This repository offers a personal implementation of the "Molecular Notes" Second Brain system within Obsidian, designed for individuals seeking to organize their thoughts and knowledge. It provides a structured approach to note-taking, linking, and retrieval, leveraging Obsidian's features and custom Python scripts for enhanced functionality.

How It Works

The system utilizes a specific folder structure (Topics, Sources, Molecules, Authors) and a tagging convention to categorize and link notes. Core Obsidian plugins like Templates, Quick Switcher, and Graph View are essential for navigation and organization. Custom Python scripts automate tasks such as file organization, orphan note identification, and GPT-powered semantic search, enhancing the note-management workflow.

Quick Start & Requirements

• Install: Obsidian (desktop app) and clone this repository into your Obsidian vault.
• Prerequisites: Python 3, OpenAI API key (for GPT features), openai, tiktoken, tenacity, click, tabulate Python packages.
• Setup: Configure Obsidian's attachment and template folders. Enable core plugins.
• Resources: Python scripts require execution within the vault directory.
• Docs: [Molecular Notes Philosophy](https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=https://www.google.com/url?q=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