diff --git a/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts b/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts
new file mode 100644
index 0000000000000000000000000000000000000000..6ab4c79a204b6956f6be4facf1aad27d70f6ec0b
--- /dev/null
+++ b/src/mol-model/structure/model/properties/utils/accessible-surface-area.ts
@@ -0,0 +1,95 @@
+import { ResidueIndex } from 'mol-model/structure';
+import { MoleculeType } from 'mol-model/structure/model/types';
+import { GridLookup3D } from 'mol-math/geometry';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { SortedArray } from 'mol-data/int';
+import { ElementIndex } from 'mol-model/structure/model/indexing';
+import { AtomicHierarchy, AtomicConformation } from '../atomic';
+
+export function computeModelASA(hierarchy: AtomicHierarchy, conformation: AtomicConformation) {
+ const { lookup3d, proteinResidues } = calcAtomicTraceLookup3D(hierarchy, conformation)
+ const backboneIndices = calcBackboneAtomIndices(hierarchy, proteinResidues)
+
+ const residueCount = proteinResidues.length
+ const numberOfSpherePoints = 960
+
+ const ctx: ASAContext = {
+ probeSize: 1.4,
+ spherePoints: generateSpherePoints(numberOfSpherePoints),
+ cons: 4.0 * Math.PI / numberOfSpherePoints,
+
+ hierarchy,
+ proteinResidues
+ }
+
+ calculateASA(ctx)
+}
+
+function calculateASA(ctx: ASAContext) {
+
+}
+
+function generateSpherePoints(numberOfSpherePoints: number): Vec3[] {
+ const points: Vec3[] = []
+ const inc = Math.PI
+
+ return points
+}
+
+interface ASAContext {
+ probeSize: number,
+ spherePoints: Vec3[],
+ cons: number,
+
+ hierarchy: AtomicHierarchy,
+ proteinResidues: SortedArray<ResidueIndex>
+}
+
+interface BackboneAtomIndices {
+ cIndices: ArrayLike<ElementIndex | -1>
+ hIndices: ArrayLike<ElementIndex | -1>
+ oIndices: ArrayLike<ElementIndex | -1>
+ nIndices: ArrayLike<ElementIndex | -1>
+}
+
+function calcAtomicTraceLookup3D(hierarchy: AtomicHierarchy, conformation: AtomicConformation) {
+ const { x, y, z } = conformation;
+ const { moleculeType, traceElementIndex } = hierarchy.derived.residue
+ const indices: number[] = []
+ const _proteinResidues: number[] = []
+ for (let i = 0, il = moleculeType.length; i < il; ++i) {
+ if (moleculeType[i] === MoleculeType.protein) {
+ indices[indices.length] = traceElementIndex[i]
+ _proteinResidues[_proteinResidues.length] = i
+ }
+ }
+ const lookup3d = GridLookup3D({ x, y, z, indices: SortedArray.ofSortedArray(indices) }, 4);
+ const proteinResidues = SortedArray.ofSortedArray<ResidueIndex>(_proteinResidues)
+ return { lookup3d, proteinResidues }
+}
+
+
+function calcBackboneAtomIndices(hierarchy: AtomicHierarchy, proteinResidues: SortedArray<ResidueIndex>): BackboneAtomIndices {
+ const residueCount = proteinResidues.length
+ const { index } = hierarchy
+
+ const c = new Int32Array(residueCount)
+ const h = new Int32Array(residueCount)
+ const o = new Int32Array(residueCount)
+ const n = new Int32Array(residueCount)
+
+ for (let i = 0, il = residueCount; i < il; ++i) {
+ const rI = proteinResidues[i]
+ c[i] = index.findAtomOnResidue(rI, 'C')
+ h[i] = index.findAtomOnResidue(rI, 'H')
+ o[i] = index.findAtomOnResidue(rI, 'O')
+ n[i] = index.findAtomOnResidue(rI, 'N')
+ }
+
+ return {
+ cIndices: c as unknown as ArrayLike<ElementIndex | -1>,
+ hIndices: h as unknown as ArrayLike<ElementIndex | -1>,
+ oIndices: o as unknown as ArrayLike<ElementIndex | -1>,
+ nIndices: n as unknown as ArrayLike<ElementIndex | -1>,
+ }
+}
\ No newline at end of file
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index cab7d59fcd15c3839d33722eed8d6d929908f7ec..48eb75cc2eb2c2b5ea76e999d044cfc283c0f66e 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -7,6 +7,7 @@
import { Color } from 'mol-util/color';
import { Location } from 'mol-model/location';
import { ColorType } from 'mol-geo/geometry/color-data';
+import { AccessibleSurfaceAreaColorThemeProvider } from './color/accessible-surface-area'
import { CarbohydrateSymbolColorThemeProvider } from './color/carbohydrate-symbol';
import { UniformColorThemeProvider } from './color/uniform';
import { deepEqual } from 'mol-util';
@@ -62,6 +63,7 @@ namespace ColorTheme {
}
export const BuiltInColorThemes = {
+ 'accessible-surface-area': AccessibleSurfaceAreaColorThemeProvider,
'carbohydrate-symbol': CarbohydrateSymbolColorThemeProvider,
'chain-id': ChainIdColorThemeProvider,
'cross-link': CrossLinkColorThemeProvider,
diff --git a/src/mol-theme/color/accessible-surface-area.ts b/src/mol-theme/color/accessible-surface-area.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9f7307023902ef5291a876f1ba42862118e4204f
--- /dev/null
+++ b/src/mol-theme/color/accessible-surface-area.ts
@@ -0,0 +1,52 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorTheme } from '../color';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
+import { ThemeDataContext } from '../theme';
+import { ColorListOptions, ColorListName, ColorScale } from 'mol-util/color/scale';
+
+// const DefaultAccessibleSurfaceAreaColor = Color(0xCCCCCC)
+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> {
+ const scale = ColorScale.create({
+ listOrName: props.list,
+ minLabel: 'Start',
+ maxLabel: 'End',
+ })
+ const color = (location: Location): Color => {
+ return scale.color(Math.random())
+ // TODO impl
+ }
+
+ 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
+}
\ No newline at end of file
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 9dae8a78c7380888fce1cf4db1a64259745cba21..e16c54bf05a6bade3cf0784d640f3d3e7ad83060 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -12,7 +12,7 @@ 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 { computeModelDSSP } from 'mol-model/structure/model/properties/utils/secondary-structure';
+import { computeModelASA } from 'mol-model/structure/model/properties/utils/accessible-surface-area';
const parent = document.getElementById('app')!
parent.style.width = '100%'
@@ -62,21 +62,21 @@ function getCartoonRepr() {
}
async function init() {
- const cif = await downloadFromPdb('3j3q')
+ const cif = await downloadFromPdb('1acj')
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
+ console.time('computeModelASA')
+ const asa = computeModelASA(models[0].atomicHierarchy, models[0].atomicConformation)
+ console.timeEnd('computeModelASA');
+ (models[0].properties as any).asa = asa
const structure = await getStructure(models[0])
const cartoonRepr = getCartoonRepr()
cartoonRepr.setTheme({
- color: reprCtx.colorThemeRegistry.create('secondary-structure', { structure }),
+ color: reprCtx.colorThemeRegistry.create('accessible-surface-area', { structure }),
size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
})
await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
-
+
canvas3d.add(cartoonRepr)
canvas3d.resetCamera()
}