User Guide for the READRetro website
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This guide provides comprehensive instructions for using all features and options available on the READRetro web interface (`https://readretro.net <https://readretro.net>`_). The official code repository for the web interface is `https://github.com/pnucolab/readretro-website <https://github.com/pnucolab/readretro-website>`_.

Viewing and Interpreting Results
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Once a prediction job is complete, the "Result Page" will display the findings. This page is designed for clear visualization and interaction.

* **Pathway Visualization (Arrows)**
    Arrows connect compounds in the predicted pathways and are color-coded to indicate the source of the prediction:

    * **Red Arrows:** Represent steps generated by the READRetro deep learning models (i.e., novel predictions not found directly in the retrieval databases). This is the default for a predicted transformation.

    * **Blue Arrows:** Indicate that the specific single-step retrosynthetic reaction was found in and retrieved from the "Reaction Retriever" database.

    * **Green Arrows:** Signify that a sequence of reactions (a partial or full pathway) was retrieved by the "Pathway Retriever," often from KEGG.

* **Information Displayed with Arrows**
    Additional biochemical context is provided above and below each arrow:

    * **EC Numbers:** Enzyme Commission numbers are displayed, classifying the potential enzymes that might catalyze the reaction. These are often clickable, linking to the `BRENDA Enzyme Database <https://www.brenda-enzymes.org/>`_ for detailed enzyme information.

    * **KEGG Pathway Information:** If applicable, links or identifiers for relevant KEGG pathways are shown, allowing users to explore the broader biological context. These typically link to the `KEGG PATHWAY database <https://www.genome.jp/kegg/pathway.html>`_.

* **Compound Representation (Cards)**
    Each molecule in the pathway is shown as an interactive card with the following features and color-coding:

    * **Default Card Color:** Typically red (or a neutral color) for newly predicted intermediates.

    * **Blue Card Color:** Indicates that the molecule is a known compound found in the `KEGG COMPOUND database <https://www.genome.jp/kegg/compound/>`_.

    * **Yellow Card Color:** Applied when a user clicks on a compound card to highlight it, making it easier to trace its involvement across different suggested pathways.

    * **Information on Cards:**
        * **SMILES Notation:** The SMILES string of the compound.
        * **KEGG Entry:** If the compound is in KEGG, its KEGG ID is displayed and is clickable, redirecting to the specific entry in the KEGG COMPOUND database.
        * **Structural Diagram:** A 2D chemical structure image of the molecule.

* **Interactive Features**
    The Result Page offers several tools to aid in analysis:

    * **Highlighting Compounds:** Clicking on a compound card will highlight that compound across all displayed pathways.

    * **Changing Pathway Display Direction:** Options may be available to view pathways in the retrosynthetic (product to precursors) or biosynthetic (precursors to product) direction.

* **Saving and Re-accessing Results**
    You can save and revisit your prediction results:

    * **Unique Result Link:** Each prediction generates a unique web link. The link follows the format ``https://readretro.net/result/`` followed by your specific **[job id]** (e.g., ``https://readretro.net/result/d0bc0da8ebb245bb87e8aa161fbbd2d6``). You can bookmark or share this link to access the specific result page again later.

    * **Download Result Button:** A "Download result" button allows you to download the predicted pathway information as a  **.txt** file for offline storage, sharing, or further analysis.