data/src/Plugins/Core/RemoteMolLoaders/LoadAlphaFoldPlugin.vue

<template>
    <PluginComponent v-model="open" :infoPayload="infoPayload" actionBtnTxt="Load" @onPopupDone="onPopupDone"
        @onUserArgChanged="onUserArgChanged" @onMolCountsChanged="onMolCountsChanged"></PluginComponent>
</template>

<script lang="ts">
import { Options } from "vue-class-component";
import { loadRemoteToFileInfo } from "./RemoteMolLoadersUtils";
import {
    IContributorCredit,
    ISoftwareCredit,
} from "@/Plugins/PluginInterfaces";
import * as api from "@/Api";
import { UserArg, IUserArgText } from "@/UI/Forms/FormFull/FormFullInterfaces";
import { PluginParentClass } from "@/Plugins/Parents/PluginParentClass/PluginParentClass";
import PluginComponent from "@/Plugins/Parents/PluginComponent/PluginComponent.vue";
import { ITest } from "@/Testing/TestInterfaces";
import { TestCmdList } from "@/Testing/TestCmdList";
import { Tag } from "@/Plugins/Core/ActivityFocus/ActivityFocusUtils";
import { FileInfo } from "@/FileSystem/FileInfo";

/**
 * LoadAlphaFoldPlugin
 */
@Options({
    components: {
        PluginComponent,
    },
})
export default class LoadAlphaFoldPlugin extends PluginParentClass {
    menuPath = "File/Import/[4] AlphaFold...";
    title = "Load AlphaFold Structure";
    softwareCredits: ISoftwareCredit[] = [];
    contributorCredits: IContributorCredit[] = [
        // {
        //   name: "Jacob D. Durrant",
        //   url: "http://durrantlab.com/",
        // },
        {
            name: "AlphaFold Protein Structure Database",
            url: "https://alphafold.ebi.ac.uk/",
            citations: [
                {
                    title: "AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models",
                    authors: ["Varadi, Mihaly", "Anyango, Stephen"],
                    journal: "Nucleic Acids Res.",
                    volume: 50,
                    issue: "D1",
                    year: 2022,
                    pages: "D439-D444",
                },
                {
                    title: "Highly accurate protein structure prediction with AlphaFold",
                    authors: ["Jumper, John", "Evans, Richard"],
                    journal: "Nature",
                    volume: 596,
                    issue: 7873,
                    year: 2021,
                    pages: "583-589",
                },
            ],
        },
    ];
    pluginId = "loadalphafold";
    skipLongRunningJobMsg = true;
    intro = `Load a protein from the <a href="https://alphafold.ebi.ac.uk/" target="_blank">AlphaFold Protein Structure Database</a> of predicted protein structures.`;
    details = "This plugin retrieves AlphaFold-predicted protein models using a UniProt accession number.";
    tags = [Tag.All];

    userArgDefaults: UserArg[] = [
        {
            id: "uniprot",
            label: "",
            val: "",
            placeHolder: "UniProt Accession (e.g., P86927)...",
            description: `The UniProt Accession of the protein structure. Search the
      <a href="https://alphafold.ebi.ac.uk/" target="_blank">AlphaFold Protein Structure Database</a> if you're uncertain.`,
            filterFunc: (uniprot: string): string => {
                // https://www.uniprot.org/help/accession_numbers
                uniprot = uniprot.toUpperCase();
                uniprot = uniprot.replace(/[^A-Z\d]/g, "");
                uniprot = uniprot.substring(0, 10);
                return uniprot;
            },
            validateFunc: (uniprot: string): boolean => {
                // https://www.uniprot.org/help/accession_numbers
                let r =
                    /[OPQ]\d[A-Z\d]{3}\d|[A-NR-Z]\d([A-Z][A-Z\d]{2}\d){1,2}/;
                return uniprot.match(r) !== null;
            },
        } as IUserArgText,
    ];
    /**
     * Runs when the user presses the action button and the popup closes.
     */
    onPopupDone() {
        let uniprot = this.getUserArg("uniprot");
        this.submitJobs([uniprot]);
    }

    /**
     * Every plugin runs some job. This is the function that does the job running.
     *
     * @param {string} uniprot  The requested uniprot id.
     * @returns {Promise<void>}  A promise that resolves the file object.
     */
    async runJobInBrowser(uniprot: string): Promise<void> {
        const errorMsg =
            "Could not load AlphaFold model with UniProt ID " +
            uniprot +
            ". Are you sure the AlphaFold Protein Structure Database includes a model with this ID?";
        const spinnerId = api.messages.startWaitSpinner();
        try {
            // Use local PHP proxy to bypass CORS on the summary endpoint
            const summaryUrl = `https://molmoda.org/alphafold-proxy.php?id=${uniprot.toUpperCase()}`;
            const fileInfo = await loadRemoteToFileInfo(summaryUrl);

            let data = fileInfo.contents;
            if (typeof data === "string") {
                data = JSON.parse(data);
            }

            const structures = data.structures;
            if (structures && structures.length > 0) {
                const summary = structures[0].summary;
                const modelUrl = summary.model_url;

                if (modelUrl) {
                    // Extract filename from the URL (e.g. AF-P86927-F1-model_v6.cif)
                    const filename = modelUrl.split("/").pop();

                    if (!filename) throw new Error("Invalid model URL format.");

                    // Use local PHP proxy to download the file (also bypasses CORS if file server restricts it)
                    const proxyFileUrl = `https://molmoda.org/alphafold-proxy.php?file=${filename}`;
                    const modelFileInfo = await loadRemoteToFileInfo(proxyFileUrl);

                    // Ensure the file info has the correct name/extension for the loader
                    modelFileInfo.name = filename;

                    await this.addFileInfoToViewer({
                        fileInfo: modelFileInfo,
                        tag: this.pluginId,
                    });
                } else {
                    throw new Error("No model URL found in structure summary.");
                }
            } else {
                throw new Error("No structures found for this UniProt ID.");
            }
        } catch (err: any) {
            console.log(err);
            api.messages.popupError(errorMsg);
            // throw err;
        } finally {
            api.messages.stopWaitSpinner(spinnerId);
        }
    }
    /**
     * Gets the test commands for the plugin. For advanced use.
     *
     * @gooddefault
     * @document
     * @returns {ITest[]}  The selenium test commands.
     */
    async getTests(): Promise<ITest[]> {
        return [
            {
                pluginOpen: () => new TestCmdList().setUserArg(
                    "uniprot",
                    "P86927",
                    this.pluginId
                ),
                afterPluginCloses: () => new TestCmdList().waitUntilRegex(
                    "#navigator",
                    "P86927"
                ),

                // .waitUntilRegex("#styles", "Protein")
                // .waitUntilRegex("#log", 'Job loadalphafold.*? ended')
            },

            // Below tests errors
            {
                pluginOpen: () => new TestCmdList().setUserArg(
                    "uniprot",
                    "P11111",
                    this.pluginId
                ),
                afterPluginCloses: () => new TestCmdList().waitUntilRegex(
                    "#modal-simplemsg",
                    "Could not load"
                ),
            },
        ];
    }
}
</script>
<style scoped lang="scss">
.inverse-indent {
    text-indent: -1em;
    padding-left: 1em;
}
</style>