def _add_node(chebi_id, chebi_ids, rels, chem_manager):
'''Constructs a node from libChEBI.'''
if chebi_id not in chebi_ids:
chebi_ids.append(chebi_id)
chem_id, entity = chem_manager.add_chemical({'chebi': chebi_id})
for incoming in entity.get_incomings():
target_id = incoming.get_target_chebi_id()
chebi_ent = ChebiEntity(target_id)
if chebi_ent.get_parent_id():
target_id = chebi_ent.get_parent_id()
_add_node(target_id, chebi_ids, rels, chem_manager)
rels.append([target_id, incoming.get_type(), chem_id])
def _add_node(chebi_id, chebi_ids, rels, chem_manager):
'''Constructs a node from libChEBI.'''
if chebi_id not in chebi_ids:
chebi_ids.append(chebi_id)
chem_id, entity = chem_manager.add_chemical({'chebi': chebi_id})
for incoming in entity.get_incomings():
target_id = incoming.get_target_chebi_id()
chebi_ent = ChebiEntity(target_id)
if chebi_ent.get_parent_id():
target_id = chebi_ent.get_parent_id()
_add_node(target_id, chebi_ids, rels, chem_manager)
rels.append([target_id, incoming.get_type(), chem_id])
def _get_chebi_data(chebi_id, chebi_data):
"""Recursively extracts data from supplied ChEBI id."""
if chebi_id not in chebi_data:
chebi_entity = ChebiEntity(chebi_id)
hmdb_ids = [
db_acc.get_accession_number()
for db_acc in chebi_entity.get_database_accessions()
if db_acc.get_source() == "HMDB"
]
chebi_data[chebi_id] = {
"Name": chebi_entity.get_name(),
"ChEBI id": chebi_entity.get_id(),
"HMDB id": ";".join(hmdb_ids),
}
for incoming in chebi_entity.get_incomings():
_get_chebi_data(incoming.get_target_chebi_id(), chebi_data)
def _get_chebi_data(chebi_id, properties):
'''Gets ChEBI data.'''
chebi_ent = ChebiEntity(str(chebi_id))
if chebi_ent.get_parent_id():
chebi_id = chebi_ent.get_parent_id()
else:
chebi_id = chebi_ent.get_id()
properties['chebi'] = chebi_id
formula = chebi_ent.get_formula()
charge = chebi_ent.get_charge()
inchi = chebi_ent.get_inchi()
smiles = chebi_ent.get_smiles()
if formula:
properties['formula'] = formula
if not math.isnan(charge):
properties['charge'] = charge
if inchi:
properties['inchi'] = inchi
if smiles:
properties['smiles'] = smiles
properties['name'] = chebi_ent.get_name()
properties['names:string[]'] = \
[name.get_name() for name in chebi_ent.get_names()] + \
[chebi_ent.get_name()]
for db_acc in chebi_ent.get_database_accessions():
namespace = ns_utils.resolve_namespace(
db_acc.get_type(), True)
if namespace is not None:
properties[namespace] = db_acc.get_accession_number()
return chebi_id, chebi_ent
def _get_chebi_data(chebi_id, properties, array_delimiter):
'''Gets ChEBI data.'''
chebi_ent = ChebiEntity(str(chebi_id))
if chebi_ent.get_parent_id():
chebi_id = chebi_ent.get_parent_id()
else:
chebi_id = chebi_ent.get_id()
properties['chebi'] = chebi_id
formula = chebi_ent.get_formula()
charge = chebi_ent.get_charge()
inchi = chebi_ent.get_inchi()
smiles = chebi_ent.get_smiles()
if formula:
properties['formula'] = formula
if not math.isnan(charge):
properties['charge:float'] = charge
if inchi:
properties['inchi'] = inchi
if smiles:
properties['smiles'] = smiles
properties['name'] = chebi_ent.get_name()
properties['names:string[]'] = \
array_delimiter.join([name.get_name()
for name in chebi_ent.get_names()] +
[chebi_ent.get_name()])
for db_acc in chebi_ent.get_database_accessions():
namespace = ns_utils.resolve_namespace(db_acc.get_type(), True)
if namespace is not None:
properties[namespace] = db_acc.get_accession_number()
return chebi_id, chebi_ent