data/src/Plugins/Core/LocalMolLoadersSavers/OpenMoleculesPlugin.vue

<template>
    <PluginComponent :infoPayload="infoPayload" v-model="open" cancelBtnTxt="Cancel" actionBtnTxt="Open"
        @onPopupDone="onPopupDone" :isActionBtnEnabled="filesToLoad.length > 0" @onUserArgChanged="onUserArgChanged"
        @onMolCountsChanged="onMolCountsChanged">
        <FormFile ref="formFile" :multiple="true" @onFilesLoaded="onFilesLoaded" :accept="accept"
            id="formFile-openmolecules-item" />
        <!-- :isZip="true" -->
    </PluginComponent>
</template>

<script lang="ts">
import { Options, Vue } from "vue-class-component";
import { IContributorCredit, ISoftwareCredit } from "../../PluginInterfaces";
import FormFile from "@/UI/Forms/FormFile.vue";
import PluginComponent from "@/Plugins/Parents/PluginComponent/PluginComponent.vue";
import { PluginParentClass } from "@/Plugins/Parents/PluginParentClass/PluginParentClass";
import {
    IUserArgCheckbox,
    UserArg,
    UserArgType,
} from "@/UI/Forms/FormFull/FormFullInterfaces";
import { ITest } from "@/Testing/TestInterfaces";
import { fileTypesAccepts } from "@/FileSystem/LoadSaveMolModels/ParseMolModels/ParseMoleculeFiles";
import { filesToFileInfos } from "@/FileSystem/FileUtils";
import * as api from "@/Api";
import { FileInfo } from "@/FileSystem/FileInfo";
import { TestCmdList } from "@/Testing/TestCmdList";
import { dynamicImports } from "@/Core/DynamicImports";
import { delayForPopupOpenClose } from "@/Core/GlobalVars";
import { getDesaltUserArg } from "@/UI/Forms/FormFull/FormFullCommonEntries";
import {
    IGen3DOptions,
    WhichMolsGen3D,
    getGen3DUserArg,
} from "@/FileSystem/OpenBabel/OpenBabel";
import { getFileType } from "@/FileSystem/FileUtils2";
import {
    IFormatInfo,
    getFormatInfoGivenType,
} from "@/FileSystem/LoadSaveMolModels/Types/MolFormats";
import { Tag } from "@/Plugins/Core/ActivityFocus/ActivityFocusUtils";
import { makeEasyParser } from "@/FileSystem/LoadSaveMolModels/ParseMolModels/EasyParser";
/**
 * OpenMoleculesPlugin
 */
@Options({
    components: {
        PluginComponent,
        FormFile,
    },
})
export default class OpenMoleculesPlugin extends PluginParentClass {
    menuPath = "[3] File/[1] Project/[0] Open...";
    title = "Open Molecule Files";
    softwareCredits: ISoftwareCredit[] = [dynamicImports.obabelwasm.credit];
    contributorCredits: IContributorCredit[] = [];
    filesToLoad: FileInfo[] = [];
    pluginId = "openmolecules";
    intro = "Open (load) molecule file(s).";
    details = "This plugin allows the user to import molecular structure files from their local computer.";
    tags = [Tag.All];

    userArgDefaults: UserArg[] = [
        getDesaltUserArg(),
        {
            id: "hideOnLoad",
            type: UserArgType.Checkbox,
            label: "Loaded molecules should be invisible",
            description:
                "If checked, molecules will be initially invisible. You will have to toggle visibility by hand. Useful if you plan to load many molecules at once.",
            val: false,
        } as IUserArgCheckbox,
        getGen3DUserArg(
            "Method for generating 3D coordinates",
            "If your file lacks 3D coordinates (e.g., SMILES), choose how to generate those coordinates. Otherwise, this parameter is ignored. Try different methods only if your imported molecules have incorrect geometries."
        ),
    ];

    accept = fileTypesAccepts;
    hotkey = "o";
    skipLongRunningJobMsg = true;

    /**
     * Runs when the files are loaded.
     *
     * @param {FileInfo[]} files  The files that were loaded.
     */
    onFilesLoaded(files: FileInfo[]) {
        this.filesToLoad = files;
    }

    /**
     * Runs when the user presses the action button and the popup closes.
     */
    onPopupDone() {
        this.closePopup();

        if (this.filesToLoad.length > 0) {
            this.submitJobs(this.filesToLoad);
        }
    }

    /**
     * Runs before the popup opens. Good for initializing/resenting variables
     * (e.g., clear inputs from previous open).
     *
     * @param {any} payload  The payload passed to the plugin.
     * @returns {Promise<boolean | void>}  If false, the popup will not open.
     */
    async onBeforePopupOpen(payload: any): Promise<boolean | void> {
        // Below is hackish...
        setTimeout(() => {
            // Give the component time to render
            const formFile = this.$refs.formFile as FormFile;
            if (formFile) {
                formFile.clearFile();
            }
        }, delayForPopupOpenClose);

        if (payload !== undefined) {
            let fileList = payload as File[];
            // this.payload = undefined;
            const fileInfos = await filesToFileInfos(
                fileList,
                false,
                this.accept.split(",").map((a) => a.toUpperCase().substring(1))
            );
            if (fileInfos === undefined) return;

            const errorMsgs = fileInfos.filter((a) => typeof a === "string");

            if (errorMsgs.length > 0) {
                api.messages.popupError(
                    "<p>" + errorMsgs.join("</p><p>") + "</p>"
                );
            }

            const toLoad = fileInfos.filter(
                (a) => typeof a !== "string"
            ) as FileInfo[];

            this.filesToLoad = toLoad;
            this.onPopupDone();

            return false; // To prevent popup from opening.
        }
        // this.windowClosing = this.payload !== undefined;
    }

    /**
     * Every plugin runs some job. This is the function that does the job running.
     *
     * @param {FileInfo} fileInfo  Information about the molecules to save.
     * @returns {Promise<void>}  A promise that resolves when the job is
     *     done. TODO: These are wrong throughout.
     */
    runJobInBrowser(fileInfo: FileInfo): Promise<void> {
        // It's not a molmoda file (e.g., a PDB file). NOTE: When loading a
        // multi-frame file, this fileInfo contains all frames (not yet
        // separated).

        const gen3DParams = {
            whichMols: WhichMolsGen3D.OnlyIfLacks3D,
            level: this.getUserArg("gen3D"),
        } as IGen3DOptions;

        // MOL2 and SDF files can be both 2D and 3D.
        const typ = getFileType(fileInfo);
        if (typ !== undefined) {
            const frmt = getFormatInfoGivenType(typ);
            // If a format is not explicitly 2D (like SMILES) but this particular
            // file instance appears to be flat (e.g., a 2D SDF), we should
            // force 3D coordinate generation.
            if (frmt && !frmt.lacks3D) {
                try {
                    const parser = makeEasyParser(fileInfo);
                    if (parser.isFlat()) {
                        gen3DParams.whichMols = WhichMolsGen3D.All;
                    }
                } catch (error) {
                    console.warn(
                        `Could not parse ${fileInfo.name} to check if flat, proceeding with default 3D generation settings.`,
                        error
                    );
                }
            }
        }

        // Note that below not only adds to viewer, but performs necessary
        // files conversions, generates 3D geometry, etc.
        return this.addFileInfoToViewer(
            {
                fileInfo,
                desalt: this.getUserArg("desalt"),
                gen3D: gen3DParams,
                defaultTitle: "",
                tag: this.pluginId,
            },
            this.getUserArg("hideOnLoad")
        );
    }

    /**
     * Gets the test commands for the plugin. For advanced use.
     *
     * @gooddefault
     * @document
     * @returns {ITest[]}  The selenium test commands.
     */
    async getTests(): Promise<ITest[]> {
        const filesToTest = [
            // File, title-clicks,
            // ["two_files.zip", ["ligs"ompounds", "A"], "UNL:1"],
            ["four_mols.zip", ":ligs"],
            // ["ligs.smi.zip", "ligs.smi:3"],
            ["ligs.can", ":ligs"],
            ["test_old_format.molmoda", "ATP:501"],
            ["test_old_format.biotite", "ATP:501"],
            ["test_new_format.molmoda", "ATP:501"],

            // NOTE: OpenBabel parser a bit broken here. Only keeps first frame.
            ["ligs.cif", "UNL:1"],

            ["ligs.mol2", "frame3"],
            ["ligs.pdb", "UN3:1"],
            ["ligs.pdbqt", "UN3:1"],
            ["ligs.sdf", ":ligs"],
            ["ligs.smi", ":ligs"],
            ["4WP4.pdb", "TOU:101"],
            ["4WP4.pdb.zip", "TOU:101"],
            ["4WP4.pdbqt", "A"],
            ["4WP4.pqr", "TOU:101"], //
            ["4WP4.xyz", "4WP4"], //
            ["flat.mol2", "flat"],
        ];

        const tests = filesToTest.map((fileToTest, idx) => {
            const name = fileToTest[0];
            // const titles = fileToTest[1] as string[];
            // const count = (fileToTest[2] as number) - 1;
            let navSubstrng = fileToTest[1] as string;
            let stylesSubstrng = "Atoms";
            const pluginOpenCmdList = new TestCmdList().setUserArg(
                "formFile",
                "file://./src/Testing/mols/" + name,
                this.pluginId
            );

            // Make some invisible to test that functionality, though molmoda
            // files define their own visibility.
            // debugger
            if ((idx % 2 === 0) && (fileToTest[0].indexOf(".molmoda") === -1)) {
                pluginOpenCmdList.click("#hideOnLoad-openmolecules-item");
                navSubstrng = 'eye-slash'; // To check invisible.
                stylesSubstrng = 'No molecules are currently visible.';
            }

            // if (fileToTest[0].indexOf(".molmoda") !== -1) {
            //     // It's a molmoda file, so the filename won't appear in the
            //     // title. Pick something else what will.
            //     navSubstrng = "ATP:501";
            // }

            return {
                pluginOpen: () => pluginOpenCmdList,
                afterPluginCloses: () =>
                    new TestCmdList()
                        .waitUntilRegex("#styles", stylesSubstrng)
                        .openPlugin("expandall")
                        // .expandMoleculesTree(titles)
                        .waitUntilRegex("#navigator", navSubstrng),
            };
        });
        // Final test to verify error catching.
        tests.push({
            pluginOpen: () => new TestCmdList().setUserArg(
                "formFile",
                "file://./src/Testing/mols/nonsense_format.can",
                this.pluginId
            ),
            afterPluginCloses: () => new TestCmdList().waitUntilRegex(
                "#modal-simplemsg",
                "Could not process"
            ),
            // .expandMoleculesTree(titles)
            // .waitUntilRegex("#navigator", substrng),
        });

        return tests;
    }
}
</script>

<style scoped lang="scss">
.inverse-indent {
    text-indent: -1em;
    padding-left: 1em;
}
</style>