pymol-skills

cc-toolkit

Unified Claude Code plugin marketplace for development workflows, scientific content creation, and document processing.

Overview

cc-toolkit is a modular plugin marketplace following the official Claude Code plugin system. Each plugin is self-contained and can include skills, agents, hooks, and commands.

Repository Structure

cc-toolkit/
├── .claude-plugin/
│   └── marketplace.json           # Plugin registry
├── dev-skills/                     # Development workflow plugin
│   ├── .claude-plugin/
│   │   └── plugin.json
│   └── skills/
│       ├── problem-solving-cycle/
│       └── step-workflow/
├── creator-skills/                 # Scientific content creation plugin
│   ├── .claude-plugin/
│   │   └── plugin.json
│   └── skills/
│       ├── sci-figure-format/
│       └── sci-slides/
├── doc-skills/                     # Document processing plugin
│   ├── .claude-plugin/
│   │   └── plugin.json
│   ├── skills/
│   │   ├── docling-pdf/
│   │   └── paper-rename/
│   └── agents/
│       ├── paper-reader.md
│       └── paper-consolidator.md
├── core-hooks/                     # Safety and workflow hooks plugin
│   ├── .claude-plugin/
│   │   └── plugin.json
│   ├── hooks/
│   │   └── hooks.json
│   └── scripts/
│       ├── safety_guard.py
│       ├── pre_git_hook.py
│       ├── post_tool_use.py
│       └── system_notification.py
├── productivity-skills/            # Personal productivity plugin
│   ├── .claude-plugin/
│   │   └── plugin.json
│   └── skills/
│       ├── calendar-manager/
│       └── reminder-manager/
└── pymol-skills/                   # PyMOL molecular visualization plugin
    ├── .claude-plugin/
    │   └── plugin.json
    ├── skills/
    │   └── pymol-mcp/
    └── commands/
        └── setup.md

Available Plugins

Development Skills (dev-skills)

Development workflow automation and systematic problem-solving.

Skills:

• problem-solving-cycle: Systematic development workflow from brainstorming to PR merge, including issue creation, branch management, and cleanup
• step-workflow: Step-based file naming and folder organization using numbered prefixes (01_, 02_, 03_) for clear workflow order

Creator Skills (creator-skills)

Scientific content creation for figures and presentations.

Skills:

• sci-figure-format: Publication-quality scientific figure formatting for major journals (Nature, Science, ACS, RSC)
• sci-slides: Academic presentation slide creation for STEM fields

Document Skills (doc-skills)

Document processing and AI-accessible content extraction.

Skills:

• docling-pdf: PDF to markdown conversion using IBM's Docling library
• paper-rename: Intelligent PDF renaming based on extracted titles and metadata

Agents:

• paper-reader: Analyzes research papers and answers questions about content
• paper-consolidator: Consolidates multiple paper analysis outputs into unified reports

Core Hooks (core-hooks)

Safety guards and workflow enforcement hooks.

Hooks:

• safety_guard.py: Blocks dangerous rm commands and .env file access
• pre_git_hook.py: Enforces branch naming conventions, blocks bulk git add, prevents Claude attribution in commits
• post_tool_use.py: Logs tool executions to logs/post_tool_use.json
• system_notification.py: Plays sound notifications on task completion

Productivity Skills (productivity-skills)

Personal productivity automation using macOS Calendar and Reminders.

Skills:

• calendar-manager: Manage macOS Calendar events via EventKit CLI
• reminder-manager: Manage macOS Reminders via EventKit CLI

PyMOL Skills (pymol-skills)

PyMOL molecular visualization control via MCP server.

Skills:

• pymol-mcp: Control PyMOL through natural language for protein visualization and structural analysis

Commands:

• /pymol-skills:setup: Installation instructions for PyMOL socket plugin

Plugin System Benefits

1. Modular: Each plugin is self-contained and portable
2. Scalable: Easy to add new skills, agents, hooks, or commands to any plugin
3. Standard: Follows official Claude Code plugin system architecture
4. Maintainable: Clear separation of concerns between plugins
5. Shareable: Individual plugins can be distributed independently

Usage

As a Marketplace

Install the entire marketplace by linking to this repository in your Claude Code configuration.

Individual Plugins

Each plugin can be used independently by referencing its directory:

• ./dev-skills
• ./creator-skills
• ./doc-skills
• ./core-hooks
• ./productivity-skills
• ./pymol-skills