Borrowing it
Nothing to install: this file belongs to pluskal-lab/EnzymeExplorer. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/pluskal-lab/EnzymeExplorer/main/AGENTS.mdgit clone --depth 1 https://github.com/pluskal-lab/EnzymeExplorerWrote 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.
[](https://agentmods.dev/instructions/pluskal-lab/enzymeexplorer/agents-md)<a href="https://agentmods.dev/instructions/pluskal-lab/enzymeexplorer/agents-md"><img src="https://agentmods.dev/badge/instructions/pluskal-lab/enzymeexplorer/agents-md/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.
<a href="https://agentmods.dev/instructions/pluskal-lab/enzymeexplorer/agents-md"><img src="https://agentmods.dev/badge/instructions/pluskal-lab/enzymeexplorer/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.01746 | $0.01746 |
| Opus 5.5 | $0.00698 | $0.00698 |
| Sonnet 5.5 | $0.00349 | $0.00349 |
| Haiku 4.5 | $0.00175 | $0.00175 |
Grade A, and why
EnzymeExplorer AGENTS.md 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 23d 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.
How it starts
The opening of the file, as written. The whole thing — 185 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md — EnzymeExplorer
This file provides project-specific instructions for AI coding agents (e.g., Cursor agents). Follow these rules when reading, modifying, or adding code in this repository.
What this repo is
EnzymeExplorer is a Python codebase for terpene synthase (TPS) discovery and downstream classification. It supports:
- running predictions (full model requiring structures, and a sequence-only variant),
- data preparation and workflow steps used in the paper,
- model training/evaluation utilities and structural-domain analysis.
Repository layout (high-level)
enzymeexplorer/— main Python package (core logic lives here).scripts/— command-line / convenience scripts (e.g.,predict_*.py,bundle_fold_checkpoints.py).data/— small, versioned artifacts for reproducibility (some.pkl, curated CSVs, etc.).outputs/— logs, intermediate artifacts, trained models/results (often large).notebooks/— notebooks / colab-related material.build/— generated build artifacts (do not edit manually).app_faster_with_foldseek.py— app/entry script related to Foldseek-accelerated workflow.
Coding standards (must match CI)
Before proposing changes, run the same checks CI runs:
Formatting
black --check .
Lint
flake8 . --max-line-length 88 --extend-ignore E203 --select B950
Pylint
pylint ./enzymeexplorer --disable C0301,E0401,E1136,R0914,R1728,R0912,R0917,R0915,R0913,R0902,W0640
Typing
mypy --implicit-optional --explicit-package-bases .
Additional agent check
ruff check .
Do not reformat large unrelated parts of the repo. Keep diffs minimal and targeted.
Python coding rules for agents
-
Prefer minimal changes
- Make the smallest correct change that fixes the bug or adds the feature.
- Do not mix unrelated refactors into the same patch.
- Do not rename/move modules unless necessary for the requested change.
-
Keep structure readable
- Prefer small helpers over deeply nested logic.
- Reuse existing patterns in the repo before inventing new abstractions.
- Keep control flow simple and explicit.
- Choose clear names over clever code.
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.
- 23d ago First seen · 185 lines · 1,746 tokens per session scan A dc23ae364aa6
EnzymeExplorer AGENTS.md is an instructions file published in the GitHub repository pluskal-lab/EnzymeExplorer (18 stars, last pushed 1mo ago), licensed MIT. It adds 1,746 tokens to every session, about $0.0070 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 2026-10-02.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
deno copilot-instructions.md
Copilot instructions for denoland/deno, covering deno development guide for github copilot, network access, high level overview, key directories and key files to understand first.