A chemistry toolkit for working with molecules represented as SMILES, a compact text format for chemical structures. It calculates molecular properties, checks common drug-design rules, creates molecular fingerprints, and compares molecular similarity.

Inspecting molecules, estimating properties such as molecular weight and fat solubility, screening for drug-likeness, generating fingerprints, and comparing compounds.

It turns chemical structures into measurable values and comparable representations that software can analyse consistently.

How omar-A-hassan/medsci-agent configures OpenCode

Reuse

Borrowing it

Nothing to install: this file belongs to omar-A-hassan/medsci-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/.opencode/skills/rdkit/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/omar-A-hassan/medsci-agent

Made for: OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/omar-a-hassan/medsci-agent/rdkit/github.svg)](https://agentmods.dev/skills/omar-a-hassan/medsci-agent/rdkit)

Your own site

<a href="https://agentmods.dev/skills/omar-a-hassan/medsci-agent/rdkit"><img src="https://agentmods.dev/badge/skills/omar-a-hassan/medsci-agent/rdkit/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/omar-a-hassan/medsci-agent/rdkit"><img src="https://agentmods.dev/badge/skills/omar-a-hassan/medsci-agent/rdkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 26 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 424 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00026	$0.00424
Opus 5.5	$0.00010	$0.00170
Sonnet 5.5	$0.00005	$0.00085
Haiku 4.5	$0.00003	$0.00042

Measured 2mo ago against content hash 5ab02d0c31a2, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

rdkit scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.opencode/skills/rdkit/SKILL.md · 36 lines

What it actually says

RDKit — Cheminformatics

When to Use

Analyzing molecules from SMILES strings
Computing physicochemical properties (MW, LogP, TPSA, etc.)
Drug-likeness assessment (Lipinski, Veber, etc.)
Molecular similarity (Tanimoto with Morgan fingerprints)
Molecular fingerprint generation

Available Tools

analyze_molecule(smiles) — Full property profile
lipinski_filter(smiles) — Rule of Five check
molecular_similarity(smiles1, smiles2) — Tanimoto similarity

SMILES Reference

SMILES (Simplified Molecular Input Line Entry System) is a line notation for molecular structures:

CC(=O)OC1=CC=CC=C1C(=O)O — Aspirin
CC(C)CC1=CC=C(C=C1)C(C)C(=O)O — Ibuprofen
CN1C=NC2=C1C(=O)N(C(=O)N2C)C — Caffeine

Drug-Likeness Rules

Lipinski's Rule of Five: MW≤500, LogP≤5, HBD≤5, HBA≤10 (≤1 violation)
Veber: RotBonds≤10, TPSA≤140
Lead-like: MW 250-350, LogP -1 to 3, RotBonds≤7

Similarity Interpretation

Tanimoto > 0.85 — Very similar, likely same scaffold
Tanimoto 0.7-0.85 — Similar, may share target activity
Tanimoto 0.4-0.7 — Moderate, may share pharmacophore features
Tanimoto < 0.4 — Dissimilar

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 36 lines · 26 tokens per session scan A 5ab02d0c31a2

Subscribe to this mod's changes

rdkit is a skill published in the GitHub repository omar-A-hassan/medsci-agent (17 stars, last pushed 2mo ago), licensed MIT. It adds 26 tokens to every session and 424 once invoked, about $0.0001 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific agents mcp medgemma ollama opencode txgemma

rdkit next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
rdkitomar-A-hassan/medsci-agent	Skill	17	2mo ago	MIT	A	26	OpenCode
build-expression-treejimmc414/claude-code-plugin-marketplace	Skill	4	yesterday	MIT	A	24	Claude Code
find-convex-hulljimmc414/claude-code-plugin-marketplace	Skill	4	yesterday	MIT	A	31	Claude Code
dfam-checkearthtojake/text-to-cad	Skill	26k	yesterday	MIT	A	117	Claude Code, Codex
peer-reviewxintaofei/codeg	Skill	4.2k	6d ago	Apache-2.0	A	71	Claude Code
scientific-critical-thinkingxintaofei/codeg	Skill	4.2k	6d ago	Apache-2.0	A	63	Claude Code
tooluniverse-phylogeneticsmims-harvard/ToolUniverse	Skill	1.8k	yesterday	Apache-2.0	A	155	Claude Code

medsci-agent: Skill for OpenCode