CLI Anything Chromadb
HKUDS/CLI-Anything
Command-line interface for ChromaDB - A stateless CLI for managing vector database collections, documents, and semantic search.
Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
Install Chem Similarity Search
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-search --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-similarity-search .claude/skills/chem-similarity-search && rm -rf skills-srcUse ~/.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/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .claude/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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 install https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-searchType 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-search --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/chem-similarity-search .agents/skills/chem-similarity-search && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .agents/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-search --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/chem-similarity-search .cursor/skills/chem-similarity-search && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .cursor/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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 https://github.com/learningmatter-mit/AtomisticSkills.git --path skills/chem-similarity-search--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-search --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/chem-similarity-search .gemini/skills/chem-similarity-search && rm -rf skills-srcUse ~/.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/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .gemini/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-searchInstalls 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).
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/chem-similarity-search .github/skills/chem-similarity-search && rm -rf skills-srcUse ~/.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/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .github/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-similarity-search --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/chem-similarity-search .opencode/skills/chem-similarity-search && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "chem-similarity-search" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-similarity-search into .opencode/skills/chem-similarity-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-similarity-search", 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
chem-similarity-search- GitHub stars
- 176
- Token cost
- ~614 tokens
- SKILL.md length
- 186 words
- Files
- 4 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
- Works in 2 steps: Search by SMILES String → Search by PubChem CID
- Tasks that involve Vector databases
- SKILL.md covers Goal, Instructions, Examples and Constraints
- Runs Python scripts from its folder
What it does
Chem Similarity Search is an agent skill from learningmatter-mit/AtomisticSkills. Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
Its SKILL.md is about 610 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/aspirin_analogs/README.md`, `examples/aspirin_analogs/aspirin_analogs.json` and `scripts/similarity_search.py`).
It sits in Backend & APIs, covering Vector databases, REST APIs and Drug discovery and cheminformatics. 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 Vector databases
- Tasks that involve REST APIs
- Tasks that involve Drug discovery and cheminformatics
Example prompts
- “/chem-similarity-search”
Requirements
- Python 3
Workflow steps
2 steps, taken from the step headings in SKILL.md.
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
Ships 1 file in scripts/ (Python), which the agent can run.
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
Chem Similarity Search loads about 614 tokens when it runs. Until then it costs about 33 tokens; SKILL.md has 186 words of instructions outside code blocks.
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); the scripts in this folder are not scanned.
SKILL.md
The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 186 words, ~614 tokens.
Download SKILL.mdSave it as
.claude/skills/chem-similarity-search/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- chem-similarity-search
- description
- Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
- metadata.category
- chemistry, drug-discovery
- metadata.venv
- cpu
Chemical Similarity Search
Goal
To programmatically find chemical analogs, alternative precursors, and structurally similar compounds for a given target molecule using PubChem's "fastsimilarity_2d" endpoint. The skill retrieves lists of similar compounds ranked by sequence alignment of their 2D molecular fingerprints, providing CIDs, molecular weights, formulas, and SMILES strings.
Instructions
1. Search by SMILES String
Search for similar compounds by providing the canonical or isomeric SMILES.
Adjust the --threshold (similarity cutoff 0-100, default is 95) to widen or narrow the search radius. Higher threshold equals higher similarity.
Adjust --max_records to limit the output length.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/similarity_search.py \
--smiles "CC(=O)Oc1ccccc1C(=O)O" \
--threshold 95 \
--max_records 5 \
--outdir research/aspirin_similar \
--output aspirin_similar.json2. Search by PubChem CID
Search directly using an exact compound's CID. This avoids translation steps for SMILES parsing.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/similarity_search.py \
--cid 2244 \
--threshold 90 \
--max_records 10 \
--outdir research/aspirin_similar \
--output cid_2244_similar.jsonExamples
We can test extracting highly similar analogs (Threshold 95) for Aspirin (CID: 2244 or SMILES: CC(=O)Oc1ccccc1C(=O)O).
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/similarity_search.py \
--cid 2244 \
--threshold 95 \
--max_records 5 \
--outdir ${CLAUDE_SKILL_DIR}/examples/aspirin_analogs \
--output aspirin_analogs.jsonConstraints
- Rate Limiting: PubChem PUG REST API enforces per-user throttling limits. Heavy bursts will result in
HTTP 503 Server Busyerrors. The script implements an exponential backoff retry mechanism. - 2D Similarity: Uses exact structural bit-vector fingerprints. Stereochemical and 3D properties do not strongly affect the score.
- Network: Internet access is required.
Author: Bowen Deng Contact: GitHub @learningmatter-mit
© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 3 other files (scripts) in skills/chem-similarity-search of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/aspirin_analogs/README.md
- examples/aspirin_analogs/aspirin_analogs.json
- scripts/similarity_search.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
Chem Similarity Search 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Chem Similarity Search this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~614 | Automated safety check: Pass | MIT | |
| CLI Anything ChromadbHKUDS/CLI-Anything | 52k | — | ~727 | Automated safety check: Pass | Apache-2.0 | |
| Pubchem Database Skillaipoch/medical-research-skills | 1.9k | — | ~954 | Automated safety check: Pass | MIT | |
| CohesivityAnil-matcha/awesome-muse-connectors | 1.3k | — | ~1.1k | Automated safety check: Pass | MIT | |
| Ncbi Blast APIwentorai/research-plugins | 298 | 1 repos | ~1.6k | Automated safety check: Pass | MIT | |
| DBoracle/skills | 877 | — | ~1.4k | Automated safety check: Pass | UPL-1.0 |
Similar skills
Pubchem Database Skill
aipoch/medical-research-skills
Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure…
Cohesivity
Anil-matcha/awesome-muse-connectors
Backend infrastructure for a project via Cohesivity (cohesivity.ai).
Ncbi Blast API
wentorai/research-plugins
Run sequence similarity searches via the NCBI BLAST REST API
- Official
DB
oracle/skills
Oracle Database guidance for SQL, PL/SQL, SQLcl, ORDS, Oracle Vector SDK, administration, app development, performance, security, migrations, and agent-safe database workflows.
Open Notebook
K-Dense-AI/scientific-agent-skills
Organizes research with the self-hosted Open Notebook alternative to NotebookLM.
More from learningmatter-mit/AtomisticSkills
All 129 skills in this repoDrug Binding Site Definition
learningmatter-mit/AtomisticSkills
Define a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification.
Drug Complex System Builder
learningmatter-mit/AtomisticSkills
Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation.
Drug Pocket Detection
learningmatter-mit/AtomisticSkills
Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank).
Chem Bond Dissociation
learningmatter-mit/AtomisticSkills
Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
Chem Conformer Search
learningmatter-mit/AtomisticSkills
Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.
Chem DB Mof
learningmatter-mit/AtomisticSkills
Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al.
Related
Categories
Questions about Chem Similarity Search
What does Chem Similarity Search do?
Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API. Chem Similarity Search is an agent skill from learningmatter-mit/AtomisticSkills. Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
When should I use Chem Similarity Search?
Chem Similarity Search fits situations like: tasks that involve Vector databases; tasks that involve REST APIs; tasks that involve Drug discovery and cheminformatics.
How do I install Chem Similarity Search in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a claude-code`. Or copy the skill folder (skills/chem-similarity-search in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-similarity-search in your project. Claude Code loads it when a task matches its description.
How do I install Chem Similarity Search in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-similarity-search -a codex`. Or copy the skill folder (skills/chem-similarity-search in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-similarity-search in your project. Codex loads it when a task matches its description.
Can I use Chem Similarity Search 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 chem-similarity-search -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-similarity-search, .gemini/skills/chem-similarity-search, .github/skills/chem-similarity-search and .opencode/skills/chem-similarity-search in your project.
What does Chem Similarity Search need to run?
Going by SKILL.md and its folder, Chem Similarity Search needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Chem Similarity Search 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 Chem Similarity Search 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Chem Similarity Search use?
Chem Similarity Search 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 Chem Similarity Search use?
About 614 tokens (SKILL.md is roughly 2.5k 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 Chem Similarity Search?
Skills that share tags, products or a category with Chem Similarity Search: CLI Anything Chromadb (HKUDS/CLI-Anything, 52k stars), Pubchem Database Skill (aipoch/medical-research-skills, 1.9k stars), Cohesivity (Anil-matcha/awesome-muse-connectors, 1.3k stars) and Ncbi Blast API (wentorai/research-plugins, 298 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Chem Similarity Search?
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.