molstar
Version:
A comprehensive macromolecular library.
401 lines (400 loc) • 26.2 kB
JavaScript
;
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.StructureGaussianSurfaceTextureMeshVisual = exports.GaussianSurfaceTextureMeshVisual = exports.StructureGaussianSurfaceMeshVisual = exports.GaussianSurfaceMeshVisual = exports.StructureGaussianSurfaceVisual = exports.GaussianSurfaceVisual = exports.StructureGaussianSurfaceMeshParams = exports.GaussianSurfaceMeshParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../../mol-util/param-definition");
var units_visual_1 = require("../units-visual");
var gaussian_1 = require("./util/gaussian");
var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
var algorithm_1 = require("../../../mol-geo/util/marching-cubes/algorithm");
var element_1 = require("./util/element");
var texture_mesh_1 = require("../../../mol-geo/geometry/texture-mesh/texture-mesh");
var isosurface_1 = require("../../../mol-gl/compute/marching-cubes/isosurface");
var geometry_1 = require("../../../mol-math/geometry");
var complex_visual_1 = require("../complex-visual");
var common_1 = require("./util/common");
var color_smoothing_1 = require("../../../mol-geo/geometry/mesh/color-smoothing");
var color_smoothing_2 = require("../../../mol-geo/geometry/texture-mesh/color-smoothing");
var base_1 = require("../../../mol-geo/geometry/base");
var linear_algebra_1 = require("../../../mol-math/linear-algebra");
var debug_1 = require("../../../mol-util/debug");
var value_cell_1 = require("../../../mol-util/value-cell");
var SharedParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
exports.GaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsTextureMeshParams), SharedParams);
exports.StructureGaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexTextureMeshParams), SharedParams);
function gpuSupport(webgl) {
return webgl.extensions.colorBufferFloat && webgl.extensions.textureFloat && webgl.extensions.blendMinMax && webgl.extensions.drawBuffers;
}
function suitableForGpu(structure, props, webgl) {
// lower resolutions are about as fast on CPU vs integrated GPU,
// very low resolutions have artifacts when calculated on GPU
if (props.resolution > 1)
return false;
// the GPU is much more memory contraint, especially true for integrated GPUs,
// being conservative here still allows for small and medium sized assemblies
var d = webgl.maxTextureSize / 3;
var _a = (0, common_1.getVolumeSliceInfo)(structure.boundary.box, props.resolution, d * d), areaCells = _a.areaCells, maxAreaCells = _a.maxAreaCells;
return areaCells < maxAreaCells;
}
function GaussianSurfaceVisual(materialId, structure, props, webgl) {
if (props.tryUseGpu && webgl && gpuSupport(webgl) && suitableForGpu(structure, props, webgl)) {
return GaussianSurfaceTextureMeshVisual(materialId);
}
return GaussianSurfaceMeshVisual(materialId);
}
exports.GaussianSurfaceVisual = GaussianSurfaceVisual;
function StructureGaussianSurfaceVisual(materialId, structure, props, webgl) {
if (props.tryUseGpu && webgl && gpuSupport(webgl) && suitableForGpu(structure, props, webgl)) {
return StructureGaussianSurfaceTextureMeshVisual(materialId);
}
return StructureGaussianSurfaceMeshVisual(materialId);
}
exports.StructureGaussianSurfaceVisual = StructureGaussianSurfaceVisual;
//
function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
smoothness = props.smoothness;
return [4 /*yield*/, (0, gaussian_1.computeUnitGaussianDensity)(structure, unit, theme.size, props).runInContext(ctx.runtime)];
case 1:
_a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
params = {
isoLevel: Math.exp(-smoothness) / radiusFactor,
scalarField: field,
idField: idField
};
return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesMesh)(params, mesh).runAsChild(ctx.runtime)];
case 2:
surface = _b.sent();
surface.meta.resolution = resolution;
mesh_1.Mesh.transform(surface, transform);
if (ctx.webgl && !ctx.webgl.isWebGL2) {
mesh_1.Mesh.uniformTriangleGroup(surface);
value_cell_1.ValueCell.updateIfChanged(surface.varyingGroup, false);
}
else {
value_cell_1.ValueCell.updateIfChanged(surface.varyingGroup, true);
}
sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
return [2 /*return*/, surface];
}
});
});
}
function GaussianSurfaceMeshVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianSurfaceMeshParams),
createGeometry: createGaussianSurfaceMesh,
createLocationIterator: element_1.ElementIterator.fromGroup,
getLoci: element_1.getElementLoci,
eachLocation: element_1.eachElement,
setUpdateState: function (state, newProps, currentProps) {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.radiusOffset !== currentProps.radiusOffset)
state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
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;
}
},
mustRecreate: function (structureGroup, props, webgl) {
return props.tryUseGpu && !!webgl && suitableForGpu(structureGroup.structure, props, webgl);
},
processValues: function (values, geometry, props, theme, webgl) {
var _a = geometry.meta, resolution = _a.resolution, colorTexture = _a.colorTexture;
var csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp) {
(0, color_smoothing_1.applyMeshColorSmoothing)(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: function (geometry) {
var _a;
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}
exports.GaussianSurfaceMeshVisual = GaussianSurfaceMeshVisual;
//
function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
smoothness = props.smoothness;
return [4 /*yield*/, (0, gaussian_1.computeStructureGaussianDensity)(structure, theme.size, props).runInContext(ctx.runtime)];
case 1:
_a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
params = {
isoLevel: Math.exp(-smoothness) / radiusFactor,
scalarField: field,
idField: idField
};
return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesMesh)(params, mesh).runAsChild(ctx.runtime)];
case 2:
surface = _b.sent();
surface.meta.resolution = resolution;
mesh_1.Mesh.transform(surface, transform);
if (ctx.webgl && !ctx.webgl.isWebGL2) {
mesh_1.Mesh.uniformTriangleGroup(surface);
value_cell_1.ValueCell.updateIfChanged(surface.varyingGroup, false);
}
else {
value_cell_1.ValueCell.updateIfChanged(surface.varyingGroup, true);
}
sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
return [2 /*return*/, surface];
}
});
});
}
function StructureGaussianSurfaceMeshVisual(materialId) {
return (0, complex_visual_1.ComplexMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.StructureGaussianSurfaceMeshParams),
createGeometry: createStructureGaussianSurfaceMesh,
createLocationIterator: element_1.ElementIterator.fromStructure,
getLoci: element_1.getSerialElementLoci,
eachLocation: element_1.eachSerialElement,
setUpdateState: function (state, newProps, currentProps) {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.radiusOffset !== currentProps.radiusOffset)
state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly)
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;
}
},
mustRecreate: function (structure, props, webgl) {
return props.tryUseGpu && !!webgl && suitableForGpu(structure, props, webgl);
},
processValues: function (values, geometry, props, theme, webgl) {
var _a = geometry.meta, resolution = _a.resolution, colorTexture = _a.colorTexture;
var csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp) {
(0, color_smoothing_1.applyMeshColorSmoothing)(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: function (geometry) {
var _a;
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}
exports.StructureGaussianSurfaceMeshVisual = StructureGaussianSurfaceMeshVisual;
//
var GaussianSurfaceName = 'gaussian-surface';
function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, textureMesh) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, groupCount, boundingSphere, surface;
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0:
if (!ctx.webgl)
throw new Error('webgl context required to create gaussian surface texture-mesh');
if (debug_1.isTimingMode)
ctx.webgl.timer.mark('createGaussianSurfaceTextureMesh');
_a = ctx.webgl, namedTextures = _a.namedTextures, resources = _a.resources, _b = _a.extensions, colorBufferFloat = _b.colorBufferFloat, textureFloat = _b.textureFloat, colorBufferHalfFloat = _b.colorBufferHalfFloat, textureHalfFloat = _b.textureHalfFloat;
if (!namedTextures[GaussianSurfaceName]) {
namedTextures[GaussianSurfaceName] = colorBufferHalfFloat && textureHalfFloat
? resources.texture('image-float16', 'rgba', 'fp16', 'linear')
: colorBufferFloat && textureFloat
? resources.texture('image-float32', 'rgba', 'float', 'linear')
: resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
}
return [4 /*yield*/, (0, gaussian_1.computeUnitGaussianDensityTexture2d)(structure, unit, theme.size, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
case 1:
densityTextureData = _c.sent();
isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
gv = (0, isosurface_1.extractIsosurface)(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, true, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
if (debug_1.isTimingMode)
ctx.webgl.timer.markEnd('createGaussianSurfaceTextureMesh');
groupCount = unit.elements.length;
boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, densityTextureData.maxRadius);
surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
surface.meta.resolution = densityTextureData.resolution;
return [2 /*return*/, surface];
}
});
});
}
function GaussianSurfaceTextureMeshVisual(materialId) {
return (0, units_visual_1.UnitsTextureMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianSurfaceMeshParams),
createGeometry: createGaussianSurfaceTextureMesh,
createLocationIterator: element_1.ElementIterator.fromGroup,
getLoci: element_1.getElementLoci,
eachLocation: element_1.eachElement,
setUpdateState: function (state, newProps, currentProps) {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.radiusOffset !== currentProps.radiusOffset)
state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
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;
}
},
mustRecreate: function (structureGroup, props, webgl) {
return !props.tryUseGpu || !webgl || !suitableForGpu(structureGroup.structure, props, webgl);
},
processValues: function (values, geometry, props, theme, webgl) {
var _a = geometry.meta, resolution = _a.resolution, colorTexture = _a.colorTexture;
var csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp && webgl) {
(0, color_smoothing_2.applyTextureMeshColorSmoothing)(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: function (geometry) {
var _a;
geometry.vertexTexture.ref.value.destroy();
geometry.groupTexture.ref.value.destroy();
geometry.normalTexture.ref.value.destroy();
geometry.doubleBuffer.destroy();
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}
exports.GaussianSurfaceTextureMeshVisual = GaussianSurfaceTextureMeshVisual;
//
function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props, textureMesh) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, groupCount, boundingSphere, surface;
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0:
if (!ctx.webgl)
throw new Error('webgl context required to create structure gaussian surface texture-mesh');
if (debug_1.isTimingMode)
ctx.webgl.timer.mark('createStructureGaussianSurfaceTextureMesh');
_a = ctx.webgl, namedTextures = _a.namedTextures, resources = _a.resources, _b = _a.extensions, colorBufferFloat = _b.colorBufferFloat, textureFloat = _b.textureFloat, colorBufferHalfFloat = _b.colorBufferHalfFloat, textureHalfFloat = _b.textureHalfFloat;
if (!namedTextures[GaussianSurfaceName]) {
namedTextures[GaussianSurfaceName] = colorBufferHalfFloat && textureHalfFloat
? resources.texture('image-float16', 'rgba', 'fp16', 'linear')
: colorBufferFloat && textureFloat
? resources.texture('image-float32', 'rgba', 'float', 'linear')
: resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
}
return [4 /*yield*/, (0, gaussian_1.computeStructureGaussianDensityTexture2d)(structure, theme.size, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
case 1:
densityTextureData = _c.sent();
isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
gv = (0, isosurface_1.extractIsosurface)(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, true, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
if (debug_1.isTimingMode)
ctx.webgl.timer.markEnd('createStructureGaussianSurfaceTextureMesh');
groupCount = structure.elementCount;
boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, densityTextureData.maxRadius);
surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
surface.meta.resolution = densityTextureData.resolution;
return [2 /*return*/, surface];
}
});
});
}
function StructureGaussianSurfaceTextureMeshVisual(materialId) {
return (0, complex_visual_1.ComplexTextureMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.StructureGaussianSurfaceMeshParams),
createGeometry: createStructureGaussianSurfaceTextureMesh,
createLocationIterator: element_1.ElementIterator.fromStructure,
getLoci: element_1.getSerialElementLoci,
eachLocation: element_1.eachSerialElement,
setUpdateState: function (state, newProps, currentProps) {
if (newProps.resolution !== currentProps.resolution)
state.createGeometry = true;
if (newProps.radiusOffset !== currentProps.radiusOffset)
state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness)
state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
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;
}
},
mustRecreate: function (structure, props, webgl) {
return !props.tryUseGpu || !webgl || !suitableForGpu(structure, props, webgl);
},
processValues: function (values, geometry, props, theme, webgl) {
var _a = geometry.meta, resolution = _a.resolution, colorTexture = _a.colorTexture;
var csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, theme.color.preferSmoothing, resolution);
if (csp && webgl) {
(0, color_smoothing_2.applyTextureMeshColorSmoothing)(values, csp.resolution, csp.stride, webgl, colorTexture);
geometry.meta.colorTexture = values.tColorGrid.ref.value;
}
},
dispose: function (geometry) {
var _a;
geometry.vertexTexture.ref.value.destroy();
geometry.groupTexture.ref.value.destroy();
geometry.normalTexture.ref.value.destroy();
geometry.doubleBuffer.destroy();
(_a = geometry.meta.colorTexture) === null || _a === void 0 ? void 0 : _a.destroy();
}
}, materialId);
}
exports.StructureGaussianSurfaceTextureMeshVisual = StructureGaussianSurfaceTextureMeshVisual;