Source code for tooluniverse.peplife2_tool
"""PEPlife 2.0 peptide half-life / stability tool (live REST, keyless).
PEPlife 2.0 (Raghava lab, IIITD) is an updated repository of experimentally
measured peptide half-lives (bioRxiv 2025). This tool informs
therapeutic-peptide stability / druggability — a non-immune capability absent
from ToolUniverse: given a linear/cyclic form, organism/media, or sequence it
returns the measured half-life (value + units), the protease, incubation
time, concentration, and assay used.
The public API is keyless. It is queried with a ``dataType`` (the field to
filter on) and a ``dataValue`` (the value to match), e.g.::
api.php?dataType=lin_cyc&dataValue=Linear (or Cyclic)
api.php?dataType=org&dataValue=<organism/media>
api.php?dataType=seq&dataValue=<sequence>
A successful response is a JSON object ``{"status": 200, "count": int,
"data": [ ... ]}``. A no-match query returns ``{"status": 404,
"message": "Record Not Found"}``.
"""
from typing import Any, Dict
import requests
from .base_tool import BaseTool
from .tool_registry import register_tool
_BASE_URL = "https://webs.iiitd.edu.in/raghava/peplife2/api/api.php"
_TIMEOUT = 30
_HEADERS = {"Accept": "application/json"}
_VALID_DATA_TYPES = ("lin_cyc", "org", "seq")
def _err(message: str, **extra: Any) -> Dict[str, Any]:
out: Dict[str, Any] = {"status": "error", "error": message}
out.update(extra)
return out
[docs]
@register_tool(
"PEPlife2SearchPeptidesTool",
config={
"name": "PEPlife2_search_peptides",
"type": "PEPlife2SearchPeptidesTool",
"description": (
"Search PEPlife 2.0 (Raghava lab, IIITD) for experimentally "
"measured peptide HALF-LIFE / proteolytic-stability records. "
"Filter by 'lin_cyc' (Linear or Cyclic), 'org' (origin organism / "
"incubation media), or 'seq' (sequence). Each record returns the "
"peptide sequence, half-life value and units, protease, incubation "
"time, concentration, assay, linear/cyclic form, chirality, "
"chemical and N/C-terminus modifications, origin, nature, PubMed "
"ID, and year. Use to assess therapeutic-peptide stability / "
"druggability. Keyless public API."
),
"parameter": {
"type": "object",
"properties": {
"dataType": {
"type": "string",
"description": (
"Field to filter on. One of: 'lin_cyc' (Linear or "
"Cyclic), 'org' (origin organism / incubation media), "
"or 'seq' (sequence). Default: 'lin_cyc'."
),
"enum": ["lin_cyc", "org", "seq"],
},
"dataValue": {
"type": "string",
"description": (
"Value to match for the chosen dataType. Examples: "
"'Linear' (with dataType=lin_cyc) -> ~3777 records; "
"'Cyclic' (with dataType=lin_cyc) -> ~49 records."
),
},
},
"required": ["dataValue"],
},
"return_schema": {
"oneOf": [
{
"type": "object",
"properties": {
"status": {"const": "success"},
"data": {
"type": "array",
"items": {"type": "object"},
"description": (
"Matching half-life records. Each has id, "
"pmid, year, seq, name, length, lin_cyc, "
"chiral, chem_mod, cter, nter, origin, nature, "
"incubation_time, conc, half_life, units_half, "
"protease, assay."
),
},
"metadata": {"type": "object"},
},
"required": ["status", "data", "metadata"],
},
{
"type": "object",
"properties": {
"status": {"const": "error"},
"error": {"type": "string"},
},
"required": ["status", "error"],
},
]
},
"test_examples": [
{"dataType": "lin_cyc", "dataValue": "Linear"},
{"dataType": "lin_cyc", "dataValue": "Cyclic"},
],
},
)
class PEPlife2SearchPeptidesTool(BaseTool):
"""Search PEPlife 2.0 peptide half-life / stability records."""
[docs]
def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
arguments = arguments or {}
data_value = arguments.get("dataValue")
if data_value is None or str(data_value).strip() == "":
return _err("dataValue is required (e.g. 'Linear' or 'Cyclic')")
data_type = str(arguments.get("dataType") or "lin_cyc").strip()
if data_type not in _VALID_DATA_TYPES:
return _err(
f"Invalid dataType {data_type!r}. "
f"Choose one of: {', '.join(_VALID_DATA_TYPES)}."
)
params = {"dataType": data_type, "dataValue": str(data_value)}
try:
resp = requests.get(
_BASE_URL, params=params, headers=_HEADERS, timeout=_TIMEOUT
)
except requests.exceptions.RequestException as exc:
return _err(f"Request to PEPlife 2.0 failed: {exc}")
if resp.status_code != 200:
return _err(
f"PEPlife 2.0 returned HTTP {resp.status_code}",
url=resp.url,
response_snippet=(resp.text or "")[:200],
)
try:
payload = resp.json()
except ValueError:
return _err(
"PEPlife 2.0 returned a non-JSON response",
url=resp.url,
response_snippet=(resp.text or "")[:200],
)
if not isinstance(payload, dict):
return _err("Unexpected PEPlife 2.0 response shape", url=resp.url)
if payload.get("status") == 404 or "data" not in payload:
return _err(
payload.get("message")
or f"No PEPlife 2.0 records for {data_type}={data_value!r}",
url=resp.url,
)
records = payload.get("data") or []
if not isinstance(records, list):
return _err("Unexpected PEPlife 2.0 data shape", url=resp.url)
return {
"status": "success",
"data": records,
"metadata": {
"source": "PEPlife 2.0 (Raghava lab, IIITD)",
"url": resp.url,
"data_type": data_type,
"data_value": str(data_value),
"total_count": payload.get("count", len(records)),
"returned_count": len(records),
},
}