molstar
Version:
A comprehensive macromolecular library.
144 lines (143 loc) • 8.05 kB
JavaScript
;
/**
* Copyright (c) 2018-2025 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.UnitsGaussianDensityVolumeParams = exports.GaussianDensityVolumeParams = void 0;
exports.GaussianDensityVolumeVisual = GaussianDensityVolumeVisual;
exports.UnitsGaussianDensityVolumeVisual = UnitsGaussianDensityVolumeVisual;
const param_definition_1 = require("../../../mol-util/param-definition");
const gaussian_1 = require("./util/gaussian");
const direct_volume_1 = require("../../../mol-geo/geometry/direct-volume/direct-volume");
const complex_visual_1 = require("../complex-visual");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const element_1 = require("./util/element");
const geometry_1 = require("../../../mol-math/geometry");
const units_visual_1 = require("../units-visual");
function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
const { webgl } = ctx;
if (!webgl) {
// gpu gaussian density also needs blendMinMax but there is no fallback here so
// we allow it here with the results that there is no group id assignment and
// hence no group-based coloring or picking
throw new Error('GaussianDensityVolume requires `webgl`');
}
const axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
const stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
const create = (directVolume) => {
const oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
const densityTextureData = (0, gaussian_1.computeStructureGaussianDensityTexture)(structure, theme.size, props, webgl, oldTexture);
const { transform, texture, bbox, gridDim } = densityTextureData;
const unitToCartn = linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), transform, linear_algebra_1.Mat4.fromScaling((0, linear_algebra_1.Mat4)(), gridDim));
const cellDim = linear_algebra_1.Mat4.getScaling((0, linear_algebra_1.Vec3)(), transform);
const vol = direct_volume_1.DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, 'byte', directVolume);
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, densityTextureData.maxRadius);
vol.setBoundingSphere(sphere);
return vol;
};
const vol = create(directVolume);
vol.meta.reset = () => {
create(vol);
};
return vol;
}
exports.GaussianDensityVolumeParams = {
...complex_visual_1.ComplexDirectVolumeParams,
...gaussian_1.GaussianDensityParams,
ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])),
includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }),
};
function GaussianDensityVolumeVisual(materialId) {
return (0, complex_visual_1.ComplexDirectVolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianDensityVolumeParams),
createGeometry: createGaussianDensityVolume,
createLocationIterator: element_1.ElementIterator.fromStructure,
getLoci: element_1.getSerialElementLoci,
eachLocation: element_1.eachSerialElement,
setUpdateState: (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.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly)
state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent)
state.createGeometry = true;
},
dispose: (geometry) => {
geometry.gridTexture.ref.value.destroy();
}
}, materialId);
}
//
function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, directVolume) {
const { webgl } = ctx;
if (!webgl) {
// gpu gaussian density also needs blendMinMax but there is no fallback here so
// we allow it here with the results that there is no group id assignment and
// hence no group-based coloring or picking
throw new Error('GaussianDensityVolume requires `webgl`');
}
const axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
const stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
const create = (directVolume) => {
const oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
const densityTextureData = (0, gaussian_1.computeUnitGaussianDensityTexture)(structure, unit, theme.size, props, webgl, oldTexture);
const { transform, texture, bbox, gridDim } = densityTextureData;
const unitToCartn = linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), transform, linear_algebra_1.Mat4.fromScaling((0, linear_algebra_1.Mat4)(), gridDim));
const cellDim = linear_algebra_1.Mat4.getScaling((0, linear_algebra_1.Vec3)(), transform);
const vol = direct_volume_1.DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, 'byte', directVolume);
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, densityTextureData.maxRadius);
vol.setBoundingSphere(sphere);
return vol;
};
const vol = create(directVolume);
vol.meta.reset = () => {
create(vol);
};
return vol;
}
exports.UnitsGaussianDensityVolumeParams = {
...units_visual_1.UnitsDirectVolumeParams,
...gaussian_1.GaussianDensityParams,
ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])),
includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }),
};
function UnitsGaussianDensityVolumeVisual(materialId) {
return (0, units_visual_1.UnitsDirectVolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.UnitsGaussianDensityVolumeParams),
createGeometry: createUnitsGaussianDensityVolume,
createLocationIterator: element_1.ElementIterator.fromGroup,
getLoci: element_1.getElementLoci,
eachLocation: element_1.eachElement,
setUpdateState: (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.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly)
state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent)
state.createGeometry = true;
},
dispose: (geometry) => {
geometry.gridTexture.ref.value.destroy();
}
}, materialId);
}