molstar
Version:
A comprehensive macromolecular library.
169 lines (168 loc) • 8.47 kB
JavaScript
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
import { MolecularSurfaceCalculationParams } from '../../../mol-math/geometry/molecular-surface';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { computeStructureMolecularSurface, computeUnitMolecularSurface } from './util/molecular-surface';
import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
import { ElementIterator, getElementLoci, eachElement, getSerialElementLoci, eachSerialElement } from './util/element';
import { CommonSurfaceParams } from './util/common';
import { Sphere3D } from '../../../mol-math/geometry';
import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
import { ValueCell } from '../../../mol-util';
import { ComplexMeshVisual } from '../complex-visual';
export const MolecularSurfaceMeshParams = {
...UnitsMeshParams,
...MolecularSurfaceCalculationParams,
...CommonSurfaceParams,
...ColorSmoothingParams,
};
//
async function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
const { transform, field, idField, resolution, maxRadius } = await computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: props.probeRadius,
scalarField: field,
idField
};
const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime);
if (props.includeParent) {
const iterations = Math.ceil(2 / props.resolution);
Mesh.smoothEdges(surface, { iterations, maxNewEdgeLength: Math.sqrt(2) });
}
Mesh.transform(surface, transform);
if (ctx.webgl && !ctx.webgl.isWebGL2) {
Mesh.uniformTriangleGroup(surface);
ValueCell.updateIfChanged(surface.varyingGroup, false);
}
else {
ValueCell.updateIfChanged(surface.varyingGroup, true);
}
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
surface.meta.resolution = resolution;
return surface;
}
export function MolecularSurfaceMeshVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(MolecularSurfaceMeshParams),
createGeometry: createMolecularSurfaceMesh,
createLocationIterator: ElementIterator.fromGroup,
getLoci: getElementLoci,
eachLocation: eachElement,
setUpdateState: (state, newProps, currentProps) => {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.probeRadius !== currentProps.probeRadius)
state.createGeometry = true;
if (newProps.probePositions !== currentProps.probePositions)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
state.createGeometry = true;
if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly)
state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent)
state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
state.updateColor = true;
}
else if (newProps.smoothColors.name === 'on' && currentProps.smoothColors.name === 'on') {
if (newProps.smoothColors.params.resolutionFactor !== currentProps.smoothColors.params.resolutionFactor)
state.updateColor = true;
if (newProps.smoothColors.params.sampleStride !== currentProps.smoothColors.params.sampleStride)
state.updateColor = true;
}
},
processValues: (values, geometry, props, theme, webgl) => {
const { resolution, colorTexture } = geometry.meta;
const csp = getColorSmoothingProps(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp) {
applyMeshColorSmoothing(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: (geometry) => {
var _a;
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}
//
async function createStructureMolecularSurfaceMesh(ctx, structure, theme, props, mesh) {
const { transform, field, idField, resolution, maxRadius } = await computeStructureMolecularSurface(structure, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: props.probeRadius,
scalarField: field,
idField
};
const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime);
if (props.includeParent) {
const iterations = Math.ceil(2 / props.resolution);
Mesh.smoothEdges(surface, { iterations, maxNewEdgeLength: Math.sqrt(2) });
}
Mesh.transform(surface, transform);
if (ctx.webgl && !ctx.webgl.isWebGL2) {
Mesh.uniformTriangleGroup(surface);
ValueCell.updateIfChanged(surface.varyingGroup, false);
}
else {
ValueCell.updateIfChanged(surface.varyingGroup, true);
}
const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
surface.meta.resolution = resolution;
return surface;
}
export function StructureMolecularSurfaceMeshVisual(materialId) {
return ComplexMeshVisual({
defaultProps: PD.getDefaultValues(MolecularSurfaceMeshParams),
createGeometry: createStructureMolecularSurfaceMesh,
createLocationIterator: ElementIterator.fromStructure,
getLoci: getSerialElementLoci,
eachLocation: eachSerialElement,
setUpdateState: (state, newProps, currentProps) => {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.probeRadius !== currentProps.probeRadius)
state.createGeometry = true;
if (newProps.probePositions !== currentProps.probePositions)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
state.createGeometry = true;
if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly)
state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent)
state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
state.updateColor = true;
}
else if (newProps.smoothColors.name === 'on' && currentProps.smoothColors.name === 'on') {
if (newProps.smoothColors.params.resolutionFactor !== currentProps.smoothColors.params.resolutionFactor)
state.updateColor = true;
if (newProps.smoothColors.params.sampleStride !== currentProps.smoothColors.params.sampleStride)
state.updateColor = true;
}
},
processValues: (values, geometry, props, theme, webgl) => {
const { resolution, colorTexture } = geometry.meta;
const csp = getColorSmoothingProps(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp) {
applyMeshColorSmoothing(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: (geometry) => {
var _a;
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}