Molecode
AtomFlow-AI/MoleCode
A skill your agent uses for deterministic molecule understanding, graph-level editing, generation, and validation with MoleCode — an explicit Mermaid graph in which every atom and bond is a typed…
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Install Pubchem Database
$ npx skills add google-deepmind/science-skills --skill pubchem-database -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install google-deepmind/science-skills pubchem-database --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/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/pubchem_database .claude/skills/pubchem-database && 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 "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .claude/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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/google-deepmind/science-skills/tree/main/skills/pubchem_databaseType 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 google-deepmind/science-skills --skill pubchem-database -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install google-deepmind/science-skills pubchem-database --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/pubchem_database .agents/skills/pubchem-database && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .agents/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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 google-deepmind/science-skills --skill pubchem-database -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install google-deepmind/science-skills pubchem-database --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/pubchem_database .cursor/skills/pubchem-database && 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 "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .cursor/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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/google-deepmind/science-skills.git --path skills/pubchem_database--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 google-deepmind/science-skills --skill pubchem-database -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install google-deepmind/science-skills pubchem-database --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/pubchem_database .gemini/skills/pubchem-database && 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 "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .gemini/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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 google-deepmind/science-skills pubchem-databaseInstalls 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 google-deepmind/science-skills --skill pubchem-database -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pubchem_database .github/skills/pubchem-database && 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 "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .github/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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 google-deepmind/science-skills --skill pubchem-database -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install google-deepmind/science-skills pubchem-database --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pubchem_database .opencode/skills/pubchem-database && 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 "pubchem-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database into .opencode/skills/pubchem-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubchem-database", 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
pubchem-database- GitHub stars
- 3.2k
- Used in
- 2 other repos
- Token cost
- ~1.4k tokens
- SKILL.md length
- 493 words
- Files
- 5 (incl. scripts, references)
- Skills in repo
- 40
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
- Works in 2 steps: uv: Read the uv skill and follow its… → User Notification: If…
- A user asks about a specific chemical
- SKILL.md covers Prerequisites, Quick Start, Core Rules and Core Capabilities, plus 5 more sections
- Runs Python scripts from its folder; calls uv
What it does
Pubchem Database is an agent skill from google-deepmind/science-skills. Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `references/endpoints.md`, `references/workflows.md` and `scripts/pubchem_api.py`).
It sits in Research & Science, covering Drug discovery and cheminformatics. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.
When your agent uses it
- A user asks about a specific chemical
- Tasks that involve Drug discovery and cheminformatics
Example prompts
- “/pubchem-database”
Requirements
- Python 3
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- uv: Read the uv skill and follow its Setup instructions to ensure
- User Notification: If .licenses/pubchem_database_LICENSE.txt does not
What it can do on your machine
Read from SKILL.md and the folder at commit 6883275. 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.
Shell commands in SKILL.md call:
uv
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):
pubchem.ncbi.nlm.nih.gov
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
Pubchem Database loads about 1.4k tokens when it runs, and up to ~2.9k if it reads all its reference files. Until then it costs about 54 tokens; SKILL.md has 493 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 google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 493 words, ~1,404 tokens.
Download SKILL.mdSave it as
.claude/skills/pubchem-database/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.- name
- pubchem-database
- description
- Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
PubChem Database
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/pubchem_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp.
Quick Start
PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs.
Example: Resolve a chemical name to its Compound ID (CID)
uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.jsonCore Rules
- Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
- Read the generated JSON output file, and process it with jq or code.
- Verify Facts: ALWAYS verify information retrieved from memory with a database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge.
- Notification: If this skill is used, ensure this is mentioned in the output.
Core Capabilities
1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys.
uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json
# OR
uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA).
uv run scripts/pubchem_api.py properties --cid 2244 --output result.json3. Synonyms and Trade Names Find alternative names and brand names.
uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.jsonAdvanced Context
4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View).
uv run scripts/pubchem_api.py safety --cid 2244 --output result.json5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View).
uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json6. Custom Heading (PUG-View) Retrieve any specific heading from the PUG-View system (e.g., 'Geometry', 'Crystal Structures').
uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json7. Image Generation Retrieve 2D chemical structure images. The script returns a Markdown-formatted image link.
uv run scripts/pubchem_api.py image --cid 2244 --output result.jsonShow full SKILL.md (193 more words)Show less
Complex Search & Biology
8. Structure-Based Searching (Similarity & Substructure) Find molecules similar to a SMILES string or containing a specific substructure.
uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.jsonand
uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.
uv run scripts/pubchem_api.py assays --cid 2244 --output result.jsonAdvanced Usage & Workflows
10. Cross-references (Xrefs) Fetch identifiers cross-referenced with a CID (e.g., PatentID, PubMedID).
uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json11. Property Range Search Find CIDs within a specific property range.
Supported features include: molecular_weight, heavy_atom_count, xlogp,
tpsa, h_bond_donor_count, h_bond_acceptor_count, rotatable_bond_count,
exact_mass, monoisotopic_mass, and complexity.
uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json12. Custom PUG-REST Query Execute a raw path against the PUG-REST API.
uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.jsonFallback Search Strategies
If direct resolution by name or formula fails (e.g., for complex compounds or specific ions):
- Search for parent/neutral molecule: If searching for an ion or salt, try searching for the neutral parent compound.
- Deconstruct complex formulas: If a complex formula returns no results, try searching for major components or ligands.
- Use substructure or similarity search: If you have a SMILES string or can generate one for a component, use it to find related compounds.
Complex Queries and Multi-Step Tasks
- Custom/Complex Queries: For more details, read references/endpoints.md to construct raw PUG-REST URLs.
- Multi-Step Tasks: For complex tasks like drug discovery pipelines, follow the checklists in references/workflows.md.
© google-deepmind, Apache-2.0. 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 4 other files (scripts, references) in skills/pubchem_database of google-deepmind/science-skills.
- SKILL.md
- references/citation.bib
- references/endpoints.md
- references/workflows.md
- scripts/pubchem_api.py
Open the folder on GitHubat commit 6883275
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Pubchem Database 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 |
|---|---|---|---|---|---|---|
| Pubchem Database this skillgoogle-deepmind/science-skills | 3.2k | 2 repos | ~1.4k | Automated safety check: Pass | Apache-2.0 | |
| MolecodeAtomFlow-AI/MoleCode | 305 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Drug DiscoveryTommy-yw/RunbookHermes | 546 | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| Edu Chem Reactionwy51ai/edulab | 1.4k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 |
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Related
Categories
Questions about Pubchem Database
What does Pubchem Database do?
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Pubchem Database is an agent skill from google-deepmind/science-skills. Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
When should I use Pubchem Database?
Pubchem Database fits situations like: A user asks about a specific chemical; tasks that involve Drug discovery and cheminformatics.
How do I install Pubchem Database in Claude Code?
Run `npx skills add google-deepmind/science-skills --skill pubchem-database -a claude-code`. Or copy the skill folder (skills/pubchem_database in google-deepmind/science-skills) into .claude/skills/pubchem-database in your project. Claude Code loads it when a task matches its description.
How do I install Pubchem Database in Codex?
Run `npx skills add google-deepmind/science-skills --skill pubchem-database -a codex`. Or copy the skill folder (skills/pubchem_database in google-deepmind/science-skills) into .agents/skills/pubchem-database in your project. Codex loads it when a task matches its description.
Can I use Pubchem Database 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 google-deepmind/science-skills --skill pubchem-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pubchem-database, .gemini/skills/pubchem-database, .github/skills/pubchem-database and .opencode/skills/pubchem-database in your project.
What does Pubchem Database need to run?
Going by SKILL.md and its folder, Pubchem Database needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Pubchem Database access the network?
SKILL.md names 1 domain. As links in the text: pubchem.ncbi.nlm.nih.gov. This is read from the text; nothing was executed.
Is Pubchem Database 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 Pubchem Database use?
Pubchem Database is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Pubchem Database use?
About 1.4k tokens (SKILL.md is roughly 5.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.5k tokens, read only when the agent opens those files.
What are the alternatives to Pubchem Database?
Skills that share tags, products or a category with Pubchem Database: Molecode (AtomFlow-AI/MoleCode, 305 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Pubchem Database?
google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,216 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on September 15, 2026.
Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.