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parse_proteins.py — extracts drug–protein binding data (targets, enzymes,
carriers, transporters) and the underlying polypeptides.
Tables populated:
interactants — BE-ID binding entity records (deduplicated)
drug_interactants — drug ↔ interactant junction (role, position, actions inlined)
polypeptides — UniProt protein records (deduplicated by UniProt ID)
interactant_polypeptides — interactant ↔ polypeptide junction
polypeptide_attributes — polypeptide synonyms, Pfam domains, GO classifiers (merged)
external_identifiers — polypeptide-level cross-database IDs (entity_type='polypeptide')
references — references cited in interactant entries (global dedup)
reference_associations — links refs to (drugbank_id, interactant_id) context
"""
from config import NP
from utils import t, a, clean, extract_ref_list
# Roles and their corresponding XML container/child tag pairs
_ROLES = [
("target", "targets", "target"),
("enzyme", "enzymes", "enzyme"),
("carrier", "carriers", "carrier"),
("transporter", "transporters", "transporter"),
]
def extract(drug_el, primary_id, state):
results = {
"interactants": [],
"drug_interactants": [],
"polypeptides": [],
"interactant_polypeptides": [],
"polypeptide_attributes": [],
"external_identifiers": [],
"references": [],
"reference_associations": [],
}
for role, container_tag, child_tag in _ROLES:
container = drug_el.find(f"{NP}{container_tag}")
if container is None:
continue
for item in container.findall(f"{NP}{child_tag}"):
_process_interactant(item, primary_id, role, state, results)
return results
# ── interactant processing ────────────────────────────────────────────────────
def _process_interactant(item_el, primary_id, role, state, out):
interactant_id = t(item_el, "id")
if not interactant_id:
return
# interactants table (deduplicated by BE-ID)
if interactant_id not in state.interactants_seen:
state.interactants_seen.add(interactant_id)
out["interactants"].append({
"interactant_id": interactant_id,
"name": t(item_el, "name"),
"organism": t(item_el, "organism"),
})
# Actions: collect all <action> children, pipe-delimited
actions_el = item_el.find(f"{NP}actions")
action_list = []
if actions_el is not None:
for act in actions_el.findall(f"{NP}action"):
v = clean(act.text)
if v:
action_list.append(v)
# drug_interactants junction
out["drug_interactants"].append({
"drugbank_id": primary_id,
"interactant_id": interactant_id,
"role": role,
"position": clean(item_el.get("position")),
"known_action": t(item_el, "known-action"),
"actions": "|".join(action_list) if action_list else None,
"inhibition_strength": t(item_el, "inhibition-strength"), # enzyme only
"induction_strength": t(item_el, "induction-strength"), # enzyme only
})
# References for this interactant entry
refs_el = item_el.find(f"{NP}references")
new_refs, ref_pks = extract_ref_list(refs_el, state)
out["references"].extend(new_refs)
for rpk in ref_pks:
out["reference_associations"].append({
"ref_pk": rpk,
"drugbank_id": primary_id,
"interactant_id": interactant_id,
})
# Polypeptides inside this interactant
for poly_el in item_el.findall(f"{NP}polypeptide"):
_process_polypeptide(poly_el, interactant_id, state, out)
# ── polypeptide processing ────────────────────────────────────────────────────
def _process_polypeptide(poly_el, interactant_id, state, out):
poly_id = clean(poly_el.get("id"))
if not poly_id:
return
# interactant_polypeptides (always write — same polypeptide under different interactants)
out["interactant_polypeptides"].append({
"interactant_id": interactant_id,
"polypeptide_id": poly_id,
})
# polypeptides table (deduplicated by UniProt ID)
if poly_id not in state.polypeptides_seen:
state.polypeptides_seen.add(poly_id)
organism_el = poly_el.find(f"{NP}organism")
organism_name = clean(organism_el.text) if organism_el is not None else None
ncbi_tax_id = clean(organism_el.get("ncbi-taxonomy-id")) if organism_el is not None else None
aa_seq_el = poly_el.find(f"{NP}amino-acid-sequence")
gene_seq_el = poly_el.find(f"{NP}gene-sequence")
out["polypeptides"].append({
"polypeptide_id": poly_id,
"source": clean(poly_el.get("source")),
"name": t(poly_el, "name"),
"general_function": t(poly_el, "general-function"),
"specific_function": t(poly_el, "specific-function"),
"gene_name": t(poly_el, "gene-name"),
"locus": t(poly_el, "locus"),
"cellular_location": t(poly_el, "cellular-location"),
"transmembrane_regions": t(poly_el, "transmembrane-regions"),
"signal_regions": t(poly_el, "signal-regions"),
"theoretical_pi": t(poly_el, "theoretical-pi"),
"molecular_weight": t(poly_el, "molecular-weight"),
"chromosome_location": t(poly_el, "chromosome-location"),
"organism": organism_name,
"ncbi_taxonomy_id": ncbi_tax_id,
"amino_acid_sequence": clean(aa_seq_el.text) if aa_seq_el is not None else None,
"gene_sequence": clean(gene_seq_el.text) if gene_seq_el is not None else None,
})
# polypeptide_attributes: synonyms
syns_el = poly_el.find(f"{NP}synonyms")
if syns_el is not None:
for syn in syns_el.findall(f"{NP}synonym"):
v = clean(syn.text)
if v:
out["polypeptide_attributes"].append({
"polypeptide_id": poly_id,
"attr_type": "synonym", "value": v, "value2": None,
})
# polypeptide_attributes: Pfam domains
pfams_el = poly_el.find(f"{NP}pfams")
if pfams_el is not None:
for pfam in pfams_el.findall(f"{NP}pfam"):
pid = t(pfam, "identifier")
pname = t(pfam, "name")
if pid:
out["polypeptide_attributes"].append({
"polypeptide_id": poly_id,
"attr_type": "pfam", "value": pid, "value2": pname,
})
# polypeptide_attributes: GO classifiers
go_el = poly_el.find(f"{NP}go-classifiers")
if go_el is not None:
for go in go_el.findall(f"{NP}go-classifier"):
cat = t(go, "category")
desc = t(go, "description")
if cat:
out["polypeptide_attributes"].append({
"polypeptide_id": poly_id,
"attr_type": "go_classifier", "value": cat, "value2": desc,
})
# external_identifiers: polypeptide-level
ext_ids = poly_el.find(f"{NP}external-identifiers")
if ext_ids is not None:
for ei in ext_ids.findall(f"{NP}external-identifier"):
resource = t(ei, "resource")
identifier = t(ei, "identifier")
if resource and identifier:
out["external_identifiers"].append({
"entity_type": "polypeptide",
"entity_id": poly_id,
"resource": resource,
"identifier": identifier,
})
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