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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * 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.CarbohydrateSymbolVisual = exports.CarbohydrateSymbolParams = void 0; var tslib_1 = require("tslib"); var linear_algebra_1 = require("../../../mol-math/linear-algebra"); var box_1 = require("../../../mol-geo/primitive/box"); var pyramid_1 = require("../../../mol-geo/primitive/pyramid"); var star_1 = require("../../../mol-geo/primitive/star"); var octahedron_1 = require("../../../mol-geo/primitive/octahedron"); var prism_1 = require("../../../mol-geo/primitive/prism"); var structure_1 = require("../../../mol-model/structure"); var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder"); var constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants"); var sphere_1 = require("../../../mol-geo/geometry/mesh/builder/sphere"); var complex_visual_1 = require("../complex-visual"); var param_definition_1 = require("../../../mol-util/param-definition"); var location_iterator_1 = require("../../../mol-geo/util/location-iterator"); var int_1 = require("../../../mol-data/int"); var loci_1 = require("../../../mol-model/loci"); var common_1 = require("./util/common"); var base_1 = require("../../../mol-geo/geometry/base"); var t = linear_algebra_1.Mat4.identity(); var sVec = (0, linear_algebra_1.Vec3)(); var pd = (0, linear_algebra_1.Vec3)(); var SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4) var box = (0, box_1.Box)(); var perforatedBox = (0, box_1.PerforatedBox)(); var octagonalPyramid = (0, pyramid_1.OctagonalPyramid)(); var perforatedOctagonalPyramid = (0, pyramid_1.PerforatedOctagonalPyramid)(); var star = (0, star_1.Star)({ outerRadius: 1, innerRadius: 0.5, thickness: 0.5, pointCount: 5 }); var octahedron = (0, octahedron_1.Octahedron)(); var perforatedOctahedron = (0, octahedron_1.PerforatedOctahedron)(); var diamondPrism = (0, prism_1.DiamondPrism)(); var pentagonalPrism = (0, prism_1.PentagonalPrism)(); var hexagonalPrism = (0, prism_1.HexagonalPrism)(); var shiftedHexagonalPrism = (0, prism_1.ShiftedHexagonalPrism)(); var heptagonalPrism = (0, prism_1.HeptagonalPrism)(); function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) { var builderState = mesh_builder_1.MeshBuilder.createState(256, 128, mesh); var detail = props.detail, sizeFactor = props.sizeFactor; var carbohydrates = structure.carbohydrates; var n = carbohydrates.elements.length; var l = structure_1.StructureElement.Location.create(structure); for (var i = 0; i < n; ++i) { var c = carbohydrates.elements[i]; var ring = c.unit.rings.all[c.ringIndex]; var shapeType = (0, constants_1.getSaccharideShape)(c.component.type, ring.length); l.unit = c.unit; l.element = c.unit.elements[ring[0]]; var size = theme.size.size(l); var radius = size * sizeFactor; var side = size * sizeFactor * SideFactor; var _a = c.geometry, center = _a.center, normal = _a.normal, direction = _a.direction; linear_algebra_1.Vec3.add(pd, center, direction); linear_algebra_1.Mat4.targetTo(t, center, pd, normal); linear_algebra_1.Mat4.setTranslation(t, center); builderState.currentGroup = i * 2; switch (shapeType) { case 0 /* SaccharideShape.FilledSphere */: (0, sphere_1.addSphere)(builderState, center, radius, detail); break; case 1 /* SaccharideShape.FilledCube */: linear_algebra_1.Mat4.scaleUniformly(t, t, side); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box); break; case 2 /* SaccharideShape.CrossedCube */: linear_algebra_1.Mat4.scaleUniformly(t, t, side); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedBox); linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZ90X180); builderState.currentGroup += 1; mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedBox); break; case 4 /* SaccharideShape.FilledCone */: linear_algebra_1.Mat4.scaleUniformly(t, t, side * 1.2); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, octagonalPyramid); break; case 5 /* SaccharideShape.DevidedCone */: linear_algebra_1.Mat4.scaleUniformly(t, t, side * 1.2); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid); linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZ90); builderState.currentGroup += 1; mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid); break; case 6 /* SaccharideShape.FlatBox */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box); break; case 7 /* SaccharideShape.FilledStar */: linear_algebra_1.Mat4.scaleUniformly(t, t, side); linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, star); break; case 8 /* SaccharideShape.FilledDiamond */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, octahedron); break; case 3 /* SaccharideShape.DividedDiamond */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron); linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotY90); builderState.currentGroup += 1; mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron); break; case 9 /* SaccharideShape.FlatDiamond */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side / 2, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, diamondPrism); break; case 12 /* SaccharideShape.DiamondPrism */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, diamondPrism); break; case 13 /* SaccharideShape.PentagonalPrism */: case 11 /* SaccharideShape.Pentagon */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, pentagonalPrism); break; case 14 /* SaccharideShape.HexagonalPrism */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, hexagonalPrism); break; case 15 /* SaccharideShape.HeptagonalPrism */: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, heptagonalPrism); break; case 10 /* SaccharideShape.FlatHexagon */: default: linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZYZ90); linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side / 1.5, side, side / 2)); mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, shiftedHexagonalPrism); break; } } return mesh_builder_1.MeshBuilder.getMesh(builderState); } exports.CarbohydrateSymbolParams = tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), { detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), sizeFactor: param_definition_1.ParamDefinition.Numeric(1.75, { min: 0, max: 10, step: 0.01 }) }); function CarbohydrateSymbolVisual(materialId) { return (0, complex_visual_1.ComplexMeshVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateSymbolParams), createGeometry: createCarbohydrateSymbolMesh, createLocationIterator: CarbohydrateElementIterator, getLoci: getCarbohydrateLoci, eachLocation: eachCarbohydrate, setUpdateState: function (state, newProps, currentProps) { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.detail !== currentProps.detail); } }, materialId); } exports.CarbohydrateSymbolVisual = CarbohydrateSymbolVisual; function CarbohydrateElementIterator(structure) { var carbElements = structure.carbohydrates.elements; var groupCount = carbElements.length * 2; var instanceCount = 1; var location = structure_1.StructureElement.Location.create(structure); function getLocation(groupIndex, instanceIndex) { var carb = carbElements[Math.floor(groupIndex / 2)]; var ring = carb.unit.rings.all[carb.ringIndex]; location.unit = carb.unit; location.element = carb.unit.elements[ring[0]]; return location; } function isSecondary(elementIndex, instanceIndex) { return (elementIndex % 2) === 1; } return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation, true, isSecondary); } /** Return a Loci for the elements of the whole residue of a carbohydrate. */ function getCarbohydrateLoci(pickingId, structure, id) { var objectId = pickingId.objectId, groupId = pickingId.groupId; if (id === objectId) { var carb = structure.carbohydrates.elements[Math.floor(groupId / 2)]; return (0, common_1.getAltResidueLociFromId)(structure, carb.unit, carb.residueIndex, carb.altId); } return loci_1.EmptyLoci; } var __elementIndicesSet = new Set(); /** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */ function eachCarbohydrate(loci, structure, apply) { var getElementIndices = structure.carbohydrates.getElementIndices; var changed = false; if (!structure_1.StructureElement.Loci.is(loci)) return false; if (!structure_1.Structure.areEquivalent(loci.structure, structure)) return false; var _loop_1 = function (unit, indices) { if (!structure_1.Unit.isAtomic(unit)) return "continue"; __elementIndicesSet.clear(); int_1.OrderedSet.forEach(indices, function (v) { var elementIndices = getElementIndices(unit, unit.elements[v]); for (var i = 0, il = elementIndices.length; i < il; ++i) { if (!__elementIndicesSet.has(elementIndices[i])) { __elementIndicesSet.add(elementIndices[i]); if (apply(int_1.Interval.ofSingleton(elementIndices[i] * 2))) changed = true; } } }); }; for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) { var _b = _a[_i], unit = _b.unit, indices = _b.indices; _loop_1(unit, indices); } return changed; }