molstar
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A comprehensive macromolecular library.
354 lines (353 loc) • 19.4 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2024 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.Spheres = void 0;
const mol_util_1 = require("../../../mol-util");
const param_definition_1 = require("../../../mol-util/param-definition");
const location_iterator_1 = require("../../../mol-geo/util/location-iterator");
const color_data_1 = require("../color-data");
const marker_data_1 = require("../marker-data");
const util_1 = require("../../../mol-gl/renderable/util");
const geometry_1 = require("../../../mol-math/geometry");
const size_data_1 = require("../size-data");
const base_1 = require("../base");
const overpaint_data_1 = require("../overpaint-data");
const transparency_data_1 = require("../transparency-data");
const util_2 = require("../../../mol-data/util");
const util_3 = require("../../util");
const clipping_data_1 = require("../clipping-data");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const substance_data_1 = require("../substance-data");
const emissive_data_1 = require("../emissive-data");
var Spheres;
(function (Spheres) {
function create(centers, groups, sphereCount, spheres) {
return spheres ?
update(centers, groups, sphereCount, spheres) :
fromArrays(centers, groups, sphereCount);
}
Spheres.create = create;
function createEmpty(spheres) {
const cb = spheres ? spheres.centerBuffer.ref.value : new Float32Array(0);
const gb = spheres ? spheres.groupBuffer.ref.value : new Float32Array(0);
return create(cb, gb, 0, spheres);
}
Spheres.createEmpty = createEmpty;
function hashCode(spheres) {
return (0, util_2.hashFnv32a)([
spheres.sphereCount,
spheres.centerBuffer.ref.version,
spheres.groupBuffer.ref.version
]);
}
function fromArrays(centers, groups, sphereCount) {
const boundingSphere = (0, geometry_1.Sphere3D)();
let groupMapping;
let currentHash = -1;
let currentGroup = -1;
const positionGroup = mol_util_1.ValueCell.create((0, util_1.createTextureImage)(1, 4, Float32Array));
const texDim = mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(0, 0));
const lodLevels = mol_util_1.ValueCell.create([]);
const sizeFactor = mol_util_1.ValueCell.create(0);
const spheres = {
kind: 'spheres',
sphereCount,
centerBuffer: mol_util_1.ValueCell.create(centers),
groupBuffer: mol_util_1.ValueCell.create(groups),
get boundingSphere() {
const newHash = hashCode(spheres);
if (newHash !== currentHash) {
const b = (0, util_1.calculateInvariantBoundingSphere)(spheres.centerBuffer.ref.value, spheres.sphereCount, 1);
geometry_1.Sphere3D.copy(boundingSphere, b);
currentHash = newHash;
}
return boundingSphere;
},
get groupMapping() {
if (spheres.groupBuffer.ref.version !== currentGroup) {
groupMapping = (0, util_3.createGroupMapping)(spheres.groupBuffer.ref.value, spheres.sphereCount);
currentGroup = spheres.groupBuffer.ref.version;
}
return groupMapping;
},
setBoundingSphere(sphere) {
geometry_1.Sphere3D.copy(boundingSphere, sphere);
currentHash = hashCode(spheres);
},
shaderData: {
positionGroup,
texDim,
lodLevels,
sizeFactor,
update(props) {
var _a, _b;
const lodLevelsProp = (_a = props === null || props === void 0 ? void 0 : props.lodLevels) !== null && _a !== void 0 ? _a : getLodLevels(lodLevels.ref.value);
const sizeFactorProp = (_b = props === null || props === void 0 ? void 0 : props.sizeFactor) !== null && _b !== void 0 ? _b : sizeFactor.ref.value;
const strides = getStrides(lodLevelsProp, sizeFactorProp);
const pgt = (0, util_1.createTextureImage)(spheres.sphereCount, 4, Float32Array, positionGroup.ref.value.array);
const offsets = getStrideOffsetsAndSetPositionGroup(pgt, spheres.centerBuffer.ref.value, spheres.groupBuffer.ref.value, spheres.sphereCount, strides);
const newLodLevels = offsets ? getLodLevelsValue(lodLevelsProp, sizeFactorProp, offsets, spheres.sphereCount) : [];
mol_util_1.ValueCell.update(positionGroup, pgt);
mol_util_1.ValueCell.update(texDim, linear_algebra_1.Vec2.set(texDim.ref.value, pgt.width, pgt.height));
mol_util_1.ValueCell.update(lodLevels, newLodLevels);
mol_util_1.ValueCell.update(sizeFactor, sizeFactorProp);
}
},
};
spheres.shaderData.update();
return spheres;
}
function update(centers, groups, sphereCount, spheres) {
spheres.sphereCount = sphereCount;
mol_util_1.ValueCell.update(spheres.centerBuffer, centers);
mol_util_1.ValueCell.update(spheres.groupBuffer, groups);
spheres.shaderData.update();
return spheres;
}
function getStrideOffsetsAndSetPositionGroup(out, centers, groups, count, strides) {
const { array } = out;
if (strides.length === 0) {
for (let i = 0; i < count; ++i) {
array[i * 4 + 0] = centers[i * 3 + 0];
array[i * 4 + 1] = centers[i * 3 + 1];
array[i * 4 + 2] = centers[i * 3 + 2];
array[i * 4 + 3] = groups[i];
}
return;
}
const offsets = [0];
let o = 0;
for (let i = 0, il = strides.length; i < il; ++i) {
const s = strides[i];
for (let j = 0; j < count; ++j) {
let handled = false;
for (let k = 0; k < i; ++k) {
if (j % strides[k] === 0) {
handled = true;
break;
}
}
if (!handled && j % s === 0) {
array[o * 4 + 0] = centers[j * 3 + 0];
array[o * 4 + 1] = centers[j * 3 + 1];
array[o * 4 + 2] = centers[j * 3 + 2];
array[o * 4 + 3] = groups[j];
o += 1;
}
}
offsets.push(o * 6);
}
return offsets;
}
function areLodLevelsEqual(a, b) {
if (a.length !== b.length)
return false;
for (let i = 0, il = a.length; i < il; ++i) {
if (a[i].maxDistance !== b[i].maxDistance)
return false;
if (a[i].minDistance !== b[i].minDistance)
return false;
if (a[i].overlap !== b[i].overlap)
return false;
if (a[i].stride !== b[i].stride)
return false;
if (a[i].scaleBias !== b[i].scaleBias)
return false;
}
return true;
}
function getLodLevelsValue(prop, sizeFactor, offsets, count) {
return prop.map((l, i) => {
const stride = getAdjustedStride(l, sizeFactor);
return [
l.minDistance,
l.maxDistance,
l.overlap,
offsets[offsets.length - 1 - i],
Math.pow(Math.min(count, stride), 1 / l.scaleBias),
l.stride,
l.scaleBias,
];
});
}
function getLodLevels(lodLevelsValue) {
return lodLevelsValue.map(l => ({
minDistance: l[0],
maxDistance: l[1],
overlap: l[2],
stride: l[5],
scaleBias: l[6],
}));
}
function getAdjustedStride(lodLevel, sizeFactor) {
return Math.max(1, Math.round(lodLevel.stride / Math.pow(sizeFactor, lodLevel.scaleBias)));
}
function getStrides(lodLevels, sizeFactor) {
return lodLevels.map(l => getAdjustedStride(l, sizeFactor)).reverse();
}
Spheres.Params = {
...base_1.BaseGeometry.Params,
sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }),
doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo),
ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory),
celShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory),
xrayShaded: param_definition_1.ParamDefinition.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], base_1.BaseGeometry.ShadingCategory),
transparentBackfaces: param_definition_1.ParamDefinition.Select('off', param_definition_1.ParamDefinition.arrayToOptions(['off', 'on', 'opaque']), base_1.BaseGeometry.ShadingCategory),
solidInterior: param_definition_1.ParamDefinition.Boolean(true, base_1.BaseGeometry.ShadingCategory),
clipPrimitive: param_definition_1.ParamDefinition.Boolean(false, { ...base_1.BaseGeometry.ShadingCategory, description: 'Clip whole sphere instead of cutting it.' }),
approximate: param_definition_1.ParamDefinition.Boolean(false, { ...base_1.BaseGeometry.ShadingCategory, description: 'Faster rendering, but has artifacts.' }),
alphaThickness: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 20, step: 1 }, { ...base_1.BaseGeometry.ShadingCategory, description: 'If not zero, adjusts alpha for radius.' }),
bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory),
bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory),
lodLevels: param_definition_1.ParamDefinition.ObjectList({
minDistance: param_definition_1.ParamDefinition.Numeric(0),
maxDistance: param_definition_1.ParamDefinition.Numeric(0),
overlap: param_definition_1.ParamDefinition.Numeric(0),
stride: param_definition_1.ParamDefinition.Numeric(0),
scaleBias: param_definition_1.ParamDefinition.Numeric(3, { min: 0.1, max: 10, step: 0.1 }),
}, o => `${o.stride}`, {
...base_1.BaseGeometry.CullingLodCategory,
defaultValue: []
})
};
Spheres.Utils = {
Params: Spheres.Params,
createEmpty,
createValues,
createValuesSimple,
updateValues,
updateBoundingSphere,
createRenderableState,
updateRenderableState,
createPositionIterator
};
function createPositionIterator(spheres, transform) {
const groupCount = spheres.sphereCount;
const instanceCount = transform.instanceCount.ref.value;
const location = (0, location_iterator_1.PositionLocation)();
const p = location.position;
const v = spheres.centerBuffer.ref.value;
const m = transform.aTransform.ref.value;
const getLocation = (groupIndex, instanceIndex) => {
if (instanceIndex < 0) {
linear_algebra_1.Vec3.fromArray(p, v, groupIndex * 3);
}
else {
linear_algebra_1.Vec3.transformMat4Offset(p, v, m, 0, groupIndex * 3, instanceIndex * 16);
}
return location;
};
return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation);
}
function createValues(spheres, transform, locationIt, theme, props) {
const { instanceCount, groupCount } = locationIt;
const positionIt = createPositionIterator(spheres, transform);
const color = (0, color_data_1.createColors)(locationIt, positionIt, theme.color);
const size = (0, size_data_1.createSizes)(locationIt, theme.size);
const marker = props.instanceGranularity
? (0, marker_data_1.createMarkers)(instanceCount, 'instance')
: (0, marker_data_1.createMarkers)(instanceCount * groupCount, 'groupInstance');
const overpaint = (0, overpaint_data_1.createEmptyOverpaint)();
const transparency = (0, transparency_data_1.createEmptyTransparency)();
const emissive = (0, emissive_data_1.createEmptyEmissive)();
const material = (0, substance_data_1.createEmptySubstance)();
const clipping = (0, clipping_data_1.createEmptyClipping)();
const counts = { drawCount: spheres.sphereCount * 2 * 3, vertexCount: spheres.sphereCount * 6, groupCount, instanceCount };
const padding = spheres.boundingSphere.radius ? (0, size_data_1.getMaxSize)(size) * props.sizeFactor : 0;
const invariantBoundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), spheres.boundingSphere, padding);
const boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
spheres.shaderData.update({ lodLevels: props.lodLevels, sizeFactor: props.sizeFactor });
return {
dGeometryType: mol_util_1.ValueCell.create('spheres'),
uTexDim: spheres.shaderData.texDim,
tPositionGroup: spheres.shaderData.positionGroup,
boundingSphere: mol_util_1.ValueCell.create(boundingSphere),
invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere),
uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)),
...color,
...size,
...marker,
...overpaint,
...transparency,
...emissive,
...material,
...clipping,
...transform,
padding: mol_util_1.ValueCell.create(padding),
...base_1.BaseGeometry.createValues(props, counts),
uSizeFactor: spheres.shaderData.sizeFactor,
uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided),
dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight),
dCelShaded: mol_util_1.ValueCell.create(props.celShaded),
dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'),
dTransparentBackfaces: mol_util_1.ValueCell.create(props.transparentBackfaces),
dSolidInterior: mol_util_1.ValueCell.create(props.solidInterior),
dClipPrimitive: mol_util_1.ValueCell.create(props.clipPrimitive),
dApproximate: mol_util_1.ValueCell.create(props.approximate),
uAlphaThickness: mol_util_1.ValueCell.create(props.alphaThickness),
uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency),
uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude),
lodLevels: spheres.shaderData.lodLevels,
centerBuffer: spheres.centerBuffer,
groupBuffer: spheres.groupBuffer,
};
}
function createValuesSimple(spheres, props, colorValue, sizeValue, transform) {
const s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
const p = { ...param_definition_1.ParamDefinition.getDefaultValues(Spheres.Params), ...props };
return createValues(spheres, s.transform, s.locationIterator, s.theme, p);
}
function updateValues(values, props) {
base_1.BaseGeometry.updateValues(values, props);
mol_util_1.ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor);
mol_util_1.ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
mol_util_1.ValueCell.updateIfChanged(values.dCelShaded, props.celShaded);
mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off');
mol_util_1.ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
mol_util_1.ValueCell.updateIfChanged(values.dSolidInterior, props.solidInterior);
mol_util_1.ValueCell.updateIfChanged(values.dClipPrimitive, props.clipPrimitive);
mol_util_1.ValueCell.updateIfChanged(values.dApproximate, props.approximate);
mol_util_1.ValueCell.updateIfChanged(values.uAlphaThickness, props.alphaThickness);
mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
const lodLevels = getLodLevels(values.lodLevels.ref.value);
if (!areLodLevelsEqual(props.lodLevels, lodLevels)) {
const count = values.uVertexCount.ref.value / 6;
const strides = getStrides(props.lodLevels, props.sizeFactor);
const offsets = getStrideOffsetsAndSetPositionGroup(values.tPositionGroup.ref.value, values.centerBuffer.ref.value, values.groupBuffer.ref.value, count, strides);
const lodLevels = offsets ? getLodLevelsValue(props.lodLevels, props.sizeFactor, offsets, count) : [];
mol_util_1.ValueCell.update(values.tPositionGroup, values.tPositionGroup.ref.value);
mol_util_1.ValueCell.update(values.lodLevels, lodLevels);
}
}
function updateBoundingSphere(values, spheres) {
const padding = spheres.boundingSphere.radius
? (0, size_data_1.getMaxSize)(values) * values.uSizeFactor.ref.value
: 0;
const invariantBoundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), spheres.boundingSphere, padding);
const boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
if (!geometry_1.Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
mol_util_1.ValueCell.update(values.boundingSphere, boundingSphere);
}
if (!geometry_1.Sphere3D.equals(invariantBoundingSphere, values.invariantBoundingSphere.ref.value)) {
mol_util_1.ValueCell.update(values.invariantBoundingSphere, invariantBoundingSphere);
mol_util_1.ValueCell.update(values.uInvariantBoundingSphere, linear_algebra_1.Vec4.fromSphere(values.uInvariantBoundingSphere.ref.value, invariantBoundingSphere));
}
mol_util_1.ValueCell.update(values.padding, padding);
}
function createRenderableState(props) {
const state = base_1.BaseGeometry.createRenderableState(props);
updateRenderableState(state, props);
return state;
}
function updateRenderableState(state, props) {
base_1.BaseGeometry.updateRenderableState(state, props);
state.opaque = state.opaque && !props.xrayShaded;
state.writeDepth = state.opaque;
}
})(Spheres || (exports.Spheres = Spheres = {}));