diff --git a/package-lock.json b/package-lock.json
index 234311741bcb83cce482b6b4833806dafdeddea4..25839c99f0e4801877e5323717bc726ccf6d8e19 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index fe60146857eda7801a1381f1c119551b13256d7e..f9391796ea11f2467d2a04af2daeb5ef05f24054 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "1.1.3",
+ "version": "1.1.5",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -86,48 +86,48 @@
],
"license": "MIT",
"devDependencies": {
- "@graphql-codegen/add": "^1.14.0",
- "@graphql-codegen/cli": "^1.14.0",
- "@graphql-codegen/time": "^1.14.0",
- "@graphql-codegen/typescript": "^1.14.0",
- "@graphql-codegen/typescript-graphql-files-modules": "^1.14.0",
- "@graphql-codegen/typescript-graphql-request": "^1.14.0",
- "@graphql-codegen/typescript-operations": "^1.14.0",
+ "@graphql-codegen/add": "^1.17.3",
+ "@graphql-codegen/cli": "^1.17.3",
+ "@graphql-codegen/time": "^1.17.3",
+ "@graphql-codegen/typescript": "^1.17.3",
+ "@graphql-codegen/typescript-graphql-files-modules": "^1.17.3",
+ "@graphql-codegen/typescript-graphql-request": "^1.17.3",
+ "@graphql-codegen/typescript-operations": "^1.17.3",
"@types/cors": "^2.8.6",
- "@typescript-eslint/eslint-plugin": "^3.0.0",
- "@typescript-eslint/parser": "^3.0.0",
+ "@typescript-eslint/eslint-plugin": "^3.7.0",
+ "@typescript-eslint/parser": "^3.7.0",
"benchmark": "^2.1.4",
"concurrently": "^5.2.0",
"cpx2": "^2.0.0",
- "css-loader": "^3.5.3",
- "eslint": "^7.0.0",
+ "css-loader": "^3.6.0",
+ "eslint": "^7.5.0",
"extra-watch-webpack-plugin": "^1.0.3",
"file-loader": "^6.0.0",
- "fs-extra": "^9.0.0",
- "graphql": "^15.0.0",
+ "fs-extra": "^9.0.1",
+ "graphql": "^15.3.0",
"http-server": "^0.12.3",
- "jest": "^26.0.1",
+ "jest": "^26.1.0",
"mini-css-extract-plugin": "^0.9.0",
"node-sass": "^4.14.1",
"raw-loader": "^4.0.1",
"sass-loader": "^8.0.2",
- "simple-git": "^2.5.0",
+ "simple-git": "^2.14.0",
"style-loader": "^1.2.1",
- "ts-jest": "^26.0.0",
- "typescript": "^3.9.3",
+ "ts-jest": "^26.1.3",
+ "typescript": "^3.9.7",
"webpack": "^4.43.0",
- "webpack-cli": "^3.3.11",
+ "webpack-cli": "^3.3.12",
"webpack-version-file-plugin": "^0.4.0"
},
"dependencies": {
"@types/argparse": "^1.0.38",
"@types/benchmark": "^1.0.33",
"@types/compression": "1.7.0",
- "@types/express": "^4.17.6",
+ "@types/express": "^4.17.7",
"@types/jest": "^25.2.3",
- "@types/node": "^14.0.5",
+ "@types/node": "^14.0.24",
"@types/node-fetch": "^2.5.7",
- "@types/react": "^16.9.35",
+ "@types/react": "^16.9.43",
"@types/react-dom": "^16.9.8",
"@types/swagger-ui-dist": "3.0.5",
"argparse": "^1.0.10",
@@ -135,13 +135,13 @@
"compression": "^1.7.4",
"cors": "^2.8.5",
"express": "^4.17.1",
- "immer": "^6.0.6",
+ "immer": "^7.0.5",
"immutable": "^3.8.2",
"node-fetch": "^2.6.0",
"react": "^16.13.1",
"react-dom": "^16.13.1",
- "rxjs": "^6.5.5",
- "swagger-ui-dist": "^3.25.4",
+ "rxjs": "^6.6.0",
+ "swagger-ui-dist": "^3.30.1",
"tslib": "^2.0.0",
"util.promisify": "^1.0.1",
"xhr2": "^0.2.0"
diff --git a/src/examples/docking-viewer/index.html b/src/apps/docking-viewer/index.html
similarity index 65%
rename from src/examples/docking-viewer/index.html
rename to src/apps/docking-viewer/index.html
index 24e6504181db342b753449065b662b0377c1f575..2c0d1567925400dbef3bb702de3e39fae292e784 100644
--- a/src/examples/docking-viewer/index.html
+++ b/src/apps/docking-viewer/index.html
@@ -17,22 +17,9 @@
</head>
<body>
<div id="app"></div>
- <script type="text/javascript" src="./index.js"></script>
+ <script type="text/javascript" src="./molstar.js"></script>
<script type="text/javascript">
- var viewer = new DockingViewer('app', {
- layoutIsExpanded: false,
- layoutShowControls: false,
- layoutShowRemoteState: false,
- layoutShowSequence: true,
- layoutShowLog: false,
- layoutShowLeftPanel: true,
-
- viewportShowExpand: true,
- viewportShowControls: false,
- viewportShowSettings: false,
- viewportShowSelectionMode: false,
- viewportShowAnimation: false,
- });
+ var viewer = new DockingViewer('app', [0x33DD22, 0x1133EE], true);
function getParam(name, regex) {
var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
diff --git a/src/examples/docking-viewer/index.ts b/src/apps/docking-viewer/index.ts
similarity index 64%
rename from src/examples/docking-viewer/index.ts
rename to src/apps/docking-viewer/index.ts
index 96f25a55215da3067318c0ef9d4eb4a61ff43561..c288b158acc3927f496cb4a6fc8011857f83b519 100644
--- a/src/examples/docking-viewer/index.ts
+++ b/src/apps/docking-viewer/index.ts
@@ -11,12 +11,8 @@ import './index.html';
import { PluginContext } from '../../mol-plugin/context';
import { PluginCommands } from '../../mol-plugin/commands';
import { PluginSpec } from '../../mol-plugin/spec';
-import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
import { PluginConfig } from '../../mol-plugin/config';
-import { Asset } from '../../mol-util/assets';
import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginState } from '../../mol-plugin/state';
-import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
import { Structure } from '../../mol-model/structure';
@@ -24,9 +20,10 @@ import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Task } from '../../mol-task';
import { StateObject } from '../../mol-state';
-import { ViewportComponent, StructurePreset } from './viewport';
+import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
import { PluginBehaviors } from '../../mol-plugin/behavior';
import { ColorNames } from '../../mol-util/color/names';
+import { Color } from '../../mol-util/color';
require('mol-plugin-ui/skin/light.scss');
@@ -53,13 +50,25 @@ const DefaultViewerOptions = {
pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
};
-type ViewerOptions = typeof DefaultViewerOptions;
class Viewer {
plugin: PluginContext
- constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
- const o = { ...DefaultViewerOptions, ...options };
+ constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
+ const o = { ...DefaultViewerOptions, ...{
+ layoutIsExpanded: false,
+ layoutShowControls: false,
+ layoutShowRemoteState: false,
+ layoutShowSequence: true,
+ layoutShowLog: false,
+ layoutShowLeftPanel: true,
+
+ viewportShowExpand: true,
+ viewportShowControls: false,
+ viewportShowSettings: false,
+ viewportShowSelectionMode: false,
+ viewportShowAnimation: false,
+ } };
const spec: PluginSpec = {
actions: [...DefaultPluginSpec.actions],
@@ -104,7 +113,8 @@ class Viewer {
[PluginConfig.State.CurrentServer, o.pluginStateServer],
[PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
[PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
- [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
+ [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+ [ShowButtons, showButtons]
]
};
@@ -114,40 +124,27 @@ class Viewer {
if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
this.plugin = createPlugin(element, spec);
- PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
- renderer: {
- ...this.plugin.canvas3d!.props.renderer,
- backgroundColor: ColorNames.white,
- },
- camera: {
- ...this.plugin.canvas3d!.props.camera,
- helper: { axes: { name: 'off', params: {} } }
+ (this.plugin.customState as any) = {
+ colorPalette: {
+ name: 'colors',
+ params: { list: { colors } }
}
- } });
- }
-
- setRemoteSnapshot(id: string) {
- const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
- return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
- }
-
- loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
- return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
- }
+ };
- loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false) {
- const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
- return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
- source: {
- name: 'url',
- params: {
- url: Asset.Url(url),
- format: format as any,
- isBinary,
- options: params.source.params.options,
- }
+ this.plugin.behaviors.canvas3d.initialized.subscribe(v => {
+ if (v) {
+ PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
+ renderer: {
+ ...this.plugin.canvas3d!.props.renderer,
+ backgroundColor: ColorNames.white,
+ },
+ camera: {
+ ...this.plugin.canvas3d!.props.camera,
+ helper: { axes: { name: 'off', params: {} } }
+ }
+ } });
}
- }));
+ });
}
async loadStructuresFromUrlsAndMerge(sources: { url: string, format: BuiltInTrajectoryFormat, isBinary?: boolean }[]) {
@@ -162,69 +159,19 @@ class Viewer {
structures.push({ ref: structureProperties?.ref || structure.ref });
}
+
+ // remove current structuresfrom hierarchy as they will be merged
+ // TODO only works with using loadStructuresFromUrlsAndMerge once
+ // need some more API metho to work with the hierarchy
+ this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');
+
const dependsOn = structures.map(({ ref }) => ref);
const data = this.plugin.state.data.build().toRoot().apply(MergeStructures, { structures }, { dependsOn });
const structure = await data.commit();
const structureProperties = await this.plugin.builders.structure.insertStructureProperties(structure);
- await this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, StructurePreset);
- }
-
- async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
- const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
- const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
- await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
- }
-
- loadPdb(pdb: string) {
- const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
- const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
- return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
- source: {
- name: 'pdb' as const,
- params: {
- provider: {
- id: pdb,
- server: {
- name: provider,
- params: PdbDownloadProvider[provider].defaultValue as any
- }
- },
- options: params.source.params.options,
- }
- }
- }));
- }
-
- loadPdbDev(pdbDev: string) {
- const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
- return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
- source: {
- name: 'pdb-dev' as const,
- params: {
- provider: {
- id: pdbDev,
- encoding: 'bcif',
- },
- options: params.source.params.options,
- }
- }
- }));
- }
-
- loadEmdb(emdb: string) {
- const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
- return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
- source: {
- name: 'pdb-emd-ds' as const,
- params: {
- provider: {
- id: emdb,
- server: provider,
- },
- detail: 3,
- }
- }
- }));
+ this.plugin.behaviors.canvas3d.initialized.subscribe(async v => {
+ await this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, StructurePreset);
+ });
}
}
@@ -260,4 +207,5 @@ const MergeStructures = PluginStateTransform.BuiltIn({
}
});
-(window as any).DockingViewer = Viewer;
\ No newline at end of file
+(window as any).DockingViewer = Viewer;
+export { Viewer as DockingViewer };
\ No newline at end of file
diff --git a/src/examples/docking-viewer/viewport.tsx b/src/apps/docking-viewer/viewport.tsx
similarity index 63%
rename from src/examples/docking-viewer/viewport.tsx
rename to src/apps/docking-viewer/viewport.tsx
index 8e11e6b5ef168bc2efeac6615ac7effdc461b909..ed41fd7542c9cfae40414619c591060151ad052b 100644
--- a/src/examples/docking-viewer/viewport.tsx
+++ b/src/apps/docking-viewer/viewport.tsx
@@ -17,10 +17,11 @@ import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-pl
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
-import { compile } from '../../mol-script/runtime/query/compiler';
-import { StructureSelection, QueryContext, Structure } from '../../mol-model/structure';
import { PluginCommands } from '../../mol-plugin/commands';
import { PluginContext } from '../../mol-plugin/context';
+import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
+import { Color } from '../../mol-util/color';
+import { PluginConfig } from '../../mol-plugin/config';
function shinyStyle(plugin: PluginContext) {
return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
@@ -76,6 +77,8 @@ const PresetParams = {
...StructureRepresentationPresetProvider.CommonParams,
};
+
+
export const StructurePreset = StructureRepresentationPresetProvider({
id: 'preset-structure',
display: { name: 'Structure' },
@@ -89,10 +92,10 @@ export const StructurePreset = StructureRepresentationPresetProvider({
polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
};
- const { update, builder, typeParams, color } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+ const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
const representations = {
- ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color }, { tag: 'ligand' }),
- polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams }, color }, { tag: 'polymer' }),
+ ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+ polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
};
await update.commit({ revertOnError: true });
@@ -112,12 +115,14 @@ export const IllustrativePreset = StructureRepresentationPresetProvider({
if (!structureCell) return {};
const components = {
- all: await presetStaticComponent(plugin, structureCell, 'all')
+ ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+ polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
};
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
const representations = {
- all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: { ...typeParams }, color: 'illustrative' }, { tag: 'all' }),
+ ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: { ...typeParams }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+ polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: { ...typeParams }, color: 'illustrative', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
};
await update.commit({ revertOnError: true });
@@ -128,6 +133,34 @@ export const IllustrativePreset = StructureRepresentationPresetProvider({
}
});
+const SurfacePreset = StructureRepresentationPresetProvider({
+ id: 'preset-surface',
+ display: { name: 'Surface' },
+ params: () => PresetParams,
+ async apply(ref, params, plugin) {
+ const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+ const structure = structureCell?.obj?.data;
+ if (!structureCell || !structure) return {};
+
+ const components = {
+ ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+ polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
+ };
+
+ const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+ const representations = {
+ ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+ polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
+ };
+
+ await update.commit({ revertOnError: true });
+ await shinyStyle(plugin);
+ plugin.managers.interactivity.setProps({ granularity: 'residue' });
+
+ return { components, representations };
+ }
+});
+
const PocketPreset = StructureRepresentationPresetProvider({
id: 'preset-pocket',
display: { name: 'Pocket' },
@@ -144,7 +177,7 @@ const PocketPreset = StructureRepresentationPresetProvider({
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
const representations = {
- ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'partial-charge' }, { tag: 'ligand' }),
+ ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
};
@@ -152,11 +185,6 @@ const PocketPreset = StructureRepresentationPresetProvider({
await shinyStyle(plugin);
plugin.managers.interactivity.setProps({ granularity: 'element' });
- const compiled = compile<StructureSelection>(StructureSelectionQueries.ligand.expression);
- const result = compiled(new QueryContext(structure));
- const selection = StructureSelection.unionStructure(result);
- plugin.managers.camera.focusLoci(Structure.toStructureElementLoci(selection));
-
return { components, representations };
}
});
@@ -172,56 +200,46 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
const components = {
ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
- selection: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `selection`)
+ surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
+ interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
};
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
const representations = {
- ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'partial-charge' }, { tag: 'ligand' }),
- ballAndStick: builder.buildRepresentation(update, components.selection, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'partial-charge' }, { tag: 'ball-and-stick' }),
- interactions: builder.buildRepresentation(update, components.selection, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+ ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+ ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
+ interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+ label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
};
await update.commit({ revertOnError: true });
await shinyStyle(plugin);
plugin.managers.interactivity.setProps({ granularity: 'element' });
- const compiled = compile<StructureSelection>(StructureSelectionQueries.ligand.expression);
- const result = compiled(new QueryContext(structure));
- const selection = StructureSelection.unionStructure(result);
- plugin.managers.camera.focusLoci(Structure.toStructureElementLoci(selection));
-
return { components, representations };
}
});
+export const ShowButtons = PluginConfig.item('showButtons', true);
+
export class ViewportComponent extends PluginUIComponent {
- structurePreset = () => {
- this.plugin.managers.structure.component.applyPreset(
- this.plugin.managers.structure.hierarchy.selection.structures,
- StructurePreset
- );
+ async _set(structures: readonly StructureRef[], preset: StructureRepresentationPresetProvider) {
+ await this.plugin.managers.structure.component.clear(structures);
+ await this.plugin.managers.structure.component.applyPreset(structures, preset);
}
- illustrativePreset = () => {
- this.plugin.managers.structure.component.applyPreset(
- this.plugin.managers.structure.hierarchy.selection.structures,
- IllustrativePreset
- );
+ set = async (preset: StructureRepresentationPresetProvider) => {
+ await this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset);
}
- pocketPreset = () => {
- this.plugin.managers.structure.component.applyPreset(
- this.plugin.managers.structure.hierarchy.selection.structures,
- PocketPreset
- );
- }
+ structurePreset = () => this.set(StructurePreset);
+ illustrativePreset = () => this.set(IllustrativePreset);
+ surfacePreset = () => this.set(SurfacePreset);
+ pocketPreset = () => this.set(PocketPreset);
+ interactionsPreset = () => this.set(InteractionsPreset);
- interactionsPreset = () => {
- this.plugin.managers.structure.component.applyPreset(
- this.plugin.managers.structure.hierarchy.selection.structures,
- InteractionsPreset
- );
+ get showButtons () {
+ return this.plugin.config.get(ShowButtons);
}
render() {
@@ -229,7 +247,7 @@ export class ViewportComponent extends PluginUIComponent {
return <>
<Viewport />
- <div className='msp-viewport-top-left-controls'>
+ {this.showButtons && <div className='msp-viewport-top-left-controls'>
<div style={{ marginBottom: '4px' }}>
<Button onClick={this.structurePreset} >Structure</Button>
</div>
@@ -237,12 +255,15 @@ export class ViewportComponent extends PluginUIComponent {
<Button onClick={this.illustrativePreset}>Illustrative</Button>
</div>
<div style={{ marginBottom: '4px' }}>
- <Button onClick={this.pocketPreset}>Pocket</Button>
+ <Button onClick={this.surfacePreset}>Surface</Button>
</div>
+ {/* <div style={{ marginBottom: '4px' }}>
+ <Button onClick={this.pocketPreset}>Pocket</Button>
+ </div> */}
<div style={{ marginBottom: '4px' }}>
<Button onClick={this.interactionsPreset}>Interactions</Button>
</div>
- </div>
+ </div>}
<VPControls />
<BackgroundTaskProgress />
<div className='msp-highlight-toast-wrapper'>
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index f64698cf11d0e1f44a0ecb55780df8f7e81bf891..a476588db89e170020d270d79c1649c97c65a2e4 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -92,7 +92,7 @@ export class Viewer {
},
components: {
...DefaultPluginSpec.components,
- remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+ remoteState: o.layoutShowRemoteState ? 'default' : 'none'
},
config: [
[PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index 8cb502e3616404709ba9b16fc93a1805026de819..3c4b587af398b0c6a1136b53e40f635b7ee01958 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -66,6 +66,7 @@ export const Canvas3DParams = {
};
export const DefaultCanvas3DParams = PD.getDefaultValues(Canvas3DParams);
export type Canvas3DProps = PD.Values<typeof Canvas3DParams>
+export type PartialCanvas3DProps = { [K in keyof Canvas3DProps]?: Partial<Canvas3DProps[K]> }
export { Canvas3D };
@@ -97,7 +98,7 @@ interface Canvas3D {
readonly camera: Camera
readonly boundingSphere: Readonly<Sphere3D>
getPixelData(variant: GraphicsRenderVariant): PixelData
- setProps(props: Partial<Canvas3DProps> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void)): void
+ setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void)): void
getImagePass(props: Partial<ImageProps>): ImagePass
/** Returns a copy of the current Canvas3D instance props */
@@ -530,7 +531,7 @@ namespace Canvas3D {
didDraw,
reprCount,
setProps: (properties) => {
- const props: Partial<Canvas3DProps> = typeof properties === 'function'
+ const props: PartialCanvas3DProps = typeof properties === 'function'
? produce(getProps(), properties)
: properties;
@@ -538,7 +539,7 @@ namespace Canvas3D {
if (props.camera && props.camera.mode !== undefined && props.camera.mode !== camera.state.mode) {
cameraState.mode = props.camera.mode;
}
- if (props.cameraFog !== undefined) {
+ if (props.cameraFog !== undefined && props.cameraFog.params) {
const newFog = props.cameraFog.name === 'on' ? props.cameraFog.params.intensity : 0;
if (newFog !== camera.state.fog) cameraState.fog = newFog;
}
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index 3cc29133e9442ec5de6fd1d4ca94704bd80c13ac..f9a4f4213a1d42cb38ecbb6371d89c2d1f97cdfa 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -265,6 +265,10 @@ export namespace CifField {
toFloatArray: params => ColumnHelpers.createAndFillArray(rowCount, float, params)
};
}
+
+ export function ofUndefined(rowCount: number, schema: Column.Schema): CifField {
+ return ofColumn(Column.Undefined(rowCount, schema));
+ }
}
export function tensorFieldNameGetter(field: string, rank: number, zeroIndexed: boolean, namingVariant: 'brackets' | 'underscore') {
diff --git a/src/mol-model-formats/structure/basic/atomic.ts b/src/mol-model-formats/structure/basic/atomic.ts
index 4cfb2634ddce122882d06060121fac44b195092f..d2fbfa69f055a6170862ea2ca88a82556e280556 100644
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -67,13 +67,27 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
});
const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
+ const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
+
+ if (!residues.label_seq_id.isDefined) {
+ const seqIds = new Int32Array(residues.label_seq_id.rowCount);
+ const { residues: residueOffsets, chains: chainOffsets } = offsets;
+ let cI = 0;
+ let seqId = 0;
+ for (let i = 0, il = seqIds.length; i < il; ++i) {
+ if (chainOffsets[cI] > residueOffsets[i]) {
+ cI += 1;
+ seqId = 0;
+ }
+ seqIds[i] = ++seqId;
+ }
+ residues.label_seq_id = Column.ofIntArray(seqIds);
+ }
// Optimize the numeric columns
Table.columnToArray(residues, 'label_seq_id', Int32Array);
Table.columnToArray(residues, 'auth_seq_id', Int32Array);
- const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
-
// Fix possibly missing auth_/label_ columns
substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
diff --git a/src/mol-model-formats/structure/pdb/atom-site.ts b/src/mol-model-formats/structure/pdb/atom-site.ts
index 3ffacc79b74a608669cb96960847f9d94181159f..933499f755aa3e6cc2697996d348a371a90af13e 100644
--- a/src/mol-model-formats/structure/pdb/atom-site.ts
+++ b/src/mol-model-formats/structure/pdb/atom-site.ts
@@ -9,6 +9,7 @@ import { CifField } from '../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { guessElementSymbolTokens } from '../util';
+import { Column } from '../../../mol-data/db';
type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
export function getAtomSiteTemplate(data: string, count: number) {
@@ -42,13 +43,12 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
const auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
- const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
return {
auth_asym_id,
auth_atom_id,
auth_comp_id,
- auth_seq_id,
+ auth_seq_id: CifField.ofTokens(sites.auth_seq_id),
B_iso_or_equiv: CifField.ofTokens(sites.B_iso_or_equiv),
Cartn_x: CifField.ofTokens(sites.Cartn_x),
Cartn_y: CifField.ofTokens(sites.Cartn_y),
@@ -61,7 +61,7 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
- label_seq_id: auth_seq_id,
+ label_seq_id: CifField.ofUndefined(sites.count, Column.Schema.int),
label_entity_id: CifField.ofStrings(sites.label_entity_id),
occupancy: CifField.ofTokens(sites.occupancy),
diff --git a/src/mol-model-formats/structure/pdb/secondary-structure.ts b/src/mol-model-formats/structure/pdb/secondary-structure.ts
index f9b005ad2fc49909653aa2eeb79322dd1f31c370..e6e93062983fa24cae1ee5d54e281cc3db41c7e2 100644
--- a/src/mol-model-formats/structure/pdb/secondary-structure.ts
+++ b/src/mol-model-formats/structure/pdb/secondary-structure.ts
@@ -7,6 +7,7 @@
import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { Tokens } from '../../../mol-io/reader/common/text/tokenizer';
+import { Column } from '../../../mol-data/db';
const HelixTypes: {[k: string]: mmCIF_Schema['struct_conf']['conf_type_id']['T']} = {
// CLASS NUMBER
@@ -99,29 +100,27 @@ export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): C
const beg_auth_asym_id = CifField.ofStrings(helices.map(h => h.initChainID));
const beg_auth_comp_id = CifField.ofStrings(helices.map(h => h.initResName));
- const beg_auth_seq_id = CifField.ofStrings(helices.map(h => h.initSeqNum));
const end_auth_asym_id = CifField.ofStrings(helices.map(h => h.endChainID));
- const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));
- const end_auth_seq_id = CifField.ofStrings(helices.map(h => h.endSeqNum));
+ const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));;
const struct_conf: CifCategory.Fields<mmCIF_Schema['struct_conf']> = {
beg_label_asym_id: beg_auth_asym_id,
beg_label_comp_id: beg_auth_comp_id,
- beg_label_seq_id: beg_auth_seq_id,
+ beg_label_seq_id: CifField.ofUndefined(helices.length, Column.Schema.int),
beg_auth_asym_id,
beg_auth_comp_id,
- beg_auth_seq_id,
+ beg_auth_seq_id: CifField.ofStrings(helices.map(h => h.initSeqNum)),
conf_type_id: CifField.ofStrings(helices.map(h => getStructConfTypeId(h.helixClass))),
details: CifField.ofStrings(helices.map(h => h.comment)),
end_label_asym_id: end_auth_asym_id,
- end_label_comp_id: end_auth_asym_id,
- end_label_seq_id: end_auth_seq_id,
+ end_label_comp_id: end_auth_comp_id,
+ end_label_seq_id: CifField.ofUndefined(helices.length, Column.Schema.int),
end_auth_asym_id,
end_auth_comp_id,
- end_auth_seq_id,
+ end_auth_seq_id: CifField.ofStrings(helices.map(h => h.endSeqNum)),
id: CifField.ofStrings(helices.map(h => h.serNum)),
pdbx_beg_PDB_ins_code: CifField.ofStrings(helices.map(h => h.initICode)),
diff --git a/src/mol-model-formats/structure/property/secondary-structure.ts b/src/mol-model-formats/structure/property/secondary-structure.ts
index 616cd18bf2a6fbbf5eabe1a7475b6f1914537467..3bf1f068554faeef60f2e2ed05afe882723c0e84 100644
--- a/src/mol-model-formats/structure/property/secondary-structure.ts
+++ b/src/mol-model-formats/structure/property/secondary-structure.ts
@@ -62,8 +62,8 @@ type SecondaryStructureData = { type: SecondaryStructureType[], key: number[], e
function addHelices(cat: StructConf, map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
- const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
- const { end_label_seq_id, pdbx_end_PDB_ins_code } = cat;
+ const { beg_label_asym_id, beg_auth_seq_id, pdbx_beg_PDB_ins_code } = cat;
+ const { end_auth_seq_id, pdbx_end_PDB_ins_code } = cat;
const { pdbx_PDB_helix_class, conf_type_id, details } = cat;
for (let i = 0, _i = cat._rowCount; i < _i; i++) {
@@ -81,9 +81,9 @@ function addHelices(cat: StructConf, map: SecondaryStructureMap, elements: Secon
details: details.valueKind(i) === Column.ValueKind.Present ? details.value(i) : void 0
};
const entry: SecondaryStructureEntry = {
- startSeqNumber: beg_label_seq_id.value(i),
+ startSeqNumber: beg_auth_seq_id.value(i),
startInsCode: pdbx_beg_PDB_ins_code.value(i),
- endSeqNumber: end_label_seq_id.value(i),
+ endSeqNumber: end_auth_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
type,
key: elements.length
@@ -108,8 +108,8 @@ function addHelices(cat: StructConf, map: SecondaryStructureMap, elements: Secon
function addSheets(cat: StructSheetRange, map: SecondaryStructureMap, sheetCount: number, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
- const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
- const { end_label_seq_id, pdbx_end_PDB_ins_code } = cat;
+ const { beg_label_asym_id, beg_auth_seq_id, pdbx_beg_PDB_ins_code } = cat;
+ const { end_auth_seq_id, pdbx_end_PDB_ins_code } = cat;
const { sheet_id } = cat;
const sheet_id_key = new Map<string, number>();
@@ -132,9 +132,9 @@ function addSheets(cat: StructSheetRange, map: SecondaryStructureMap, sheetCount
symmetry: void 0
};
const entry: SecondaryStructureEntry = {
- startSeqNumber: beg_label_seq_id.value(i),
+ startSeqNumber: beg_auth_seq_id.value(i),
startInsCode: pdbx_beg_PDB_ins_code.value(i),
- endSeqNumber: end_label_seq_id.value(i),
+ endSeqNumber: end_auth_seq_id.value(i),
endInsCode: pdbx_end_PDB_ins_code.value(i),
type,
key: elements.length
@@ -159,12 +159,12 @@ function addSheets(cat: StructSheetRange, map: SecondaryStructureMap, sheetCount
}
function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: SecondaryStructureEntry, resStart: ResidueIndex, resEnd: ResidueIndex, data: SecondaryStructureData) {
- const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
+ const { auth_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
const { endSeqNumber, endInsCode, key, type } = entry;
let rI = resStart;
while (rI < resEnd) {
- const seqNumber = label_seq_id.value(rI);
+ const seqNumber = auth_seq_id.value(rI);
data.type[rI] = type;
data.key[rI] = key;
@@ -180,7 +180,7 @@ function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: Second
function assignSecondaryStructureRanges(hierarchy: AtomicHierarchy, map: SecondaryStructureMap, data: SecondaryStructureData) {
const { count: chainCount } = hierarchy.chainAtomSegments;
const { label_asym_id } = hierarchy.chains;
- const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
+ const { auth_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
for (let cI = 0 as ChainIndex; cI < chainCount; cI++) {
const resStart = AtomicHierarchy.chainStartResidueIndex(hierarchy, cI), resEnd = AtomicHierarchy.chainEndResidueIndexExcl(hierarchy, cI);
@@ -189,7 +189,7 @@ function assignSecondaryStructureRanges(hierarchy: AtomicHierarchy, map: Seconda
const entries = map.get(asymId)!;
for (let rI = resStart; rI < resEnd; rI++) {
- const seqNumber = label_seq_id.value(rI);
+ const seqNumber = auth_seq_id.value(rI);
if (entries.has(seqNumber)) {
const entryList = entries.get(seqNumber)!;
for (const entry of entryList) {
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 1013bbaa221bbfe474bbad780d3be4d1829c557b..3f8354fb354388e6922eafa9cb432b2b93384708 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -52,6 +52,7 @@ const atom_site_fields = CifWriter.fields<StructureElement.Location, Structure>(
.float('Cartn_y', P.atom.y, { digitCount: 3, encoder: E.fixedPoint3 })
.float('Cartn_z', P.atom.z, { digitCount: 3, encoder: E.fixedPoint3 })
.float('occupancy', P.atom.occupancy, { digitCount: 2, encoder: E.fixedPoint2 })
+ .float('B_iso_or_equiv', P.atom.B_iso_or_equiv, { digitCount: 2, encoder: E.fixedPoint2 })
.int('pdbx_formal_charge', P.atom.pdbx_formal_charge, {
encoder: E.deltaRLE,
valueKind: (k, d) => k.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.valueKind(k.element)
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 62d0c844f7155422b8509b336f5947628dd00786..d8f36ff6837b308fbabebdc40e84f59c1382c416 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -52,7 +52,7 @@ const atom = {
auth_atom_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.auth_atom_id.value(l.element)),
label_alt_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.label_alt_id.value(l.element)),
label_comp_id: p(compId),
- auth_comp_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.auth_comp_id.value(l.unit.residueIndex[l.element])),
+ auth_comp_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.auth_comp_id.value(l.element)),
pdbx_formal_charge: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.value(l.element)),
// Derived
@@ -93,7 +93,7 @@ const residue = {
pdbx_PDB_ins_code: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element])),
// Properties
- isNonStandard: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : microheterogeneityCompIds(l).some(c => l.unit.model.properties.chemicalComponentMap.get(c)!.mon_nstd_flag[0] !== 'y')),
+ isNonStandard: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : microheterogeneityCompIds(l).some(c => l.unit.model.properties.chemicalComponentMap.get(c)!.mon_nstd_flag[0] === 'n')),
hasMicroheterogeneity: p(hasMicroheterogeneity),
microheterogeneityCompIds: p(microheterogeneityCompIds),
secondary_structure_type: p(l => {
diff --git a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
index d220f1f1b8b27cf6e7096e01912d0d418aaa4830..e007906d1c82084e0cbe60bfacf235dce91a1c86 100644
--- a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
+++ b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
@@ -16,6 +16,7 @@ import { PluginContext } from '../../../mol-plugin/context';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { Model } from '../../../mol-model/structure';
import { getStructureQuality } from '../../../mol-repr/util';
+import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operator-name';
export interface TrajectoryHierarchyPresetProvider<P = any, S = {}> extends PresetProvider<PluginStateObject.Molecule.Trajectory, P, S> { }
export function TrajectoryHierarchyPresetProvider<P, S>(preset: TrajectoryHierarchyPresetProvider<P, S>) { return preset; }
@@ -100,7 +101,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
structures.push(structure);
const quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.length }) : 'medium';
- await builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { globalThemeName: 'model-index', quality });
+ await builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'model-index' }, quality });
}
return { models, structures };
@@ -125,7 +126,7 @@ async function applyCrystalSymmetry(props: { ijkMin: Vec3, ijkMax: Vec3, theme?:
const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: false });
- const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { globalThemeName: props.theme });
+ const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: props.theme } });
return {
model,
@@ -167,10 +168,52 @@ const supercell = TrajectoryHierarchyPresetProvider({
}
});
+const CrystalContactsParams = (a: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext) => ({
+ model: PD.Optional(PD.Group(StateTransformer.getParamDefinition(StateTransforms.Model.ModelFromTrajectory, a, plugin))),
+ ...CommonParams(a, plugin)
+});
+
+const crystalContacts = TrajectoryHierarchyPresetProvider({
+ id: 'preset-trajectory-crystal-contacts',
+ display: {
+ name: 'Crystal Contacts', group: 'Preset',
+ description: 'Showsasymetric unit and chains from neighbours within 5 \u212B, i.e., symmetry mates.'
+ },
+ isApplicable: o => {
+ return Model.hasCrystalSymmetry(o.data[0]);
+ },
+ params: CrystalContactsParams,
+ async apply(trajectory, params, plugin) {
+ const builder = plugin.builders.structure;
+
+ const model = await builder.createModel(trajectory, params.model);
+ const modelProperties = await builder.insertModelProperties(model, params.modelProperties);
+
+ const structure = await builder.createStructure(modelProperties || model, {
+ name: 'symmetry-mates',
+ params: { radius: 5 }
+ });
+ const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
+
+ const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });
+ const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } });
+
+ return {
+ model,
+ modelProperties,
+ unitcell,
+ structure,
+ structureProperties,
+ representation
+ };
+ }
+});
+
export const PresetTrajectoryHierarchy = {
'default': defaultPreset,
'all-models': allModels,
unitcell,
supercell,
+ crystalContacts,
};
export type PresetTrajectoryHierarchy = typeof PresetTrajectoryHierarchy;
\ No newline at end of file
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 3eb9bdf539867ef6e5057fcd4afcd37a877ac820..d8d83bbdc685a29b92c8ccd33121df77871cb057 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -18,6 +18,8 @@ import { StructureSelectionQueries as Q } from '../../helpers/structure-selectio
import { PluginConfig } from '../../../mol-plugin/config';
import { StructureFocusRepresentation } from '../../../mol-plugin/behavior/dynamic/selection/structure-focus-representation';
import { createStructureColorThemeParams } from '../../helpers/structure-representation-params';
+import { ChainIdColorThemeProvider } from '../../../mol-theme/color/chain-id';
+import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operator-name';
export interface StructureRepresentationPresetProvider<P = any, S extends _Result = _Result> extends PresetProvider<PluginStateObject.Molecule.Structure, P, S> { }
export function StructureRepresentationPresetProvider<P, S extends _Result>(repr: StructureRepresentationPresetProvider<P, S>) { return repr; }
@@ -34,7 +36,7 @@ export namespace StructureRepresentationPresetProvider {
quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
theme: PD.Optional(PD.Group({
globalName: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
- carbonByChainId: PD.Optional(PD.Boolean(true)),
+ carbonColor: PD.Optional(PD.Select('chain-id', PD.arrayToOptions(['chain-id', 'operator-name', 'element-symbol'] as const))),
focus: PD.Optional(PD.Group({
name: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
params: PD.Optional(PD.Value<ColorTheme.BuiltInParams<ColorTheme.BuiltIn>>({} as any))
@@ -43,6 +45,14 @@ export namespace StructureRepresentationPresetProvider {
};
export type CommonParams = PD.ValuesFor<typeof CommonParams>
+ function getCarbonColorParams(name: 'chain-id' | 'operator-name' | 'element-symbol') {
+ return name === 'chain-id'
+ ? { name, params: ChainIdColorThemeProvider.defaultValues }
+ : name === 'operator-name'
+ ? { name, params: OperatorNameColorThemeProvider.defaultValues }
+ : { name, params: {} };
+ }
+
export function reprBuilder(plugin: PluginContext, params: CommonParams) {
const update = plugin.state.data.build();
const builder = plugin.builders.structure.representation;
@@ -53,16 +63,16 @@ export namespace StructureRepresentationPresetProvider {
if (params.quality && params.quality !== 'auto') typeParams.quality = params.quality;
if (params.ignoreHydrogens !== void 0) typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
- const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = typeof params.theme?.carbonByChainId !== 'undefined' ? { carbonByChainId: !!params.theme?.carbonByChainId } : { };
+ const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
+ ? { carbonColor: getCarbonColorParams(params.theme?.carbonColor) }
+ : { };
return { update, builder, color, typeParams, ballAndStickColor };
}
export function updateFocusRepr<T extends ColorTheme.BuiltIn>(plugin: PluginContext, structure: Structure, themeName: T | undefined, themeParams: ColorTheme.BuiltInParams<T> | undefined) {
- if (!themeName && !themeParams) return;
-
return plugin.state.updateBehavior(StructureFocusRepresentation, p => {
- const c = createStructureColorThemeParams(plugin, structure, 'ball-and-stick', themeName, themeParams);
+ const c = createStructureColorThemeParams(plugin, structure, 'ball-and-stick', themeName || 'element-symbol', themeParams);
p.surroundingsParams.colorTheme = c;
p.targetParams.colorTheme = c;
});
@@ -155,8 +165,8 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6 }, color }, { tag: 'water' }),
- ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonByChainId: false } }, { tag: 'ion' }),
- lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonByChainId: false } }, { tag: 'lipid' }),
+ ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
+ lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
};
diff --git a/src/mol-plugin-state/manager/loci-label.ts b/src/mol-plugin-state/manager/loci-label.ts
index 5193912b4bf3ce11ed652f0da69791b1298ba1e3..a5ee1eba6cd8184ea6b7495bd58e06e036e6c938 100644
--- a/src/mol-plugin-state/manager/loci-label.ts
+++ b/src/mol-plugin-state/manager/loci-label.ts
@@ -22,6 +22,12 @@ export type LociLabelProvider = {
export class LociLabelManager {
providers: LociLabelProvider[] = [];
+ clearProviders() {
+ this.providers = [];
+ this.isDirty = true;
+ this.showLabels();
+ }
+
addProvider(provider: LociLabelProvider) {
this.providers.push(provider);
this.providers.sort((a, b) => (b.priority || 0) - (a.priority || 0));
diff --git a/src/mol-plugin-state/transforms/data.ts b/src/mol-plugin-state/transforms/data.ts
index 7c28a8c7b4be3e82d0b25ed8f8a85636641b04cf..178d678e6ce919b4b2f3103ae98c06b69cf93b64 100644
--- a/src/mol-plugin-state/transforms/data.ts
+++ b/src/mol-plugin-state/transforms/data.ts
@@ -5,7 +5,6 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { isTypedArray } from '../../mol-data/db/column-helpers';
import * as CCP4 from '../../mol-io/reader/ccp4/parser';
import { CIF } from '../../mol-io/reader/cif';
import * as DSN6 from '../../mol-io/reader/dsn6/parser';
@@ -135,18 +134,23 @@ const RawData = PluginStateTransform.BuiltIn({
from: [SO.Root],
to: [SO.Data.String, SO.Data.Binary],
params: {
- data: PD.Value<string | number[]>('', { isHidden: true }),
+ data: PD.Value<string | number[] | ArrayBuffer | Uint8Array>('', { isHidden: true }),
label: PD.Optional(PD.Text(''))
}
})({
apply({ params: p }) {
return Task.create('Raw Data', async () => {
- if (typeof p.data !== 'string' && isTypedArray(p.data)) {
- throw new Error('Supplied binary data must be a plain array.');
+ if (typeof p.data === 'string') {
+ return new SO.Data.String(p.data as string, { label: p.label ? p.label : 'String' });
+ } else if (Array.isArray(p.data)) {
+ return new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
+ } else if (p.data instanceof ArrayBuffer) {
+ return new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
+ } else if (p.data instanceof Uint8Array) {
+ return new SO.Data.Binary(p.data, { label: p.label ? p.label : 'Binary' });
+ } else {
+ throw new Error('Supplied binary data must be a plain array, ArrayBuffer, or Uint8Array.');
}
- return typeof p.data === 'string'
- ? new SO.Data.String(p.data as string, { label: p.label ? p.label : 'String' })
- : new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
});
},
update({ oldParams, newParams, b }) {
@@ -156,6 +160,25 @@ const RawData = PluginStateTransform.BuiltIn({
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
+ },
+ customSerialization: {
+ toJSON(p) {
+ if (typeof p.data === 'string' || Array.isArray(p.data)) {
+ return p;
+ } else if (p.data instanceof ArrayBuffer) {
+ const v = new Uint8Array(p.data);
+ const data = new Array(v.length);
+ for (let i = 0, _i = v.length; i < _i; i++) data[i] = v[i];
+ return { data, label: p.label };
+ } else if (p.data instanceof Uint8Array) {
+ const data = new Array(p.data.length);
+ for (let i = 0, _i = p.data.length; i < _i; i++) data[i] = p.data[i];
+ return { data, label: p.label };
+ }
+ },
+ fromJSON(data: any) {
+ return data;
+ }
}
});
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 9450a2469678aa9339982aa020a7cfb33a6a84e5..eb7fc71008d9c2f481997477a52e9ed2ce0e0d0e 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -182,8 +182,7 @@ export class PluginContext {
(this.canvas3d as Canvas3D) = Canvas3D.fromCanvas(canvas);
this.canvas3dInit.next(true);
- const renderer = this.canvas3d!.props.renderer;
- PluginCommands.Canvas3D.SetSettings(this, { settings: { renderer: { ...renderer, backgroundColor: Color(0xFCFBF9) } } });
+ this.canvas3d?.setProps(this.spec.components?.viewport?.canvas3d || { renderer: { backgroundColor: Color(0xFCFBF9) } });
this.canvas3d!.animate();
(this.helpers.viewportScreenshot as ViewportScreenshotHelper) = new ViewportScreenshotHelper(this);
return true;
@@ -346,29 +345,31 @@ export class PluginContext {
}
}
- constructor(public spec: PluginSpec) {
- // the reason for this is that sometimes, transform params get modified inline (i.e. palette.valueLabel)
- // and freezing the params object causes "read-only exception"
- // TODO: is this the best place to do it?
- setAutoFreeze(false);
-
+ async init() {
this.events.log.subscribe(e => this.log.entries = this.log.entries.push(e));
this.initBehaviorEvents();
this.initBuiltInBehavior();
- this.initBehaviors();
+ (this.managers.interactivity as InteractivityManager) = new InteractivityManager(this);
+ (this.managers.lociLabels as LociLabelManager) = new LociLabelManager(this);
+ (this.builders.structure as StructureBuilder) = new StructureBuilder(this);
+
this.initDataActions();
this.initAnimations();
this.initCustomParamEditors();
- (this.managers.interactivity as InteractivityManager) = new InteractivityManager(this);
- (this.managers.lociLabels as LociLabelManager) = new LociLabelManager(this);
-
- (this.builders.structure as StructureBuilder) = new StructureBuilder(this);
+ await this.initBehaviors();
this.log.message(`Mol* Plugin ${PLUGIN_VERSION} [${PLUGIN_VERSION_DATE.toLocaleString()}]`);
if (!isProductionMode) this.log.message(`Development mode enabled`);
if (isDebugMode) this.log.message(`Debug mode enabled`);
}
+
+ constructor(public spec: PluginSpec) {
+ // the reason for this is that sometimes, transform params get modified inline (i.e. palette.valueLabel)
+ // and freezing the params object causes "read-only exception"
+ // TODO: is this the best place to do it?
+ setAutoFreeze(false);
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index c1b568029e0dcbe7676fbffd70d54cac011a6475..288db73b74ac69038d1b8f4ebad103cb5730abd1 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -94,6 +94,16 @@ export const DefaultPluginSpec: PluginSpec = {
export function createPlugin(target: HTMLElement, spec?: PluginSpec): PluginContext {
const ctx = new PluginContext(spec || DefaultPluginSpec);
+ ctx.init();
ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
return ctx;
+}
+
+/** Returns the instance of the plugin after all behaviors have been initialized */
+export async function createPluginAsync(target: HTMLElement, spec?: PluginSpec) {
+ const ctx = new PluginContext(spec || DefaultPluginSpec);
+ const init = ctx.init();
+ ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
+ await init;
+ return ctx;
}
\ No newline at end of file
diff --git a/src/mol-plugin/spec.ts b/src/mol-plugin/spec.ts
index 0b6e08d118e8255b23ea425bf2884482f18f4fd5..437dca7679402518ba175a58d33ed3e7b737c3a3 100644
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -10,6 +10,7 @@ import { StateTransformParameters } from '../mol-plugin-ui/state/common';
import { PluginLayoutStateProps } from './layout';
import { PluginStateAnimation } from '../mol-plugin-state/animation/model';
import { PluginConfigItem } from './config';
+import { PartialCanvas3DProps } from '../mol-canvas3d/canvas3d';
export { PluginSpec };
@@ -27,7 +28,8 @@ interface PluginSpec {
structureTools?: React.ComponentClass,
viewport?: {
view?: React.ComponentClass,
- controls?: React.ComponentClass
+ controls?: React.ComponentClass,
+ canvas3d?: PartialCanvas3DProps
}
},
config?: [PluginConfigItem, unknown][]
diff --git a/src/mol-state/transform.ts b/src/mol-state/transform.ts
index c1cce1fa255569073595944ae90969038e390d9f..536fa51ba0120bbe6bd0e5c3acac6f9e88976d44 100644
--- a/src/mol-state/transform.ts
+++ b/src/mol-state/transform.ts
@@ -194,7 +194,7 @@ namespace Transform {
export function fromJSON(t: Serialized): Transform {
const transformer = StateTransformer.get(t.transformer);
const pFromJson = transformer.definition.customSerialization
- ? transformer.definition.customSerialization.toJSON
+ ? transformer.definition.customSerialization.fromJSON
: _id;
return {
parent: t.parent as Ref,
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index 18e3eb2a20d8a704c814c80c00170a02b841bc1e..990aaa1034f3cfe2372244270a94eaefe7f67a98 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -24,6 +24,9 @@ export const ChainIdColorThemeParams = {
export type ChainIdColorThemeParams = typeof ChainIdColorThemeParams
export function getChainIdColorThemeParams(ctx: ThemeDataContext) {
const params = PD.clone(ChainIdColorThemeParams);
+ if (ctx.structure?.models.some(m => m.coarseHierarchy.isDefined)) {
+ params.asymId.defaultValue = 'label';
+ }
return params;
}
diff --git a/src/mol-theme/color/element-symbol.ts b/src/mol-theme/color/element-symbol.ts
index c0a96088e1f8778dbea90316635bbff088d53902..4f21b908ae02dadbefccb0e9b1d21f88e75c54f9 100644
--- a/src/mol-theme/color/element-symbol.ts
+++ b/src/mol-theme/color/element-symbol.ts
@@ -13,7 +13,8 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ThemeDataContext } from '../theme';
import { TableLegend } from '../../mol-util/legend';
import { getAdjustedColorMap } from '../../mol-util/color/color';
-import { ChainIdColorTheme, getChainIdColorThemeParams } from './chain-id';
+import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
+import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
export const ElementSymbolColors = ColorMap({
@@ -24,8 +25,14 @@ export type ElementSymbolColors = typeof ElementSymbolColors
const DefaultElementSymbolColor = Color(0xFFFFFF);
const Description = 'Assigns a color to every atom according to its chemical element.';
+// TODO generalise `carbonColor` param to all themes?
+
export const ElementSymbolColorThemeParams = {
- carbonByChainId: PD.Boolean(true),
+ carbonColor: PD.MappedStatic('chain-id', {
+ 'chain-id': PD.Group({ ...ChainIdColorThemeParams }),
+ 'operator-name': PD.Group({ ...OperatorNameColorThemeParams }),
+ 'element-symbol': PD.Group({})
+ }, { description: 'Use chain-id coloring for carbon atoms.' }),
saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
};
@@ -42,11 +49,15 @@ export function elementSymbolColor(colorMap: ElementSymbolColors, element: Eleme
export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams> {
const colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
- const chainIdColor = ChainIdColorTheme(ctx, PD.getDefaultValues(getChainIdColorThemeParams(ctx))).color;
+ const carbonColor = props.carbonColor.name === 'chain-id'
+ ? ChainIdColorTheme(ctx, props.carbonColor.params).color
+ : props.carbonColor.name === 'operator-name'
+ ? OperatorNameColorTheme(ctx, props.carbonColor.params).color
+ : undefined;
function elementColor(element: ElementSymbol, location: Location) {
- return (props.carbonByChainId && element === 'C')
- ? chainIdColor(location, false)
+ return (carbonColor && element === 'C')
+ ? carbonColor(location, false)
: elementSymbolColor(colorMap, element);
}
@@ -68,7 +79,7 @@ export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<
return {
factory: ElementSymbolColorTheme,
- granularity: 'group',
+ granularity: 'groupInstance',
color,
props,
description: Description,
diff --git a/src/mol-theme/color/illustrative.ts b/src/mol-theme/color/illustrative.ts
index 9f53e45a203b6e3d32e11a6cf37aa98d3fd3624e..d756df828adf5034d6efd7a9da7f76e851d7164c 100644
--- a/src/mol-theme/color/illustrative.ts
+++ b/src/mol-theme/color/illustrative.ts
@@ -11,19 +11,21 @@ import { Location } from '../../mol-model/location';
import { ColorTheme } from '../color';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ThemeDataContext } from '../theme';
-import { ChainIdColorTheme, getChainIdColorThemeParams } from './chain-id';
+import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
const DefaultIllustrativeColor = Color(0xEEEEEE);
const Description = `Assigns an illustrative color that gives every chain a unique color with lighter carbons (inspired by David Goodsell's Molecule of the Month style).`;
-export const IllustrativeColorThemeParams = {};
+export const IllustrativeColorThemeParams = {
+ ...ChainIdColorThemeParams
+};
export type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams
export function getIllustrativeColorThemeParams(ctx: ThemeDataContext) {
return IllustrativeColorThemeParams; // TODO return copy
}
export function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<IllustrativeColorThemeParams>): ColorTheme<IllustrativeColorThemeParams> {
- const { color: chainIdColor, legend } = ChainIdColorTheme(ctx, PD.getDefaultValues(getChainIdColorThemeParams(ctx)));
+ const { color: chainIdColor, legend } = ChainIdColorTheme(ctx, props);
function illustrativeColor(location: Location, typeSymbol: ElementSymbol) {
const baseColor = chainIdColor(location, false);
diff --git a/src/mol-theme/color/operator-name.ts b/src/mol-theme/color/operator-name.ts
index 1e1b91ac34dd0c0eb9f2c75b1e1b0e240c81f3cf..e6e2f432d9f8c383d6fe17fe73be1ecd525a1e47 100644
--- a/src/mol-theme/color/operator-name.ts
+++ b/src/mol-theme/color/operator-name.ts
@@ -12,9 +12,8 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ThemeDataContext } from '../theme';
import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { ScaleLegend, TableLegend } from '../../mol-util/legend';
-import { ColorLists, getColorListFromName } from '../../mol-util/color/lists';
-const DefaultList = 'dark-2';
+const DefaultList = 'many-distinct';
const DefaultColor = Color(0xCCCCCC);
const Description = `Assigns a color based on the operator name of a transformed chain.`;
@@ -24,15 +23,6 @@ export const OperatorNameColorThemeParams = {
export type OperatorNameColorThemeParams = typeof OperatorNameColorThemeParams
export function getOperatorNameColorThemeParams(ctx: ThemeDataContext) {
const params = PD.clone(OperatorNameColorThemeParams);
- if (ctx.structure) {
- if (getOperatorNameSerialMap(ctx.structure.root).size > ColorLists[DefaultList].list.length) {
- params.palette.defaultValue.name = 'colors';
- params.palette.defaultValue.params = {
- ...params.palette.defaultValue.params,
- list: { kind: 'interpolate', colors: getColorListFromName(DefaultList).list }
- };
- }
- }
return params;
}
diff --git a/src/mol-theme/color/sequence-id.ts b/src/mol-theme/color/sequence-id.ts
index 0520e0677a6e0fb110a167d39e81cb0f81b371f9..ec262ad0a932b580dc1051ffec21dd925320ae09 100644
--- a/src/mol-theme/color/sequence-id.ts
+++ b/src/mol-theme/color/sequence-id.ts
@@ -58,9 +58,14 @@ function getSequenceLength(unit: Unit, element: ElementIndex) {
break;
}
if (entityId === '') return 0;
+
const entityIndex = model.entities.getEntityIndex(entityId);
if (entityIndex === -1) return 0;
- return model.sequence.byEntityKey[entityIndex].sequence.length;
+
+ const entity = model.sequence.byEntityKey[entityIndex];
+ if (entity === undefined) return 0;
+
+ return entity.sequence.length;
}
export function SequenceIdColorTheme(ctx: ThemeDataContext, props: PD.Values<SequenceIdColorThemeParams>): ColorTheme<SequenceIdColorThemeParams> {
@@ -74,15 +79,21 @@ export function SequenceIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Seq
const { unit, element } = location;
const seq_id = getSeqId(unit, element);
if (seq_id > 0) {
- scale.setDomain(0, getSequenceLength(unit, element) - 1);
- return scale.color(seq_id);
+ const seqLen = getSequenceLength(unit, element);
+ if (seqLen) {
+ scale.setDomain(0, seqLen - 1);
+ return scale.color(seq_id);
+ }
}
} else if (Bond.isLocation(location)) {
const { aUnit, aIndex } = location;
const seq_id = getSeqId(aUnit, aUnit.elements[aIndex]);
if (seq_id > 0) {
- scale.setDomain(0, getSequenceLength(aUnit, aUnit.elements[aIndex]) - 1);
- return scale.color(seq_id);
+ const seqLen = getSequenceLength(aUnit, aUnit.elements[aIndex]);
+ if (seqLen) {
+ scale.setDomain(0, seqLen - 1);
+ return scale.color(seq_id);
+ }
}
}
return DefaultColor;
diff --git a/src/servers/volume/server/web-api.ts b/src/servers/volume/server/web-api.ts
index 845c18a52f47c0767f4012d556ce48997d100cf3..26baf0ee328e522a8b6cdeb723155417243fb038 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.ts
@@ -153,7 +153,7 @@ function getQueryParams(req: express.Request, isCell: boolean): Data.QueryParams
const a = [+req.params.a1, +req.params.a2, +req.params.a3];
const b = [+req.params.b1, +req.params.b2, +req.params.b3];
- const detail = Math.min(Math.max(0, (+req.query.detail) | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
+ const detail = Math.min(Math.max(0, (+req.query.detail!) | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
const isCartesian = (req.query.space as string || '').toLowerCase() !== 'fractional';
const box: Data.QueryParamsBox = isCell
diff --git a/webpack.config.js b/webpack.config.js
index f4cdb9f476a93b24a76405c2f722c92cc6b226cb..47813da69b9151f09f5d267436f96e88027c931d 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -1,6 +1,6 @@
const { createApp, createExample, createBrowserTest } = require('./webpack.config.common.js');
-const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting', 'docking-viewer'];
+const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting'];
const tests = [
'font-atlas',
'marching-cubes',
@@ -10,6 +10,7 @@ const tests = [
module.exports = [
createApp('viewer', 'molstar'),
+ createApp('docking-viewer', 'molstar'),
...examples.map(createExample),
...tests.map(createBrowserTest)
]
\ No newline at end of file
diff --git a/webpack.config.production.js b/webpack.config.production.js
index a5298d65ed0430b7bde4cf6587df78833146c389..94952ee5519c428d0a33dba676142cc6582d1d28 100644
--- a/webpack.config.production.js
+++ b/webpack.config.production.js
@@ -4,5 +4,6 @@ const examples = ['proteopedia-wrapper', 'basic-wrapper', 'lighting'];
module.exports = [
createApp('viewer', 'molstar'),
+ createApp('docking-viewer', 'molstar'),
...examples.map(createExample)
]
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