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.
A skill your agent uses for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration…
Install Data CLI Integration
$ npx skills add VectorSpaceLab/AREX-Skill --skill data-cli-integration -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill data-cli-integration --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/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .claude/skills/data-cli-integration && 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 "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .claude/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integrationType 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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill data-cli-integration --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .agents/skills/data-cli-integration && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .agents/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill data-cli-integration --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .cursor/skills/data-cli-integration && 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 "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .cursor/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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/VectorSpaceLab/AREX-Skill.git --path skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration--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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill data-cli-integration --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .gemini/skills/data-cli-integration && 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 "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .gemini/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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 VectorSpaceLab/AREX-Skill data-cli-integrationInstalls 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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .github/skills/data-cli-integration && 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 "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .github/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill data-cli-integration --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration .opencode/skills/data-cli-integration && 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 "data-cli-integration" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration into .opencode/skills/data-cli-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-cli-integration", 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
data-cli-integration- GitHub stars
- 328
- Token cost
- ~946 tokens
- SKILL.md length
- 347 words
- Files
- 5 (incl. scripts, references)
- Skills in repo
- 159
- Repo updated
- First seen
- Licence
- BSD-3-Clause
At a glance
A skill your agent uses for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration…
- RDKit data-file discovery
- SKILL.md covers Route Here, Route Elsewhere, Start With These References and Common Patterns, plus 1 more section
- Runs Python scripts from its folder; calls python
- Pharmacophore feature-definition files
What it does
Data CLI Integration is an agent skill from VectorSpaceLab/AREX-Skill. Use for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration workflows.
Its SKILL.md is about 950 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/data-files-and-features.md`, `references/pandas-and-database.md` and `references/troubleshooting.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics and DataFrames. It works with RDKit, pandas and Microsoft Excel. The repository describes itself as: A Skill Library for Automated Machine Learning. The licence is BSD-3-Clause.
When your agent uses it
- RDKit data-file discovery
- Pharmacophore feature-definition files
- PandasTools molecule DataFrames
- Lightweight database helpers
Example prompts
- “/data-cli-integration”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit ac3fe1a. 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:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Data CLI Integration loads about 946 tokens when it runs, and up to ~4.1k if it reads all its reference files. Until then it costs about 51 tokens; SKILL.md has 347 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 VectorSpaceLab/AREX-Skill at commit ac3fe1a, republished under its BSD-3-Clause licence (© VectorSpaceLab). 347 words, ~946 tokens.
Download SKILL.mdSave it as
.claude/skills/data-cli-integration/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.- name
- data-cli-integration
- description
- Use for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration workflows.
- disable-model-invocation
- true
- metadata.disco-role
- operating
- license
- BSD 3-Clause
RDKit Data, CLI, and Integration
Use this sub-skill when a task asks an agent to connect RDKit chemistry code to package data files, tabular data, pandas workflows, feature-definition files, SQL/database helpers, or small command-line workflows around installed RDKit.
Route Here
- Locate package data with
rdkit.RDConfig.RDDataDir, includingBaseFeatures.fdef,FunctionalGroups.txt,Salts.txt,RDData.sqlt,RDTests.sqlt, and sampleNCI/files. - Build pharmacophore feature factories with
rdkit.Chem.ChemicalFeatures.BuildFeatureFactoryorBuildFeatureFactoryFromString. - Annotate molecules from SMILES with feature families, types, atom ids, and coordinates using the bundled
scripts/feature_finder.pyhelper. - Use
rdkit.Chem.PandasToolsfor SDF-to-DataFrame, SMILES-to-molecule columns, substructure filtering, SDF/SMILES/XLSX export, and HTML molecule rendering. - Use
rdkit.Dbasehelpers for SQLite-style RDKit data tables or for understanding legacy DB utility boundaries. - Triage installed-package integration issues such as missing data files, optional pandas/XLSX dependencies, database backend availability, or local checkout shadowing.
Route Elsewhere
- Basic molecule parsing, SDF/SMILES suppliers, sanitization, and molecule validation:
../molecule-io-core/. - Descriptor calculation, fingerprints, similarity, clustering, or ML feature engineering:
../descriptors-fingerprints/. - 2D/3D coordinates, conformers, drawing APIs, and image generation outside pandas export:
../conformers-drawing/. - Reactions, standardization, salt stripping chemistry policy, tautomer handling, or R-group workflows:
../reactions-standardization/. - Optional contributed utilities and standalone contributed scorers:
../contrib-utilities/.
Start With These References
references/data-files-and-features.mdforRDConfig, installed data files, FDef feature factories, and feature-finder usage.references/pandas-and-database.mdforPandasTools, SDF/SMILES table round-trips, HTML/XLSX export, and DB helper boundaries.references/troubleshooting.mdfor missing data, pandas optional behavior, DB backend problems, and checkout-shadowing diagnostics.scripts/feature_finder.pyfor a safe installed-package CLI that reports RDKit chemical features for SMILES strings.
Common Patterns
- Prefer
os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef")for the default pharmacophore feature-definition file instead of hard-coding install paths. - Check
os.path.isdir(RDConfig.RDDataDir)andos.path.exists(...)before assuming sample data or.fdeffiles are present in minimal packages. - Import
PandasToolsonly when pandas-backed behavior is needed, and catchImportErrorfor environments without pandas. - Keep database examples SQLite-oriented unless the task explicitly asks for legacy PostgreSQL/DbCLI behavior; RDKit PostgreSQL cartridge work is outside this sub-skill's runtime scope.
- Treat
Projects/DbCLIas historical/reference-only guidance unless the installed RDKit distribution exposes the same modules and dependencies.
Quick Smoke
Run the bundled feature helper in any environment where RDKit is importable:
python scripts/feature_finder.py --smiles "CC(=O)O" "c1ccncc1" --summaryUse an explicit feature-definition file when testing custom pharmacophore rules:
python scripts/feature_finder.py --fdef custom.fdef --smiles "CCO"© VectorSpaceLab, BSD-3-Clause. 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/repositories/repo-skills/rdkit/sub-skills/data-cli-integration of VectorSpaceLab/AREX-Skill.
- SKILL.md
- references/data-files-and-features.md
- references/pandas-and-database.md
- references/troubleshooting.md
- scripts/feature_finder.py
Open the folder on GitHubat commit ac3fe1a
Compare with similar skills
Data CLI Integration 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 |
|---|---|---|---|---|---|---|
| Data CLI Integration this skillVectorSpaceLab/AREX-Skill | 328 | — | ~946 | Automated safety check: Pass | BSD-3-Clause | |
| RDKit Descriptors and Fingerprintsjinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~2.3k | Automated safety check: Pass | LGPL-3.0 | |
| RDKit Conformer Generatorjinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~2.4k | Automated safety check: Pass | LGPL-3.0 | |
| ADMET Prediction for Drug CandidatesGPTomics/bioSkills | 1.2k | 1 repos | ~5k | Automated safety check: Pass | MIT | |
| Verified Data Analysis with pandaspipeshub-ai/pipeshub-ai | 3.8k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Topic Model ConsolidationTyrealQ/q-skills | 108 | — | ~1k | Automated safety check: Pass | MIT |
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Questions about Data CLI Integration
What does Data CLI Integration do?
A skill your agent uses for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration…. Data CLI Integration is an agent skill from VectorSpaceLab/AREX-Skill. Use for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration workflows.
When should I use Data CLI Integration?
Data CLI Integration fits situations like: RDKit data-file discovery; pharmacophore feature-definition files; pandasTools molecule DataFrames; lightweight database helpers.
How do I install Data CLI Integration in Claude Code?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill data-cli-integration -a claude-code`. Or copy the skill folder (skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration in VectorSpaceLab/AREX-Skill) into .claude/skills/data-cli-integration in your project. Claude Code loads it when a task matches its description.
How do I install Data CLI Integration in Codex?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill data-cli-integration -a codex`. Or copy the skill folder (skills/repositories/repo-skills/rdkit/sub-skills/data-cli-integration in VectorSpaceLab/AREX-Skill) into .agents/skills/data-cli-integration in your project. Codex loads it when a task matches its description.
Can I use Data CLI Integration 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 VectorSpaceLab/AREX-Skill --skill data-cli-integration -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/data-cli-integration, .gemini/skills/data-cli-integration, .github/skills/data-cli-integration and .opencode/skills/data-cli-integration in your project.
What does Data CLI Integration need to run?
Going by SKILL.md and its folder, Data CLI Integration needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Data CLI Integration access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Data CLI Integration 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 Data CLI Integration use?
Data CLI Integration is published under the BSD-3-Clause licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Data CLI Integration use?
About 946 tokens (SKILL.md is roughly 3.8k 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 3.2k tokens, read only when the agent opens those files.
What are the alternatives to Data CLI Integration?
Skills that share tags, products or a category with Data CLI Integration: RDKit Descriptors and Fingerprints (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars), RDKit Conformer Generator (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars), ADMET Prediction for Drug Candidates (GPTomics/bioSkills, 1.2k stars) and Verified Data Analysis with pandas (pipeshub-ai/pipeshub-ai, 3.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Data CLI Integration?
VectorSpaceLab (a GitHub organization) maintains it in VectorSpaceLab/AREX-Skill, which has 328 GitHub stars. The repository holds 159 skills in this directory. The repository was last updated on September 3, 2026.
Source: VectorSpaceLab/AREX-Skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.