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molmcp: Instructions file for Claude Code

CLAUDE.md

molmcp CLAUDE.md is an instructions file for Claude Code from MolCrafts/molmcp. It costs 1,691 tokens per session, scanned A, original, BSD-3-Clause.

A set of instructions for coding agents working on MolCrafts/molmcp, a Python project that combines knowledge and science-data providers through MCP. It explains the repository layout, configuration, and usual development workflow.

In plain words
What is it for?
Use it when planning, implementing, fixing, reviewing, or recording decisions in the molmcp repository.
Why use it?
It gives an agent the project context it needs to find files, follow the repository’s process, and avoid breaking its MCP and FastMCP setup.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: reads .claude/ paths; mentions CLAUDE.md; mentions Claude Code.

This is MolCrafts/molmcp's own configuration. It tells Claude Code how to work on molmcp itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything molmcp configures →

not rated 0repo 1mo ago A scan 1,691 tokens original BSD-3-Clause
View source ↗ MolCrafts/molmcp
Reuse

Borrowing it

Nothing to install: this file belongs to MolCrafts/molmcp. 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/MolCrafts/molmcp/master/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/MolCrafts/molmcp

Made for: Claude Code.

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Per session 1,691 This file is loaded in full into every session.
When invoked 1,691 The same file — it is already loaded in full.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.01691 $0.01691
Opus 5.5 $0.00676 $0.00676
Sonnet 5.5 $0.00338 $0.00338
Haiku 4.5 $0.00169 $0.00169

Measured 2mo ago against content hash 3b09ed42e1f2, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

molmcp CLAUDE.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 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.

CLAUDE.md · 147 lines

How it starts

The opening of the file, as written. The whole thing — 147 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md

What this repo is

molmcp is FastMCP-composed MCP for MolCrafts: molmcp serve starts the molcrafts core (knowledge plus list_planes / route) and mounts enabled providers with official namespaces (molvis_open). molmcp init <host> installs the usage skill and one MCP entry. Science APIs are discovered via the core and never mirrored as MCP tools. Pure Python (>= 3.12), src/ layout, managed with uv.

Protocol: MCP 2026-07-28 via FastMCP 4.0.0b5 + MCP Python SDK v2 (mcp>=2). Do not pin FastMCP back to 3.x without an explicit decision.

Where things live

  • Source code: src/molmcp/
  • Tests: tests/
  • Public documentation: docs/ (zensical site; concepts / guides / reference)
  • Passive project knowledge (notes, decisions, blueprint): .claude/notes/
  • Active runtime specs (alive, deleted on completion): .claude/specs/
  • Claude Code runtime config: .claude/settings.local.json

Default workflow

For non-trivial work, prefer:

  1. plan (/mol:spec or write to .claude/notes/)
  2. implement (/mol:impl or /mol:fix)
  3. review (/mol:review)
  4. capture decisions (/mol:note)

Configuration

Settings live in ~/.molmcp/settings.json, with optional per-project .molmcp/settings.json and .molmcp/settings.local.json layered over it, edited via molmcp config get|set|add|remove (see src/molmcp/settings.py).

No environment variables. tests/test_no_env_switches.py fails the build if a module reads one. Three exemptions are listed there with their reason. Two are secrets — the bearer token an HTTP-transport server compares against, and GITHUB_TOKEN for github: sources; the third builds a child process environment and reads nothing. Each names a variable in config rather than storing its value — a settings file that can be committed is the wrong place for a credential. Configuration that lives only in one shell cannot be reported by molmcp config list, and two plane servers launched by different clients would silently disagree about it.

Read the full file on GitHub · 147 lines

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. 2mo ago First seen · 147 lines · 1,691 tokens per session scan A 3b09ed42e1f2

Subscribe to this mod's changes

molmcp CLAUDE.md is an instructions file published in the GitHub repository MolCrafts/molmcp (0 stars, last pushed 1mo ago), licensed BSD-3-Clause. It adds 1,691 tokens to every session, about $0.0068 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 2026-08-31.

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