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.
Use this Chemprop sub-skill for reaction SMILES, reaction-plus-molecule multicomponent data, atom/bond targets, constrained MolAtomBond prediction, spectral tasks, and specialized descriptor/feature…
Install Specialized Molecular Tasks
$ npx skills add VectorSpaceLab/AREX-Skill --skill specialized-molecular-tasks -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill specialized-molecular-tasks --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/chemprop/sub-skills/specialized-molecular-tasks .claude/skills/specialized-molecular-tasks && 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 "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .claude/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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/chemprop/sub-skills/specialized-molecular-tasksType 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 specialized-molecular-tasks -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill specialized-molecular-tasks --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/chemprop/sub-skills/specialized-molecular-tasks .agents/skills/specialized-molecular-tasks && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .agents/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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 specialized-molecular-tasks -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill specialized-molecular-tasks --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/chemprop/sub-skills/specialized-molecular-tasks .cursor/skills/specialized-molecular-tasks && 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 "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .cursor/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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/chemprop/sub-skills/specialized-molecular-tasks--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 specialized-molecular-tasks -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill specialized-molecular-tasks --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/chemprop/sub-skills/specialized-molecular-tasks .gemini/skills/specialized-molecular-tasks && 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 "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .gemini/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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 specialized-molecular-tasksInstalls 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 specialized-molecular-tasks -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/chemprop/sub-skills/specialized-molecular-tasks .github/skills/specialized-molecular-tasks && 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 "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .github/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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 specialized-molecular-tasks -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 specialized-molecular-tasks --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/chemprop/sub-skills/specialized-molecular-tasks .opencode/skills/specialized-molecular-tasks && 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 "specialized-molecular-tasks" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks into .opencode/skills/specialized-molecular-tasks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "specialized-molecular-tasks", 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
specialized-molecular-tasks- GitHub stars
- 331
- Token cost
- ~1.2k tokens
- SKILL.md length
- 414 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 157
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Use this Chemprop sub-skill for reaction SMILES, reaction-plus-molecule multicomponent data, atom/bond targets, constrained MolAtomBond prediction, spectral tasks, and specialized descriptor/feature…
- Tasks that involve Drug discovery and cheminformatics
- SKILL.md covers Route Here For, Route Elsewhere, Quick Starts and References, plus 1 more section
- Runs Python scripts from its folder
What it does
Specialized Molecular Tasks is an agent skill from VectorSpaceLab/AREX-Skill. Use this Chemprop sub-skill for reaction SMILES, reaction-plus-molecule multicomponent data, atom/bond targets, constrained MolAtomBond prediction, spectral tasks, and specialized descriptor/feature schemas.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `references/mol-atom-bond.md`, `references/reaction-multicomponent.md` and `references/spectral-and-special-tasks.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics. It works with Python. The repository describes itself as: A Skill Library for Automated Machine Learning.
When your agent uses it
- Tasks that involve Drug discovery and cheminformatics
Example prompts
- “/specialized-molecular-tasks”
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.
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
Specialized Molecular Tasks loads about 1.2k tokens when it runs, and up to ~6.3k if it reads all its reference files. Until then it costs about 59 tokens; SKILL.md has 414 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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 414 words (~1,209 tokens).
“Use this sub-skill when a Chemprop request needs specialized molecular schemas or flags rather than ordinary molecule-level training/prediction.”
- name
- specialized-molecular-tasks
- disable-model-invocation
- true
- metadata.disco-role
- operating
- license
- NOASSERTION
Files
SKILL.md and 5 other files (scripts, references) in skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks of VectorSpaceLab/AREX-Skill.
- SKILL.md
- references/mol-atom-bond.md
- references/reaction-multicomponent.md
- references/spectral-and-special-tasks.md
- references/troubleshooting.md
- scripts/chemprop_specialized_command_builder.py
Open the folder on GitHubat commit ac3fe1a
Compare with similar skills
Specialized Molecular Tasks 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 |
|---|---|---|---|---|---|---|
| Specialized Molecular Tasks this skillVectorSpaceLab/AREX-Skill | 331 | — | ~1.2k | Automated safety check: Pass | Custom licence | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Edu Chem Reactionwy51ai/edulab | 1.4k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Rowanlamm-mit/scienceclaw | 246 | 4 repos | ~3.1k | Automated safety check: Warn | Proprietary | |
| Coot Rdkitpemsley/coot | 168 | — | ~981 | Automated safety check: Pass | GPL-3.0 | |
| RDKit Cheminformaticsdavila7/claude-code-templates | 33k | 14 repos | ~5k | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Specialized Molecular Tasks
What does Specialized Molecular Tasks do?
Use this Chemprop sub-skill for reaction SMILES, reaction-plus-molecule multicomponent data, atom/bond targets, constrained MolAtomBond prediction, spectral tasks, and specialized descriptor/feature…. Specialized Molecular Tasks is an agent skill from VectorSpaceLab/AREX-Skill. Use this Chemprop sub-skill for reaction SMILES, reaction-plus-molecule multicomponent data, atom/bond targets, constrained MolAtomBond prediction, spectral tasks, and specialized descriptor/feature schemas.
When should I use Specialized Molecular Tasks?
Specialized Molecular Tasks fits situations like: tasks that involve Drug discovery and cheminformatics.
How do I install Specialized Molecular Tasks in Claude Code?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill specialized-molecular-tasks -a claude-code`. Or copy the skill folder (skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks in VectorSpaceLab/AREX-Skill) into .claude/skills/specialized-molecular-tasks in your project. Claude Code loads it when a task matches its description.
How do I install Specialized Molecular Tasks in Codex?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill specialized-molecular-tasks -a codex`. Or copy the skill folder (skills/repositories/repo-skills/chemprop/sub-skills/specialized-molecular-tasks in VectorSpaceLab/AREX-Skill) into .agents/skills/specialized-molecular-tasks in your project. Codex loads it when a task matches its description.
Can I use Specialized Molecular Tasks 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 specialized-molecular-tasks -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/specialized-molecular-tasks, .gemini/skills/specialized-molecular-tasks, .github/skills/specialized-molecular-tasks and .opencode/skills/specialized-molecular-tasks in your project.
What does Specialized Molecular Tasks need to run?
Going by SKILL.md and its folder, Specialized Molecular Tasks needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Specialized Molecular Tasks 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 Specialized Molecular Tasks 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 Specialized Molecular Tasks use?
Specialized Molecular Tasks has a licence file (declared in SKILL.md) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Specialized Molecular Tasks use?
About 1.2k tokens (SKILL.md is roughly 4.8k 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 5.1k tokens, read only when the agent opens those files.
What are the alternatives to Specialized Molecular Tasks?
Skills that share tags, products or a category with Specialized Molecular Tasks: DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars), Edu Chem Reaction (wy51ai/edulab, 1.4k stars), Rowan (lamm-mit/scienceclaw, 246 stars) and Coot Rdkit (pemsley/coot, 168 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Specialized Molecular Tasks?
VectorSpaceLab (a GitHub organization) maintains it in VectorSpaceLab/AREX-Skill, which has 331 GitHub stars. The repository holds 157 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.