resolves conflict with master

src/tests/browser/render-asa.ts

@@ -0,0 +1,145 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import './index.html'
+import { Canvas3D } from 'mol-canvas3d/canvas3d';
+import CIF, { CifFrame } from 'mol-io/reader/cif'
+import { Model, Structure, StructureElement, Unit } from 'mol-model/structure';
+import { ColorTheme, LocationColor } from 'mol-theme/color';
+import { SizeTheme } from 'mol-theme/size';
+import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
+import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
+import { AccessibleSurfaceArea } from 'mol-model/structure/structure/accessible-surface-area';
+import { Color, ColorScale } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ThemeDataContext } from 'mol-theme/theme';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { ColorListName, ColorListOptions } from 'mol-util/color/scale';
+
+const parent = document.getElementById('app')!
+parent.style.width = '100%'
+parent.style.height = '100%'
+
+const canvas = document.createElement('canvas')
+canvas.style.width = '100%'
+canvas.style.height = '100%'
+parent.appendChild(canvas)
+
+const canvas3d = Canvas3D.create(canvas, parent)
+canvas3d.animate()
+
+
+async function parseCif(data: string|Uint8Array) {
+    const comp = CIF.parse(data);
+    const parsed = await comp.run();
+    if (parsed.isError) throw parsed;
+    return parsed.result;
+}
+
+async function downloadCif(url: string, isBinary: boolean) {
+    const data = await fetch(url);
+    return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
+}
+
+async function downloadFromPdb(pdb: string) {
+    // const parsed = await downloadCif(`https://files.rcsb.org/download/${pdb}.cif`, false);
+    const parsed = await downloadCif(`https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${pdb}`, true);
+    return parsed.blocks[0];
+}
+
+async function getModels(frame: CifFrame) {
+    return await trajectoryFromMmCIF(frame).run();
+}
+
+async function getStructure(model: Model) {
+    return Structure.ofModel(model);
+}
+
+const reprCtx = {
+    colorThemeRegistry: ColorTheme.createRegistry(),
+    sizeThemeRegistry: SizeTheme.createRegistry()
+}
+function getCartoonRepr() {
+    return CartoonRepresentationProvider.factory(reprCtx, CartoonRepresentationProvider.getParams)
+}
+
+let accessibleSurfaceArea: AccessibleSurfaceArea;
+async function init(props = {}) {
+    const cif = await downloadFromPdb(
+        // '3j3q'
+        // '1aon'
+        // '1acj'
+        // '1pga'
+        '1brr'
+        )
+    const models = await getModels(cif)
+    const structure = await getStructure(models[0])
+
+    // async compute ASA
+    accessibleSurfaceArea = await AccessibleSurfaceArea.compute(structure)
+
+    const cartoonRepr = getCartoonRepr()
+
+    // create color theme
+    cartoonRepr.setTheme({
+        color: AccessibleSurfaceAreaColorTheme(reprCtx, { ...PD.getDefaultValues(AccessibleSurfaceAreaColorThemeParams), ...props }),
+        size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
+    })
+    await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
+
+    canvas3d.add(cartoonRepr)
+    canvas3d.resetCamera()
+}
+
+init()
+
+const DefaultColor = Color(0xFFFFFF)
+const Description = 'Assigns a color based on the relative accessible surface area of a residue.'
+
+export const AccessibleSurfaceAreaColorThemeParams = {
+    list: PD.ColorScale<ColorListName>('Rainbow', ColorListOptions)
+}
+export type AccessibleSurfaceAreaColorThemeParams = typeof AccessibleSurfaceAreaColorThemeParams
+export function getAccessibleSurfaceAreaColorThemeParams(ctx: ThemeDataContext) {
+    return AccessibleSurfaceAreaColorThemeParams // TODO return copy
+}
+
+export function AccessibleSurfaceAreaColorTheme(ctx: ThemeDataContext, props: PD.Values<AccessibleSurfaceAreaColorThemeParams>): ColorTheme<AccessibleSurfaceAreaColorThemeParams> {
+    let color: LocationColor = () => DefaultColor
+    const scale = ColorScale.create({
+        listOrName: props.list,
+        minLabel: '0.0 (buried)',
+        maxLabel: '1.0 (exposed)',
+        domain: [0.0, 1.0]
+    })
+    color = (location: Location): Color => {
+        if (StructureElement.isLocation(location)) {
+            if (Unit.isAtomic(location.unit)) {
+                const value = accessibleSurfaceArea.relativeAccessibleSurfaceArea![location.unit.residueIndex[location.element]];
+                return value !== AccessibleSurfaceArea.VdWLookup[0] /* signals missing value */ ? scale.color(value) : DefaultColor;
+            }
+        }
+
+        return DefaultColor
+    }
+
+    return {
+        factory: AccessibleSurfaceAreaColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        description: Description,
+        legend: scale ? scale.legend : undefined
+    }
+}
+
+export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<AccessibleSurfaceAreaColorThemeParams> = {
+    label: 'Accessible Surface Area',
+    factory: AccessibleSurfaceAreaColorTheme,
+    getParams: getAccessibleSurfaceAreaColorThemeParams,
+    defaultValues: PD.getDefaultValues(AccessibleSurfaceAreaColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}

src/tests/browser/render-structure.ts

@@ -7,17 +7,12 @@
 import './index.html'
 import { Canvas3D } from 'mol-canvas3d/canvas3d';
 import CIF, { CifFrame } from 'mol-io/reader/cif'
-import { Model, Structure, StructureElement, Unit } from 'mol-model/structure';
-import { ColorTheme, LocationColor } from 'mol-theme/color';
+import { Model, Structure } from 'mol-model/structure';
+import { ColorTheme } from 'mol-theme/color';
 import { SizeTheme } from 'mol-theme/size';
 import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
 import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
-import { AccessibleSurfaceArea } from 'mol-model/structure/structure/accessible-surface-area';
-import { Color, ColorScale } from 'mol-util/color';
-import { Location } from 'mol-model/location';
-import { ThemeDataContext } from 'mol-theme/theme';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { ColorListName, ColorListOptions } from 'mol-util/color/scale';
+import { computeModelDSSP } from 'mol-model/structure/model/properties/utils/secondary-structure';
 
 const parent = document.getElementById('app')!
 parent.style.width = '100%'
@@ -66,79 +61,24 @@ function getCartoonRepr() {
     return CartoonRepresentationProvider.factory(reprCtx, CartoonRepresentationProvider.getParams)
 }
 
-let accessibleSurfaceArea: AccessibleSurfaceArea;
-async function init(props = {}) {
-    const cif = await downloadFromPdb(
-        // '3j3q'
-        '1aon'
-        // '1acj'
-        // '1pga'
-        )
+async function init() {
+    const cif = await downloadFromPdb('3j3q')
     const models = await getModels(cif)
+    console.time('computeModelDSSP')
+    const secondaryStructure = computeModelDSSP(models[0].atomicHierarchy, models[0].atomicConformation)
+    console.timeEnd('computeModelDSSP')
+    ;(models[0].properties as any).secondaryStructure = secondaryStructure
     const structure = await getStructure(models[0])
-
-    // async compute ASA
-    accessibleSurfaceArea = await AccessibleSurfaceArea.compute(structure)
-
     const cartoonRepr = getCartoonRepr()
 
-    // create color theme
     cartoonRepr.setTheme({
-        color: AccessibleSurfaceAreaColorTheme(reprCtx, { ...PD.getDefaultValues(AccessibleSurfaceAreaColorThemeParams), ...props }),
+        color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
         size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
     })
     await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
-
+    
     canvas3d.add(cartoonRepr)
     canvas3d.resetCamera()
 }
 
-init()
-
-const DefaultColor = Color(0xFFFFFF)
-const Description = 'Assigns a color based on the relative accessible surface area of a residue.'
-
-export const AccessibleSurfaceAreaColorThemeParams = {
-    list: PD.ColorScale<ColorListName>('Rainbow', ColorListOptions)
-}
-export type AccessibleSurfaceAreaColorThemeParams = typeof AccessibleSurfaceAreaColorThemeParams
-export function getAccessibleSurfaceAreaColorThemeParams(ctx: ThemeDataContext) {
-    return AccessibleSurfaceAreaColorThemeParams // TODO return copy
-}
-
-export function AccessibleSurfaceAreaColorTheme(ctx: ThemeDataContext, props: PD.Values<AccessibleSurfaceAreaColorThemeParams>): ColorTheme<AccessibleSurfaceAreaColorThemeParams> {
-    let color: LocationColor = () => DefaultColor
-    const scale = ColorScale.create({
-        listOrName: props.list,
-        minLabel: '0.0 (buried)',
-        maxLabel: '1.0 (exposed)',
-        domain: [0.0, 1.0]
-    })
-    color = (location: Location): Color => {
-        if (StructureElement.isLocation(location)) {
-            if (Unit.isAtomic(location.unit)) {
-                const value = accessibleSurfaceArea.relativeAccessibleSurfaceArea![location.unit.residueIndex[location.element]];
-                return value !== AccessibleSurfaceArea.VdWLookup[0] /* signals missing value */ ? scale.color(value) : DefaultColor;
-            }
-        }
-
-        return DefaultColor
-    }
-
-    return {
-        factory: AccessibleSurfaceAreaColorTheme,
-        granularity: 'group',
-        color,
-        props,
-        description: Description,
-        legend: scale ? scale.legend : undefined
-    }
-}
-
-export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<AccessibleSurfaceAreaColorThemeParams> = {
-    label: 'Accessible Surface Area',
-    factory: AccessibleSurfaceAreaColorTheme,
-    getParams: getAccessibleSurfaceAreaColorThemeParams,
-    defaultValues: PD.getDefaultValues(AccessibleSurfaceAreaColorThemeParams),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
-}
+init()

webpack.config.js

@@ -102,6 +102,7 @@ module.exports = [
     createApp('model-server-query'),
 
     createBrowserTest('font-atlas'),
+    createBrowserTest('render-asa'),
     createBrowserTest('render-lines'),
     createBrowserTest('render-mesh'),
     createBrowserTest('render-shape'),