data/src/Plugins/Optional/FPocketWeb/FPocketWebPlugin.vue

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

<script lang="ts">
import { FileInfo } from "@/FileSystem/FileInfo";
import { checkProteinLoaded } from "@/Plugins/CheckUseAllowedUtils";
import PluginComponent from "@/Plugins/Parents/PluginComponent/PluginComponent.vue";
import { PluginParentClass } from "@/Plugins/Parents/PluginParentClass/PluginParentClass";
import {
    IContributorCredit,
    ISoftwareCredit,
    Licenses,
} from "@/Plugins/PluginInterfaces";
import {
    UserArg,
    UserArgType,
    IUserArgAlert,
    IUserArgCheckbox,
    IUserArgGroup,
    IUserArgMoleculeInputParams,
    IUserArgNumber,
    IUserArgSelect,
} from "@/UI/Forms/FormFull/FormFullInterfaces";
import { MoleculeInput } from "@/UI/Forms/MoleculeInputParams/MoleculeInput";
import Alert from "@/UI/Layout/Alert.vue";
import { Options } from "vue-class-component";
import { TreeNode } from "@/TreeNodes/TreeNode/TreeNode";
import {
    ITreeNodeData,
    TreeNodeDataType,
    TreeNodeType,
    // IBox,
    SelectedType,
    TableHeaderSort,
} from "@/UI/Navigation/TreeView/TreeInterfaces";
import { randomPastelColor } from "@/Core/Styling/Colors/ColorUtils";
import { messagesApi } from "@/Api/Messages";
import { TreeNodeList } from "@/TreeNodes/TreeNodeList/TreeNodeList";
import { ITest } from "@/Testing/TestInterfaces";
import { TestCmdList } from "@/Testing/TestCmdList";
import { FPocketWebQueue } from "./FPocketWebQueue";
import { getSetting } from "@/Plugins/Core/Settings/LoadSaveSettings";
import { dynamicImports } from "@/Core/DynamicImports";
import { Tag } from "@/Plugins/Core/ActivityFocus/ActivityFocusUtils";
import { ISelAndStyle } from "@/Core/Styling/SelAndStyleInterfaces";
import { IColorScheme } from "@/Core/Styling/Colors/ColorInterfaces";
import { parseAndLoadMoleculeFile } from "@/FileSystem/LoadSaveMolModels/ParseMolModels/ParseMoleculeFiles";

/**
 * FPocketWebPlugin
 */
@Options({
    components: {
        PluginComponent,
        Alert,
    },
})
export default class FPocketWebPlugin extends PluginParentClass {
    menuPath = "Proteins/[7] Detect Pockets...";
    title = "Pocket Detection";
    tags = [Tag.Docking];
    softwareCredits: ISoftwareCredit[] = [
        dynamicImports.fpocketweb.credit,
        {
            name: "fpocket",
            url: "https://github.com/Discngine/fpocket",
            license: Licenses.MIT,
            citations: [
                {
                    title: "Fpocket: An open source platform for ligand pocket detection",
                    authors: [
                        "Le Guilloux, V.",
                        "Schmidtke, P.",
                        "Tuffery, P.",
                    ],
                    journal: "BMC Bioinformatics",
                    year: 2009,
                    volume: 10,
                    issue: 1,
                    pages: "1-1",
                },
            ],
        },
    ];
    contributorCredits: IContributorCredit[] = [
        // {
        //     name: "Jacob D. Durrant",
        //     url: "http://durrantlab.com/",
        // },
    ];
    pluginId = "fpocketweb";

    intro = `Identify small-molecule binding pockets on protein surfaces.`;
    details = `This plugin also calculates pocket properties using the fpocket algorithm (FPocketWeb).`;
    msgOnJobsFinished =
        "Finished detecting pockets (see molecular viewer). Some pockets might be hidden. You can toggle visibility using the Navigator panel. The Data panel includes additional information about the detected pockets (e.g., volume).";

    userArgDefaults: UserArg[] = [
        {
            // type: UserArgType.MoleculeInputParams,
            id: "makemolinputparams",
            val: new MoleculeInput({
                considerCompounds: false,
                considerProteins: true,
                proteinFormat: "pdb",
                includeSolventAsProtein: false,
                allowUserToToggleIncludeSolventAsProtein: false,
                includeMetalsAsProtein: true,
                allowUserToToggleIncludeMetalsAsProtein: true,
            }),
        } as IUserArgMoleculeInputParams,
        {
            id: "providePseudoAtoms",
            type: UserArgType.Checkbox,
            label: "Provide pocket-filling pseudo atoms for visualization",
            val: false,
        } as IUserArgCheckbox,
        {
            id: "pocketDetectionParams",
            type: UserArgType.Group,
            label: "Optional Pocket Detection Parameters",
            val: [
                {
                    id: "warning",
                    type: UserArgType.Alert,
                    val: "Unless you are an expert user, these advanced parameters are best left unmodified",
                    alertType: "warning",
                } as IUserArgAlert,
                {
                    id: "min_alpha_size",
                    type: UserArgType.Number,
                    label: "Minimum radius of an alpha-sphere",
                    val: 3.4,
                } as IUserArgNumber,

                {
                    id: "max_alpha_size",
                    type: UserArgType.Number,
                    label: "Maximum radius of an alpha-sphere",
                    val: 6.2,
                } as IUserArgNumber,

                {
                    id: "clustering_distance",
                    type: UserArgType.Number,
                    label: "Distance threshold for clustering algorithm",
                    val: 2.4,
                } as IUserArgNumber,

                {
                    id: "clustering_method",
                    type: UserArgType.Select,
                    label: "Clustering method for grouping voronoi vertices",
                    options: [
                        {
                            description: "s : single linkage clustering",
                            val: "s",
                        },
                        {
                            description: "m : complete linkage clustering",
                            val: "m",
                        },
                        {
                            description: "a : average linkage clustering",
                            val: "a",
                        },
                    ],
                    val: "s",
                } as IUserArgSelect,

                {
                    id: "clustering_measure",
                    type: UserArgType.Select,
                    label: "Distance measure for clustering",
                    options: [
                        { description: "e : euclidean distance", val: "e" },
                        { description: "b : Manhattan distance", val: "b" },
                    ],
                    val: "e",
                } as IUserArgSelect,

                {
                    id: "min_spheres_per_pocket",
                    type: UserArgType.Number,
                    label: "Minimum number of a-sphere per pocket",
                    val: 15,
                } as IUserArgNumber,

                {
                    id: "ratio_apol_spheres_pocket",
                    type: UserArgType.Number,
                    label: "Minimum proportion of apolar sphere in a pocket (remove otherwise)",
                    val: 0.0,
                } as IUserArgNumber,

                {
                    id: "number_apol_asph_pocket",
                    type: UserArgType.Number,
                    label: "Minimum number of apolar neighbor for an a-sphere to be considered as apolar",
                    val: 3,
                } as IUserArgNumber,

                {
                    id: "iterations_volume_mc",
                    type: UserArgType.Number,
                    label: "Number of Monte-Carlo iterations for calculating each pocket volume",
                    val: 300,
                } as IUserArgNumber,
            ],
            startOpened: false,
        } as IUserArgGroup,
    ];

    /**
     * Runs before the popup opens. Starts importing the modules needed for the
     * plugin.
     */
    async onBeforePopupOpen() {
        // You're probably going to need fpocketweb
        // dynamicImports.fpocketweb.module;
    }

    /**
     * Check if this plugin can currently be used.
     *
     * @returns {string | null}  If it returns a string, show that as an error
     *     message. If null, proceed to run the plugin.
     */
    checkPluginAllowed(): string | null {
        return checkProteinLoaded();
    }

    /**
     * Runs when the user presses the action button and the popup closes.
     */
    async onPopupDone(): Promise<void> {
        const pdbFiles: FileInfo[] = this.getUserArg("makemolinputparams");

        const userArgsNotFpocketArgs = [
            "providePseudoAtoms",
            "makemolinputparams",
            "warning",
        ];

        // Convert to IFpocketParams format
        const fpocketParams: { [key: string]: any } = {}; // IFpocketParams
        this.getUserArgsFlat().forEach((arg) => {
            if (userArgsNotFpocketArgs.indexOf(arg.id) === -1) {
                fpocketParams[arg.id] = (arg as UserArg).val;
            }
        });

        // Combine into payloads
        const payloads: any[] = pdbFiles.map((pdbFile) => {
            // Put path in auxData
            pdbFile.auxData = pdbFile.treeNode?.descriptions.pathName(":");

            // Remove treenodes from payloads because doesn't serialize.
            delete pdbFile.treeNode;
            return {
                pdbFile,
                fpocketParams,
            };
        });

        const maxProcs = await getSetting("maxProcs");

        try {
            const fpocketOuts: any = await new FPocketWebQueue(
                "fpocket",
                payloads,
                maxProcs,
                undefined,
                1
            ).done;

            // Add the original name and whether to return points too. NOTE:
            // This is per protein.
            fpocketOuts.forEach((fpocketOut: any, i: number) => {
                fpocketOut.origFileName = pdbFiles[i].name;
                // fpocketOut.label =
                //     pdbFiles[i].treeNode?.descriptions.pathName(":");
                fpocketOut.label = pdbFiles[i].auxData;
                fpocketOut.providePseudoAtoms = (
                    this.userArgs.filter(
                        (u) => u.id === "providePseudoAtoms"
                    )[0] as UserArg
                ).val;
            });

            this.submitJobs(fpocketOuts);
            return;
        } catch (err: any) {
            // Intentionally not rethrowing error here.
            messagesApi.popupError(
                `<p>FPocketWeb threw an error, likely because it could not detect any pockets.</p><p>Error details: ${err.message}</p>`
            );
        }
    }

    /**
     * Every plugin runs some job. This is the function that does the job
     * running.
     *
     * @param {any} payload     The user arguments to pass to the "executable."
     *                          Contains compound information.
     * @returns {Promise<void>}  A promise that resolves when the job is done.
     */
    async runJobInBrowser(payload: any): Promise<void> {
        if (payload.stdErr !== "") {
            throw new Error(payload.stdErr);
        }

        const outPdbFileTxt = payload.outPdbFileTxt;
        // const stdOut = payload.stdOut;
        const stdErr = payload.stdErr;
        const pocketProps = payload.pocketProps;
        const providePseudoAtoms = payload.providePseudoAtoms;

        if (stdErr !== "") {
            console.warn(stdErr);
        }

        const promises = [
            parseAndLoadMoleculeFile({
                fileInfo: new FileInfo({
                    name: payload.origFileName,
                    contents: outPdbFileTxt,
                }),
                tag: this.pluginId,
                addToTree: false
            }),
            Promise.resolve(pocketProps),
        ];

        const payload2: any[] = await Promise.all(promises);
        const outPdbFileTreeNodeList = payload2[0] as TreeNodeList | void;
        const pocketProps2 = payload2[1] as any[];

        if (outPdbFileTreeNodeList === undefined || !outPdbFileTreeNodeList) {
            return;
        }

        const outPdbFileTreeNode = outPdbFileTreeNodeList.get(0);
        outPdbFileTreeNode.title = "Pockets: " + payload.label;

        // const numInitiallyVisible = 5;

        // Update the compounds (names, style)
        // let firstNodeId = "";

        // Make everything visible to start.
        outPdbFileTreeNode.visible = true;

        if (outPdbFileTreeNode.nodes) {
            await this._addBoxes(outPdbFileTreeNode, pocketProps2);

            await this._processPocketPseudoAtoms(
                outPdbFileTreeNode,
                providePseudoAtoms
            );

            // Title "Compounds"
            const compoundsNode = outPdbFileTreeNode.nodes
                .lookup([TreeNodeType.Compound])
                .get(0);
            compoundsNode.title = "Pockets";
            // compoundsNode.visible = true;

            // Hide anything that isn't Pockets, since it's probably also in
            // another molecule.
            for (const node of outPdbFileTreeNode.nodes._nodes) {
                if (node.title !== "Pockets") {
                    node.visible = false;
                }
                // else {
                //     firstNodeId = node.id as string;
                // }
            }
        }

        // Remove protein
        outPdbFileTreeNode.nodes = outPdbFileTreeNode.nodes?.filter(
            (treeNode) => treeNode.type !== TreeNodeType.Protein
        );

        outPdbFileTreeNode.addToMainTree(this.pluginId);

        // this.$store.commit("pushToMolecules", outPdbFileTreeNode);

        // this.$nextTick(() => {
        //     selectProgramatically(firstNodeId);
        // });
        return;
    }

    /**
     * Adds boxes surrounding the pockets to the tree.
     *
     * @param {TreeNode} outPdbFileTreeNode    The tree node to add the boxes to.
     * @param {any[]} pocketProps              The properties of the pockets.
     */
    async _addBoxes(outPdbFileTreeNode: TreeNode, pocketProps: any[]) {
        const numInitiallyVisible = await getSetting("initialCompoundsVisible");
        const pseudoAtomNodes = outPdbFileTreeNode.nodes?.lookup([
            TreeNodeType.Compound,
            "*",
            "*",
        ]);

        // Get the pocket-box regions and properties
        const shapesNode = new TreeNode({
            title: "Pocket Boxes",
            type: TreeNodeType.Region,
            treeExpanded: true,
            visible: true,
            selected: SelectedType.False,
            focused: false,
            viewerDirty: true,
            nodes: new TreeNodeList([]),
        });

        pseudoAtomNodes?.forEach((node: TreeNode, idx: number) => {
            const box = node.getBoxRegion();
            box.opacity = 0.9;
            box.color = randomPastelColor();

            const newNode = new TreeNode({
                title: "Pocket" + (idx + 1).toString() + "Box",
                type: TreeNodeType.Region,
                region: box,
                treeExpanded: false,
                visible: idx < numInitiallyVisible,
                selected: SelectedType.False,
                focused: false,
                viewerDirty: true,
                data: {
                    "FPocketWeb Properties": {
                        data: pocketProps[idx],
                        type: TreeNodeDataType.Table,
                        treeNodeId: node.id,
                        headerSort: TableHeaderSort.None,
                    } as ITreeNodeData,
                },
            });

            shapesNode.nodes?.push(newNode);
        });

        const ps = outPdbFileTreeNode.nodes
            ?.lookup(TreeNodeType.Compound)
            .get(0);
        if (ps && ps.nodes) {
            // Insert at top
            ps.nodes._nodes.splice(0, 0, shapesNode);
        }

        // return pseudoAtomNodes;
    }

    /**
     * Processes the pseudo atoms in the tree.
     *
     * @param {TreeNode} outPdbFileTreeNode    The tree node to process.
     * @param {boolean} providePseudoAtoms     Whether to provide pseudo atoms.
     */
    async _processPocketPseudoAtoms(
        outPdbFileTreeNode: TreeNode,
        providePseudoAtoms: boolean
    ): Promise<void> {
        if (outPdbFileTreeNode.nodes === undefined) {
            return;
        }

        const numInitiallyVisible = await getSetting("initialCompoundsVisible");

        // Get the index of the node with type compound
        const compoundNodeIdx = outPdbFileTreeNode.nodes._nodes.findIndex(
            (node: TreeNode) => node.type === TreeNodeType.Compound
        );

        if (!providePseudoAtoms) {
            // Remove it

            // eslint-disable-next-line @typescript-eslint/ban-ts-comment
            // @ts-ignore  // TODO: Fix this
            outPdbFileTreeNode.nodes._nodes[compoundNodeIdx].nodes._nodes =
                outPdbFileTreeNode.nodes._nodes[
                    compoundNodeIdx
                ].nodes?._nodes.slice(0, -1);

            return;
        }

        // Title "Compounds"
        const pseudoAtomNodeTree =
            outPdbFileTreeNode.nodes._nodes[compoundNodeIdx];

        if (!pseudoAtomNodeTree) {
            return;
        }

        if (!pseudoAtomNodeTree.nodes) {
            return;
        }

        pseudoAtomNodeTree.nodes.get(1).title = "Pocket Pseudo Atoms";

        // eslint-disable-next-line sonarjs/no-empty-collection
        pseudoAtomNodeTree.nodes
            .get(1)
            .nodes?.forEach((node: TreeNode, idx: number) => {
                // Should be surface
                node.styles = [
                    {
                        surface: {
                            color: randomPastelColor(),
                            opacity: 0.9,
                        } as IColorScheme,
                    } as ISelAndStyle,
                ];

                // Rename it too. TODO: This should be the region...
                node.title = "PocketPseudoAtoms" + (idx + 1);

                // Hide unless it's the first few ones.
                if (idx >= numInitiallyVisible) {
                    node.visible = false;
                }

                node.type = TreeNodeType.Other;
            });
    }

    /**
     * Gets the test commands for the plugin. For advanced use.
     *
     * @gooddefault
     * @document
     * @returns {ITest[]}  The selenium test commands.
     */
    async getTests(): Promise<ITest[]> {
        return [
            // Including pseudo atoms
            {
                beforePluginOpens: () => new TestCmdList().loadExampleMolecule(),
                pluginOpen: () => new TestCmdList().click(
                    "#providePseudoAtoms-fpocketweb-item"
                ),
                afterPluginCloses: () => new TestCmdList()
                    .openPlugin("expandall")
                    .waitUntilRegex(
                        "#navigator",
                        "PocketPseudoAtoms1"
                    ),
            },
            // without pseudo atoms
            {
                beforePluginOpens: () => new TestCmdList().loadExampleMolecule(),
                afterPluginCloses: () => new TestCmdList()
                    .openPlugin("expandall")
                    .waitUntilRegex(
                        "#navigator",
                        "Pocket1Box"
                    ),
            },
        ];
    }
}
</script>

<style scoped lang="scss"></style>