Skip to content
Snippets Groups Projects
Commit f49c34c5 authored by JonStargaryen's avatar JonStargaryen
Browse files

cleanup

parent ad3c07c6
No related branches found
No related tags found
No related merge requests found
Show whitespace changes
Inline Side-by-side
src/mol-model-props/computed/topology.ts → src/mol-model-props/computed/membrane.ts
+ 12
− 14
View file @ f49c34c5
...@@ -10,30 +10,28 @@ import { Structure } from '../../mol-model/structure'; ...@@ -10,30 +10,28 @@ import { Structure } from '../../mol-model/structure';
import { CustomStructureProperty } from '../common/custom-structure-property'; import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property'; import { CustomProperty } from '../common/custom-property';
import { CustomPropertyDescriptor } from '../../mol-model/custom-property'; import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
import { ANVILParams, Topology } from './topology/ANVIL'; import { ANVILParams, Membrane } from './membrane/ANVIL';
export const TopologyParams = { export const MembraneParams = {
...ANVILParams ...ANVILParams
}; };
export type TopologyParams = typeof TopologyParams export type MembraneParams = typeof MembraneParams
export type TopologyProps = PD.Values<TopologyParams> export type MembraneProps = PD.Values<MembraneParams>
export type TopologyValue = Map<number, Topology> export const MembraneProvider: CustomStructureProperty.Provider<MembraneParams, Membrane> = CustomStructureProperty.createProvider({
label: 'Predicted Membrane',
export const TopologyProvider: CustomStructureProperty.Provider<TopologyParams, Topology> = CustomStructureProperty.createProvider({
label: 'Predicted Membrane Topology',
descriptor: CustomPropertyDescriptor({ descriptor: CustomPropertyDescriptor({
name: 'molstar_topology', name: 'molstar_membrane',
// TODO `cifExport` // TODO `cifExport`
}), }),
type: 'root', type: 'root',
defaultParams: TopologyParams, defaultParams: MembraneParams,
getParams: (data: Structure) => TopologyParams, getParams: (data: Structure) => MembraneParams,
isApplicable: (data: Structure) => true, isApplicable: (data: Structure) => true,
// TODO needs ASA to be computed (or 'resolved' before trying computing topology) - how to achieve? // TODO needs ASA to be computed (or 'resolved' before trying computing topology) - how to achieve?
// TODO potentially, this could behave like secondary structure info where data can be either parsed or computed // TODO potentially, this could behave like secondary structure info where data can be either parsed or computed
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<TopologyProps>) => { obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneProps>) => {
const p = { ...PD.getDefaultValues(TopologyParams), ...props }; const p = { ...PD.getDefaultValues(MembraneParams), ...props };
return { value: await Topology.compute(data, p).runInContext(ctx.runtime) }; return { value: await Membrane.compute(data, p).runInContext(ctx.runtime) };
} }
}); });
\ No newline at end of file
src/mol-model-props/computed/topology/ANVIL.ts → src/mol-model-props/computed/membrane/ANVIL.ts
+ 58
− 48
View file @ f49c34c5
...@@ -14,6 +14,7 @@ import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper'; ...@@ -14,6 +14,7 @@ import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
import { Vec3 } from '../../../mol-math/linear-algebra'; import { Vec3 } from '../../../mol-math/linear-algebra';
import { AccessibleSurfaceArea } from '../accessible-surface-area/shrake-rupley'; import { AccessibleSurfaceArea } from '../accessible-surface-area/shrake-rupley';
import { AccessibleSurfaceAreaProvider } from '../accessible-surface-area'; import { AccessibleSurfaceAreaProvider } from '../accessible-surface-area';
import { ANVILContext } from './anvil/common';
export const ANVILParams = { export const ANVILParams = {
numberOfSpherePoints: PD.Numeric(350), numberOfSpherePoints: PD.Numeric(350),
...@@ -26,13 +27,10 @@ export const ANVILParams = { ...@@ -26,13 +27,10 @@ export const ANVILParams = {
export type ANVILParams = typeof ANVILParams export type ANVILParams = typeof ANVILParams
export type ANVILProps = PD.Values<ANVILParams> export type ANVILProps = PD.Values<ANVILParams>
export { Topology }; export { Membrane };
interface Membrane extends Array<Vec3> {}
interface Topology { namespace Membrane {
readonly membrane: Vec3[]
}
namespace Topology {
/** /**
* Implements: * Implements:
* Membrane positioning for high- and low-resolution protein structures through a binary classification approach * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
...@@ -50,9 +48,8 @@ namespace Topology { ...@@ -50,9 +48,8 @@ namespace Topology {
const l = StructureElement.Location.create(void 0); const l = StructureElement.Location.create(void 0);
const centroidHelper = new CentroidHelper(); const centroidHelper = new CentroidHelper();
const vec = Vec3(); const vec = Vec3();
export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<Topology> { function initialize(structure: Structure, params: ANVILProps): ANVILContext {
const { label_atom_id, x, y, z } = StructureProperties.atom; const { label_atom_id, x, y, z } = StructureProperties.atom;
const { label_comp_id } = StructureProperties.residue;
const elementCount = structure.polymerResidueCount; const elementCount = structure.polymerResidueCount;
centroidHelper.reset(); centroidHelper.reset();
l.structure = structure; l.structure = structure;
...@@ -110,26 +107,43 @@ namespace Topology { ...@@ -110,26 +107,43 @@ namespace Topology {
} }
const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq); const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
const initialHphobHphil = HphobHphil.filtered(offsets, exposed, structure, label_comp_id); return {
const initialMembrane = findMembrane(generateSpherePoints(params.numberOfSpherePoints, centroid, extent), centroid, params, initialHphobHphil, offsets, exposed, structure, label_comp_id); structure: structure,
const refinedMembrane = findMembrane(findProximateAxes(initialMembrane, params.numberOfSpherePoints, centroid, extent), centroid, params, initialHphobHphil, offsets, exposed, structure, label_comp_id); numberOfSpherePoints: params.numberOfSpherePoints,
stepSize: params.stepSize,
minThickness: params.maxThickness,
maxThickness: params.minThickness,
afilter: params.afilter,
membranePointDensity: params.membranePointDensity,
offsets: offsets,
exposed: exposed,
centroid: centroid,
extent: extent
}
}
export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<Membrane> {
const { label_comp_id } = StructureProperties.residue;
const ctx = initialize(structure, params);
const initialHphobHphil = HphobHphil.filtered(ctx, label_comp_id);
const initialMembrane = findMembrane(ctx, generateSpherePoints(ctx, ctx.numberOfSpherePoints), initialHphobHphil, label_comp_id);
const refinedMembrane = findMembrane(ctx, findProximateAxes(ctx, initialMembrane), initialHphobHphil, label_comp_id);
const membrane = initialMembrane.qmax! > refinedMembrane.qmax! ? initialMembrane : refinedMembrane; const membrane = initialMembrane.qmax! > refinedMembrane.qmax! ? initialMembrane : refinedMembrane;
return { return createMembraneLayers(ctx, membrane);
membrane: createMembraneLayers(membrane, extent, params)
};
} }
function createMembraneLayers(membrane: Membrane, extent: number, params: ANVILProps): Vec3[] { function createMembraneLayers(ctx: ANVILContext, membrane: MembraneCandidate): Vec3[] {
console.time('create membrane layers'); const { extent, membranePointDensity } = ctx;
const out: Vec3[] = []; const out: Vec3[] = [];
const radius = extent * extent; const radius = extent * extent;
const normalVector = membrane.normalVector!; const normalVector = membrane.normalVector!;
createMembraneLayer(out, membrane.planePoint1, normalVector, params.membranePointDensity, radius); createMembraneLayer(out, membrane.planePoint1, normalVector, membranePointDensity, radius);
createMembraneLayer(out, membrane.planePoint2, normalVector, params.membranePointDensity, radius); createMembraneLayer(out, membrane.planePoint2, normalVector, membranePointDensity, radius);
console.timeEnd('create membrane layers');
return out; return out;
} }
...@@ -139,13 +153,14 @@ namespace Topology { ...@@ -139,13 +153,14 @@ namespace Topology {
for (let j = -1000, jl = 1000; j < jl; j += density) { for (let j = -1000, jl = 1000; j < jl; j += density) {
const rep = Vec3.create(i, j, -(d + i * normalVector[0] + j * normalVector[1]) / normalVector[2]); const rep = Vec3.create(i, j, -(d + i * normalVector[0] + j * normalVector[1]) / normalVector[2]);
if (Vec3.squaredDistance(rep, point) < radius) { if (Vec3.squaredDistance(rep, point) < radius) {
// TODO it has a nice effect to ensure that membrane points don't overlap with structure representation
out.push(rep); out.push(rep);
} }
} }
} }
} }
interface Membrane { interface MembraneCandidate {
planePoint1: Vec3, planePoint1: Vec3,
planePoint2: Vec3, planePoint2: Vec3,
stats: HphobHphil, stats: HphobHphil,
...@@ -156,8 +171,8 @@ namespace Topology { ...@@ -156,8 +171,8 @@ namespace Topology {
membraneAtoms?: Vec3[] membraneAtoms?: Vec3[]
} }
namespace Membrane { namespace MembraneCandidate {
export function initial(c1: Vec3, c2: Vec3, stats: HphobHphil): Membrane { export function initial(c1: Vec3, c2: Vec3, stats: HphobHphil): MembraneCandidate {
return { return {
planePoint1: c1, planePoint1: c1,
planePoint2: c2, planePoint2: c2,
...@@ -165,7 +180,7 @@ namespace Topology { ...@@ -165,7 +180,7 @@ namespace Topology {
} }
} }
export function scored(spherePoint: Vec3, c1: Vec3, c2: Vec3, stats: HphobHphil, qmax: number, centroid: Vec3): Membrane { export function scored(spherePoint: Vec3, c1: Vec3, c2: Vec3, stats: HphobHphil, qmax: number, centroid: Vec3): MembraneCandidate {
const diam_vect = Vec3(); const diam_vect = Vec3();
Vec3.sub(diam_vect, centroid, spherePoint); Vec3.sub(diam_vect, centroid, spherePoint);
return { return {
...@@ -181,13 +196,13 @@ namespace Topology { ...@@ -181,13 +196,13 @@ namespace Topology {
} }
} }
function findMembrane(spherePoints: Vec3[], centroid: Vec3, params: ANVILProps, initialStats: HphobHphil, offsets: ArrayLike<number>, exposed: ArrayLike<boolean>, structure: Structure, label_comp_id: StructureElement.Property<string>): Membrane { function findMembrane(ctx: ANVILContext, spherePoints: Vec3[], initialStats: HphobHphil, label_comp_id: StructureElement.Property<string>): MembraneCandidate {
const { centroid, stepSize, minThickness, maxThickness } = ctx;
// best performing membrane // best performing membrane
let membrane: Membrane; let membrane: MembraneCandidate;
// score of the best performing membrane // score of the best performing membrane
let qmax = 0; let qmax = 0;
console.time('membrane placement iteration');
// construct slices of thickness 1.0 along the axis connecting the centroid and the spherePoint // construct slices of thickness 1.0 along the axis connecting the centroid and the spherePoint
for (let i = 0, il = spherePoints.length; i < il; i++) { for (let i = 0, il = spherePoints.length; i < il; i++) {
const spherePoint = spherePoints[i]; const spherePoint = spherePoints[i];
...@@ -197,20 +212,20 @@ namespace Topology { ...@@ -197,20 +212,20 @@ namespace Topology {
const diamNorm = Vec3.magnitude(diam); const diamNorm = Vec3.magnitude(diam);
const qvartemp = []; const qvartemp = [];
for (let i = 0, il = diamNorm - params.stepSize; i < il; i += params.stepSize) { for (let i = 0, il = diamNorm - stepSize; i < il; i += stepSize) {
const c1 = Vec3(); const c1 = Vec3();
const c2 = Vec3(); const c2 = Vec3();
Vec3.scaleAndAdd(c1, spherePoint, diam, i / diamNorm); Vec3.scaleAndAdd(c1, spherePoint, diam, i / diamNorm);
Vec3.scaleAndAdd(c2, spherePoint, diam, (i + params.stepSize) / diamNorm); Vec3.scaleAndAdd(c2, spherePoint, diam, (i + stepSize) / diamNorm);
// evaluate how well this membrane slice embeddeds the peculiar residues // evaluate how well this membrane slice embeddeds the peculiar residues
const stats = HphobHphil.filtered(offsets, exposed, structure, label_comp_id, (testPoint: Vec3) => isInMembranePlane(testPoint, diam, c1, c2)); const stats = HphobHphil.filtered(ctx, label_comp_id, (testPoint: Vec3) => isInMembranePlane(testPoint, diam, c1, c2));
qvartemp.push(Membrane.initial(c1, c2, stats)); qvartemp.push(MembraneCandidate.initial(c1, c2, stats));
} }
let jmax = (params.minThickness / params.stepSize) - 1; let jmax = (minThickness / stepSize) - 1;
for (let width = 0, widthl = params.maxThickness; width < widthl;) { for (let width = 0, widthl = maxThickness; width < widthl;) {
const imax = qvartemp.length - 1 - jmax; const imax = qvartemp.length - 1 - jmax;
for (let i = 0, il = imax; i < il; i++) { for (let i = 0, il = imax; i < il; i++) {
...@@ -238,18 +253,15 @@ namespace Topology { ...@@ -238,18 +253,15 @@ namespace Topology {
const qvaltest = qValue(stats, initialStats); const qvaltest = qValue(stats, initialStats);
if (qvaltest > qmax) { if (qvaltest > qmax) {
qmax = qvaltest; qmax = qvaltest;
membrane = Membrane.scored(spherePoint, c1, c2, HphobHphil.of(hphob, hphil, total), qmax, centroid); membrane = MembraneCandidate.scored(spherePoint, c1, c2, HphobHphil.of(hphob, hphil, total), qmax, centroid);
} }
} }
} }
jmax++; jmax++;
width = (jmax + 1) * params.stepSize width = (jmax + 1) * stepSize
} }
} }
console.timeEnd('membrane placement iteration');
console.log(`new qvalue: ${ membrane!.qmax }`);
return membrane!; return membrane!;
} }
...@@ -262,11 +274,9 @@ namespace Topology { ...@@ -262,11 +274,9 @@ namespace Topology {
initialStats.hphil += 1; initialStats.hphil += 1;
} }
const tot = initialStats.hphob + initialStats.hphil;
const part_tot = currentStats.hphob + currentStats.hphil; const part_tot = currentStats.hphob + currentStats.hphil;
return (currentStats.hphob * (initialStats.hphil - currentStats.hphil) - currentStats.hphil * (initialStats.hphob - currentStats.hphob)) / return (currentStats.hphob * (initialStats.hphil - currentStats.hphil) - currentStats.hphil * (initialStats.hphob - currentStats.hphob)) /
Math.sqrt(part_tot * initialStats.hphob * initialStats.hphil * (tot - part_tot)); Math.sqrt(part_tot * initialStats.hphob * initialStats.hphil * (initialStats.hphob + initialStats.hphil - part_tot));
} }
function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean { function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean {
...@@ -277,9 +287,9 @@ namespace Topology { ...@@ -277,9 +287,9 @@ namespace Topology {
} }
// generates a defined number of points on a sphere with radius = extent around the specified centroid // generates a defined number of points on a sphere with radius = extent around the specified centroid
function generateSpherePoints(numberOfSpherePoints: number, centroid: Vec3, extent: number): Vec3[] { function generateSpherePoints(ctx: ANVILContext, numberOfSpherePoints: number): Vec3[] {
const points = new Array<Vec3>(numberOfSpherePoints); const { centroid, extent } = ctx;
const points = [];
let oldPhi = 0, h, theta, phi; let oldPhi = 0, h, theta, phi;
for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) { for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
h = -1 + 2 * (k - 1) / (numberOfSpherePoints - 1); h = -1 + 2 * (k - 1) / (numberOfSpherePoints - 1);
...@@ -299,9 +309,9 @@ namespace Topology { ...@@ -299,9 +309,9 @@ namespace Topology {
} }
// generates sphere points close to that of the initial membrane // generates sphere points close to that of the initial membrane
function findProximateAxes(membrane: Membrane, numberOfSpherePoints: number, centroid: Vec3, extent: number): Vec3[] { function findProximateAxes(ctx: ANVILContext, membrane: MembraneCandidate): Vec3[] {
console.time('find proximate axes'); const { numberOfSpherePoints, extent } = ctx;
const points = generateSpherePoints(30000, centroid, extent); const points = generateSpherePoints(ctx, 30000);
let j = 4; let j = 4;
let sphere_pts2: Vec3[] = []; let sphere_pts2: Vec3[] = [];
while (sphere_pts2.length < numberOfSpherePoints) { while (sphere_pts2.length < numberOfSpherePoints) {
...@@ -315,7 +325,6 @@ namespace Topology { ...@@ -315,7 +325,6 @@ namespace Topology {
} }
j += 0.2; j += 0.2;
} }
console.timeEnd('find proximate axes');
return sphere_pts2; return sphere_pts2;
} }
...@@ -335,7 +344,8 @@ namespace Topology { ...@@ -335,7 +344,8 @@ namespace Topology {
} }
const testPoint = Vec3(); const testPoint = Vec3();
export function filtered(offsets: ArrayLike<number>, exposed: ArrayLike<boolean>, structure: Structure, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil { export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
const { offsets, exposed, structure } = ctx;
const { x, y, z } = StructureProperties.atom; const { x, y, z } = StructureProperties.atom;
let hphob = 0; let hphob = 0;
let hphil = 0; let hphil = 0;
......
src/mol-model-props/computed/topology/anvil/common.ts → src/mol-model-props/computed/membrane/anvil/common.ts
+ 6
− 6
View file @ f49c34c5
...@@ -5,7 +5,6 @@ ...@@ -5,7 +5,6 @@
*/ */
import { Structure } from '../../../../mol-model/structure'; import { Structure } from '../../../../mol-model/structure';
import { Topology } from '../ANVIL';
import { Vec3 } from '../../../../mol-math/linear-algebra'; import { Vec3 } from '../../../../mol-math/linear-algebra';
export interface ANVILContext { export interface ANVILContext {
...@@ -16,8 +15,9 @@ export interface ANVILContext { ...@@ -16,8 +15,9 @@ export interface ANVILContext {
maxThickness: number, maxThickness: number,
afilter: number, afilter: number,
membranePointDensity: number, membranePointDensity: number,
centerOfMass: Vec3,
maxExtent: number, offsets: ArrayLike<number>,
serialResidueIndex: Int32Array, exposed: ArrayLike<boolean>,
exposure: ArrayLike<Topology> centroid: Vec3,
} extent: number
\ No newline at end of file };
\ No newline at end of file
src/mol-theme/color.ts
+ 0
− 2
View file @ f49c34c5
...@@ -32,7 +32,6 @@ import { ModelIndexColorThemeProvider } from './color/model-index'; ...@@ -32,7 +32,6 @@ import { ModelIndexColorThemeProvider } from './color/model-index';
import { OccupancyColorThemeProvider } from './color/occupancy'; import { OccupancyColorThemeProvider } from './color/occupancy';
import { OperatorNameColorThemeProvider } from './color/operator-name'; import { OperatorNameColorThemeProvider } from './color/operator-name';
import { OperatorHklColorThemeProvider } from './color/operator-hkl'; import { OperatorHklColorThemeProvider } from './color/operator-hkl';
import { AccessibleSurfaceAreaColorThemeProvider } from '../mol-model-props/computed/themes/accessible-surface-area';
export type LocationColor = (location: Location, isSecondary: boolean) => Color export type LocationColor = (location: Location, isSecondary: boolean) => Color
...@@ -101,7 +100,6 @@ namespace ColorTheme { ...@@ -101,7 +100,6 @@ namespace ColorTheme {
'uncertainty': UncertaintyColorThemeProvider, 'uncertainty': UncertaintyColorThemeProvider,
'unit-index': UnitIndexColorThemeProvider, 'unit-index': UnitIndexColorThemeProvider,
'uniform': UniformColorThemeProvider, 'uniform': UniformColorThemeProvider,
'accessible-surface-area': AccessibleSurfaceAreaColorThemeProvider,
}; };
type _BuiltIn = typeof BuiltIn type _BuiltIn = typeof BuiltIn
export type BuiltIn = keyof _BuiltIn export type BuiltIn = keyof _BuiltIn
......
src/tests/browser/render-structure.ts
+ 14
− 25
View file @ f49c34c5
...@@ -27,12 +27,12 @@ import { SecondaryStructureProvider } from '../../mol-model-props/computed/secon ...@@ -27,12 +27,12 @@ import { SecondaryStructureProvider } from '../../mol-model-props/computed/secon
import { SyncRuntimeContext } from '../../mol-task/execution/synchronous'; import { SyncRuntimeContext } from '../../mol-task/execution/synchronous';
import { AssetManager } from '../../mol-util/assets'; import { AssetManager } from '../../mol-util/assets';
import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area'; import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
import { TopologyProvider } from '../../mol-model-props/computed/topology'; import { MembraneProvider } from '../../mol-model-props/computed/membrane';
import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder'; import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder';
import { Spheres } from '../../mol-geo/geometry/spheres/spheres'; import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
import { Color } from '../../mol-util/color'; import { Color } from '../../mol-util/color';
import { createRenderObject } from '../../mol-gl/render-object'; import { createRenderObject } from '../../mol-gl/render-object';
import { Topology } from '../../mol-model-props/computed/topology/ANVIL'; import { Membrane } from '../../mol-model-props/computed/membrane/ANVIL';
const parent = document.getElementById('app')!; const parent = document.getElementById('app')!;
parent.style.width = '100%'; parent.style.width = '100%';
...@@ -123,14 +123,14 @@ function getGaussianSurfaceRepr() { ...@@ -123,14 +123,14 @@ function getGaussianSurfaceRepr() {
return GaussianSurfaceRepresentationProvider.factory(reprCtx, GaussianSurfaceRepresentationProvider.getParams); return GaussianSurfaceRepresentationProvider.factory(reprCtx, GaussianSurfaceRepresentationProvider.getParams);
} }
function getMembraneRepr(topology: Topology) { function getMembraneRepr(membrane: Membrane) {
const spheresBuilder = SpheresBuilder.create(topology.membrane.length, 1); const spheresBuilder = SpheresBuilder.create(membrane.length, 1);
for (let i = 0, il = topology.membrane.length; i < il; i++) { for (let i = 0, il = membrane.length; i < il; i++) {
spheresBuilder.add(topology.membrane[i][0], topology.membrane[i][1], topology.membrane[i][2], 0); spheresBuilder.add(membrane[i][0], membrane[i][1], membrane[i][2], 0);
} }
const spheres = spheresBuilder.getSpheres(); const spheres = spheresBuilder.getSpheres();
const values = Spheres.Utils.createValuesSimple(spheres, {}, Color(0xFF0000/*666666*/), 1); const values = Spheres.Utils.createValuesSimple(spheres, {}, Color(0xCCCCCC), 1);
const state = Spheres.Utils.createRenderableState({}); const state = Spheres.Utils.createRenderableState({});
const renderObject = createRenderObject('spheres', values, state, -1); const renderObject = createRenderObject('spheres', values, state, -1);
console.log(renderObject); console.log(renderObject);
...@@ -141,7 +141,7 @@ function getMembraneRepr(topology: Topology) { ...@@ -141,7 +141,7 @@ function getMembraneRepr(topology: Topology) {
async function init() { async function init() {
const ctx = { runtime: SyncRuntimeContext, assetManager: new AssetManager() }; const ctx = { runtime: SyncRuntimeContext, assetManager: new AssetManager() };
const cif = await downloadFromPdb('1brr'); const cif = await downloadFromPdb('3pqr');
const models = await getModels(cif); const models = await getModels(cif);
const structure = await getStructure(models[0]); const structure = await getStructure(models[0]);
...@@ -153,9 +153,9 @@ async function init() { ...@@ -153,9 +153,9 @@ async function init() {
await AccessibleSurfaceAreaProvider.attach(ctx, structure); await AccessibleSurfaceAreaProvider.attach(ctx, structure);
console.timeEnd('compute AccessibleSurfaceArea'); console.timeEnd('compute AccessibleSurfaceArea');
console.time('compute Topology'); console.time('compute Membrane');
await TopologyProvider.attach(ctx, structure); await MembraneProvider.attach(ctx, structure);
console.timeEnd('compute Topology'); console.timeEnd('compute Membrane');
console.time('compute Interactions'); console.time('compute Interactions');
await InteractionsProvider.attach(ctx, structure); await InteractionsProvider.attach(ctx, structure);
...@@ -176,12 +176,11 @@ async function init() { ...@@ -176,12 +176,11 @@ async function init() {
const ballAndStickRepr = getBallAndStickRepr(); const ballAndStickRepr = getBallAndStickRepr();
const molecularSurfaceRepr = getMolecularSurfaceRepr(); const molecularSurfaceRepr = getMolecularSurfaceRepr();
const gaussianSurfaceRepr = getGaussianSurfaceRepr(); const gaussianSurfaceRepr = getGaussianSurfaceRepr();
const membraneRepr = getMembraneRepr(TopologyProvider.get(structure).value!); const membraneRepr = getMembraneRepr(MembraneProvider.get(structure).value!);
if (show.cartoon) { if (show.cartoon) {
cartoonRepr.setTheme({ cartoonRepr.setTheme({
// TODO remove from mol-theme/color.ts again color: reprCtx.colorThemeRegistry.create('element-symbol', { structure }),
color: reprCtx.colorThemeRegistry.create('accessible-surface-area', { structure }),
size: reprCtx.sizeThemeRegistry.create('uniform', { structure }) size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
}); });
await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run(); await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run();
...@@ -223,16 +222,6 @@ async function init() { ...@@ -223,16 +222,6 @@ async function init() {
console.timeEnd('gaussian surface'); console.timeEnd('gaussian surface');
} }
// if (show.membrane) {
// membraneRepr.setTheme({
// color: reprCtx.colorThemeRegistry.create('uniform', { structure }),
// size: reprCtx.sizeThemeRegistry.create('physical', { structure })
// });
// console.time('membrane layer');
// await membraneRepr.createOrUpdate({ ...MembraneRepresentationProvider.defaultValues, quality: 'custom', alpha: 1.0, flatShaded: true, doubleSided: true, resolution: 0.3 }, structure).run();
// console.timeEnd('membrane layer');
// }
if (show.cartoon) canvas3d.add(cartoonRepr); if (show.cartoon) canvas3d.add(cartoonRepr);
if (show.interaction) canvas3d.add(interactionRepr); if (show.interaction) canvas3d.add(interactionRepr);
if (show.ballAndStick) canvas3d.add(ballAndStickRepr); if (show.ballAndStick) canvas3d.add(ballAndStickRepr);
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment