jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/dist/ProteinView/structureModel.d.ts

@@ -0,0 +1,183 @@
+import { Region as IRegion } from '@jbrowse/core/util/types';
+import { Instance } from 'mobx-state-tree';
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { PairwiseAlignment } from '../mappings';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+type LGV = LinearGenomeViewModel;
+type MaybeLGV = LGV | undefined;
+type MaybePairwiseAlignment = PairwiseAlignment | undefined;
+type StructureModel = Awaited<ReturnType<PluginContext['builders']['structure']['createModel']>>;
+declare const Structure: import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
+    url: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    data: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    pairwiseAlignment: import("mobx-state-tree").IType<MaybePairwiseAlignment, MaybePairwiseAlignment, MaybePairwiseAlignment>;
+    /**
+     * #property
+     */
+    feature: import("mobx-state-tree").IType<SimpleFeatureSerialized | undefined, SimpleFeatureSerialized | undefined, SimpleFeatureSerialized | undefined>;
+    /**
+     * #property
+     */
+    userProvidedTranscriptSequence: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    /**
+     * #volatile
+     */
+    model: StructureModel | undefined;
+    /**
+     * #volatile
+     */
+    clickGenomeHighlights: IRegion[];
+    /**
+     * #volatile
+     */
+    hoverGenomeHighlights: IRegion[];
+    /**
+     * #volatile
+     */
+    clickPosition: {
+        structureSeqPos: number;
+        code: string;
+        chain: string;
+    } | undefined;
+    /**
+     * #volatile
+     */
+    hoverPosition: {
+        structureSeqPos?: number;
+        code?: string;
+        chain?: string;
+    } | undefined;
+    /**
+     * #volatile
+     */
+    pairwiseAlignmentStatus: string;
+    /**
+     * #volatile
+     */
+    structureSequences: string[] | undefined;
+} & {
+    /**
+     * #action
+     */
+    setModel(model: StructureModel): void;
+    setSequences(str?: string[]): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly connectedView: MaybeLGV;
+} & {
+    /**
+     * #action
+     */
+    setClickedPosition(arg?: {
+        structureSeqPos: number;
+        code: string;
+        chain: string;
+    }): void;
+    /**
+     * #action
+     */
+    setClickGenomeHighlights(r: IRegion[]): void;
+    /**
+     * #action
+     */
+    clearClickGenomeHighlights(): void;
+    /**
+     * #action
+     */
+    setHoverGenomeHighlights(r: IRegion[]): void;
+    /**
+     * #action
+     */
+    clearHoverGenomeHighlights(): void;
+    /**
+     * #action
+     */
+    setHoveredPosition(arg?: {
+        structureSeqPos?: number;
+        chain?: string;
+        code?: string;
+    }): void;
+    /**
+     * #action
+     */
+    setAlignment(r?: PairwiseAlignment): void;
+    /**
+     * #action
+     */
+    setAlignmentStatus(str: string): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly structureSeqToTranscriptSeqPosition: Record<string, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly transcriptSeqToStructureSeqPosition: Record<string, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly structurePositionToAlignmentMap: Record<string, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly transcriptPositionToAlignmentMap: Record<string, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly pairwiseAlignmentToTranscriptPosition: Record<number, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly pairwiseAlignmentToStructurePosition: Record<number, number> | undefined;
+    /**
+     * #getter
+     */
+    readonly clickString: string;
+    /**
+     * #getter
+     */
+    readonly hoverString: string;
+    /**
+     * #getter
+     */
+    readonly genomeToTranscriptSeqMapping: {
+        g2p: Record<number, number | undefined>;
+        p2g: Record<number, number | undefined>;
+        refName: string;
+        strand: number;
+    } | undefined;
+    /**
+     * #getter
+     */
+    readonly structureSeqHoverPos: number | undefined;
+    /**
+     * #getter
+     */
+    readonly exactMatch: boolean;
+    readonly zoomToBaseLevel: boolean;
+    readonly showHighlight: boolean;
+    readonly molstarPluginContext: PluginContext | undefined;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default Structure;
+export type JBrowsePluginProteinStructureStateModel = typeof Structure;
+export type JBrowsePluginProteinStructureModel = Instance<JBrowsePluginProteinStructureStateModel>;

package/dist/ProteinView/structureModel.js

@@ -0,0 +1,407 @@
+import { autorun } from 'mobx';
+import { addDisposer, getParent, types } from 'mobx-state-tree';
+import { SimpleFeature, getSession, } from '@jbrowse/core/util';
+// locals
+import { checkHovered, invertMap, toStr } from './util';
+import { launchPairwiseAlignment } from './launchRemotePairwiseAlignment';
+import { genomeToTranscriptSeqMapping, structureSeqVsTranscriptSeqMap, structurePositionToAlignmentMap, transcriptPositionToAlignmentMap, } from '../mappings';
+import { StructureElement, StructureProperties, } from 'molstar/lib/mol-model/structure';
+import { clickProteinToGenome, hoverProteinToGenome, } from './proteinToGenomeMapping';
+import selectResidue from './selectResidue';
+import clearSelection from './clearSelection';
+import highlightResidue from './highlightResidue';
+const Structure = types
+    .model({
+    /**
+     * #property
+     */
+    url: types.maybe(types.string),
+    /**
+     * #property
+     */
+    data: types.maybe(types.string),
+    /**
+     * #property
+     */
+    connectedViewId: types.maybe(types.string),
+    /**
+     * #property
+     */
+    pairwiseAlignment: types.frozen(),
+    /**
+     * #property
+     */
+    feature: types.frozen(),
+    /**
+     * #property
+     */
+    userProvidedTranscriptSequence: types.string,
+})
+    .volatile(() => ({
+    /**
+     * #volatile
+     */
+    model: undefined,
+    /**
+     * #volatile
+     */
+    clickGenomeHighlights: [],
+    /**
+     * #volatile
+     */
+    hoverGenomeHighlights: [],
+    /**
+     * #volatile
+     */
+    clickPosition: undefined,
+    /**
+     * #volatile
+     */
+    hoverPosition: undefined,
+    /**
+     * #volatile
+     */
+    pairwiseAlignmentStatus: '',
+    /**
+     * #volatile
+     */
+    structureSequences: undefined,
+}))
+    .actions(self => ({
+    /**
+     * #action
+     */
+    setModel(model) {
+        self.model = model;
+    },
+    setSequences(str) {
+        self.structureSequences = str;
+    },
+}))
+    .views(self => ({
+    /**
+     * #getter
+     */
+    get connectedView() {
+        const { views } = getSession(self);
+        return views.find(f => f.id === self.connectedViewId);
+    },
+}))
+    .actions(self => ({
+    /**
+     * #action
+     */
+    setClickedPosition(arg) {
+        self.clickPosition = arg;
+    },
+    /**
+     * #action
+     */
+    setClickGenomeHighlights(r) {
+        self.clickGenomeHighlights = r;
+    },
+    /**
+     * #action
+     */
+    clearClickGenomeHighlights() {
+        self.clickGenomeHighlights = [];
+    },
+    /**
+     * #action
+     */
+    setHoverGenomeHighlights(r) {
+        self.hoverGenomeHighlights = r;
+    },
+    /**
+     * #action
+     */
+    clearHoverGenomeHighlights() {
+        self.hoverGenomeHighlights = [];
+    },
+    /**
+     * #action
+     */
+    setHoveredPosition(arg) {
+        self.hoverPosition = arg;
+    },
+    /**
+     * #action
+     */
+    setAlignment(r) {
+        self.pairwiseAlignment = r;
+    },
+    /**
+     * #action
+     */
+    setAlignmentStatus(str) {
+        self.pairwiseAlignmentStatus = str;
+    },
+}))
+    .views(self => ({
+    /**
+     * #getter
+     */
+    get structureSeqToTranscriptSeqPosition() {
+        return self.pairwiseAlignment
+            ? structureSeqVsTranscriptSeqMap(self.pairwiseAlignment)
+                .structureSeqToTranscriptSeqPosition
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get transcriptSeqToStructureSeqPosition() {
+        return self.pairwiseAlignment
+            ? structureSeqVsTranscriptSeqMap(self.pairwiseAlignment)
+                .transcriptSeqToStructureSeqPosition
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get structurePositionToAlignmentMap() {
+        return self.pairwiseAlignment
+            ? structurePositionToAlignmentMap(self.pairwiseAlignment)
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get transcriptPositionToAlignmentMap() {
+        return self.pairwiseAlignment
+            ? transcriptPositionToAlignmentMap(self.pairwiseAlignment)
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get pairwiseAlignmentToTranscriptPosition() {
+        return this.transcriptPositionToAlignmentMap
+            ? invertMap(this.transcriptPositionToAlignmentMap)
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get pairwiseAlignmentToStructurePosition() {
+        return this.structurePositionToAlignmentMap
+            ? invertMap(this.structurePositionToAlignmentMap)
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get clickString() {
+        const r = self.clickPosition;
+        return r === undefined ? '' : toStr(r);
+    },
+    /**
+     * #getter
+     */
+    get hoverString() {
+        const r = self.hoverPosition;
+        return r === undefined ? '' : toStr(r);
+    },
+    /**
+     * #getter
+     */
+    get genomeToTranscriptSeqMapping() {
+        return self.feature
+            ? genomeToTranscriptSeqMapping(new SimpleFeature(self.feature))
+            : undefined;
+    },
+    /**
+     * #getter
+     */
+    get structureSeqHoverPos() {
+        return self.hoverPosition?.structureSeqPos;
+    },
+    /**
+     * #getter
+     */
+    get exactMatch() {
+        const r1 = self.userProvidedTranscriptSequence.replaceAll('*', '');
+        const r2 = self.structureSequences?.[0]?.replaceAll('*', '');
+        return r1 === r2;
+    },
+    get zoomToBaseLevel() {
+        // @ts-expect-error
+        return getParent(self, 2).zoomToBaseLevel;
+    },
+    get showHighlight() {
+        // @ts-expect-error
+        return getParent(self, 2).showHighlight;
+    },
+    get molstarPluginContext() {
+        // @ts-expect-error
+        return getParent(self, 2).molstarPluginContext;
+    },
+}))
+    .actions(self => ({
+    afterAttach() {
+        // pairwise align transcript sequence to structure residues
+        addDisposer(self, autorun(async () => {
+            try {
+                const { userProvidedTranscriptSequence, structureSequences, exactMatch, } = self;
+                const seq1 = userProvidedTranscriptSequence;
+                const seq2 = structureSequences?.[0];
+                if (!!self.pairwiseAlignment || !seq1 || !seq2) {
+                    return;
+                }
+                const r1 = seq1.replaceAll('*', '');
+                const r2 = seq2.replaceAll('*', '');
+                if (exactMatch) {
+                    let consensus = '';
+                    // eslint-disable-next-line @typescript-eslint/prefer-for-of
+                    for (let i = 0; i < r1.length; i++) {
+                        consensus += '|';
+                    }
+                    self.setAlignment({
+                        consensus,
+                        alns: [
+                            { id: 'seq1', seq: r1 },
+                            { id: 'seq2', seq: r2 },
+                        ],
+                    });
+                }
+                else {
+                    const pairwiseAlignment = await launchPairwiseAlignment({
+                        seq1: r1,
+                        seq2: r2,
+                        algorithm: 'emboss_needle',
+                        onProgress: arg => {
+                            self.setAlignmentStatus(arg);
+                        },
+                    });
+                    self.setAlignment(pairwiseAlignment.pairwiseAlignment);
+                    // showHighlight when we are
+                    // @ts-expect-error
+                    getParent(self, 2).setShowHighlight(true);
+                    // @ts-expect-error
+                    getParent(self, 2).setShowAlignment(true);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                // @ts-expect-error
+                getParent(self, 2).setError(e);
+            }
+        }));
+        // convert hover over the genome to structure position
+        addDisposer(self, autorun(() => {
+            const { hovered } = getSession(self);
+            const { transcriptSeqToStructureSeqPosition, genomeToTranscriptSeqMapping, connectedView, } = self;
+            if (connectedView?.initialized &&
+                genomeToTranscriptSeqMapping &&
+                checkHovered(hovered)) {
+                const { hoverPosition } = hovered;
+                const pos = genomeToTranscriptSeqMapping.g2p[hoverPosition.coord];
+                const c0 = pos === undefined
+                    ? undefined
+                    : transcriptSeqToStructureSeqPosition?.[pos];
+                if (c0 !== undefined) {
+                    self.setHoveredPosition({
+                        structureSeqPos: c0,
+                    });
+                }
+            }
+        }));
+        addDisposer(self, autorun(() => {
+            const { molstarPluginContext } = self;
+            if (molstarPluginContext) {
+                const ret = molstarPluginContext.behaviors.interaction.click.subscribe(e => {
+                    if (StructureElement.Loci.is(e.current.loci)) {
+                        const loc = StructureElement.Loci.getFirstLocation(e.current.loci);
+                        if (loc) {
+                            const pos = StructureProperties.residue.auth_seq_id(loc);
+                            const code = StructureProperties.atom.label_comp_id(loc);
+                            const chain = StructureProperties.chain.auth_asym_id(loc);
+                            self.setHoveredPosition({
+                                structureSeqPos: pos - 1,
+                                code,
+                                chain,
+                            });
+                            clickProteinToGenome({
+                                model: self,
+                                structureSeqPos: pos - 1,
+                            }).catch((e) => {
+                                console.error(e);
+                                // @ts-expect-error
+                                getParent(self, 2).setError(e);
+                            });
+                        }
+                    }
+                });
+                return () => {
+                    ret.unsubscribe();
+                };
+            }
+            return () => { };
+        }));
+        addDisposer(self, autorun(() => {
+            const { molstarPluginContext } = self;
+            if (molstarPluginContext) {
+                const ret = molstarPluginContext.behaviors.interaction.hover.subscribe(e => {
+                    if (StructureElement.Loci.is(e.current.loci)) {
+                        const loc = StructureElement.Loci.getFirstLocation(e.current.loci);
+                        if (loc) {
+                            // example code for this label
+                            // https://github.com/molstar/molstar/blob/60550cfea1f62a50a764d5714307d6d1049be71d/src/mol-theme/label.ts#L255-L264
+                            const pos = StructureProperties.residue.auth_seq_id(loc);
+                            const code = StructureProperties.atom.label_comp_id(loc);
+                            const chain = StructureProperties.chain.auth_asym_id(loc);
+                            self.setHoveredPosition({
+                                structureSeqPos: pos - 1,
+                                code,
+                                chain,
+                            });
+                            hoverProteinToGenome({
+                                model: self,
+                                structureSeqPos: pos - 1,
+                            });
+                        }
+                    }
+                });
+                return () => {
+                    ret.unsubscribe();
+                };
+            }
+            return () => { };
+        }));
+        addDisposer(self, autorun(() => {
+            const { showHighlight, structureSeqToTranscriptSeqPosition, molstarPluginContext, } = self;
+            const structure = molstarPluginContext?.managers.structure.hierarchy.current
+                .structures[0]?.cell.obj?.data;
+            if (structure && structureSeqToTranscriptSeqPosition) {
+                if (showHighlight) {
+                    for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) {
+                        selectResidue({
+                            structure,
+                            plugin: molstarPluginContext,
+                            selectedResidue: +coord + 1,
+                        });
+                    }
+                }
+                else {
+                    clearSelection({
+                        plugin: molstarPluginContext,
+                    });
+                }
+            }
+        }));
+        addDisposer(self, autorun(() => {
+            const { structureSeqHoverPos, molstarPluginContext } = self;
+            const structure = molstarPluginContext?.managers.structure.hierarchy.current
+                .structures[0]?.cell.obj?.data;
+            if (structure && structureSeqHoverPos !== undefined) {
+                highlightResidue({
+                    structure,
+                    plugin: molstarPluginContext,
+                    selectedResidue: structureSeqHoverPos,
+                });
+            }
+        }));
+    },
+}));
+export default Structure;
+//# sourceMappingURL=structureModel.js.map

package/dist/ProteinView/structureModel.js.map

@@ -0,0 +1 @@
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package/dist/ProteinView/useProteinView.d.ts

@@ -1,11 +1,8 @@
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
-export default function useProteinView({ url, data, showControls, }: {
-    url?: string;
-    data?: string;
+export default function useProteinView({ showControls, }: {
     showControls: boolean;
 }): {
     parentRef: import("react").RefObject<HTMLDivElement>;
     error: unknown;
     plugin: PluginContext | undefined;
-    seq: string;
 };

package/dist/ProteinView/useProteinView.js

@@ -2,14 +2,10 @@ import { useState, useEffect, useRef } from 'react';
 import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
 import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
 import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
-// locals
-import { loadStructureFromURL } from './loadStructureFromURL';
-import { loadStructureFromData } from './loadStructureFromData';
-export default function useProteinView({ url, data, showControls, }) {
+export default function useProteinView({ showControls, }) {
     const parentRef = useRef(null);
     const [plugin, setPlugin] = useState();
     const [error, setError] = useState();
-    const [seq, setSeq] = useState('');
     useEffect(() => {
         let p;
         (async () => {
@@ -34,14 +30,6 @@ export default function useProteinView({ url, data, showControls, }) {
                 });
                 await p.initialized;
                 setPlugin(p);
-                if (url) {
-                    const { seq } = await loadStructureFromURL({ url, plugin: p });
-                    setSeq(seq);
-                }
-                else if (data) {
-                    const { seq } = await loadStructureFromData({ data, plugin: p });
-                    setSeq(seq);
-                }
             }
             catch (e) {
                 console.error(e);
@@ -51,7 +39,7 @@ export default function useProteinView({ url, data, showControls, }) {
         return () => {
             p?.unmount();
         };
-    }, [url, data, showControls]);
-    return { parentRef, error, plugin, seq };
+    }, [showControls]);
+    return { parentRef, error, plugin };
 }
 //# sourceMappingURL=useProteinView.js.map

package/dist/ProteinView/useProteinView.js.map

@@ -1 +1 @@
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package/dist/ProteinView/util.d.ts

@@ -11,9 +11,9 @@ export declare function getMolstarStructureSelection({ structure, selectedResidu
     structure: Structure;
     selectedResidue: number;
 }): import("molstar/lib/mol-model/structure").StructureSelection;
-export declare function toStr(r: {
-    structureSeqPos: number;
+export declare function toStr({ chain, code, structureSeqPos, }: {
+    structureSeqPos?: number;
     code?: string;
     chain?: string;
 }): string;
-export declare function invertMap(arg: Record<number, number | undefined>): any;
+export declare function invertMap(arg: Record<number, number>): Record<number, number>;