molstar
Version:
A comprehensive macromolecular library.
201 lines (200 loc) • 11.2 kB
JavaScript
;
/**
* Copyright (c) 2020-2022 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.Volume = void 0;
var grid_1 = require("./grid");
var int_1 = require("../../mol-data/int");
var geometry_1 = require("../../mol-math/geometry");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
var boundary_helper_1 = require("../../mol-math/geometry/boundary-helper");
var cube_1 = require("../../mol-model-formats/volume/cube");
var common_1 = require("../../mol-math/linear-algebra/3d/common");
var custom_property_1 = require("../custom-property");
var param_definition_1 = require("../../mol-util/param-definition");
var number_1 = require("../../mol-util/number");
var density_server_1 = require("../../mol-model-formats/volume/density-server");
var Volume;
(function (Volume) {
function is(x) {
var _a, _b, _c, _d;
// TODO: improve
return (((_d = (_c = (_b = (_a = x === null || x === void 0 ? void 0 : x.grid) === null || _a === void 0 ? void 0 : _a.cells) === null || _b === void 0 ? void 0 : _b.space) === null || _c === void 0 ? void 0 : _c.dimensions) === null || _d === void 0 ? void 0 : _d.length) &&
(x === null || x === void 0 ? void 0 : x.sourceData) &&
(x === null || x === void 0 ? void 0 : x.customProperties) &&
(x === null || x === void 0 ? void 0 : x._propertyData));
}
Volume.is = is;
var IsoValue;
(function (IsoValue) {
function areSame(a, b, stats) {
return (0, common_1.equalEps)(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
}
IsoValue.areSame = areSame;
function absolute(value) { return { kind: 'absolute', absoluteValue: value }; }
IsoValue.absolute = absolute;
function relative(value) { return { kind: 'relative', relativeValue: value }; }
IsoValue.relative = relative;
function calcAbsolute(stats, relativeValue) {
return relativeValue * stats.sigma + stats.mean;
}
IsoValue.calcAbsolute = calcAbsolute;
function calcRelative(stats, absoluteValue) {
return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
}
IsoValue.calcRelative = calcRelative;
function toAbsolute(value, stats) {
return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: IsoValue.calcAbsolute(stats, value.relativeValue) };
}
IsoValue.toAbsolute = toAbsolute;
function toRelative(value, stats) {
return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: IsoValue.calcRelative(stats, value.absoluteValue) };
}
IsoValue.toRelative = toRelative;
function toString(value) {
return value.kind === 'relative'
? "".concat(value.relativeValue.toFixed(2), " \u03C3")
: "".concat(value.absoluteValue.toPrecision(4));
}
IsoValue.toString = toString;
})(IsoValue = Volume.IsoValue || (Volume.IsoValue = {}));
// Converts iso value to relative if using downsample VolumeServer data
function adjustedIsoValue(volume, value, kind) {
if (kind === 'relative')
return IsoValue.relative(value);
var absolute = IsoValue.absolute(value);
if (density_server_1.DscifFormat.is(volume.sourceData)) {
var stats = {
min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
};
return Volume.IsoValue.toRelative(absolute, stats);
}
return absolute;
}
Volume.adjustedIsoValue = adjustedIsoValue;
var defaultStats = { min: -1, max: 1, mean: 0, sigma: 0.1 };
function createIsoValueParam(defaultValue, stats) {
var sts = stats || defaultStats;
var min = sts.min, max = sts.max, mean = sts.mean, sigma = sts.sigma;
// using ceil/floor could lead to "ouf of bounds" when converting
var relMin = (min - mean) / sigma;
var relMax = (max - mean) / sigma;
var def = defaultValue;
if (defaultValue.kind === 'absolute') {
if (defaultValue.absoluteValue < min)
def = Volume.IsoValue.absolute(min);
else if (defaultValue.absoluteValue > max)
def = Volume.IsoValue.absolute(max);
}
else {
if (defaultValue.relativeValue < relMin)
def = Volume.IsoValue.relative(relMin);
else if (defaultValue.relativeValue > relMax)
def = Volume.IsoValue.relative(relMax);
}
return param_definition_1.ParamDefinition.Conditioned(def, {
'absolute': param_definition_1.ParamDefinition.Converted(function (v) { return Volume.IsoValue.toAbsolute(v, grid_1.Grid.One.stats).absoluteValue; }, function (v) { return Volume.IsoValue.absolute(v); }, param_definition_1.ParamDefinition.Numeric(mean, { min: min, max: max, step: (0, number_1.toPrecision)(sigma / 100, 2) }, { immediateUpdate: true })),
'relative': param_definition_1.ParamDefinition.Converted(function (v) { return Volume.IsoValue.toRelative(v, grid_1.Grid.One.stats).relativeValue; }, function (v) { return Volume.IsoValue.relative(v); }, param_definition_1.ParamDefinition.Numeric(Math.min(1, relMax), { min: relMin, max: relMax, step: (0, number_1.toPrecision)(Math.round(((max - min) / sigma)) / 100, 2) }, { immediateUpdate: true }))
}, function (v) { return v.kind === 'absolute' ? 'absolute' : 'relative'; }, function (v, c) { return c === 'absolute' ? Volume.IsoValue.toAbsolute(v, sts) : Volume.IsoValue.toRelative(v, sts); }, { isEssential: true });
}
Volume.createIsoValueParam = createIsoValueParam;
Volume.IsoValueParam = createIsoValueParam(Volume.IsoValue.relative(2));
Volume.One = {
label: '',
grid: grid_1.Grid.One,
sourceData: { kind: '', name: '', data: {} },
customProperties: new custom_property_1.CustomProperties(),
_propertyData: Object.create(null),
};
function areEquivalent(volA, volB) {
return grid_1.Grid.areEquivalent(volA.grid, volB.grid);
}
Volume.areEquivalent = areEquivalent;
function isEmpty(vol) {
return grid_1.Grid.isEmpty(vol.grid);
}
Volume.isEmpty = isEmpty;
function isOrbitals(volume) {
if (!cube_1.CubeFormat.is(volume.sourceData))
return false;
return volume.sourceData.data.header.orbitals;
}
Volume.isOrbitals = isOrbitals;
function Loci(volume) { return { kind: 'volume-loci', volume: volume }; }
Volume.Loci = Loci;
function isLoci(x) { return !!x && x.kind === 'volume-loci'; }
Volume.isLoci = isLoci;
function areLociEqual(a, b) { return a.volume === b.volume; }
Volume.areLociEqual = areLociEqual;
function isLociEmpty(loci) { return grid_1.Grid.isEmpty(loci.volume.grid); }
Volume.isLociEmpty = isLociEmpty;
function getBoundingSphere(volume, boundingSphere) {
return grid_1.Grid.getBoundingSphere(volume.grid, boundingSphere);
}
Volume.getBoundingSphere = getBoundingSphere;
var Isosurface;
(function (Isosurface) {
function Loci(volume, isoValue) { return { kind: 'isosurface-loci', volume: volume, isoValue: isoValue }; }
Isosurface.Loci = Loci;
function isLoci(x) { return !!x && x.kind === 'isosurface-loci'; }
Isosurface.isLoci = isLoci;
function areLociEqual(a, b) { return a.volume === b.volume && Volume.IsoValue.areSame(a.isoValue, b.isoValue, a.volume.grid.stats); }
Isosurface.areLociEqual = areLociEqual;
function isLociEmpty(loci) { return loci.volume.grid.cells.data.length === 0; }
Isosurface.isLociEmpty = isLociEmpty;
function getBoundingSphere(volume, isoValue, boundingSphere) {
// TODO get bounding sphere for subgrid with values >= isoValue
return Volume.getBoundingSphere(volume, boundingSphere);
}
Isosurface.getBoundingSphere = getBoundingSphere;
})(Isosurface = Volume.Isosurface || (Volume.Isosurface = {}));
var Cell;
(function (Cell) {
function Loci(volume, indices) { return { kind: 'cell-loci', volume: volume, indices: indices }; }
Cell.Loci = Loci;
function isLoci(x) { return !!x && x.kind === 'cell-loci'; }
Cell.isLoci = isLoci;
function areLociEqual(a, b) { return a.volume === b.volume && int_1.OrderedSet.areEqual(a.indices, b.indices); }
Cell.areLociEqual = areLociEqual;
function isLociEmpty(loci) { return int_1.OrderedSet.size(loci.indices) === 0; }
Cell.isLociEmpty = isLociEmpty;
var boundaryHelper = new boundary_helper_1.BoundaryHelper('98');
var tmpBoundaryPos = (0, linear_algebra_1.Vec3)();
function getBoundingSphere(volume, indices, boundingSphere) {
boundaryHelper.reset();
var transform = grid_1.Grid.getGridToCartesianTransform(volume.grid);
var getCoords = volume.grid.cells.space.getCoords;
for (var i = 0, _i = int_1.OrderedSet.size(indices); i < _i; i++) {
var o = int_1.OrderedSet.getAt(indices, i);
getCoords(o, tmpBoundaryPos);
linear_algebra_1.Vec3.transformMat4(tmpBoundaryPos, tmpBoundaryPos, transform);
boundaryHelper.includePosition(tmpBoundaryPos);
}
boundaryHelper.finishedIncludeStep();
for (var i = 0, _i = int_1.OrderedSet.size(indices); i < _i; i++) {
var o = int_1.OrderedSet.getAt(indices, i);
getCoords(o, tmpBoundaryPos);
linear_algebra_1.Vec3.transformMat4(tmpBoundaryPos, tmpBoundaryPos, transform);
boundaryHelper.radiusPosition(tmpBoundaryPos);
}
var bs = boundaryHelper.getSphere(boundingSphere);
return geometry_1.Sphere3D.expand(bs, bs, linear_algebra_1.Mat4.getMaxScaleOnAxis(transform) * 10);
}
Cell.getBoundingSphere = getBoundingSphere;
})(Cell = Volume.Cell || (Volume.Cell = {}));
Volume.PickingGranularity = {
set: function (volume, granularity) {
volume._propertyData['__picking_granularity__'] = granularity;
},
get: function (volume) {
var _a;
return (_a = volume._propertyData['__picking_granularity__']) !== null && _a !== void 0 ? _a : 'voxel';
}
};
})(Volume = exports.Volume || (exports.Volume = {}));