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867861-core.cif

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  • gaussian.ts 4.50 KiB
    /**
     * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
     *
     * @author Alexander Rose <alexander.rose@weirdbyte.de>
     */
    
    import { Unit, StructureElement, ElementIndex, Structure } from 'mol-model/structure';
    import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
    import { Task } from 'mol-task';
    import { ParamDefinition as PD } from 'mol-util/param-definition';
    import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
    import { Texture } from 'mol-gl/webgl/texture';
    import { WebGLContext } from 'mol-gl/webgl/context';
    import { PhysicalSizeTheme } from 'mol-theme/size/physical';
    import { OrderedSet } from 'mol-data/int';
    
    export const GaussianDensityParams = {
        resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
        radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
        smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
        useGpu: PD.Boolean(false),
    }
    export const DefaultGaussianDensityProps = PD.getDefaultValues(GaussianDensityParams)
    export type GaussianDensityProps = typeof DefaultGaussianDensityProps
    
    function getConformation(unit: Unit) {
        switch (unit.kind) {
            case Unit.Kind.Atomic: return unit.model.atomicConformation
            case Unit.Kind.Spheres: return unit.model.coarseConformation.spheres
            case Unit.Kind.Gaussians: return unit.model.coarseConformation.gaussians
        }
    }
    
    function getUnitConformationAndRadius(unit: Unit) {
        const conformation = getConformation(unit)
        const { elements } = unit
        const position = {
            indices: elements,
            x: conformation.x,
            y: conformation.y,
            z: conformation.z
        }
    
        const l = StructureElement.create(unit)
        const sizeTheme = PhysicalSizeTheme({}, {})
        const radius = (index: number) => {
            l.element = index as ElementIndex
            return sizeTheme.size(l)
        }
    
        return { position, radius }
    }
    
    export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
        const { position, radius } = getUnitConformationAndRadius(unit)
        return Task.create('Gaussian Density', async ctx => {
            return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props, webgl);
        });
    }
    
    export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
        const { position, radius } = getUnitConformationAndRadius(unit)
        return Task.create('Gaussian Density', async ctx => {
            return await GaussianDensityTexture(ctx, webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
        });
    }
    
    //
    
    function getStructureConformationAndRadius(structure: Structure) {
        const n = structure.elementCount
    
        const xs = new Float32Array(n)
        const ys = new Float32Array(n)
        const zs = new Float32Array(n)
        const rs = new Float32Array(n)
    
        const l = StructureElement.create()
        const sizeTheme = PhysicalSizeTheme({}, {})
    
        let m = 0
        for (let i = 0, il = structure.units.length; i < il; ++i) {
            const unit = structure.units[i]
            const { elements } = unit
            const { x, y, z } = unit.conformation
            l.unit = unit
            for (let j = 0, jl = elements.length; j < jl; ++j) {
                const eI = elements[j]
                xs[m + j] = x(eI)
                ys[m + j] = y(eI)
                zs[m + j] = z(eI)
                l.element = eI
                rs[m + j] = sizeTheme.size(l)
            }
            m += elements.length
        }
    
        const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
        const radius = (index: number) => rs[index]
    
        return { position, radius }
    }
    
    export const GaussianDensityTextureParams = {
        resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
        radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
        smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
    }
    export const DefaultGaussianDensityTextureProps = PD.getDefaultValues(GaussianDensityTextureParams)
    export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTextureProps
    
    // TODO calculate by combining unit volumes
    export function computeStructureGaussianDensityTexture(structure: Structure, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
        const { position, radius } = getStructureConformationAndRadius(structure)
        return Task.create('Gaussian Density', async ctx => {
            return await GaussianDensityTexture(ctx, webgl, position, structure.lookup3d.boundary.box, radius, props, texture);
        });
    }