Issue #820: refactorings; clean ups

src/examples/assembly-tm/FeatureViewConfig.ts

@@ -1,4 +1,8 @@
-import { FeatureViewInterface } from "../../RcsbFvSequence/SequenceViews/CustomView/CustomView";
+import {
+    CustomViewInterface,
+    FeatureBlockInterface,
+    FeatureViewInterface
+} from "../../RcsbFvSequence/SequenceViews/CustomView/CustomView";
 import {
     RcsbFv,
     RcsbFvDisplayTypes,
@@ -17,16 +21,10 @@ import {
 import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
 
 import {RcsbFvStructureConfigInterface} from "../../RcsbFvStructure/RcsbFvStructure";
-import {
-    CustomViewInterface,
-    FeatureBlockInterface
-} from "../../RcsbFvSequence/SequenceViews/CustomView/CustomView";
-import {
-} from "../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import { updateSiteColors } from "./UniTmpColor";
 import { fetchHtpDescriptor, fetchPdbtmJsvLibDescriptor, htpDescriptorToTrackData, jsvLibDescriptorToTrackData } from "./UniTmpHelper";
-import { TmDetRcsbPreset } from "./preset2";
+import { TmDetRcsbPreset } from "./TmTrajectoryHierarchyPreset";
 import { TmDetDescriptorCache } from "./tmdet-extension/prop";
 
 export async function createFeatureViewerConfing(
@@ -86,11 +84,11 @@ export async function createFeatureViewerConfing(
             plugin.clearSelection("select", {modelId: modelId, labelAsymId: params.labelAsymId})
             plugin.resetCamera();
         }
-    },
+    };
     fvConfig.sequenceElementClickCallback = (plugin: StructureViewerPublicInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
         if(d!=null)
             plugin.cameraFocus(modelId, params.labelAsymId, d.begin, d.end ?? d.begin);
-    },
+    };
     fvConfig.sequenceHoverCallback = (plugin: StructureViewerPublicInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
         if(elements == null || elements.length == 0)
             plugin.clearSelection("hover");
@@ -103,7 +101,7 @@ export async function createFeatureViewerConfing(
                 end: e.end ?? e.begin
             })), "hover", "set");
         }
-    },
+    };
     fvConfig.structureSelectionCallback = (plugin: StructureViewerPublicInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition(modelId, params.labelAsymId, "select");
         if(sel == null) {
@@ -112,14 +110,14 @@ export async function createFeatureViewerConfing(
         }else {
             pfv.setSelection({elements: sel.regions, mode: "select"});
         }
-    },
+    };
     fvConfig.structureHoverCallback = (plugin: StructureViewerPublicInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition(modelId, params.labelAsymId, "hover");
         if(sel == null)
             pfv.clearSelection("hover");
         else
             pfv.setSelection({elements:sel.regions, mode:"hover"});
-    }
+    };
 
     const block: FeatureBlockInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType> = {
         blockId: `${params.pdbEntry}_${params.labelAsymId}_block_id`,

src/examples/assembly-tm/index.ts

@@ -34,7 +34,7 @@ async function createConfig(configParams: any): Promise<RcsbFv3DCustomInterface>
 
     if (pdbEntry) {
         const descriptorUrl = `/${pdbEntry}.json`;
-        registerRegionDescriptorData(descriptorUrl, params.side1 as any);
+        registerRegionDescriptorData(descriptorUrl, params.side1);
     }
     if (configParams.configData) {
         params.fvConfigData = (await fetchDescriptor(configParams.configData))

src/examples/assembly-tm/preset.ts

@@ -1,235 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
-import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
-import { RootStructureDefinition } from 'molstar/lib/mol-plugin-state/helpers/root-structure';
-import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';
-import {
-    StateObjectSelector,
-    StateObject,
-    StateTransformer
-} from 'molstar/lib/mol-state';
-import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
-import { MembraneOrientationPreset } from 'molstar/lib/extensions/anvil/behavior';
-import { Target } from '@rcsb/rcsb-molstar/build/src/viewer/helpers/selection';
-import { TMDET_STRUCTURE_PRESET_ID } from './tmdet-extension/behavior';
-import { TmDetDescriptorCache } from './tmdet-extension/prop';
-import { DebugUtil } from './tmdet-extension/debug-utils';
-import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
-import { applyTransformations } from './tmdet-extension/transformation';
-
-type BaseProps = {
-    assemblyId?: string
-    modelIndex?: number
-    plddt?: 'off' | 'single-chain' | 'on'
-}
-
-export { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
-
-export type AlignmentProps = {
-    kind: 'alignment',
-    targets?: (Target & {
-        matrix?: Mat4
-    })[],
-    colors: {
-        value: number,
-        targets: Target[]
-    }[]
-} & BaseProps
-
-export type EmptyProps = {
-    kind: 'empty'
-} & BaseProps
-
-type ValidationProps = {
-    kind: 'validation'
-    colorTheme?: string
-    showClashes?: boolean
-} & BaseProps
-
-type StandardProps = {
-    kind: 'standard'
-} & BaseProps
-
-type SymmetryProps = {
-    kind: 'symmetry'
-    symmetryIndex?: number
-} & BaseProps
-
-type FeatureProps = {
-    kind: 'feature'
-    target: Target
-} & BaseProps
-
-type DensityProps = {
-    kind: 'density'
-} & BaseProps
-
-type MembraneProps = {
-    kind: 'membrane',
-} & BaseProps
-
-type FeatureDensityProps = {
-    kind: 'feature-density',
-    target: Target,
-    radius?: number,
-    hiddenChannels?: string[]
-} & BaseProps
-
-export type MotifProps = {
-    kind: 'motif',
-    label?: string,
-    targets: Target[],
-    color?: number
-} & BaseProps
-
-export type NakbProps = {
-    kind: 'nakb'
-} & BaseProps
-
-export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | AlignmentProps |
-MembraneProps | FeatureDensityProps | MotifProps | NakbProps | EmptyProps;
-
-const RcsbParams = () => ({
-    preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
-});
-
-type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>
-
-export const TmDetRcsbPreset = TrajectoryHierarchyPresetProvider({
-    id: 'tmdet-preset-trajectory-rcsb',
-    display: { name: 'TMDET RCSB Preset' },
-    isApplicable: () => true,
-    params: RcsbParams,
-    async apply(trajectory, params, plugin) {
-        console.log('TMDET RCSB PRESET: apply start');
-        const builder = plugin.builders.structure;
-        const p = params.preset;
-
-        const modelParams = { modelIndex: p.modelIndex || 0 };
-
-        const structureParams: RootStructureDefinition.Params = { name: 'model', params: {} };
-        if (p.assemblyId && p.assemblyId !== '' && p.assemblyId !== '0') {
-            Object.assign(structureParams, {
-                name: 'assembly',
-                params: { id: p.assemblyId }
-            } as RootStructureDefinition.Params);
-        }
-
-        const model = await builder.createModel(trajectory, modelParams);
-        const modelProperties = await builder.insertModelProperties(model);
-
-        let structure: StructureObject | undefined = undefined;
-        let structureProperties: StructureObject | undefined = undefined;
-        let unitcell: StateObjectSelector | undefined = undefined;
-        // If flexible transformation is allowed, we may need to create a single structure component
-        // from transformed substructures
-        structure = await builder.createStructure(modelProperties || model, structureParams);
-        structureProperties = await builder.insertStructureProperties(structure);
-
-        // default to pLDDT coloring when category present && single chain
-        const presetParams = Object.create(null);
-        let representation: StructureRepresentationPresetProvider.Result | undefined = undefined;
-        console.log('PRESET params:', params);
-        console.log('PRESET p:', p);
-
-        if (p.kind === 'alignment') {
-            console.warn('alignment case not implemented in TmDetRcsbPreset');
-        } else if (p.kind === 'motif' && structure?.obj) {
-            console.warn('motif case not implemented in TmDetRcsbPreset');
-        } else if (p.kind === 'validation') {
-            console.warn('validation case not implemented in TmDetRcsbPreset');
-        } else if (p.kind === 'symmetry' && structure?.obj) {
-            console.warn('symmetry case not implemented in TmDetRcsbPreset');
-        } else if (p.kind === 'empty') {
-            console.warn('Using empty representation in TmDetRcsbPreset');
-        } else if (p.kind === 'membrane') {
-            try {
-                representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, MembraneOrientationPreset, presetParams);
-
-                // reset the camera because the membranes render 1st and the structure might not be fully visible
-                requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset());
-            } catch (error) {
-                const msg = 'Membrane calculation failed! - This can happen for tiny structures with only a dozen of residues.';
-                plugin.log.error(msg);
-                console.error(msg);
-                console.error(error);
-
-                // fall back to default representation to show something
-                representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', presetParams);
-            }
-        } else if (p.kind === 'nakb') {
-            console.warn('nakb case not implemented in TmDetRcsbPreset');
-        } else {
-            // Transformation:
-            const pdbtmDescriptor = TmDetDescriptorCache.get('1afo'); // TODO
-            let matrix = undefined;
-            if (pdbtmDescriptor) {
-                matrix = DebugUtil.descriptorMxToMat4(pdbtmDescriptor!.additional_entry_annotations.membrane.transformation_matrix as any);
-                //applyTransformations(plugin, pdbtmDescriptor!);
-            }
-
-            console.log('HERE WE GO:', { structure: structure, structureProps: structureProperties, presetParams: presetParams });
-            //representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', presetParams);
-            representation = await plugin.builders.structure.representation.applyPreset(
-                structureProperties!, 'empty', { theme: { globalName: 'tmdet-custom-color-theme' } });
-            const selector = await plugin.builders.structure.hierarchy.applyPreset(
-                trajectory, 'default', { representationPreset: TMDET_STRUCTURE_PRESET_ID as any });
-
-
-            console.log('PRESET apply result', {
-                matrix: matrix,
-//                selector: selector,
-                model: model,
-                modelProperties: modelProperties,
-                unitcell: unitcell,
-                structure: structure,
-                structureProperties: structureProperties,
-                representation: representation
-            });
-
-            // if (matrix && selector?.structureProperties) {
-            //     const params = {
-            //         transform: {
-            //             name: 'matrix' as const,
-            //             params: { data: matrix, transpose: false }
-            //         }
-            //     };
-            //     setTimeout(async () => {
-            //             console.log(this.plugin);
-            //             // const b = this.plugin.state.data.build().to(selector.structureProperties)
-            //             //     .insert(StateTransforms.Model.TransformStructureConformation, params);
-            //             // await this.plugin.runTask(this.plugin.state.data.updateTree(b));
-            //         },
-            //         2000
-            //     );
-            // }
-
-        }
-
-        console.log('STRUCTURE REPRESENTATION:', representation);
-
-        // TODO align with 'motif'?
-        if ((p.kind === 'feature' || p.kind === 'feature-density') && structure?.obj) {
-            console.warn('feature/feature-density case not implemented in TmDetRcsbPreset');
-        }
-
-        if (p.kind === 'density' && structure) {
-            console.warn('density case not implemented in TmDetRcsbPreset');
-        }
-
-        return {
-            model,
-            modelProperties,
-            unitcell,
-            structure,
-            structureProperties,
-            representation
-        };
-    }
-});

src/examples/assembly-tm/tmdet-extension/README.md

@@ -1,3 +1,8 @@
+# Caution
+
+This doc written for TmMol* viewer.
+Things changed due to heavy refactoring to adjust for saguaro usage.
+
 # TMDET Extension
 
 TmMol* is a Mol* extension to visualize transmembrane regions and topology

src/examples/assembly-tm/tmdet-extension/behavior.ts

@@ -25,7 +25,6 @@ import { StructureSelectionQuery, StructureSelectionCategory } from 'molstar/lib
 import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
 import { GenericRepresentationRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
 import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
-// import { Gunzip } from "zlibt2";
 
 
 // TMDET imports
@@ -239,30 +238,18 @@ async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor:
 
 async function downloadData(ctx: PluginUIContext, params: any, pdbtmDescriptor: PDBTMDescriptor) {
 
-    // let gzipped: boolean = false;
-    // if (params.compression || params.structureUrl.endsWith('gz')) {
-    //     gzipped = true;
-    // }
-
     const builders = ctx.builders;
     let downloadResult = await ctx.runTask(ctx.fetch({ url: params.structureUrl, type: "string" }));
     DebugUtil.log('First 50 chars of input data', downloadResult.slice(0, 50));
-    // TODO: temporary solution
-    // TODO: downloadResult = downloadResult.replace(/HETATM.+\n/mg, ''); // remove all hetatom stuffs
-    // TODO: const uncompressed: string = await ungzip(downloadResult); // it does not work right now
-    // console.log(uncompressed.slice(0, 100));
 
     return await builders.data.rawData({
         data: downloadResult,
         label: `${pdbtmDescriptor.pdb_id}`,
     }); // , { state: { isGhost: true } });
-
 }
 
-// async function ungzip(data: Uint8Array) {
-//     // TODO: it does not work :(
-//     return new Gunzip(data).decompress();
-// }
+
+
 
 //
 // //////////////////////////// END OF TMDET VIEWER SECTION

src/examples/assembly-tm/tmdet-extension/transformation.ts

@@ -8,11 +8,11 @@
  */
 
 import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
-import { Mat4, Quat, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+import { Mat4, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
 import { PDBTMDescriptor, PDBTMTransformationMatrix, PMS } from './types';
 import { createStructureRepresentationParams } from 'molstar/lib/mol-plugin-state/helpers/structure-representation-params';
 import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
-import { StateObjectRef, StateBuilder, StateObjectSelector } from 'molstar/lib/mol-state';
+import { StateObjectRef, StateBuilder } from 'molstar/lib/mol-state';
 import { Expression } from 'molstar/lib/mol-script/language/expression';
 import { MembraneOrientation } from './prop';
 import { TmDetColorThemeProvider } from './tmdet-color-theme';
@@ -67,7 +67,6 @@ export function transformWholeModel(plugin: PluginContext, membraneMatrix: PDBTM
 export function chainTransformation(plugin: PluginContext, transformationMatrix: Mat4, chainId: string, newId: string): void {
     const query: Expression = getChainExpression(chainId);
 
-//    const transformation = transformationForStateTransform(transformationMatrix);
     const transformation = transformationMatrix;
     const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
     const update: StateBuilder.To<any, any> = plugin.build().to(structure);

src/examples/assembly-tm/tmdet-viewer/TmFv3DCustom.tsx

@@ -1,6 +1,5 @@
 
-import {RcsbFvStructure, RcsbFvStructureConfigInterface} from "../../../RcsbFvStructure/RcsbFvStructure";
-import {CustomViewInterface} from "../../../RcsbFvSequence/SequenceViews/CustomView/CustomView";
+import {RcsbFvStructure} from "../../../RcsbFvStructure/RcsbFvStructure";
 import uniqid from "uniqid";
 import {
     LoadMolstarInterface,
@@ -8,24 +7,12 @@ import {
 } from "../../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {StructureViewer} from "../../../RcsbFvStructure/StructureViewers/StructureViewer";
-import {RcsbFv3DCssConfig} from "../../../RcsbFv3D/RcsbFv3DComponent";
 import {NullBehaviourObserver} from "../../../RcsbFvStructure/StructureViewerBehaviour/NullBehaviour";
 import {MolstarTools} from "../../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
 import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
 import {RcsbFv3DCustomAbstract} from "../../../RcsbFv3D/RcsbFv3DCustomAbstract";
 import { TmMolstarManagerFactory } from "./TmMolstarManagerFactory";
-
-export interface RcsbFv3DCustomInterface  {
-    elementId?: string;
-    structurePanelConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface<unknown,unknown>,{viewerProps:Partial<ViewerProps>}>;
-    sequencePanelConfig: {
-        config: CustomViewInterface<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType>;
-        title?: string;
-        subtitle?: string;
-    }
-    cssConfig?: RcsbFv3DCssConfig;
-
-}
+import { RcsbFv3DCustomInterface } from "../../../RcsbFv3D/RcsbFv3DCustom";
 
 export class TmFv3DCustom extends RcsbFv3DCustomAbstract<LoadMolstarInterface<unknown,unknown>,LoadMolstarReturnType,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}> {
 

src/examples/assembly-tm/tmdet-viewer/TmViewer.ts

@@ -13,7 +13,7 @@ import { MembraneOrientationPreset } from '../tmdet-extension/behavior';
 import { TmDetLabelProvider } from '../tmdet-extension/labeling';
 import { loadInitialSnapshot, rotateCamera, storeCameraSnapshot } from '../tmdet-extension/camera';
 import { BuiltInTrajectoryFormat } from 'molstar/lib/mol-plugin-state/formats/trajectory';
-import { PresetProps } from '../preset2';
+import { PresetProps } from '../TmTrajectoryHierarchyPreset';
 import { Mat4 } from 'molstar/lib/commonjs/mol-math/linear-algebra';
 import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';