| name | rdkit-molecular-descriptors |
| description | Use this skill to compute compact cheminformatics descriptors from one SMILES string with RDKit. Do not use it for docking, quantum chemistry, or large library screening. |
Purpose
Turn a SMILES string into a compact descriptor summary suitable for quick triage, featurization, and metadata enrichment.
When to use
- You need a local RDKit-backed molecular summary from a SMILES string.
- You want canonical SMILES, formula, weight, and simple physicochemical descriptors.
When not to use
- You need conformer generation, docking, or reaction modeling.
- You need batch-scale descriptor computation for millions of compounds.
Inputs
- One SMILES string
- Optional molecule name
- Optional JSON output path
Outputs
- JSON summary with canonical SMILES, formula, exact mass, logP, TPSA, HBA/HBD, rotatable bonds, ring count, and heavy-atom count
Requirements
slurm/envs/chem-tools with RDKit available
Procedure
- Run
slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecular-descriptors/scripts/compute_rdkit_descriptors.py --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --name aspirin.
- Inspect
canonical_smiles, formula, molecular_weight, and tpsa.
- Reuse the JSON payload for downstream filtering or reporting.
Validation
- The command exits successfully.
canonical_smiles is non-empty for a known valid molecule.- Descriptor fields are numeric where expected.
Failure modes and fixes
- Invalid SMILES: verify the input string and quoting.
- Missing RDKit environment: run the script with
slurm/envs/chem-tools/bin/python.
Safety and limits
- Descriptor calculation only.
- No medicinal-chemistry or safety interpretation is implied.
Provenance
Related skills
