diff --git a/src/mol-plugin/behavior/dynamic/volume.ts b/src/mol-plugin/behavior/dynamic/volume.ts
deleted file mode 100644
index 9808a806afb4a1d402cac2274eb90593b789421b..0000000000000000000000000000000000000000
--- a/src/mol-plugin/behavior/dynamic/volume.ts
+++ /dev/null
@@ -1,149 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import CIF from 'mol-io/reader/cif';
-import { Box3D } from 'mol-math/geometry';
-import { Vec3 } from 'mol-math/linear-algebra';
-import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
-import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
-import { PluginContext } from 'mol-plugin/context';
-import { PluginStateObject } from 'mol-plugin/state/objects';
-import { createIsoValueParam } from 'mol-repr/volume/isosurface';
-import { Color } from 'mol-util/color';
-import { LRUCache } from 'mol-util/lru-cache';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { PluginBehavior } from '../behavior';
-import { Structure } from 'mol-model/structure';
-
-export namespace VolumeStreaming {
- function channelParam(label: string, color: Color, defaultValue: number) {
- return PD.Group({
- color: PD.Color(color),
- isoValue: createIsoValueParam(VolumeIsoValue.relative(defaultValue))
- }, { label });
- }
-
- export const Params = {
- id: PD.Text('1tqn'),
- levels: PD.MappedStatic('x-ray', {
- 'em': channelParam('EM', Color(0x638F8F), 1.5),
- 'x-ray': PD.Group({
- '2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), 1.5),
- 'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), 3),
- 'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), -3),
- })
- }),
- box: PD.MappedStatic('static-box', {
- 'static-box': PD.Group({
- bottomLeft: PD.Vec3(Vec3.create(-22.4, -33.4, -21.6)),
- topRight: PD.Vec3(Vec3.create(-7.1, -10, -0.9))
- }, { description: 'Static box defined by cartesian coords.' }),
- // 'around-selection': PD.Group({ radius: PD.Numeric(5, { min: 0, max: 10 }) }),
- 'cell': PD.Group({ }),
- // 'auto': PD.Group({ }), // based on camera distance/active selection/whatever, show whole structure or slice.
- }),
- detailLevel: PD.Numeric(3, { min: 0, max: 7 }),
- serverUrl: PD.Text('https://webchem.ncbr.muni.cz/DensityServer'),
- }
- export type Params = PD.Values<typeof Params>
-
- export type ChannelData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: VolumeData }
- export type LevelType = 'em' | '2fo-fc' | 'fo-fc(+ve)' | 'fo-fc(-ve)'
-
- export class Behavior implements PluginBehavior<Params> {
- // TODO: have special value for "cell"?
- private cache = LRUCache.create<ChannelData>(25);
- // private ref: string = '';
-
- currentData: ChannelData = { }
-
- private async queryData(box?: Box3D) {
- let url = `${this.params.serverUrl}/${this.params.levels.name}/${this.params.id}`
-
- if (box) {
- const { min: a, max: b } = box;
- url += `/box`
- + `/${a.map(v => Math.round(1000 * v) / 1000).join(',')}`
- + `/${b.map(v => Math.round(1000 * v) / 1000).join(',')}`;
- } else {
- url += `/cell`;
- }
- url += `?detail=${this.params.detailLevel}`;
-
- let data = LRUCache.get(this.cache, url);
- if (data) {
- return data;
- }
-
- const cif = await this.ctx.runTask(this.ctx.fetch({ url, type: 'binary' }));
- data = await this.parseCif(cif as Uint8Array);
- if (!data) {
- return;
- }
-
- LRUCache.set(this.cache, url, data);
- return data;
- }
-
- private async parseCif(data: Uint8Array): Promise<ChannelData | undefined> {
- const parsed = await this.ctx.runTask(CIF.parseBinary(data));
- if (parsed.isError) {
- this.ctx.log.error('VolumeStreaming, parsing CIF: ' + parsed.toString());
- return;
- }
- if (parsed.result.blocks.length < 2) {
- this.ctx.log.error('VolumeStreaming: Invalid data.');
- return;
- }
-
- const ret: ChannelData = { };
- for (let i = 1; i < parsed.result.blocks.length; i++) {
- const block = parsed.result.blocks[i];
-
- const densityServerCif = CIF.schema.densityServer(block);
- const volume = await this.ctx.runTask(await volumeFromDensityServerData(densityServerCif));
- (ret as any)[block.header as any] = volume;
- }
- return ret;
- }
-
- register(ref: string): void {
- // TODO: register camera movement/loci so that "around selection box works"
- // alternatively, and maybe a better solution, write a global behavior that modifies this node from the outside
- }
-
- async update(params: Params): Promise<boolean> {
- this.params = params;
-
- let box: Box3D | undefined = void 0;
-
- switch (params.box.name) {
- case 'static-box':
- box = Box3D.create(params.box.params.bottomLeft, params.box.params.topRight);
- break;
- case 'cell':
- box = this.params.levels.name === 'x-ray'
- ? this.structure.boundary.box
- : void 0;
- break;
- }
-
- const data = await this.queryData(box);
- this.currentData = data || { };
-
- return true;
- }
-
- unregister(): void {
- // TODO unsubscribe to events
- }
-
- constructor(public ctx: PluginContext, public params: Params, private structure: Structure) {
- }
- }
-
- export class Obj extends PluginStateObject.CreateBehavior<Behavior>({ name: 'Volume Streaming' }) { }
-}
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/volume.ts b/src/mol-plugin/state/actions/volume.ts
index ab07fd80a3098c5d9b303dbcb1fa4d26a1148ee7..baf6e0ded64d08c380cf907bd4a671302cbeac5a 100644
--- a/src/mol-plugin/state/actions/volume.ts
+++ b/src/mol-plugin/state/actions/volume.ts
@@ -16,7 +16,6 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { VolumeRepresentation3DHelpers } from '../transforms/representation';
-import { VolumeStreaming } from 'mol-plugin/behavior/dynamic/volume';
import { DataFormatProvider } from './data-format';
export const Ccp4Provider: DataFormatProvider<any> = {
@@ -201,24 +200,4 @@ const DownloadDensity = StateAction.build({
const b = state.build().to(data.ref);
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx)
-}));
-
-export const InitVolumeStreaming = StateAction.build({
- display: { name: 'Volume Streaming' },
- from: PluginStateObject.Molecule.Structure,
- params: VolumeStreaming.Params
-})(({ ref, state, params }, ctx: PluginContext) => {
- // TODO: specify simpler params
- // TODO: try to determine if the input is x-ray or emd (in params provider)
- // TODO: for EMD, use PDBe API to determine controur level https://github.com/dsehnal/LiteMol/blob/master/src/Viewer/Extensions/DensityStreaming/Entity.ts#L168
- // TODO: custom react view for this and the VolumeStreamingBehavior transformer
-
- const root = state.build().to(ref)
- .apply(StateTransforms.Volume.VolumeStreamingBehavior, params);
-
- root.apply(StateTransforms.Volume.VolumeStreamingVisual, { channel: '2FO-FC', level: '2fo-fc' }, { props: { isGhost: true } });
- root.apply(StateTransforms.Volume.VolumeStreamingVisual, { channel: 'FO-FC', level: 'fo-fc(+ve)' }, { props: { isGhost: true } });
- root.apply(StateTransforms.Volume.VolumeStreamingVisual, { channel: 'FO-FC', level: 'fo-fc(-ve)' }, { props: { isGhost: true } });
-
- return state.updateTree(root);
-});
\ No newline at end of file
+}));
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/volume.ts b/src/mol-plugin/state/transforms/volume.ts
index 6c682e4a13cc9df01cea36e51391ae1e832e8259..2401cb0cf18fa0bff435a1e8a430841d65a1f2f9 100644
--- a/src/mol-plugin/state/transforms/volume.ts
+++ b/src/mol-plugin/state/transforms/volume.ts
@@ -13,14 +13,6 @@ import { volumeFromDsn6 } from 'mol-model-formats/volume/dsn6';
import { Task } from 'mol-task';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
-import { VolumeStreaming } from 'mol-plugin/behavior/dynamic/volume';
-import { PluginContext } from 'mol-plugin/context';
-import { StateTransformer } from 'mol-state';
-import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
-import { BuiltInVolumeRepresentations } from 'mol-repr/volume/registry';
-import { createTheme } from 'mol-theme/theme';
-import { VolumeRepresentation3DHelpers } from './representation';
-import { Color } from 'mol-util/color';
export { VolumeFromCcp4 };
export { VolumeFromDsn6 };
@@ -97,99 +89,4 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
return new SO.Volume.Data(volume, props);
});
}
-});
-
-export { VolumeStreamingBehavior }
-type VolumeStreamingBehavior = typeof VolumeStreamingBehavior
-const VolumeStreamingBehavior = PluginStateTransform.BuiltIn({
- name: 'volume-streaming-behavior',
- display: { name: 'Volume Streaming Behavior', description: 'Create Volume Streaming behavior.' },
- from: SO.Molecule.Structure,
- to: VolumeStreaming.Obj,
- params: VolumeStreaming.Params
-})({
- canAutoUpdate: ({ oldParams, newParams }) => oldParams.serverUrl === newParams.serverUrl && oldParams.id === newParams.id,
- apply: ({ a, params }, plugin: PluginContext) => Task.create('Volume Streaming', async ctx => {
- const behavior = new VolumeStreaming.Behavior(plugin, params, a.data);
- // get the initial data now so that the child projections dont get empty volumes.
- await behavior.update(behavior.params);
- return new VolumeStreaming.Obj(behavior, { label: 'Volume Streaming' });
- }),
- update({ b, newParams }) {
- return Task.create('Update Volume Streaming', async _ => {
- await b.data.update(newParams);
- return StateTransformer.UpdateResult.Updated;
- });
- }
-});
-
-// export { VolumeStreamingData }
-// type VolumeStreamingData = typeof VolumeStreamingData
-// const VolumeStreamingData = PluginStateTransform.BuiltIn({
-// name: 'volume-streaming-data',
-// display: { name: 'Volume Streaming Data' },
-// from: VolumeStreaming.Obj,
-// to: SO.Volume.Data,
-// params: {
-// channel: PD.Select<keyof VolumeStreaming.ChannelData>('EM', [['EM', 'EM'], ['FO-FC', 'Fo-Fc'], ['2FO-FC', '2Fo-Fc']], { isHidden: true }),
-// level: PD.Text<VolumeStreaming.LevelType>('em')
-// }
-// })({
-// apply({ a, params }, plugin: PluginContext) {
-// const data = a.data.currentData[params.channel] || VolumeData.Empty;
-// console.log({ data });
-// return new SO.Volume.Data(a.data.currentData[params.channel] || VolumeData.Empty, { label: params.level });
-// }
-// });
-
-export { VolumeStreamingVisual }
-type VolumeStreamingVisual = typeof VolumeStreamingVisual
-const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
- name: 'volume-streaming-visual',
- display: { name: 'Volume Streaming Visual' },
- from: VolumeStreaming.Obj,
- to: SO.Volume.Representation3D,
- params: {
- channel: PD.Select<keyof VolumeStreaming.ChannelData>('EM', [['EM', 'EM'], ['FO-FC', 'Fo-Fc'], ['2FO-FC', '2Fo-Fc']], { isHidden: true }),
- level: PD.Text<VolumeStreaming.LevelType>('em')
- }
-})({
- apply: ({ a, params: srcParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
- const { data, params } = createVolumeProps(a.data, srcParams.channel, srcParams.level);
-
- const provider = BuiltInVolumeRepresentations.isosurface;
- const props = params.type.params || {}
- const repr = provider.factory({ webgl: plugin.canvas3d.webgl, ...plugin.volumeRepresentation.themeCtx }, provider.getParams)
- repr.setTheme(createTheme(plugin.volumeRepresentation.themeCtx, { volume: data }, params))
- await repr.createOrUpdate(props, data).runInContext(ctx);
- return new SO.Volume.Representation3D(repr, { label: srcParams.level, description: VolumeRepresentation3DHelpers.getDescription(props) });
- }),
- update: ({ a, b, oldParams, newParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
- // TODO : check if params/underlying data/etc have changed; maybe will need to export "data" or some other "tag" in the Representation for this to work
- const { data, params } = createVolumeProps(a.data, newParams.channel, newParams.level);
- const props = { ...b.data.props, ...params.type.params };
- b.data.setTheme(createTheme(plugin.volumeRepresentation.themeCtx, { volume: data }, params))
- await b.data.createOrUpdate(props, data).runInContext(ctx);
- return StateTransformer.UpdateResult.Updated;
- })
-});
-
-function createVolumeProps(streaming: VolumeStreaming.Behavior, channel: keyof VolumeStreaming.ChannelData, level: VolumeStreaming.LevelType) {
- const data = streaming.currentData[channel] || VolumeData.One;
- // TODO: createTheme fails when VolumeData.Empty is used for some reason.
-
- let isoValue: VolumeIsoValue, color: Color;
-
- if (level === 'em' && streaming.params.levels.name === 'em') {
- isoValue = streaming.params.levels.params.isoValue;
- color = streaming.params.levels.params.color;
- } else if (level !== 'em' && streaming.params.levels.name === 'x-ray') {
- isoValue = streaming.params.levels.params[level].isoValue;
- color = streaming.params.levels.params[level].color;
- } else {
- throw new Error(`Unsupported iso level ${level}.`);
- }
-
- const params = VolumeRepresentation3DHelpers.getDefaultParamsStatic(streaming.ctx, 'isosurface', { isoValue, alpha: 0.3 }, 'uniform', { value: color });
- return { data, params };
-}
\ No newline at end of file
+});
\ No newline at end of file