ir-spectra-simulation

ir-spectra-simulation is a skill for Claude Code, Codex from InternScience/ChemClaw. It costs 25 tokens per session (490 once invoked), scanned A, original, MIT.

A chemistry tool that calculates and displays an infrared (IR) spectrum from a molecule written as SMILES or from an XYZ coordinate file. It can also compare the result with an experimental spectrum file.

In plain words
What is it for?
Use it to optimize a molecule’s geometry, calculate its theoretical IR spectrum, summarize the results, and compare them with experimental IR data.
Why use it?
It turns a molecular structure into a calculated spectrum and ready-to-use images, avoiding manual setup of the calculation and plotting.

Skill for Claude CodeCodex

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

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.

agentmods
npx agentmods add skills/internscience/chemclaw/ir-spectra-simulation
Any agent
npx skills add InternScience/ChemClaw --skill ir-spectra-simulation
Clone the repo
git clone --depth 1 https://github.com/InternScience/ChemClaw

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 ir-spectra-simulation

README.md
[![agentmods](https://agentmods.dev/badge/skills/internscience/chemclaw/ir-spectra-simulation.svg)](https://agentmods.dev/skills/internscience/chemclaw/ir-spectra-simulation)
Your own site
<a href="https://agentmods.dev/skills/internscience/chemclaw/ir-spectra-simulation"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/ir-spectra-simulation.svg" alt="Measured on agentmods" height="20"></a>
Per session 25 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 490 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00025 $0.00490
Opus 5 $0.00013 $0.00245
Sonnet 5 $0.00005 $0.00098
Haiku 4.5 $0.00003 $0.00049

Measured 6d ago against content hash 60d2f49cccbb, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-06, from the pricing page.

Security

Grade A, and why

ir-spectra-simulation 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 6d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (ir_spectra_simulation.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/ir-spectra-simulation/SKILL.md · 57 lines

What it actually says

IR Spectra Simulation Skill

When to use this

Use this skill when the user provides a SMILES or XYZ file (coordinates) and wants:

  • Optimized geometry
  • Theoretically calculated IR spectrum in a summarized table
  • Quick overview of simulated IR
  • Publication-ready image file

Inputs

  • SMILES string (e.g. CCO for ethanol) or XYZ file path (necessary)
  • Experimental IR spectrum file (optional, .txt format)

Outputs

  • /tmp/chemclaw/optimized_geometry.md
  • /tmp/chemclaw/theoretical_ir.md
  • /tmp/chemclaw/theoretical_ir.png
  • /tmp/chemclaw/exp_ir.png (可选,提供实验数据时)
  • /tmp/chemclaw/comparison_ir.png (可选,提供实验数据时)

New environment (from zero)

conda create -n spec python=3.12 -y
conda activate spec
conda install -c conda-forge xtb -y   # macOS 必装(MLatom 内建 xTB 为 Linux 版)
pip install mlatom numpy matplotlib pyscf geometric rdkit

cd ir-spectra-simulation
python ir_spectra_simulation.py CCO
# optional: python ir_spectra_simulation.py /path/to/structure.xyz
# optional: python ir_spectra_simulation.py CCO exp.txt
  • 请在 skill 目录内执行脚本(cd ir-spectra-simulation)。
  • macOS 若仍误用 MLatom 内建 Linux 版 xTB,可确保 which xtb 指向 conda 的 xtb(必要时 export PATH="$CONDA_PREFIX/bin:$PATH")。

How to run(已装好环境时)

SMILES

cd ir-spectra-simulation
python ir_spectra_simulation.py CCO

XYZ(用户提供坐标文件)

cd ir-spectra-simulation
python ir_spectra_simulation.py /path/to/structure.xyz
Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. 6d ago First seen · 57 lines · 25 tokens per session scan A 60d2f49cccbb

Subscribe to this mod's changes

ir-spectra-simulation is a skill published in the GitHub repository InternScience/ChemClaw (52 stars, last pushed 5mo ago), licensed MIT. It adds 25 tokens to every session and 490 once invoked, about $0.0001 per session on Opus 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.

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