chemistry

chemistry is a skill for Claude Code, Codex from Zaoqu-Liu/ScienceClaw. It costs 0 tokens per session (420 once invoked), scanned A, a copy of chemistry, MIT.

A collection of tools and workflows for studying molecules, chemical properties, and possible medicines with computers.

In plain words
What is it for?
It helps search and prepare compounds, filter them for drug-like properties, predict molecular properties, dock compounds to protein targets, build activity models, and run molecular-dynamics simulations.
Why use it?
It brings together commonly needed steps instead of requiring separate tools for molecular editing, database searches, docking, and simulation.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit It helps search and prepare compounds, filter them for drug-like properties, predict molecular properties, dock compounds to protein targets, build activity models, and run molecular-dynamics simulations.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/zaoqu-liu/scienceclaw/chemistry
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Zaoqu-Liu/ScienceClaw --skill chemistry
Clone the repo
git clone --depth 1 https://github.com/Zaoqu-Liu/ScienceClaw

Made for: Claude Code, Codex.

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.

agentmods badge for chemistry

README.md
[![agentmods](https://agentmods.dev/badge/skills/zaoqu-liu/scienceclaw/chemistry/github.svg)](https://agentmods.dev/skills/zaoqu-liu/scienceclaw/chemistry)
Your own site
<a href="https://agentmods.dev/skills/zaoqu-liu/scienceclaw/chemistry"><img src="https://agentmods.dev/badge/skills/zaoqu-liu/scienceclaw/chemistry/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.

agentmods 80×15 button for chemistry

Your own site · 80×15
<a href="https://agentmods.dev/skills/zaoqu-liu/scienceclaw/chemistry"><img src="https://agentmods.dev/badge/skills/zaoqu-liu/scienceclaw/chemistry.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 420 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 95% copy Near-identical to another mod 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.00420
Opus 5 $0.00000 $0.00210
Sonnet 5 $0.00000 $0.00084
Haiku 4.5 $0.00000 $0.00042

Measured 9d ago against content hash 707227740001, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

chemistry 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 9d 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.

Origin

This is a copy

95% identical to chemistry — 5 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

skills/chemistry/SKILL.md · 50 lines

What it actually says

Chemistry & Drug Discovery

Overview

Computational chemistry, cheminformatics, and drug discovery workflows.

Key Tools

  • RDKit: Molecular manipulation, fingerprints, descriptors, substructure search
  • PubChem: Chemical compound database (100M+ compounds)
  • ChEMBL: Bioactivity database for drug-like molecules
  • Open Babel: Format conversion, 3D generation
  • AutoDock Vina: Molecular docking
  • GROMACS/OpenMM: Molecular dynamics simulations

Common Workflows

Virtual Screening

  1. Define target (protein structure from PDB)
  2. Prepare compound library (from ChEMBL/ZINC/Enamine)
  3. Filter by drug-likeness (Lipinski's Rule of Five)
  4. Docking (AutoDock Vina, GNINA)
  5. Scoring and ranking
  6. ADMET prediction (absorption, distribution, metabolism, excretion, toxicity)
  7. Hit validation

QSAR Modeling

  1. Curate activity data (ChEMBL IC50/Ki/EC50)
  2. Calculate molecular descriptors (RDKit)
  3. Feature selection
  4. Model training (Random Forest, XGBoost, neural network)
  5. Validation (cross-validation, external test set)
  6. Applicability domain assessment

Molecular Property Prediction

  • Lipophilicity (LogP)
  • Solubility (LogS)
  • Permeability (PAMPA, Caco-2)
  • Metabolic stability (CYP inhibition)
  • hERG toxicity
  • BBB penetration

Databases

Database Content Access
PubChem 100M+ compounds Free API
ChEMBL Bioactivity data Free API
PDB 200K+ protein structures Free API
ZINC Purchasable compounds Free download
DrugBank Drug information Free academic
Materials Project Inorganic materials Free API
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.

  1. 9d ago First seen · 50 lines · 0 tokens per session scan A 707227740001

Subscribe to this mod's changes

chemistry is a skill published in the GitHub repository Zaoqu-Liu/ScienceClaw (60 stars, last pushed 5mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 420 tokens. A static security scan graded it A with 0 findings. It is 95% identical to chemistry, differing in 5 lines, and is treated as a copy.

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