Welcome to the exciting world of molecular design with REINVENT! Whether you are venturing into de novo design, scaffold hopping, or molecule optimization, this user-friendly guide will walk you through the essential steps to get you started with REINVENT. Below we will cover installation, usage, and troubleshooting tips to make your experience smooth.

Installation of REINVENT

Let’s dive into how to install REINVENT on your system. Follow these steps:

• Clone the Git repository to your local system.
• Install a compatible version of Python. It is recommended to use Conda:

conda create --name reinvent4 python=3.10
conda activate reinvent4

• Change directory to the repository and install dependencies from the lockfile:

pip install -r requirements-linux-64.lock

• Optionally, for AMD GPUs on Linux, install the ROCm PyTorch version:

pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/rocm5.7

• To install the tool:

pip install --no-deps .

• Test the installation:

reinvent --help

Basic Usage of REINVENT

Once you have installed REINVENT, it’s time to put it to work. Here’s how to use it effectively:

• Start by using the command:

reinvent -l sampling.log sampling.toml

• Here, sampling.toml is your configuration file. The log can either be written to a file or displayed on the screen.
• You can find sample configuration files in the repository that will need to be adjusted based on your needs.
• For a more user-friendly configuration format, TOML is recommended over JSON.

Understanding the Reinvention Code – An Analogy

Think of REINVENT as a master chef who creates exquisite dishes. Just like a chef relies on specific ingredients (code) to create a new recipe (molecule), REINVENT uses its codebase to design novel molecules. The chef sources high-quality ingredients (input molecules), combines them per the recipe (properties defined in TOML), and produces a unique dish (optimized molecules). Each task—from selecting the right ingredients to perfecting the cooking has its specific instructions, much like the various functions and commands in the REINVENT software.

Troubleshooting Tips

Even the best chefs occasionally face challenges in the kitchen. Here are some common issues you may encounter with REINVENT and their solutions:

• Installation errors: Ensure that all dependencies are installed correctly. Double-check your Python version and try reinstalling.
• Command not found: Make sure that REINVENT is added to your PATH. Verify this by running reinvent --help again.
• Configuration errors: If your TOML or JSON files are not working, check their format, as these formats are sensitive to minor changes.

If you encounter issues you cannot resolve, don’t hesitate to reach out. For more insights, updates, or to collaborate on AI development projects, stay connected with fxis.ai.

Conclusion

At fxis.ai, we believe that such advancements are crucial for the future of AI, as they enable more comprehensive and effective solutions. Our team is continually exploring new methodologies to push the envelope in artificial intelligence, ensuring that our clients benefit from the latest technological innovations. Enjoy your molecular design journey with REINVENT!