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…
A skill your agent uses WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names.
Install Search Species
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills search-species --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/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/tools/search-species .claude/skills/search-species && 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 "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .claude/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-speciesType 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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills search-species --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/tools/search-species .agents/skills/search-species && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .agents/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills search-species --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/tools/search-species .cursor/skills/search-species && 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 "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .cursor/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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/jinzhezenggroup/computational-chemistry-agent-skills.git --path tools/search-species--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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills search-species --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/tools/search-species .gemini/skills/search-species && 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 "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .gemini/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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 jinzhezenggroup/computational-chemistry-agent-skills search-speciesInstalls 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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/tools/search-species .github/skills/search-species && 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 "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .github/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills search-species --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/tools/search-species .opencode/skills/search-species && 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 "search-species" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/search-species into .opencode/skills/search-species/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "search-species", 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
search-species- GitHub stars
- 148
- Token cost
- ~1.1k tokens
- SKILL.md length
- 353 words
- Files
- 2
- Skills in repo
- 62
- Repo updated
- First seen
- Licence
- LGPL-3.0-or-later
At a glance
A skill your agent uses WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names.
- Works in 5 steps: Acquire Target: Identify the chemical… → Select Engine: Choose the most targeted… → Execute Search: Use the search command… → …
- Requesting core chemical structural data (SMILES
- SKILL.md covers 🔄 Core Workflow (CRITICAL), Search Backend Overview, Quick Start & Command Outputs and Example, plus 2 more sections
- Calls uvx
What it does
Search Species is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. You MUST actively retrieve the data using this skill; DO NOT hallucinate or generate structures yourself. DO NOT USE WHEN asking for physical properties (melting point, solubility), safety/toxicity data (MSDS), or synthesis pathways.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `reference/backends.md`). Compatibility notes: Requires uv installed.
It sits in Research & Science, covering Drug discovery and cheminformatics. The repository describes itself as: Agent skills to run computational-chemistry tasks, used in OpenClaw. The licence is LGPL-3.0-or-later.
When your agent uses it
- Requesting core chemical structural data (SMILES
- 2D images) via IUPAC
- Multilingual names
- Asking for physical properties (melting point
Example prompts
- “/search-species”
Requirements
- Compatibility (from SKILL.md): Requires `uv` installed.
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Acquire Target: Identify the chemical name, identifier, or SMILES the user wants to query.
- Select Engine: Choose the most targeted search backend (pubchem, opsin, wikidata, or all) based on the query type. Avoid using all unless…
- Execute Search: Use the search command to query the database. You must set an appropriate max_cands limit to prevent excessively long…
- Evaluate Results: Carefully review the returned summary data in the output.
- Confirm & Iterate: Present the retrieved data to the user for confirmation. If the result is ambiguous or incorrect, communicate with the…
What it can do on your machine
Read from SKILL.md and the folder at commit 5c19e75. 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
Shell commands in SKILL.md call:
uvx
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uvx, which can reach the network depending on how they are called.
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.
Compatibility
Requires `uv` installed.
From compatibility in the SKILL.md frontmatter.
Context cost
Search Species loads about 1.1k tokens when it runs. Until then it costs about 94 tokens; SKILL.md has 353 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); files beside SKILL.md are not scanned.
SKILL.md
The full file from jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its LGPL-3.0-or-later licence (© jinzhezenggroup). 353 words, ~1,057 tokens.
Download SKILL.mdSave it as
.claude/skills/search-species/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- search-species
- description
- USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. You MUST actively retrieve the data using this skill; DO NOT hallucinate or generate structures yourself. DO NOT USE WHEN asking for physical properties (melting point, solubility), safety/toxicity data (MSDS), or synthesis pathways.
- compatibility
- Requires `uv` installed.
- license
- LGPL-3.0-or-later
- metadata.author
- light-cyan
- metadata.version
- 0.1.0
- metadata.repository
- https://github.com/light-cyan/search-species
Search Species
🔄 Core Workflow (CRITICAL)
When assisting users with chemical searches, you MUST adhere to the following step-by-step workflow. Note: Searching can be highly time-consuming; always prioritize efficiency.
- Acquire Target: Identify the chemical name, identifier, or SMILES the user wants to query.
- Select Engine: Choose the most targeted search backend (
pubchem,opsin,wikidata, orall) based on the query type. Avoid usingallunless strictly necessary, to minimize search times. - Execute Search: Use the
searchcommand to query the database. You must set an appropriatemax_candslimit to prevent excessively long processing times and reduce data noise. - Evaluate Results: Carefully review the returned summary data in the output.
- Confirm & Iterate: Present the retrieved data to the user for confirmation. If the result is ambiguous or incorrect, communicate with the user to adjust the search keywords and restart the process.
Search Backend Overview
search-species integrates three distinct backends. Each serves a specific purpose in the chemical informatics workflow:
| Feature | OPSIN | PubChem | Wikidata |
|---|---|---|---|
| Core Method | Algorithmic Parser | Curated Database | Knowledge Graph |
| Primary Input | IUPAC English Names | Names, CIDs, SMILES | Common & Multilingual Names |
| Molecular Image | Supported (Rendered) | Supported (Stored) | Rarely Available |
| Mass/Formula | Calculated via RDKit | Database Metadata | Database Metadata |
| Key Strength | Handles theoretical molecules. | Highly standardized data. | Vernacular & Cross-lingual. |
(For more detailed engine capabilities, limitations, and data normalization behavior, see reference/backends.md)
Show full SKILL.md (130 more words)Show less
Quick Start & Command Outputs
Typical search syntax:
uvx search-species <engine> "<query>" [max_cands] -o <output_dir>
Output: Prints the retrieved species data summary and the file path where each candidate's JSON is saved (e.g.,
SpeciesCandidate(...) written -> ./cache/xyz.json).
Typical render syntax:
uvx --from search-species render-species <candidate_files...> -o <output_dir>
Output: Prints the file path of the successfully generated image card (e.g.,
Successfully rendered -> ./gallery/xyz.png).
Example
PubChem (Standard database lookups):
uvx search-species pubchem "benzene" 5 -o ./results
OPSIN (Theoretical molecules & strict IUPAC):
uvx search-species opsin "2-acetyloxybenzoic acid"
Wikidata (Multilingual & common/trade names):
uvx search-species wikidata "Аспирин"
uvx search-species wikidata "TNT"
Agent Checklist
When using this toolkit for users, ensure you cross-check these points with the Core Workflow:
- Engine Match: Match the engine to the query type based on the overview table.
- Data Scope: Remember this tool only retrieves structural identity (Name, Formula, Mass, SMILES, 2D Image).
- Fallback: If
pubchemfails on a systematic name, fallback toopsin. - Quoting: Always wrap the chemical
<query>in quotes.
References
- Engine Details & Limitations:
reference/backends.md
© jinzhezenggroup, LGPL-3.0-or-later. 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 1 other file in tools/search-species of jinzhezenggroup/computational-chemistry-agent-skills.
- SKILL.md
- reference/backends.md
Open the folder on GitHubat commit 5c19e75
Compare with similar skills
Search Species 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 |
|---|---|---|---|---|---|---|
| Search Species this skilljinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~1.1k | Automated safety check: Pass | LGPL-3.0-or-later | |
| MolecodeAtomFlow-AI/MoleCode | 306 | — | ~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 | |
| Biopipelineslocbp-uzh/biopipelines | 109 | — | ~2.4k | Automated safety check: Pass | MIT |
Similar skills
Drug Discovery
Tommy-yw/RunbookHermes
Pharmaceutical research assistant for drug discovery workflows.
DiffDock Molecular Docking
K-Dense-AI/scientific-agent-skills
Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
Biomedical Analysis Dispatch
xjtulyc/MedgeClaw
Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.
Biopipelines
locbp-uzh/biopipelines
Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…
Tooluniverse Chemical Compound Retrieval
wu-yc/LabClaw
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
More from jinzhezenggroup/computational-chemistry-agent-skills
All 62 skills in this repoQuantum ESPRESSO DFT Task Builder
jinzhezenggroup/computational-chemistry-agent-skills
Turns a user-supplied atomic structure and DFT settings into a runnable Quantum ESPRESSO input file, stopping short of submitting the job.
DP-GEN Simplify Workflow
jinzhezenggroup/computational-chemistry-agent-skills
Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
LAMMPS with DeePMD-kit
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and runs molecular dynamics simulations in LAMMPS with a DeePMD machine-learning potential, writing the input script and choosing NVE, NVT or NPT.
LAMMPS ReaxFF Setup
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and explains LAMMPS input scripts for reactive molecular dynamics with the ReaxFF potential, including charge equilibration and ensemble choice.
RDKit Conformer Generator
jinzhezenggroup/computational-chemistry-agent-skills
Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.
RDKit Descriptors and Fingerprints
jinzhezenggroup/computational-chemistry-agent-skills
Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.
Related
Categories
Questions about Search Species
What does Search Species do?
A skill your agent uses WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. Search Species is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names.
When should I use Search Species?
Search Species fits situations like: requesting core chemical structural data (SMILES; 2D images) via IUPAC; multilingual names; asking for physical properties (melting point.
How do I install Search Species in Claude Code?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a claude-code`. Or copy the skill folder (tools/search-species in jinzhezenggroup/computational-chemistry-agent-skills) into .claude/skills/search-species in your project. Claude Code loads it when a task matches its description.
How do I install Search Species in Codex?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a codex`. Or copy the skill folder (tools/search-species in jinzhezenggroup/computational-chemistry-agent-skills) into .agents/skills/search-species in your project. Codex loads it when a task matches its description.
Can I use Search Species 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 jinzhezenggroup/computational-chemistry-agent-skills --skill search-species -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/search-species, .gemini/skills/search-species, .github/skills/search-species and .opencode/skills/search-species in your project.
What does Search Species need to run?
Going by SKILL.md and its folder, Search Species needs the command-line tools its instructions call (uvx). Compatibility (from SKILL.md): Requires `uv` installed..
Does Search Species access the network?
SKILL.md contains no URLs. Its commands use uvx, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Search Species 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 Search Species use?
Search Species is published under the LGPL-3.0-or-later licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Search Species use?
About 1.1k tokens (SKILL.md is roughly 4.2k 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 Search Species?
Skills that share tags, products or a category with Search Species: Molecode (AtomFlow-AI/MoleCode, 306 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 Search Species?
jinzhezenggroup (a GitHub organization) maintains it in jinzhezenggroup/computational-chemistry-agent-skills, which has 148 GitHub stars. The repository holds 62 skills in this directory. The repository was last updated on October 9, 2026.
Source: jinzhezenggroup/computational-chemistry-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.