Agent skill

Drug Molecular Fingerprints

by learningmatter-mit in learningmatter-mit/AtomisticSkills

Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

MITAuto-check passedResearch & Science

Install Drug Molecular Fingerprints

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/drug-molecular-fingerprints .claude/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .claude/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/drug-molecular-fingerprints .agents/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .agents/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/drug-molecular-fingerprints .cursor/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .cursor/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/learningmatter-mit/AtomisticSkills.git --path skills/drug-molecular-fingerprints

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/drug-molecular-fingerprints .gemini/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .gemini/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/drug-molecular-fingerprints .github/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .github/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-molecular-fingerprints --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/drug-molecular-fingerprints .opencode/skills/drug-molecular-fingerprints && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "drug-molecular-fingerprints" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-molecular-fingerprints into .opencode/skills/drug-molecular-fingerprints/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-molecular-fingerprints", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: drug-molecular-fingerprints
GitHub stars: 176
Token cost: ~1k tokens
SKILL.md length: 277 words
Files: 5
Skills in repo: 129
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

Tasks that involve Drug discovery and cheminformatics
SKILL.md covers Goal, Instructions, Examples and Output Format, plus 1 more section
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Drug Molecular Fingerprints is an agent skill from learningmatter-mit/AtomisticSkills. Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `examples/README.md` and `examples/nsaid_similarity.json`).

It sits in Research & Science, covering Drug discovery and cheminformatics. It works with Model Context Protocol. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

When your agent uses it

Tasks that involve Drug discovery and cheminformatics

Example prompts

“/drug-molecular-fingerprints”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Drug Molecular Fingerprints loads about 1k tokens when it runs. Until then it costs about 38 tokens; SKILL.md has 277 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~38
When it runs · the whole SKILL.md, loaded when a task matches: ~1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 277 words, ~1,013 tokens.

Download SKILL.mdSave it as .claude/skills/drug-molecular-fingerprints/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.

name: drug-molecular-fingerprints
description: Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.
metadata.category: drug-discovery
metadata.venv: cpu

Molecular Fingerprints

<!-- mcp-tools-note -->

[!NOTE] Steps written server.tool are MCP tool calls: drugdisc.compute_molecular_fingerprints is the compute_molecular_fingerprints tool of the drugdisc server (mcp__drugdisc__compute_molecular_fingerprints, or mcp__plugin_atomistic-skills_drugdisc__compute_molecular_fingerprints when installed as a plugin). Without a connected server, run the same tools from the shell. Tools named in one command share a process, so a model loaded by load_model stays loaded:
bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python -m src.mcp_server.cli drugdisc compute_molecular_fingerprints key=value

Goal

To compute circular Morgan fingerprints (ECFP-style; default ECFP4 with radius=2) for a set of compounds, then calculate pairwise Tanimoto similarity for library comparison. Optionally perform Butina clustering for diversity analysis and generate a similarity heatmap for small sets.

This skill is commonly used for hit expansion, SAR triage, compound library diversity assessment, and applicability-domain style analysis.

Instructions

The drugdisc MCP server provides a compute_molecular_fingerprints tool that can be called directly:

Basic usage with SMILES file:

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="compounds.smi",
    radius=2,
    fp_size=2048,
    compute_similarity=True,
    output_file="similarity.json"
)

With Butina clustering:

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="library.smi",
    cluster=True,
    cluster_cutoff=0.7,
    output_file="clustered.json"
)

With similarity heatmap (small molecule sets, ≤250 compounds):

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="hits.smi",
    save_heatmap="heatmap.png",
    output_file="similarity.json"
)

Feature Morgan (FCFP-like) fingerprints:

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="compounds.smi",
    use_features=True,
    output_file="fcfp_similarity.json"
)

Chirality-aware fingerprints:

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="enantiomers.smi",
    use_chirality=True,
    output_file="chiral_sim.json"
)

Examples

SMILES file format

text

CCO	ethanol
CCCO	propanol
c1ccccc1	benzene
c1ccc(cc1)O	phenol

Basic similarity analysis

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="${CLAUDE_SKILL_DIR}/examples/compounds.smi",
    output_file="similarity.json"
)

Diversity-based clustering for library selection

bash

drugdisc.compute_molecular_fingerprints(
    smiles_file="screening_library.smi",
    cluster=True,
    cluster_cutoff=0.5,
    output_file="diverse_clusters.json"
)

Output Format

The tool returns a JSON with:

n_compounds: Total number of input compounds
n_valid: Number of successfully processed compounds
compounds: List of compound info (SMILES, name, validity, fingerprint bits)
similarity_matrix: Pairwise Tanimoto similarity (if compute_similarity=True)
clusters: Butina clustering results (if cluster=True)

Constraints

MCP Server: Requires drugdisc MCP server
Dependencies: RDKit (Chem, rdFingerprintGenerator, DataStructs, ML.Cluster.Butina)
SMILES file format: One molecule per line, SMILES[whitespace]NAME (NAME optional), # for comments
Fingerprint defaults: Morgan radius=2 (ECFP4-like), 2048 bits
Heatmap rendering: Limited to ≤250 compounds due to memory constraints
Similarity metric: Tanimoto coefficient (Jaccard index for bit vectors)
Clustering algorithm: Butina (leader-picker style); cutoff = similarity threshold (not distance)

Author: Matthew Cox Contact: GitHub @mcox3406

Files

SKILL.md and 4 other files in skills/drug-molecular-fingerprints of learningmatter-mit/AtomisticSkills.

SKILL.md
examples/README.md
examples/nsaid_similarity.json
examples/nsaid_similarity.png
examples/nsaids.smi

Open the folder on GitHubat commit 6257444

Compare with similar skills

Drug Molecular Fingerprints next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Drug Molecular Fingerprints compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Drug Molecular Fingerprints this skilllearningmatter-mit/AtomisticSkills	176	—	~1k	Automated safety check: Pass	MIT	2 days ago
Hcls Build Agentaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~885	Automated safety check: Pass	MIT-0	8 days ago
Tooluniverseynulihao/AgentSkillOS	618	2 repos	~2.5k	Automated safety check: Pass	None	7 mo ago
Hcls Get Startedaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~607	Automated safety check: Pass	MIT-0	8 days ago
Patsnap Chemistry Small Moleculepatsnap/mcp	113	—	~643	Automated safety check: Pass	Apache-2.0	1 mo ago
Chemgraphargonne-lcf/ChemGraph	162	—	~2.7k	Automated safety check: Pass	Apache-2.0	today

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Questions about Drug Molecular Fingerprints

What does Drug Molecular Fingerprints do?

Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison. Drug Molecular Fingerprints is an agent skill from learningmatter-mit/AtomisticSkills. Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

When should I use Drug Molecular Fingerprints?

Drug Molecular Fingerprints fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Drug Molecular Fingerprints in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a claude-code`. Or copy the skill folder (skills/drug-molecular-fingerprints in learningmatter-mit/AtomisticSkills) into .claude/skills/drug-molecular-fingerprints in your project. Claude Code loads it when a task matches its description.

How do I install Drug Molecular Fingerprints in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a codex`. Or copy the skill folder (skills/drug-molecular-fingerprints in learningmatter-mit/AtomisticSkills) into .agents/skills/drug-molecular-fingerprints in your project. Codex loads it when a task matches its description.

Can I use Drug Molecular Fingerprints in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-molecular-fingerprints -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/drug-molecular-fingerprints, .gemini/skills/drug-molecular-fingerprints, .github/skills/drug-molecular-fingerprints and .opencode/skills/drug-molecular-fingerprints in your project.

What does Drug Molecular Fingerprints need to run?

SKILL.md names no scripts, command-line tools or credentials: Drug Molecular Fingerprints is instructions for the agent only. Our summary lists: Python 3.

Does Drug Molecular Fingerprints access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is Drug Molecular Fingerprints safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Drug Molecular Fingerprints use?

Drug Molecular Fingerprints is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Drug Molecular Fingerprints use?

About 1k tokens (SKILL.md is roughly 4.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Drug Molecular Fingerprints?

Skills that share tags, products or a category with Drug Molecular Fingerprints: Hcls Build Agent (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Tooluniverse (ynulihao/AgentSkillOS, 618 stars), Hcls Get Started (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars) and Patsnap Chemistry Small Molecule (patsnap/mcp, 113 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Drug Molecular Fingerprints?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Drug Molecular Fingerprints

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Molecular Fingerprints

Goal

Instructions

Examples

SMILES file format

Basic similarity analysis

Diversity-based clustering for library selection

Output Format

Constraints

Files

Compare with similar skills

Similar skills

More from learningmatter-mit/AtomisticSkills

Related

Questions about Drug Molecular Fingerprints