SMILES Profiling

Comprehensive SMILES profiling through SwissTargetPrediction, PubChem, ADMETlab 3.0, ChEMBL, and PK-Smart. Use when given a single SMILES to extract predicted targets, exact identity and physicochemical baselines, known analogs and mechanisms, ADMET properties, and pharmacokinetic estimates; handles salts/counterions and degrades gracefully when any source is unavailable.

Hendrik Schmitz@hendr15k

Install

openclaw skills install @hendr15k/smiles-profiling

SMILES Profiling

Turn one SMILES into a compact pharmacology profile.

Tool stack

Tool	Use
SwissTargetPrediction	Predicted protein targets with probabilities
PubChem	Exact CID, synonyms, MW, XLogP, TPSA, HBD/HBA, rotatable bonds
ADMETlab 3.0	ADMET flags, drug-likeness, toxicity sections
ChEMBL	Similarity hits, max phase, known mechanisms, target names
PK-Smart	Human and animal PK estimates (VDss, CL, t½, fu, MRT)

Workflow

Use the user-provided SMILES as-is unless it clearly needs cleanup.
Normalize only obvious salts/counterions.
Run SwissTargetPrediction for target hypotheses.
Run PubChem for identity and physicochemical baseline.
Run ADMETlab 3.0 for ADMET flags and drug-likeness.
Run ChEMBL for similarity hits and mechanism context.
Run PK-Smart last for PK estimates.
Merge the outputs into one short report, preferring direct database evidence over predictions.

Preferred scripts

scripts/run_smiles_profile.py <SMILES> for the full report.
scripts/run_smiles_smoke.py --cases <tsv> for regression/benchmark runs.

Extraction notes

SwissTargetPrediction: capture the top 5 targets, probabilities, and species.
PubChem: capture CID, IUPAC name, synonyms, MW, XLogP, TPSA, HBD/HBA, and rotatable bonds.
ADMETlab 3.0: capture the section list and any obvious toxicity/drug-likeness flags.
ChEMBL: capture the similarity threshold, top hits, max phase, mechanism_of_action, and target name.
PK-Smart: capture VDss, CL, t½, fu, MRT, and animal PK when available.

Handling edge cases

Salts/mixtures: strip common counterions first.
Invalid SMILES: fail cleanly, do not crash.
Missing tools: continue with the remaining sources.
PubChem miss: report the miss and continue.
ChEMBL miss: automatically fall back from 90 → 80 → 70 similarity.

Output shape

text

SMILES: CC(=O)OC1=CC=CC=C1C(=O)O

## SwissTargetPrediction
- Top target: PTGS1 (prob: 0.76)

## PubChem
- CID: 2244 | Name: 2-acetyloxybenzoic acid
- MW: 180.16 Da | XLogP: 1.2 | TPSA: 63.6 Å²

## ADMETlab 3.0
- MW: 180.04 Da | QED: N/A

## ChEMBL
- Top hit: CHEMBL25 ASPIRIN | sim 100 | phase 4
- Mechanism: Cyclooxygenase inhibitor -> Cyclooxygenase

## PK-Smart
- VDss: 0.23 L/kg | CL: 10.41 mL/min/kg
- t½: 0.34 hr | fu: 0.67