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.
npx agentmods add instructions/zichenwang114514/cdxml-toolkit-community/agents-mdgit clone --depth 1 https://github.com/ZiChenWang114514/cdxml-toolkit-communityWrote 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/zichenwang114514/cdxml-toolkit-community/agents-md)<a href="https://agentmods.dev/instructions/zichenwang114514/cdxml-toolkit-community/agents-md"><img src="https://agentmods.dev/badge/instructions/zichenwang114514/cdxml-toolkit-community/agents-md.svg" alt="Measured on agentmods" 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 | $0.00198 | $0.00198 |
| Opus 5 | $0.00099 | $0.00099 |
| Sonnet 5 | $0.00040 | $0.00040 |
| Haiku 4.5 | $0.00020 | $0.00020 |
Grade A, and why
cdxml-toolkit-community 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 4d 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.
What it actually says
Project Instructions
- Preserve the
cdxml_toolkitimport package and the 15 compatible core MCP tool names. - Use
cdxml_toolkit.mcp_runtimefor the complete service andcdxml_toolkit.mcp_serveronly for core compatibility work. - Ground molecular connectivity in a trusted user value, resolver, parser, or OCSR result. Do not invent SMILES.
- Route structural changes through
modify_moleculeand inspect its MCS diff. - Preserve inputs. Generated artifacts use new paths unless overwrite permission is explicit.
- Keep native ChemDraw work in isolated workers and under the shared native resource lock.
- Do not record molecular content, file contents, credentials, or tool arguments in metrics or health responses.
- Regenerate
docs/mcp-tools.mdanddocs/mcp-schema.jsonafter changing the tool registry. - Run
pytest -m "not network" -q, package checks, and applicable native probes before release.
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.
- 4d ago First seen · 12 lines · 198 tokens per session scan A 8850ff8062af
cdxml-toolkit-community AGENTS.md is an instructions file published in the GitHub repository ZiChenWang114514/cdxml-toolkit-community (1 stars, last pushed 10d ago), licensed MIT. It adds 198 tokens to every session, about $0.0010 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 2026-08-31.
Other instructions, from other repositories
chemdraw-mcp CLAUDE.md
Instructions for jurimaxam-dotcom/chemdraw-mcp, covering chemdraw-mcp, build / run, auto-gate (the project's green/red), the five tool areas (where a new tool goes) and architecture.
MoleCode AGENTS.md
Instructions for AtomFlow-AI/MoleCode, covering agents.md — molecode, what this repo is, use the molecode skill, molecode-first rule and cli quick start.
pubchem-mcp-server CLAUDE.md
Instructions for cyanheads/pubchem-mcp-server, covering developer protocol, what's next?, core rules, patterns and tool.
bio-gene-to-reference-tree copilot-instructions.md
Copilot instructions for Hongda-Zhao/bio-gene-to-reference-tree, a project described as: Auditable agent skill for resolving protein queries, selecting references, and planning reproducible phylogenetic trees.
braina GEMINI.md
Instructions for brainets/braina, covering project: braina (brain interaction analysis), 1. project context & purpose, 2. commands, verify environment (all core dependencies) and run the verification test suite for frites + hoi.
research-automation CLAUDE.md
Instructions for lucafusarbassini/research-automation, covering ricet - research automation framework, project overview, claude-flow mcp, workflow habits and file organization.