Rdkit Scaffold Analysis Starter

Purpose

Analyze a small local TSV of SMILES strings with RDKit Murcko scaffolds and emit a compact JSON summary that can feed later smoke integration or scaffold triage workflows.

When to use

• You need a local scaffold grouping summary for a small curated molecule set.
• You want canonical SMILES, Murcko scaffolds, generic scaffolds, and group counts from one deterministic run.

When not to use

• You need large library clustering, matched molecular pair analysis, or SAR interpretation.
• You need remote compound lookup or medicinal-chemistry recommendations.

Inputs

• A TSV file with columns name and smiles
• Optional JSON output path

Outputs

• JSON with per-molecule canonical SMILES, Murcko scaffold, generic scaffold, scaffold groups, generic scaffold groups, and summary counts

Requirements

• slurm/envs/chem-tools/bin/python
• RDKit available in that environment

Procedure

1. Inspect examples/molecules.tsv.
2. Run slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/scripts/run_rdkit_scaffold_analysis.py --input skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/examples/molecules.tsv.
3. Review molecules, scaffold_groups, and summary.

Validation

• The bundled example returns at least one scaffold group with count >= 2.
• Invalid SMILES input returns a non-zero exit code with a clear error message.

Failure modes and fixes

• Invalid SMILES: fix the offending row in the input TSV.
• Missing RDKit environment: rerun with slurm/envs/chem-tools/bin/python.
• Missing name or smiles columns: use a header row with exactly those field names.

Safety and limits

• Local scaffold computation only.
• No medicinal-chemistry conclusions are implied by the grouping.

Provenance

• RDKit docs: https://www.rdkit.org/docs/index.html
• RDKit Murcko scaffold API: https://www.rdkit.org/docs/source/rdkit.Chem.Scaffolds.MurckoScaffold.html
• RDKit repository: https://github.com/rdkit/rdkit

Related skills

• rdkit-molecular-descriptors
• rdkit-molecule-standardization

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: ma-compbio-lab
• Source: ma-compbio-lab/SkillFoundry
• License: Apache-2.0
• Homepage: https://ma-compbio-lab.github.io/SkillFoundry/

Install and usage instructions live in the source repository linked above.