Tutorial ======== Welcome to the DeepRetro tutorial! This section focuses on using the DeepRetro GUI for Retrosynthesis Analysis and Pathway Visualization .. image:: _static/landing.png :alt: DeepRetro GUI Overview :align: center :width: 800px Getting Started -------------- Prerequisites ~~~~~~~~~~~~~ - You should have the DeepRetro backend server running - You should have an API key for backend access - Try using a modern web browser (Chrome/Firefox/Safari) Setup ~~~~~ - Navigate to `viewer/index.html` - Enter your frontend API key when prompted - Choose your analysis mode (Smart Retrosynthesis or View Pathway) Advanced Settings Configuration ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. image:: _static/advanced.png :alt: Advanced Settings Panel :align: center :width: 600px | The advanced settings panel consists of multiple options that can be configured to optimize the retrosynthesis process. While the default settings are optimum, the LLM model, backend model, and validation checks can be adjusted to suit your needs. LLM Selection:: Claude 3 Opus, Claude 3.7 Sonnet, DeepSeek, Claude 4 Opus, Claude 4 Sonnet Model Backend Selection:: USPTO, Pistachio_25, Pistachio_50, Pistachio_100, Pistachio_100+ Validation Checks:: Stability validation enable/disable, Hallucination detection settings, Chemical feasibility assessment SMILES Input and Configuration ----------------------------- Target Molecule Entry ~~~~~~~~~~~~~~~~~~~~~ The SMILES input interface allows you to enter the target molecule for retrosynthesis analysis. Here we are using Cyanostilbene as an example:: "COc1ccc(-c2ccc(/C=C(\\C#N)c3ccc(-c4ccncc4)cc3)cc2)cc1" We then click "Analyze" to start the retrosynthesis process and the system will validate the SMILES and begin pathway generation. .. image:: _static/smiles.png :alt: SMILES Input Interface :align: center :width: 600px | **Input Requirements** Please make sure you are using a valid SMILES notation (Simplified Molecular Input Line Entry System) and have a chemically feasible target molecule. Visualization ------------- Pathway Visualization ~~~~~~~~~~~~~~~~~~~~ .. image:: _static/tut11.png :alt: Pathway Visualization :align: center :width: 800px .. admonition:: Chemical Context: Cyanostilbene Synthesis :class: info The example demonstrates synthesis of a cyanostilbene derivative - a valuable chromophore with aggregation-induced emission (AIE) and strong donor–acceptor charge transfer properties. **Two-Step Synthesis Approach** - **Step 1 (Knoevenagel Condensation)**: Introduces the cyano group, forming the final conjugated system - **Step 2 (Suzuki Coupling)**: Connects the donor and acceptor aromatic units Molecular Information ~~~~~~~~~~~~~~~~~~~~ The visualization provides several interactive elements to help you explore and analyze retrosynthesis pathways. When examining molecule nodes, you can hover on any node to view detailed structural information, including molecular weight, chemical formula, and access the SMILES notation along with the step metrics. .. image:: _static/info.png :alt: Molecule Information Panel :align: center :width: 500px | For reaction edges connecting the molecules, hover your mouse over them to reveal important reaction conditions and metrics. This includes the scalability index, confidence estimate and closest literature metadata along with reaction conditions such as temperature and solvent information. .. image:: _static/reaction.png :alt: Reaction Information :align: center :width: 600px | To effectively navigate complex reaction networks, the interface offers several navigation tools. You can easily switch between different proposed pathways, zoom in and out to examine specific details, and pan across larger reaction trees. The step-by-step progression view allows you to follow the synthesis route sequentially, while the comparison feature lets you evaluate multiple pathways side by side to determine the optimal route. .. image:: _static/pathways.png :alt: Multiple Pathway Support :align: center :width: 700px Interactive Editing ------------------ Partial Re-run Analysis ~~~~~~~~~~~~~~~~~~~~~~ .. image:: _static/partial.png :alt: Partial Re-run Feature :align: center :width: 600px | **Expert chemist intervention workflow:** The expert chemist can select a specific reaction step that needs modification and generate new pathway branches starting from that modified step. This allows for targeted refinement of problematic reactions while preserving successful parts of the route. Manual Pathway Editing ~~~~~~~~~~~~~~~~~~~~~ .. image:: _static/edit.png :alt: Pathway Modification :align: center :width: 700px | **Direct Modification**: The interface enables manual condition editing, reagent substitution, and protecting group addition to refine and optimize reaction pathways. Ypu can click on "Edit Data" to directly edit the JSON file and the changes will be automatically reflected in the molecule pathway. File Management --------------- Pathway File Management ~~~~~~~~~~~~~~~~~~~~~~ .. image:: _static/view.png :alt: File Upload Interface :align: center :width: 600px To upload and visualize existing pathways, first click on the "View Pathway" tab in the interface. From there, you can select your JSON file containing the pathway data. The system will automatically load and validate the pathway information. Once loaded, you can easily view the full molecular pathway. JSON Data Export ~~~~~~~~~~~~~~~ .. image:: _static/json.png :alt: JSON Data Export :align: center :width: 600px | To export and manage pathway data, click the "JSON Result" button to view the raw data in JSON format. You can then save this data for further analysis or storage by using the download JSON button provided in the interface. Multiple Pathway Support ~~~~~~~~~~~~~~~~~~~~~~~ .. image:: _static/pathways.png :alt: Multiple Pathway Support :align: center :width: 700px The interface supports handling complex syntheses through pathway switching functionality. You can easily navigate between different proposed routes, compare their efficiency metrics, and evaluate the synthetic complexity of each pathway. This allows you to systematically assess multiple synthetic strategies and select the most promising approach for your target molecule. Troubleshooting and Best Practices --------------------------------- Troubleshooting ~~~~~~~~~~~~~~ Common Issues and Solutions ^^^^^^^^^^^^^^^^^^^^^^^^^^ - **API Connection** - Solution: Verify server running and API key correct - Verification: Check network and URL configuration - **SMILES Errors** - Solution: Validate syntax and chemical validity - Verification: Check chemical structure - **Visualization Issues** - Solution: Refresh page and check browser console - Verification: Cache Clearing - **File Upload Problems** - Solution: Verify format - Verification: Valid JSON structure Best Practices ~~~~~~~~~~~~~ Optimization Guidelines ^^^^^^^^^^^^^^^^^^^^^^ When working with DeepRetro, it's important to follow best practices for optimal results. For input validation, start with simple molecules to get familiar with the system. Always verify your SMILES syntax and check chemical validity before proceeding. For model configuration, ensure you're using appropriate settings for your specific use case. Enable any relevant validation checks, and optimize the configuration based on the types of molecules you're working with. For managing your results: - Review and validate all generated pathways thoroughly - Export any important results for future reference For advanced usage: :doc:`user_guide`, :doc:`api_reference`, :doc:`development`