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40 results

polymer-backbone-cylinder.ts

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  • polymer-backbone-cylinder.ts 3.88 KiB
    /**
     * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
     *
     * @author Alexander Rose <alexander.rose@weirdbyte.de>
     */
    
    import { Unit, Structure } from 'mol-model/structure';
    import { UnitsVisual } from '../representation';
    import { VisualUpdateState } from '../../util';
    import { PolymerBackboneIterator } from './util/polymer';
    import { getElementLoci, eachElement, StructureElementIterator } from './util/element';
    import { Vec3 } from 'mol-math/linear-algebra';
    import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
    import { OrderedSet } from 'mol-data/int';
    import { ParamDefinition as PD } from 'mol-util/param-definition';
    import { Mesh } from 'mol-geo/geometry/mesh/mesh';
    import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
    import { CylinderProps } from 'mol-geo/primitive/cylinder';
    import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
    import { VisualContext } from 'mol-repr/visual';
    import { Theme } from 'mol-theme/theme';
    
    export const PolymerBackboneCylinderParams = {
        sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
        radialSegments: PD.Numeric(16, { min: 3, max: 56, step: 1 }),
    }
    export const DefaultPolymerBackboneCylinderProps = PD.getDefaultValues(PolymerBackboneCylinderParams)
    export type PolymerBackboneCylinderProps = typeof DefaultPolymerBackboneCylinderProps
    
    // TODO do group id based on polymer index not element index
    function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
        const polymerElementCount = unit.polymerElements.length
        if (!polymerElementCount) return Mesh.createEmpty(mesh)
    
        const { radialSegments, sizeFactor } = props
    
        const vertexCountEstimate = radialSegments * 2 * polymerElementCount * 2
        const builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 10, mesh)
    
        const { elements } = unit
        const pos = unit.conformation.invariantPosition
        const pA = Vec3.zero()
        const pB = Vec3.zero()
        const cylinderProps: CylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments }
    
        const polymerBackboneIt = PolymerBackboneIterator(unit)
        while (polymerBackboneIt.hasNext) {
            const { centerA, centerB } = polymerBackboneIt.move()
            pos(centerA.element, pA)
            pos(centerB.element, pB)
    
            cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerA) * sizeFactor
            builderState.currentGroup = OrderedSet.indexOf(elements, centerA.element)
            addCylinder(builderState, pA, pB, 0.5, cylinderProps)
    
            cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerB) * sizeFactor
            builderState.currentGroup = OrderedSet.indexOf(elements, centerB.element)
            addCylinder(builderState, pB, pA, 0.5, cylinderProps)
        }
    
        return MeshBuilder.getMesh(builderState)
    }
    
    export const PolymerBackboneParams = {
        ...UnitsMeshParams,
        ...PolymerBackboneCylinderParams,
    }
    export type PolymerBackboneParams = typeof PolymerBackboneParams
    
    export function PolymerBackboneVisual(materialId: number): UnitsVisual<PolymerBackboneParams> {
        return UnitsMeshVisual<PolymerBackboneParams>({
            defaultProps: PD.getDefaultValues(PolymerBackboneParams),
            createGeometry: createPolymerBackboneCylinderMesh,
            // TODO create a specialized location iterator
            createLocationIterator: StructureElementIterator.fromGroup,
            getLoci: getElementLoci,
            eachLocation: eachElement,
            setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneParams>, currentProps: PD.Values<PolymerBackboneParams>) => {
                state.createGeometry = (
                    newProps.sizeFactor !== currentProps.sizeFactor ||
                    newProps.radialSegments !== currentProps.radialSegments
                )
            }
        }, materialId)
    }