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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * Copyright (c) 2018-2023 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.PolymerBackboneCylinderParams = void 0; exports.PolymerBackboneCylinderVisual = PolymerBackboneCylinderVisual; exports.PolymerBackboneCylinderImpostorVisual = PolymerBackboneCylinderImpostorVisual; exports.PolymerBackboneCylinderMeshVisual = PolymerBackboneCylinderMeshVisual; const param_definition_1 = require("../../../mol-util/param-definition"); const structure_1 = require("../../../mol-model/structure"); const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh"); const mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder"); const linear_algebra_1 = require("../../../mol-math/linear-algebra"); const polymer_1 = require("./util/polymer"); const cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder"); const units_visual_1 = require("../units-visual"); const base_1 = require("../../../mol-geo/geometry/base"); const geometry_1 = require("../../../mol-math/geometry"); const types_1 = require("../../../mol-model/structure/model/types"); const cylinders_1 = require("../../../mol-geo/geometry/cylinders/cylinders"); const cylinders_builder_1 = require("../../../mol-geo/geometry/cylinders/cylinders-builder"); const backbone_1 = require("./util/polymer/backbone"); // avoiding namespace lookup improved performance in Chrome (Aug 2020) const v3scale = linear_algebra_1.Vec3.scale; const v3add = linear_algebra_1.Vec3.add; const v3sub = linear_algebra_1.Vec3.sub; exports.PolymerBackboneCylinderParams = { ...units_visual_1.UnitsMeshParams, ...units_visual_1.UnitsCylindersParams, sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), }; function PolymerBackboneCylinderVisual(materialId, structure, props, webgl) { return props.tryUseImpostor && webgl && webgl.extensions.fragDepth ? PolymerBackboneCylinderImpostorVisual(materialId) : PolymerBackboneCylinderMeshVisual(materialId); } function createPolymerBackboneCylinderImpostor(ctx, unit, structure, theme, props, cylinders) { const polymerElementCount = unit.polymerElements.length; if (!polymerElementCount) return cylinders_1.Cylinders.createEmpty(cylinders); const cylindersCountEstimate = polymerElementCount * 2; const builder = cylinders_builder_1.CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders); const uc = unit.conformation; const pA = (0, linear_algebra_1.Vec3)(); const pB = (0, linear_algebra_1.Vec3)(); const pM = (0, linear_algebra_1.Vec3)(); const add = function (indexA, indexB, groupA, groupB, moleculeType) { uc.invariantPosition(indexA, pA); uc.invariantPosition(indexB, pB); const isNucleicType = (0, types_1.isNucleic)(moleculeType); const shift = isNucleicType ? polymer_1.NucleicShift : polymer_1.StandardShift; v3add(pM, pA, v3scale(pM, v3sub(pM, pB, pA), shift)); builder.add(pA[0], pA[1], pA[2], pM[0], pM[1], pM[2], 1, false, false, 2, groupA); builder.add(pM[0], pM[1], pM[2], pB[0], pB[1], pB[2], 1, false, false, 2, groupB); }; (0, backbone_1.eachPolymerBackboneLink)(unit, add); const c = builder.getCylinders(); const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor); c.setBoundingSphere(sphere); return c; } function PolymerBackboneCylinderImpostorVisual(materialId) { return (0, units_visual_1.UnitsCylindersVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneCylinderParams), createGeometry: createPolymerBackboneCylinderImpostor, createLocationIterator: (structureGroup) => polymer_1.PolymerLocationIterator.fromGroup(structureGroup), getLoci: polymer_1.getPolymerElementLoci, eachLocation: polymer_1.eachPolymerElement, setUpdateState: (state, newProps, currentProps) => { }, mustRecreate: (structureGroup, props, webgl) => { return !props.tryUseImpostor || !webgl; } }, materialId); } function createPolymerBackboneCylinderMesh(ctx, unit, structure, theme, props, mesh) { const polymerElementCount = unit.polymerElements.length; if (!polymerElementCount) return mesh_1.Mesh.createEmpty(mesh); const { radialSegments, sizeFactor } = props; const vertexCountEstimate = radialSegments * 2 * polymerElementCount * 2; const builderState = mesh_builder_1.MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 10, mesh); const c = unit.conformation; const pA = (0, linear_algebra_1.Vec3)(); const pB = (0, linear_algebra_1.Vec3)(); const cylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments }; const centerA = structure_1.StructureElement.Location.create(structure, unit); const centerB = structure_1.StructureElement.Location.create(structure, unit); const add = function (indexA, indexB, groupA, groupB, moleculeType) { centerA.element = indexA; centerB.element = indexB; c.invariantPosition(centerA.element, pA); c.invariantPosition(centerB.element, pB); const isNucleicType = (0, types_1.isNucleic)(moleculeType); const shift = isNucleicType ? polymer_1.NucleicShift : polymer_1.StandardShift; cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerA) * sizeFactor; builderState.currentGroup = groupA; (0, cylinder_1.addCylinder)(builderState, pA, pB, shift, cylinderProps); cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerB) * sizeFactor; builderState.currentGroup = groupB; (0, cylinder_1.addCylinder)(builderState, pB, pA, 1 - shift, cylinderProps); }; (0, backbone_1.eachPolymerBackboneLink)(unit, add); const m = mesh_builder_1.MeshBuilder.getMesh(builderState); const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor); m.setBoundingSphere(sphere); return m; } function PolymerBackboneCylinderMeshVisual(materialId) { return (0, units_visual_1.UnitsMeshVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneCylinderParams), createGeometry: createPolymerBackboneCylinderMesh, createLocationIterator: (structureGroup) => polymer_1.PolymerLocationIterator.fromGroup(structureGroup), getLoci: polymer_1.getPolymerElementLoci, eachLocation: polymer_1.eachPolymerElement, setUpdateState: (state, newProps, currentProps) => { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.radialSegments !== currentProps.radialSegments); }, mustRecreate: (structureGroup, props, webgl) => { return props.tryUseImpostor && !!webgl; } }, materialId); }