rdkit
Analyze Molecules with RDKit
Advanced molecular workflows require careful control over parsing, descriptors, fingerprints, and structure queries. This skill provides focused RDKit guidance, references, and reusable scripts.
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Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "rdkit" from https://skillstore.io/skills/davila7-rdkit.md and its manifest at https://skillstore.io/api/skills/davila7-rdkit/manifest. Verify the artifact. Stop and obtain explicit user consent before installing or changing files.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "rdkit". Calculate drug-likeness properties for the SMILES CCO.
Expected outcome:
- Canonical SMILES: CCO
- Molecular weight: 46.07
- TPSA: 20.23
- Lipinski result: passes the standard thresholds
Using "rdkit". Filter a molecule file to retain benzene-containing structures.
Expected outcome:
- Use the benzene SMARTS pattern c1ccccc1.
- Validate each molecule before matching.
- Write passing structures to the requested SDF or SMILES output.
Using "rdkit". Plan a Morgan fingerprint similarity screen.
Expected outcome:
- Use a documented radius and fingerprint size.
- Calculate Tanimoto similarity against the query fingerprint.
- Sort matches from highest to lowest score and apply the selected threshold.
Security Audit
High RiskAll 115 static findings are false positives after contextual review. They represent Markdown syntax, chemistry notation, expected output writes, dictionary keys, or normal error messages. A separate high-severity issue remains because SKILL.md demonstrates unsafe pickle deserialization without a trust warning.
Confirmed security concerns (1)
Risk Factors
📁 Filesystem access (6)
⚡ Contains scripts (1)
⚙️ External commands (50)
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<iframe src="https://skillstore.io/embed/skills/davila7-rdkit.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
davila7. (2026). rdkit security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-rdkit/audits/9BibTeX citation
@techreport{davila7-davila7-rdkit-2026,
author = {davila7},
title = {rdkit security audit report (audit version 9)},
institution = {Skillstore},
year = {2026},
number = {9},
url = {https://skillstore.io/skills/davila7-rdkit/audits/9},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "rdkit security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
- name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-rdkit/audits/9"
identifiers:
- type: other
value: "skillstore:davila7-rdkit:audit:9"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
k-dense-ai-rdkit
2026-08-21
davila7-rdkit
2026-08-21
Skillstore Score
Why this score Evidence Confidence: MediumWhat You Can Build
Screen Compound Libraries
Calculate properties, apply structural filters, and rank compounds by fingerprint similarity.
Prepare Molecular Features
Create validated descriptors and fingerprints for modeling, clustering, or exploratory analysis.
Build Reproducible Structure Workflows
Design parsing, sanitization, conformer generation, reaction, and visualization workflows with explicit parameters.
Try These Prompts
Analyze the SMILES CCO. Report molecular weight, LogP, TPSA, hydrogen-bond donors, hydrogen-bond acceptors, and Lipinski status.
Review molecules.smi and prepare a command to calculate descriptors into properties.csv. Explain how invalid molecules are handled.
Search database.sdf for compounds similar to c1ccccc1 using Morgan fingerprints and a 0.70 Tanimoto threshold. Summarize the top hits.
Design an RDKit workflow that filters PAINS, computes custom descriptors, clusters Morgan fingerprints, generates conformers, and records validation failures.
Best Practices
- Check every parsed molecule for None before calculating properties or fingerprints.
- Validate SMARTS patterns and document fingerprint parameters, thresholds, and random seeds.
- Use exchange formats such as SDF or SMILES for untrusted data instead of pickle files.
Avoid
- Do not process invalid molecules without checking parser results.
- Do not compare similarity scores generated with different fingerprint settings.
- Do not load pickle files from untrusted or unknown sources.
Frequently Asked Questions
Does this skill install RDKit?
Which molecular formats are supported?
Can it calculate drug-likeness properties?
Can it search large molecule collections?
When should I use Datamol instead?
Are pickle molecule files safe to share?
Developer Details
Author
davila7License
MIT
Skillstore revision
r2
Version notice
The author did not declare a version.
Ref
c43861a65bb95efcae259cd161c9d6f4dc7eec6f
Maintenance freshness
7/24/2026
Usage
7 downloads · 244 views
File structure