A coding-agent guide for using MolCrafts, a computational chemistry package for modeling and analyzing molecules. It helps the agent find the package’s real programming interface before writing science code.

Use it to work with molecular structures, force fields, simulations, trajectories, and analyses such as radial distribution functions and mean squared displacement. It also supports packing or solvating systems, 3D visualization, cluster jobs, and experiment workspaces.

It reduces the risk of writing code against guessed or outdated interfaces. It also provides a way to connect molecular visualization, cluster jobs, and experiment workspaces when those services are available.

molcrafts — Skill for Claude Code by MolCrafts/molmcp

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 MolCrafts/molmcp --skill skill

Clone the repo

git clone --depth 1 https://github.com/MolCrafts/molmcp

Made for: Claude Code.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/molcrafts/molmcp/skill/github.svg)](https://agentmods.dev/skills/molcrafts/molmcp/skill)

Your own site

<a href="https://agentmods.dev/skills/molcrafts/molmcp/skill"><img src="https://agentmods.dev/badge/skills/molcrafts/molmcp/skill/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/molcrafts/molmcp/skill"><img src="https://agentmods.dev/badge/skills/molcrafts/molmcp/skill.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 58 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 663 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 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.

Model	Per session	Once invoked
Fable 5.1	$0.00058	$0.00663
Opus 5.5	$0.00023	$0.00265
Sonnet 5.5	$0.00012	$0.00133
Haiku 4.5	$0.00006	$0.00066

Measured 2mo ago against content hash d4acca1b5b29, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

molcrafts 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.

The scan reads SKILL.md. This mod also ships 1 executable file (__init__.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.

src/molmcp/skill/SKILL.md · 72 lines

What it actually says

MolCrafts usage

Managed by molmcp init. Do not edit this file.

The model loads this skill; the user should not have to invoke it. If it loaded, use the molcrafts MCP connection.

If molcrafts tools are missing

Stop. Tell the user to install or start molmcp:

pip install molcrafts-molmcp
molmcp init <host>    # grok | claude | cursor | codex

Then enable the molcrafts MCP server in the host. Do not hand-roll science code while the connection is down.

Find the capability, then call it

Science methods are not MCP tools. Discover them, then call them in agent Python (or molvis_exec on the composed server).

packages — pick sources from summaries.
outline(source=…) — module tree.
open(ref) — signature, docstring, examples. Do this before coding.
compose / search / suggest — index helpers only.

route(task) says which provider namespace a session needs (draw → molvis, jobs → molq, workspace → molexp). Default molmcp serve mounts those onto this same connection with FastMCP namespaces: molvis_open, molq_list_jobs, molexp_list_projects. Core tools stay bare (packages, open, route).

Use the package that owns the role (structure / IO / analysis → molpy, packing → molpack, plots → molplot). Do not reimplement RDF, trajectory IO, packing, or writers.

Missing API is a product gap

ok=false / SYMBOL_NOT_FOUND / no public API for the step means the capability is not there. Stop. Report three lines:

Which step is missing.
Which package or ref you opened.
What came back.

Then wait. The user may name another package — run outline / open on that source; do not skip discovery. Or they may ask to file an issue: use gh against that science package's tracker (not molmcp), body = the three lines. Do not add a workaround unless they explicitly ask.

Files

What ships with it

1 file 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.

__init__.py 93 B runs code

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.

2mo ago First seen · 72 lines · 58 tokens per session scan A d4acca1b5b29

Subscribe to this mod's changes

molcrafts is a skill published in the GitHub repository MolCrafts/molmcp (0 stars, last pushed 1mo ago), licensed BSD-3-Clause. It adds 58 tokens to every session and 663 once invoked, about $0.0002 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.

Scientific

molcrafts next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
molcraftsMolCrafts/molmcp	Skill	0	1mo ago	BSD-3-Clause	A	58	Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	yesterday	Apache-2.0	A	123	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	6d ago	MIT	A	44	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	6d ago	MIT	A	83	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	6d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	today	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	today	Apache-2.0	A	205	Claude Code