def __swap_modelseed_compound(self, model_metabolite: Metabolite,
new_compound_ontology_id: int):
"""
Method to swap a metabolite in the Model SEED database format.
This method tries to find the Model SEED format of the new compound. If it does not find, it will change into an
arbitrary id with the Model SEED or the Ontology format.
:param Model.Metabolite model_metabolite: metabolite to be replaced.
:param int new_compound_ontology_id: ontology identifier of the metabolite that will replace the other
:return:
"""
old_inchikey = ""
if "inchi_key" in model_metabolite.annotation.keys():
old_inchikey = model_metabolite.annotation["inchi_key"]
old_aliases = AnnotationUtils.get_annotation_from_cobra_annotation(
model_metabolite)
old_id = model_metabolite.id
model_metabolite.annotation = {}
compound_container = self.__compounds_ontology.get_node_by_ont_id(
new_compound_ontology_id)
new_aliases = self.__compoundsIdConverter.get_all_aliases_by_modelSeedID(
compound_container.model_seed_id)
annotation = AnnotationUtils.get_compound_annotation_format_by_aliases(
new_aliases)
model_metabolite.annotation = annotation
new_inchikey = ""
if not compound_container.generic:
model_metabolite.annotation[
"inchi_key"] = compound_container.inchikey
new_inchikey = compound_container.inchikey
model_metabolite.annotation["smiles"] = compound_container.smiles
model_metabolite.formula = compound_container.formula
model_metabolite.charge = compound_container.charge
compartment = model_metabolite.compartment
db_id = compound_container.model_seed_id
model_metabolite.name = compound_container.name
if db_id:
self.__check_if_id_is_used_in_model_and_delete_it(
compound_container.model_seed_id + "_" + compartment)
model_metabolite.id = compound_container.model_seed_id + "_" + compartment
self.mapper.update_maps(old_inchikey, new_inchikey, old_id,
model_metabolite.id,
new_compound_ontology_id, old_aliases,
new_aliases)
else:
self.__change_boimmg_format_metabolite(model_metabolite,
compound_container)
def __change_boimmg_format_metabolite(self, model_metabolite: Metabolite,
compound_container):
"""
This method changes the id of the metabolite arbitrarily. The format of the metabolite is set for the
ontology format.
It is worth noting that the :param compound_container can be either a ModelSeedCompound or an OntologyCompound
:param Model.Metabolite model_metabolite: metabolite to be replaced.
:param CompoundContainer compound_container: compound that will replace the other.
:return:
"""
old_inchikey = ""
if "inchi_key" in model_metabolite.annotation.keys():
old_inchikey = model_metabolite.annotation["inchi_key"]
old_aliases = AnnotationUtils.get_annotation_from_cobra_annotation(
model_metabolite)
old_id = model_metabolite.id
aliases = self.__compoundsIdConverter.get_all_aliases_by_modelSeedID(
compound_container.model_seed_id)
annotation = {}
if aliases:
annotation = AnnotationUtils.get_compound_annotation_format_by_aliases(
aliases)
annotation["boimmg.compound"] = self.__compoundsAnnotationConfigs["BOIMMG_ID_CONSTRUCTION"]+\
str(compound_container.id)
new_aliases = {"BOIMMG": [annotation["boimmg.compound"]]}
model_metabolite.annotation = annotation
new_inchikey = ""
if not compound_container.generic:
model_metabolite.annotation[
"inchi_key"] = compound_container.inchikey
new_inchikey = compound_container.inchikey
model_metabolite.annotation["smiles"] = compound_container.smiles
model_metabolite.formula = compound_container.formula
model_metabolite.charge = compound_container.charge
model_metabolite.name = compound_container.name
compartment = model_metabolite.compartment
id = self.__compoundsAnnotationConfigs["BOIMMG_ID_CONSTRUCTION"] + str(
compound_container.id)
new_metabolite_id = id + "_" + compartment
self.__check_if_id_is_used_in_model_and_delete_it(new_metabolite_id)
self.report_material[model_metabolite.id] = new_metabolite_id
model_metabolite.id = new_metabolite_id
self.mapper.update_maps(old_inchikey, new_inchikey, old_id,
model_metabolite.id, compound_container.id,
old_aliases, new_aliases)
def __swap_kegg_metabolite(self, model_metabolite,
new_compound_ontology_id):
"""
Method to swap a metabolite in the KEGG database format.
This method tries to find the KEGG format of the new compound. If it does not find, it will change into the
Model SEED format.
:param Model.Metabolite model_metabolite: metabolite to be replaced.
:param int new_compound_ontology_id: ontology identifier of the metabolite that will replace the other
:return:
"""
old_inchikey = ""
if "inchi_key" in model_metabolite.annotation.keys():
old_inchikey = model_metabolite.annotation["inchi_key"]
old_aliases = AnnotationUtils.get_annotation_from_cobra_annotation(
model_metabolite)
old_id = model_metabolite.id
model_metabolite.annotation = {}
compound_container = self.__compounds_ontology.get_node_by_ont_id(
new_compound_ontology_id)
model_seed_id = compound_container.model_seed_id
new_aliases = self.__compoundsIdConverter.get_all_aliases_by_modelSeedID(
model_seed_id)
if model_seed_id in self.__compoundsIdConverter.get_modelSeedIdToDb(
).keys():
if "KEGG" in self.__compoundsIdConverter.get_modelSeedIdToDb().get(
model_seed_id):
kegg_id = self.__compoundsIdConverter.convert_modelSeedId_into_other_dbID(
model_seed_id, "KEGG")[0]
kegg_metabolite = KeggCompound(kegg_id)
annotation = AnnotationUtils.get_compound_annotation_format_by_aliases(
new_aliases)
model_metabolite.annotation = annotation
new_inchikey = ""
if not compound_container.generic:
model_metabolite.annotation[
"inchi_key"] = compound_container.inchikey
new_inchikey = compound_container.inchikey
model_metabolite.annotation[
"smiles"] = compound_container.smiles
model_metabolite.formula = kegg_metabolite.get_formula()
model_metabolite.name = kegg_metabolite.get_name()
model_metabolite.charge = 0
compartment = model_metabolite.compartment
self.__check_if_id_is_used_in_model_and_delete_it(kegg_id +
"_" +
compartment)
model_metabolite.id = kegg_id + "_" + compartment
self.mapper.update_maps(old_inchikey, new_inchikey, old_id,
model_metabolite.id,
compound_container.id, old_aliases,
new_aliases)
else:
self.__change_boimmg_format_metabolite(model_metabolite,
compound_container)
else:
self.__change_boimmg_format_metabolite(model_metabolite,
compound_container)
def __swap_bigg_metabolite(self, model_metabolite,
new_compound_ontology_id):
"""
Method to swap a metabolite in the BiGG database format.
This method tries to find the BiGG format of the new compound. If it does not find, it will change into the
Model SEED format.
:param Model.Metabolite model_metabolite: metabolite to be replaced.
:param int new_compound_ontology_id: ontology identifier of the metabolite that will replace the other
:return:
"""
model_metabolite.annotation = {}
compound_container = self.__compounds_ontology.get_node_by_ont_id(
new_compound_ontology_id)
model_seed_id = compound_container.model_seed_id
if model_seed_id:
bigg_ids = None
aliases = self.__compoundsIdConverter.get_modelSeedIdToDb().get(
model_seed_id)
if "BiGG" in aliases:
bigg_ids = self.__compoundsIdConverter.convert_modelSeedId_into_other_dbID(
model_seed_id, "BiGG")
elif "BiGG1" in aliases:
bigg_ids = self.__compoundsIdConverter.convert_modelSeedId_into_other_dbID(
model_seed_id, "BiGG1")
if bigg_ids:
bigg_metabolite = None
bigg_id = None
found = False
i = 0
while not found and i < len(bigg_ids):
try:
bigg_id = bigg_ids[i]
bigg_metabolite = bigg.get_bigg_metabolite(bigg_id)
found = True
except:
i += 1
if bigg_metabolite:
old_inchikey = ""
if "inchi_key" in model_metabolite.annotation.keys():
old_inchikey = model_metabolite.annotation["inchi_key"]
old_aliases = AnnotationUtils.get_annotation_from_cobra_annotation(
model_metabolite)
old_id = model_metabolite.id
new_aliases = self.__compoundsIdConverter.get_all_aliases_by_modelSeedID(
compound_container.model_seed_id)
annotation = AnnotationUtils.get_compound_annotation_format_by_aliases(
new_aliases)
model_metabolite.annotation = annotation
new_inchikey = ""
if not compound_container.generic:
new_inchikey = compound_container.inchikey
model_metabolite.annotation[
"inchi_key"] = compound_container.inchikey
model_metabolite.annotation[
"smiles"] = compound_container.smiles
model_metabolite.formula = bigg_metabolite.get(
"formulae")[0]
charges = bigg_metabolite.get("charges")
if charges: model_metabolite.charge = charges[0]
compartment = model_metabolite.compartment
if compartment is None:
model_metabolite.compartment = "c"
model_metabolite.name = bigg_metabolite.get("name")
self.__check_if_id_is_used_in_model_and_delete_it(
bigg_id + "_" + model_metabolite.compartment)
model_metabolite.id = bigg_id + "_" + model_metabolite.compartment
self.mapper.update_maps(old_inchikey, new_inchikey, old_id,
model_metabolite.id,
new_compound_ontology_id,
old_aliases, new_aliases)
else:
self.__change_boimmg_format_metabolite(
model_metabolite, compound_container)
else:
self.__change_boimmg_format_metabolite(model_metabolite,
compound_container)
else:
self.__change_boimmg_format_metabolite(model_metabolite,
compound_container)
def check_compounds_representation_and_balance_reactions(self, reactions:list):
res = []
self.__get_hydrogen_from_model()
compounds_ontology = CompoundsDBAccessor()
to_remove = []
for reaction in reactions:
reaction_ontology_reactants = []
reaction_ontology_products = []
for compound in reaction.reactants:
aliases = AnnotationUtils.get_annotation_from_cobra_annotation(compound)
found = False
for key in aliases:
for alias in aliases[key]:
new_key = self.compoundsAnnotationConfigs.get(key)
if key == "BOIMMG":
id = self.get_boimmg_id_from_annotation(aliases[key])
container = compounds_ontology.get_node_by_ont_id(id)
reaction_ontology_reactants.append(container)
found = True
break
elif new_key in self.__mapper.compounds_aliases_indexation.keys():
entities = self.__mapper.compounds_aliases_indexation.get(new_key).get(alias)
if entities:
for entity in entities:
entity_id = entity.id
if entity_id in self.__mapper.boimmg_db_model_map:
ont_id = self.__mapper.boimmg_db_model_map.get(entity_id)
entity_container = compounds_ontology.get_node_by_ont_id(ont_id)
reaction_ontology_reactants.append(entity_container)
found = True
break
if found:
break
for compound in reaction.products:
found = False
aliases = AnnotationUtils.get_annotation_from_cobra_annotation(compound)
for key in aliases:
new_key = self.compoundsAnnotationConfigs.get(key)
for alias in aliases[key]:
if key == "BOIMMG":
id = self.get_boimmg_id_from_annotation(aliases[key])
container = compounds_ontology.get_node_by_ont_id(id)
reaction_ontology_products.append(container)
found = True
break
elif new_key in self.__mapper.compounds_aliases_indexation.keys():
entities = self.__mapper.compounds_aliases_indexation.get(new_key).get(alias)
if entities:
for entity in entities:
entity_id = entity.id
if entity_id in self.__mapper.boimmg_db_model_map:
ont_id = self.__mapper.boimmg_db_model_map.get(entity_id)
entity_container = compounds_ontology.get_node_by_ont_id(ont_id)
reaction_ontology_products.append(entity_container)
found = True
break
if found:
break
# self.__check_generic_complete_relationship(reaction_ontology_reactants,reaction_ontology_products,reaction)
# if reaction_ontology_reactants and reaction_ontology_products:
balanced = self.check_balanced_reaction(reaction)
if not balanced:
to_remove.append(reaction)
else:
res.append(reaction)
# if generalization:
# self.__check_if_generic_complete_relationship()
# print("reactions to remove: ")
# print(to_remove)
self.__model.remove_reactions(to_remove)
return res