def get_dgf_priors(mi: MaudInput) -> Tuple[pd.Series, pd.DataFrame]:
"""Given a Maud input, get a multivariate prior from equilibrator.
Returns a pandas Series of prior means and a pandas DataFrame of
covariances. Both are indexed by metabolite ids.
:param mi: A MaudInput object
"""
cc = ComponentContribution()
mu = []
sigmas_fin = []
sigmas_inf = []
external_ids = {m.id: m.inchi_key for m in mi.kinetic_model.metabolites}
met_ix = pd.Index(mi.stan_coords.metabolites, name="metabolite")
for met_id in met_ix:
external_id = external_ids[met_id]
if external_id is None:
raise ValueError(f"metabolite {met_id} has no external id.")
c = cc.get_compound(external_id)
if isinstance(c, Compound):
mu_c, sigma_fin_c, sigma_inf_c = cc.standard_dg_formation(c)
mu.append(mu_c)
sigmas_fin.append(sigma_fin_c)
sigmas_inf.append(sigma_inf_c)
else:
raise ValueError(f"cannot find compound for metabolite {met_id}"
f" with external id {external_id}.")
sigmas_fin = np.array(sigmas_fin)
sigmas_inf = np.array(sigmas_inf)
cov = sigmas_fin @ sigmas_fin.T + 1e6 * sigmas_inf @ sigmas_inf.T
return (
pd.Series(mu, index=met_ix, name="prior_mean_dgf").round(10),
pd.DataFrame(cov, index=met_ix, columns=met_ix).round(10),
)
def search_equilibrator_compound(
cc: ComponentContribution,
id: str = None,
inchikey: str = None,
inchi: str = None,
smiles: str = None,
logger: Logger = getLogger(__name__)
) -> Dict[str, str]:
def copy_data(
compound,
data: Dict,
overwrite: bool = False,
) -> Dict:
# ...copy initial data into result compound
_compound = deepcopy(data)
# fill with eQuilibrator data for empty fields
for k, v in _compound.items():
if (
overwrite
or v is None
or v == ''
): _compound[k] = getattr(compound, k)
# keep the key known by eQuilibrator
_compound['cc_key'] = key
# keep the value known by eQuilibrator
_compound[key] = val
return _compound
data = {
'id': id,
'inchi_key': inchikey,
'inchi': inchi,
'smiles': smiles
}
for key, val in data.items():
if val:
compound = cc.get_compound(val)
# If compound is found in eQuilibrator, then...
if compound is not None:
# ...copy initial data into result compound
_compound = copy_data(compound, data)
return _compound
if inchikey:
# In last resort, try to search only with the first part of inchikey
compounds = cc.search_compound_by_inchi_key(
# first part of inchikey
inchikey.split('-')[0]
)
# eQuilibrator returns a list of compounds
if compounds:
# first compound in the list, hope it is sorted by decrease relevance
_compound = copy_data(compounds[0], data, overwrite=True)
# make inchi_key the ID key
_compound['cc_key'] = 'inchi_key'
return _compound
return {}
def get_dgf_priors(mi: MaudInput) -> Tuple[pd.Series, pd.DataFrame]:
"""Given a Maud input, get a multivariate prior from equilibrator.
Returns a pandas Series of prior means and a pandas DataFrame of
covariances. Both are indexed by metabolite ids.
:param mi: A MaudInput object
"""
cc = ComponentContribution()
mu = []
sigmas_fin = []
sigmas_inf = []
met_ix = pd.Index(mi.stan_coords.metabolites, name="metabolite")
met_order = [m.id for m in mi.kinetic_model.metabolites]
for m in mi.kinetic_model.metabolites:
external_id = m.id if m.inchi_key is None else m.inchi_key
c = cc.get_compound(external_id)
if isinstance(c, Compound):
mu_c, sigma_fin_c, sigma_inf_c = cc.standard_dg_formation(c)
mu_c += c.transform(
cc.p_h, cc.ionic_strength, cc.temperature, cc.p_mg
).m_as("kJ/mol")
mu.append(mu_c)
sigmas_fin.append(sigma_fin_c)
sigmas_inf.append(sigma_inf_c)
else:
raise ValueError(
f"cannot find compound for metabolite {m.id}"
f" with external id {external_id}."
"\nConsider setting the field metabolite_inchi_key"
" if you haven't already."
)
sigmas_fin = np.array(sigmas_fin)
sigmas_inf = np.array(sigmas_inf)
cov = sigmas_fin @ sigmas_fin.T + 1e6 * sigmas_inf @ sigmas_inf.T
cov = (
pd.DataFrame(cov, index=met_order, columns=met_order)
.loc[met_ix, met_ix]
.round(10)
)
mu = (
pd.Series(mu, index=met_order, name="prior_mean_dgf")
.loc[met_ix]
.round(10)
)
return mu, cov
def runThermo(
pathway: rpPathway,
cc: ComponentContribution=None,
ph: float=DEFAULT_pH,
ionic_strength: float=DEFAULT_ionic_strength,
pMg: float=DEFAULT_pMg,
compound_substitutes: Dict = None,
logger: Logger = getLogger(__name__)
) -> Dict:
"""Given a tar input file, perform thermodynamics analysis for each rpSBML file.
:param inFile: The path to the input file
:param outFile: The path to the output file
:param pathway_id: The id of the heterologous pathway of interest
:param ph: The pH of the host organism (Default: 7.5)
:param ionic_strength: Ionic strenght of the host organism (Default: 0.25M)
:param pMg: The pMg of the host organism (Default: 3.0)
:param temp_k: The temperature of the host organism in Kelvin (Default: 298.15)
:param stdev_factor: The standard deviation factor to calculate MDF (Default: 1.96)
:type pathway: Dict
:type pathway_id: str
:type ph: float
:type ionic_strength: float
:type pMg: float
:type temp_k: float
:type logger: Logger
:rtype: Dict
:return: Pathway updated with thermodynalics values
"""
print_title(
txt='Pathway Reactions',
logger=logger,
waiting=False
)
for rxn in pathway.get_list_of_reactions():
print_reaction(
rxn=rxn,
logger=logger
)
## INTERMEDIATE COMPOUNDS
# Optimise the production of target
# and remove (if possible) intermediate compounds
reactions = remove_compounds(
compounds=pathway.get_intermediate_species(),
reactions=pathway.get_list_of_reactions(),
rxn_target_id=pathway.get_target_rxn_id(),
logger=logger
)
## eQuilibrator
if cc is None:
cc = initThermo(
ph,
ionic_strength,
pMg,
logger
)
# Search for the key ID known by eQuilibrator
cc_species = {}
substituted_species = {}
sep = '__64__'
if compound_substitutes is None:
compound_substitutes = read_compound_substitutes(
os_path.join(
os_path.dirname(os_path.realpath(__file__)),
'data',
'compound_substitutes.csv'
)
)
for spe in pathway.get_species():
spe_split = spe.get_id().split(sep)
if len(spe_split) > 1:
_compound_substitutes = {k+sep+spe_split[1]: v for k, v in compound_substitutes.items()}
else:
_compound_substitutes = deepcopy(compound_substitutes)
# If the specie is listed in substitutes file, then take search values from it
# Check if starts with in case of compound names are like CMPD_NAME__64__COMPID
if spe.get_id() in _compound_substitutes:
cc_species[spe.get_id()] = search_equilibrator_compound(
cc=cc,
id=_compound_substitutes[spe.get_id()]['id'],
inchikey=_compound_substitutes[spe.get_id()]['inchikey'],
inchi=_compound_substitutes[spe.get_id()]['inchi'],
logger=logger
)
# Else, take search values from rpCompound
else:
cc_species[spe.get_id()] = search_equilibrator_compound(
cc=cc,
id=spe.get_id(),
inchikey=spe.get_inchikey(),
inchi=spe.get_inchi(),
smiles=spe.get_smiles(),
logger=logger
)
if cc_species[spe.get_id()] != {}:
if spe.get_id() != cc_species[spe.get_id()]['id']:
substituted_species[spe.get_id()] = cc_species[spe.get_id()][cc_species[spe.get_id()]['cc_key']]
else:
logger.warning(f'Compound {spe.get_id()} has not been found within eQuilibrator cache')
# Store thermo values for the net reactions
# and for each of the reactions within the pathway
results = {
'net_reaction': {},
'optimized_net_reaction': Reaction.sum_stoichio(reactions),
'reactions': {},
'optimized_reactions': {
rxn.get_id(): rxn
for rxn in reactions
},
'species': {},
'substituted_species': substituted_species
}
# Get the formation energy for each compound
for spe_id, cc_spe in cc_species.items():
try:
value = cc.standard_dg_formation(
cc.get_compound(
cc_spe[cc_spe['cc_key']]
)
)[0] # get .mu
except Exception as e:
value = None
logger.debug(e)
if value is None:
value = 'NaN'
results['species'][spe_id] = {
'standard_dg_formation': {
'value': value,
'units': 'kilojoule / mole'
}
}
# Build the list of IDs known by eQuilibrator
species_cc_ids = {}
for spe_id, cc_spe in cc_species.items():
if cc_spe == {}:
species_cc_ids[spe_id] = spe_id
else:
species_cc_ids[spe_id] = cc_spe[cc_spe['cc_key']]
## REACTIONS
# Compute thermo for each reaction
for rxn in pathway.get_list_of_reactions():
results['reactions'][rxn.get_id()] = eQuilibrator(
species_stoichio=rxn.get_species(),
species_ids=species_cc_ids,
cc=cc,
logger=logger
)
## THERMO
print_title(
txt='Computing thermodynamics (eQuilibrator)...',
logger=logger,
waiting=True
)
results['net_reaction'] = eQuilibrator(
species_stoichio=Reaction.sum_stoichio(reactions),
species_ids=species_cc_ids,
cc=cc,
logger=logger
)
print_OK(logger)
# Write results into the pathway
write_results_to_pathway(pathway, results, logger)
return results