, compound=compound_d),
models.Reactant(coeff=1, compound=compound_c)]
sr_a2 = models.StoredReaction.HashableReactionString(reactants_a2)
# 1 d + 1 c = 1 a + 1 b
reactants_a3 = [models.Reactant(coeff=1, compound=compound_a),
models.Reactant(coeff=1, compound=compound_b),
models.Reactant(coeff=-1, compound=compound_d),
models.Reactant(coeff=-1, compound=compound_c)]
sr_a3 = models.StoredReaction.HashableReactionString(reactants_a3)
# 1 b + 3 a = 2 c
reactants_d2 = [models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=-3, compound=compound_a),
models.Reactant(coeff=2, compound=compound_c)]
sr_d2 = models.StoredReaction.HashableReactionString(reactants_d2)
# 2 c = 1 b + 3 a
reactants_d3 = [models.Reactant(coeff=1, compound=compound_b),
models.Reactant(coeff=3, compound=compound_a),
models.Reactant(coeff=-2, compound=compound_c)]
sr_d3 = models.StoredReaction.HashableReactionString(reactants_d3)
# 1 b + 3 a = 2 c + 2 h+
reactants_d4 = [models.Reactant(coeff=-1, compound=compound_b),
models.Reactant(coeff=-3, compound=compound_a),
models.Reactant(coeff=2, compound=compound_c)]
sr_d4 = models.StoredReaction.HashableReactionString(reactants_d4)
# make sure all the 4 reactions have different hashable strings
for a, b in itertools.combinations((sr_a, sr_b, sr_c, sr_d), 2):
self.assertNotEqual(a, b)
# make sure all the 3 versions of reaction a have the same
# hashable strings
for a, b in itertools.combinations((sr_a, sr_a2, sr_a3), 2):
self.assertEqual(a, b)
# make sure all the 4 versions of reaction a have the same
# hashable strings
for a, b in itertools.combinations((sr_d, sr_d2, sr_d3, sr_d4), 2):
self.assertEqual(a, b)