Rdkit scaffold analysis starter

Skill ma-compbio-lab/SkillFoundry/skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-scaffold-analysis-starter

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What its author says it does

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Use this skill to compute Murcko scaffold summaries for a small local molecule set with RDKit. Prefer it for deterministic scaffold grouping and smoke-scale cheminformatics checks.

SKILL.md

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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

Inspect examples/molecules.tsv.
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.
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