diff --git a/src/examples/ply-wrapper/annotation.ts b/src/examples/ply-wrapper/annotation.ts
deleted file mode 100644
index 66bf2ea7c0ceaec0d6eabfd6268bc4364df71713..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/annotation.ts
+++ /dev/null
@@ -1,72 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
-import { Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
-import { Color } from 'mol-util/color';
-
-const EvolutionaryConservationPalette: Color[] = [
- [255, 255, 129], // insufficient
- [160, 37, 96], // 9
- [240, 125, 171],
- [250, 201, 222],
- [252, 237, 244],
- [255, 255, 255],
- [234, 255, 255],
- [215, 255, 255],
- [140, 255, 255],
- [16, 200, 209] // 1
-].reverse().map(([r, g, b]) => Color.fromRgb(r, g, b));
-const EvolutionaryConservationDefaultColor = Color(0x999999);
-
-export const EvolutionaryConservation = CustomElementProperty.create<number>({
- isStatic: true,
- name: 'proteopedia-wrapper-evolutionary-conservation',
- display: 'Evolutionary Conservation',
- async getData(model: Model) {
- const id = model.label.toLowerCase();
- const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
- const json = await req.json();
- const annotations = (json && json.residueAnnotations) || [];
-
- const conservationMap = new Map<string, number>();
-
- for (const e of annotations) {
- for (const r of e.ids) {
- conservationMap.set(r, e.annotation);
- }
- }
-
- const map = new Map<ElementIndex, number>();
-
- const { _rowCount: residueCount } = model.atomicHierarchy.residues;
- const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
- const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
-
- for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
- const cI = chainIndex[residueOffsets[rI]];
- const key = `${model.atomicHierarchy.chains.auth_asym_id.value(cI)} ${model.atomicHierarchy.residues.auth_seq_id.value(rI)}`;
- if (!conservationMap.has(key)) continue;
- const ann = conservationMap.get(key)!;
- for (let aI = residueOffsets[rI]; aI < residueOffsets[rI + 1]; aI++) {
- map.set(aI, ann);
- }
- }
-
- return map;
- },
- coloring: {
- getColor(e: number) {
- if (e < 1 || e > 10) return EvolutionaryConservationDefaultColor;
- return EvolutionaryConservationPalette[e - 1];
- },
- defaultColor: EvolutionaryConservationDefaultColor
- },
- format(e) {
- if (e === 10) return `Evolutionary Conservation: InsufficientData`;
- return e ? `Evolutionary Conservation: ${e}` : void 0;
- }
-});
\ No newline at end of file
diff --git a/src/examples/ply-wrapper/changelog.md b/src/examples/ply-wrapper/changelog.md
deleted file mode 100644
index 041ecacd3454949a8be9e03ad2a6284c5b9f8381..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/changelog.md
+++ /dev/null
@@ -1,7 +0,0 @@
-== v2.0 ==
-
-* Changed how state saving works.
-
-== v1.0 ==
-
-* Initial version.
\ No newline at end of file
diff --git a/src/examples/ply-wrapper/helpers.ts b/src/examples/ply-wrapper/helpers.ts
deleted file mode 100644
index e9406e38a0fea12efca0eb9f194ca6807a9b6414..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/helpers.ts
+++ /dev/null
@@ -1,101 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { ResidueIndex, Model } from 'mol-model/structure';
-import { BuiltInStructureRepresentationsName } from 'mol-repr/structure/registry';
-import { BuiltInColorThemeName } from 'mol-theme/color';
-import { AminoAcidNames } from 'mol-model/structure/model/types';
-import { PluginContext } from 'mol-plugin/context';
-
-export interface ModelInfo {
- hetResidues: { name: string, indices: ResidueIndex[] }[],
- assemblies: { id: string, details: string, isPreferred: boolean }[],
- preferredAssemblyId: string | undefined
-}
-
-export namespace ModelInfo {
- async function getPreferredAssembly(ctx: PluginContext, model: Model) {
- if (model.label.length <= 3) return void 0;
- try {
- const id = model.label.toLowerCase();
- const src = await ctx.runTask(ctx.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${id}` })) as string;
- const json = JSON.parse(src);
- const data = json && json[id];
-
- const assemblies = data[0] && data[0].assemblies;
- if (!assemblies || !assemblies.length) return void 0;
-
- for (const asm of assemblies) {
- if (asm.preferred) {
- return asm.assembly_id;
- }
- }
- return void 0;
- } catch (e) {
- console.warn('getPreferredAssembly', e);
- }
- }
-
- export async function get(ctx: PluginContext, model: Model, checkPreferred: boolean): Promise<ModelInfo> {
- const { _rowCount: residueCount } = model.atomicHierarchy.residues;
- const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
- const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
- // const resn = SP.residue.label_comp_id, entType = SP.entity.type;
-
- const pref = checkPreferred
- ? getPreferredAssembly(ctx, model)
- : void 0;
-
- const hetResidues: ModelInfo['hetResidues'] = [];
- const hetMap = new Map<string, ModelInfo['hetResidues'][0]>();
-
- for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
- const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
- if (AminoAcidNames.has(comp_id)) continue;
- const mod_parent = model.properties.modifiedResidues.parentId.get(comp_id);
- if (mod_parent && AminoAcidNames.has(mod_parent)) continue;
-
- const cI = chainIndex[residueOffsets[rI]];
- const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
- if (model.entities.data.type.value(eI) === 'water') continue;
-
- let lig = hetMap.get(comp_id);
- if (!lig) {
- lig = { name: comp_id, indices: [] };
- hetResidues.push(lig);
- hetMap.set(comp_id, lig);
- }
- lig.indices.push(rI);
- }
-
- const preferredAssemblyId = await pref;
-
- return {
- hetResidues: hetResidues,
- assemblies: model.symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })),
- preferredAssemblyId
- };
- }
-}
-
-export type SupportedFormats = 'cif' | 'pdb'
-export interface LoadParams {
- plyurl: string,
- url: string,
- format?: SupportedFormats,
- assemblyId?: string,
- representationStyle?: RepresentationStyle
-}
-
-export interface RepresentationStyle {
- sequence?: RepresentationStyle.Entry,
- hetGroups?: RepresentationStyle.Entry,
- water?: RepresentationStyle.Entry
-}
-
-export namespace RepresentationStyle {
- export type Entry = { kind?: BuiltInStructureRepresentationsName, coloring?: BuiltInColorThemeName }
-}
\ No newline at end of file
diff --git a/src/examples/ply-wrapper/index.html b/src/examples/ply-wrapper/index.html
deleted file mode 100644
index f59e5745f2dabf5a47cbcc506ceaacd736617b51..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/index.html
+++ /dev/null
@@ -1,218 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8" />
- <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
- <title>Mol* PLY Wrapper</title>
- <style>
- * {
- margin: 0;
- padding: 0;
- box-sizing: border-box;
- }
- #app {
- position: absolute;
- left: 160px;
- top: 100px;
- width: 600px;
- height: 400px;
- border: 1px solid #ccc;
- }
- #select {
- position: absolute;
- left: 10px;
- top: 480px;
- }
- #diagram {
- position: absolute;
- left: 10px;
- top: 520px;
- width: 1210px;
- height: 510px;
- border: 1px solid #ccc;
- }
-
- #controls {
- position: absolute;
- width: 130px;
- top: 10px;
- left: 10px;
- }
-
- #controls > button {
- display: block;
- width: 100%;
- text-align: left;
- }
-
- #controls > hr {
- margin: 5px 0;
- }
-
- #controls > input, #controls > select {
- width: 100%;
- display: block;
- }
- </style>
- <link rel="stylesheet" type="text/css" href="app.css" />
- <script type="text/javascript" src="./index.js"></script>
- <link rel="stylesheet" type="text/css" href="/FProject5.3/style.css">
- <!--<link rel="stylesheet" type="text/css" href="/FProject5.3/dist/slimselect.css" />-->
- </head>
- <body>
- <script>var aminoAcid = 68</script>
- <div id='controls'>
- <h3>Source</h3>
- <input type='text' id='plyurl' placeholder='plyurl' style='width: 400px' />
- <input type='text' id='url' placeholder='url' style='width: 400px' />
- <input type='text' id='assemblyId' placeholder='assembly id' />
- <select id='format'>
- <option value='cif' selected>CIF</option>
- <option value='pdb'>PDB</option>
- </select>
- </div>
- <div id="app"></div>
- <script>
- // create an instance of the plugin
- var PluginWrapper = new MolStarPLYWrapper();
-
- console.log('Wrapper version', MolStarPLYWrapper.VERSION_MAJOR);
-
- function $(id) { return document.getElementById(id); }
-
- var pdbId = '1tca', assemblyId= 'preferred';
- var url = '/test-data/' + pdbId + '_updated.cif';
- var format = 'cif';
-
- var plyName = 'run_0_mesh';
- var plyurl = '/test-data/' + plyName + '.ply';
-
- $('plyurl').value = plyurl;
- $('plyurl').onchange = function (e) { url = e.target.value; }
- $('url').value = url;
- $('url').onchange = function (e) { url = e.target.value; }
- $('assemblyId').value = assemblyId;
- $('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
- $('format').value = format;
- $('format').onchange = function (e) { format = e.target.value; }
-
- // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
- // var format = 'pdb';
- // var assemblyId = 'deposited';
-
- PluginWrapper.init('app' /** or document.getElementById('app') */);
- PluginWrapper.setBackground(0xffffff);
- PluginWrapper.load({ plyurl: plyurl, url: url, format: format, assemblyId: assemblyId });
- PluginWrapper.toggleSpin();
-
- PluginWrapper.events.modelInfo.subscribe(function (info) {
- console.log('Model Info', info);
- });
-
-
-
- addControl('Load Asym Unit', () => PluginWrapper.load({ plyurl: plyurl, url: url, format: format }));
- addControl('Load Assembly', () => PluginWrapper.load({ plyurl: plyurl, url: url, format: format, assemblyId: assemblyId }));
-
- addSeparator();
-
- addHeader('Camera');
- addControl('Toggle Spin', () => PluginWrapper.toggleSpin());
-
- addSeparator();
-
- addHeader('Animation');
-
- // adjust this number to make the animation faster or slower
- // requires to "restart" the animation if changed
- PluginWrapper.animate.modelIndex.maxFPS = 30;
-
- addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
- addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());
- addControl('Play Palindrome', () => PluginWrapper.animate.modelIndex.palindrome());
- addControl('Play Loop', () => PluginWrapper.animate.modelIndex.loop());
- addControl('Stop', () => PluginWrapper.animate.modelIndex.stop());
-
- addSeparator();
- addHeader('Misc');
-
- addControl('Apply Evo Cons', () => PluginWrapper.coloring.evolutionaryConservation());
- addControl('Default Visuals', () => PluginWrapper.updateStyle());
-
- addSeparator();
- addHeader('State');
-
- var snapshot;
- addControl('Create Snapshot', () => {
- snapshot = PluginWrapper.snapshot.get();
- // could use JSON.stringify(snapshot) and upload the data
- });
- addControl('Apply Snapshot', () => {
- if (!snapshot) return;
- PluginWrapper.snapshot.set(snapshot);
-
- // or download snapshot using fetch or ajax or whatever
- // or PluginWrapper.snapshot.download(url);
- });
-
- ////////////////////////////////////////////////////////
-
- function addControl(label, action) {
- var btn = document.createElement('button');
- btn.onclick = action;
- btn.innerText = label;
- $('controls').appendChild(btn);
- }
-
- function addSeparator() {
- var hr = document.createElement('hr');
- $('controls').appendChild(hr);
- }
-
- function addHeader(header) {
- var h = document.createElement('h3');
- h.innerText = header;
- $('controls').appendChild(h);
- }
- PluginWrapper.klick;
- </script>
-
- <!-- --------- FProject start --------- -->
- <select id="select" onchange="iniciar()">
- <option value="/FProject5.3/Contact_density/run_0.json">Run 0</option>
- <option value="/FProject5.3/Contact_density/run_1.json">Run 1</option>
- <option value="/FProject5.3/Contact_density/run_2.json">Run 2</option>
- <option value="/FProject5.3/Contact_density/run_3.json">Run 3</option>
- <option value="/FProject5.3/Contact_density/run_4.json">Run 4</option>
- <option value="/FProject5.3/Contact_density/run_5.json">Run 5</option>
- <option value="/FProject5.3/Contact_density/run_6.json">Run 6</option>
- <option value="/FProject5.3/Contact_density/run_7.json">Run 7</option>
- <option value="/FProject5.3/Contact_density/run_8.json">Run 8</option>
- <option value="/FProject5.3/Contact_density/run_9.json">Run 9</option>
- <option value="/FProject5.3/Contact_density/run_total.json">Run total</option>
- </select>
- <div id="diagram">
- </div>
- <!--
- <script>
- setTimeout(function() {
- new SlimSelect({
- select: '#select'
- })
- }, 300)
- </script>
- <script src="/FProject5.3/dist/slimselect.min.js"></script>
- -->
-
- <!-- load the d3.js library -->
- <script src="/FProject5.3/d3.v4.min.js"></script>
- <script src="/FProject5.3/jquery-3.3.1.min.js"></script>
- <script src="https://d3js.org/d3-path.v1.min.js"></script>
- <script src="https://d3js.org/d3-shape.v1.min.js"></script>
-
- <script src="/FProject5.3/scriptv2.js">
- </script>
- <!-- --------- FProject end --------- -->
-
- </body>
-</html>
\ No newline at end of file
diff --git a/src/examples/ply-wrapper/index.ts b/src/examples/ply-wrapper/index.ts
deleted file mode 100644
index 955ff98e6e9b45d9dd41468961aa41eadba691b5..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/index.ts
+++ /dev/null
@@ -1,248 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { createPlugin, DefaultPluginSpec } from 'mol-plugin';
-import './index.html'
-import { PluginContext } from 'mol-plugin/context';
-import { PluginCommands } from 'mol-plugin/command';
-import { StateTransforms } from 'mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
-import { Color } from 'mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from 'mol-plugin/state/objects';
-import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
-import {StateBuilder, StateObject} from 'mol-state';
-import { EvolutionaryConservation } from './annotation';
-import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo } from './helpers';
-import { RxEventHelper } from 'mol-util/rx-event-helper';
-import { ControlsWrapper } from './ui/controls';
-import { PluginState } from 'mol-plugin/state';
-import { Canvas3D } from 'mol-canvas3d/canvas3d';
-require('mol-plugin/skin/light.scss')
-
-
-
-class MolStarPLYWrapper {
- static VERSION_MAJOR = 2;
- static VERSION_MINOR = 0;
-
- private _ev = RxEventHelper.create();
-
- readonly events = {
- modelInfo: this._ev<ModelInfo>()
- };
-
-
- plugin: PluginContext;
-
- init(target: string | HTMLElement) {
- this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
- layout: {
- initial: {
- isExpanded: false,
- showControls: false
- },
- controls: {
- right: ControlsWrapper
- }
- }
- });
-
- this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(EvolutionaryConservation.Descriptor.name, EvolutionaryConservation.colorTheme!);
- this.plugin.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
- this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider);
- }
-
- get state() {
- return this.plugin.state.dataState;
- }
-
- get klick(){
- this.plugin.canvas3d.interaction.click.subscribe(e =>{
- console.log('atomID', e)
- aminoAcid = 169;
- })
- return 0
- }
-
-
- private download(b: StateBuilder.To<PSO.Root>, url: string) {
- return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
- }
-
- private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
- const parsed = format === 'cif'
- ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
- : b.apply(StateTransforms.Model.TrajectoryFromPDB);
-
- return parsed
- .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 }, { ref: 'model' });
- }
-
- private plyData(b: StateBuilder.To<PSO.Data.String>) {
- return b.apply(StateTransforms.Data.ParsePly)
- .apply(StateTransforms.Model.ShapeFromPly)
- .apply(StateTransforms.Representation.ShapeRepresentation3D);
- }
-
- private structure(assemblyId: string) {
- const model = this.state.build().to('model');
-
- return model
- .apply(StateTransforms.Model.CustomModelProperties, { properties: [EvolutionaryConservation.Descriptor.name] }, { ref: 'props', props: { isGhost: false } })
- .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
- }
-
- private visual(ref: string, style?: RepresentationStyle) {
- const structure = this.getObj<PluginStateObject.Molecule.Structure>(ref);
- if (!structure) return;
-
- const root = this.state.build().to(ref);
-
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: 'sequence' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
- (style && style.sequence && style.sequence.kind) || 'cartoon',
- (style && style.sequence && style.sequence.coloring) || 'unit-index', structure),
- { ref: 'sequence-visual' });
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' }, { ref: 'het' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
- (style && style.hetGroups && style.hetGroups.kind) || 'ball-and-stick',
- (style && style.hetGroups && style.hetGroups.coloring), structure),
- { ref: 'het-visual' });
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' }, { ref: 'water' })
- .apply(StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
- (style && style.water && style.water.kind) || 'ball-and-stick',
- (style && style.water && style.water.coloring), structure, { alpha: 0.51 }),
- { ref: 'water-visual' });
-
- return root;
- }
-
- private getObj<T extends StateObject>(ref: string): T['data'] {
- const state = this.state;
- const cell = state.select(ref)[0];
- if (!cell || !cell.obj) return void 0;
- return (cell.obj as T).data;
- }
-
- private async doInfo(checkPreferredAssembly: boolean) {
- const model = this.getObj<PluginStateObject.Molecule.Model>('model');
- if (!model) return;
-
- const info = await ModelInfo.get(this.plugin, model, checkPreferredAssembly)
- this.events.modelInfo.next(info);
- return info;
- }
-
- private applyState(tree: StateBuilder) {
- return PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
- }
-
- private loadedParams: LoadParams = { plyurl: '', url: '', format: 'cif', assemblyId: '' };
- async load({ plyurl, url, format = 'cif', assemblyId = '', representationStyle }: LoadParams) {
- let loadType: 'full' | 'update' = 'full';
-
- const state = this.plugin.state.dataState;
-
- if (this.loadedParams.plyurl !== plyurl || this.loadedParams.url !== url || this.loadedParams.format !== format) {
- loadType = 'full';
- } else if (this.loadedParams.url === url) {
- if (state.select('asm').length > 0) loadType = 'update';
- }
-
- if (loadType === 'full') {
- await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
- // pdb/cif loading
- const modelTree = this.model(this.download(state.build().toRoot(), url), format, assemblyId);
- await this.applyState(modelTree);
- const info = await this.doInfo(true);
- const structureTree = this.structure((assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId);
- await this.applyState(structureTree);
- // ply loading
- const modelTreePly = this.plyData(this.download(state.build().toRoot(), plyurl));
- await this.applyState(modelTreePly);
- } else {
- const tree = state.build();
- tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
- await this.applyState(tree);
- }
-
- await this.updateStyle(representationStyle);
-
- this.loadedParams = { plyurl, url, format, assemblyId };
- PluginCommands.Camera.Reset.dispatch(this.plugin, { });
- }
-
- async updateStyle(style?: RepresentationStyle) {
- const tree = this.visual('asm', style);
- if (!tree) return;
- await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
- }
-
- setBackground(color: number) {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { backgroundColor: Color(color) } });
- }
-
- toggleSpin() {
- const trackball = this.plugin.canvas3d.props.trackball;
- const spinning = trackball.spin;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
- if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
- }
-
- animate = {
- modelIndex: {
- maxFPS: 8,
- onceForward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }) },
- onceBackward: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }) },
- palindrome: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }) },
- loop: () => { this.plugin.state.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }) },
- stop: () => this.plugin.state.animation.stop()
- }
- }
-
- coloring = {
- evolutionaryConservation: async () => {
- await this.updateStyle({ sequence: { kind: 'spacefill' } });
-
- const state = this.state;
-
- // const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Structure.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
- const tree = state.build();
- const colorTheme = { name: EvolutionaryConservation.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(EvolutionaryConservation.Descriptor.name).defaultValues };
-
- tree.to('sequence-visual').update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
- // for (const v of visuals) {
- // }
-
- await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
- }
- }
-
- snapshot = {
- get: () => {
- return this.plugin.state.getSnapshot();
- },
- set: (snapshot: PluginState.Snapshot) => {
- return this.plugin.state.setSnapshot(snapshot);
- },
- download: async (url: string) => {
- try {
- const data = await this.plugin.runTask(this.plugin.fetch({ url }));
- const snapshot = JSON.parse(data);
- await this.plugin.state.setSnapshot(snapshot);
- } catch (e) {
- console.log(e);
- }
- }
-
- }
-}
-
-(window as any).MolStarPLYWrapper = MolStarPLYWrapper;
diff --git a/src/examples/ply-wrapper/ui/controls.tsx b/src/examples/ply-wrapper/ui/controls.tsx
deleted file mode 100644
index d2a79e61b59b5df991b610381e77c7d9e4fe8ecc..0000000000000000000000000000000000000000
--- a/src/examples/ply-wrapper/ui/controls.tsx
+++ /dev/null
@@ -1,21 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import * as React from 'react';
-import { PluginUIComponent } from 'mol-plugin/ui/base';
-import { CurrentObject } from 'mol-plugin/ui/plugin';
-import { AnimationControls } from 'mol-plugin/ui/state/animation';
-import { CameraSnapshots } from 'mol-plugin/ui/camera';
-
-export class ControlsWrapper extends PluginUIComponent {
- render() {
- return <div className='msp-scrollable-container msp-right-controls'>
- <CurrentObject />
- <AnimationControls />
- <CameraSnapshots />
- </div>;
- }
-}
\ No newline at end of file
diff --git a/webpack.config.js b/webpack.config.js
index f23cd57bbcb5deef38db87f344634cfd6ebd1252..bda3612a92f256206750a7c20e5422ed44d57fc9 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -97,7 +97,6 @@ module.exports = [
createApp('viewer'),
createApp('basic-wrapper'),
createEntry('examples/proteopedia-wrapper/index', 'examples/proteopedia-wrapper', 'index'),
- createEntry('examples/ply-wrapper/index', 'examples/ply-wrapper', 'index'),
createNodeApp('state-docs'),
createNodeEntryPoint('preprocess', 'servers/model', 'model-server'),
createApp('model-server-query'),