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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Gianluca Tomasello <giagitom@gmail.com> */ Object.defineProperty(exports, "__esModule", { value: true }); exports.PolymerTraceParams = exports.DefaultPolymerTraceMeshProps = exports.PolymerTraceMeshParams = void 0; exports.PolymerTraceVisual = PolymerTraceVisual; 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 polymer_1 = require("./util/polymer"); const types_1 = require("../../../mol-model/structure/model/types"); const sheet_1 = require("../../../mol-geo/geometry/mesh/builder/sheet"); const tube_1 = require("../../../mol-geo/geometry/mesh/builder/tube"); const units_visual_1 = require("../units-visual"); const secondary_structure_1 = require("../../../mol-model-props/computed/secondary-structure"); const ribbon_1 = require("../../../mol-geo/geometry/mesh/builder/ribbon"); const sphere_1 = require("../../../mol-geo/geometry/mesh/builder/sphere"); const linear_algebra_1 = require("../../../mol-math/linear-algebra"); const base_1 = require("../../../mol-geo/geometry/base"); const geometry_1 = require("../../../mol-math/geometry"); exports.PolymerTraceMeshParams = { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), aspectRatio: param_definition_1.ParamDefinition.Numeric(5, { min: 0.1, max: 10, step: 0.1 }), arrowFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }), tubularHelices: param_definition_1.ParamDefinition.Boolean(false, { description: 'Draw alpha helices as tubes' }), roundCap: param_definition_1.ParamDefinition.Boolean(false, { description: 'Draw round caps on tubular alpha helices' }), helixProfile: param_definition_1.ParamDefinition.Select('elliptical', param_definition_1.ParamDefinition.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Protein helix trace profile' }), nucleicProfile: param_definition_1.ParamDefinition.Select('square', param_definition_1.ParamDefinition.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Nucleic strand trace profile' }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), linearSegments: param_definition_1.ParamDefinition.Numeric(8, { min: 1, max: 48, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo) }; exports.DefaultPolymerTraceMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerTraceMeshParams); const tmpV1 = (0, linear_algebra_1.Vec3)(); function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) { const polymerElementCount = unit.polymerElements.length; if (!polymerElementCount) return mesh_1.Mesh.createEmpty(mesh); const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor, tubularHelices, roundCap, helixProfile, nucleicProfile } = props; const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2; const builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 10, mesh); const isCoarse = structure_1.Unit.isCoarse(unit); const state = (0, polymer_1.createCurveSegmentState)(linearSegments); const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state; let i = 0; const polymerTraceIt = (0, polymer_1.PolymerTraceIterator)(unit, structure, { ignoreSecondaryStructure: false, useHelixOrientation: tubularHelices }); while (polymerTraceIt.hasNext) { const v = polymerTraceIt.move(); builderState.currentGroup = i; const isNucleicType = (0, types_1.isNucleic)(v.moleculeType); const isSheet = types_1.SecondaryStructureType.is(v.secStrucType, 4 /* SecondaryStructureType.Flag.Beta */); const isHelix = types_1.SecondaryStructureType.is(v.secStrucType, 2 /* SecondaryStructureType.Flag.Helix */); const tension = isHelix && !tubularHelices ? polymer_1.HelixTension : polymer_1.StandardTension; const shift = isNucleicType ? polymer_1.NucleicShift : polymer_1.StandardShift; (0, polymer_1.interpolateCurveSegment)(state, v, tension, shift); let w0 = theme.size.size(v.centerPrev) * sizeFactor; let w1 = theme.size.size(v.center) * sizeFactor; let w2 = theme.size.size(v.centerNext) * sizeFactor; if (isCoarse) { w0 *= aspectRatio / 2; w1 *= aspectRatio / 2; w2 *= aspectRatio / 2; } const startCap = v.secStrucFirst || v.coarseBackboneFirst || v.first; const endCap = v.secStrucLast || v.coarseBackboneLast || v.last; const hasRoundCap = isHelix && tubularHelices && roundCap; let segmentCount = linearSegments; if (v.initial) { segmentCount = Math.max(Math.round(linearSegments * shift), 1); const offset = linearSegments - segmentCount; curvePoints.copyWithin(0, offset * 3); binormalVectors.copyWithin(0, offset * 3); normalVectors.copyWithin(0, offset * 3); linear_algebra_1.Vec3.fromArray(tmpV1, curvePoints, 3); linear_algebra_1.Vec3.normalize(tmpV1, linear_algebra_1.Vec3.sub(tmpV1, v.p2, tmpV1)); linear_algebra_1.Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * polymer_1.OverhangFactor); linear_algebra_1.Vec3.toArray(tmpV1, curvePoints, 0); } else if (v.final) { segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1); linear_algebra_1.Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3); linear_algebra_1.Vec3.normalize(tmpV1, linear_algebra_1.Vec3.sub(tmpV1, v.p2, tmpV1)); linear_algebra_1.Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * polymer_1.OverhangFactor); linear_algebra_1.Vec3.toArray(tmpV1, curvePoints, segmentCount * 3); } if (v.initial === true && v.final === true) { (0, sphere_1.addSphere)(builderState, v.p2, w1 * 2, detail); } else if (isSheet) { const h0 = w0 * aspectRatio; const h1 = w1 * aspectRatio; const h2 = w2 * aspectRatio; const arrowHeight = v.secStrucLast ? h1 * arrowFactor : 0; (0, polymer_1.interpolateSizes)(state, w0, w1, w2, h0, h1, h2, shift); if (radialSegments === 2) { (0, ribbon_1.addRibbon)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight); } else { (0, sheet_1.addSheet)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, arrowHeight, startCap, endCap); } } else { let h0, h1, h2; if (isHelix) { if (tubularHelices) { w0 *= aspectRatio * 1.5; w1 *= aspectRatio * 1.5; w2 *= aspectRatio * 1.5; h0 = w0; h1 = w1; h2 = w2; } else { h0 = w0 * aspectRatio; h1 = w1 * aspectRatio; h2 = w2 * aspectRatio; } } else if (isNucleicType) { h0 = w0 * aspectRatio; h1 = w1 * aspectRatio; h2 = w2 * aspectRatio; } else { h0 = w0; h1 = w1; h2 = w2; } (0, polymer_1.interpolateSizes)(state, w0, w1, w2, h0, h1, h2, shift); const [normals, binormals] = isNucleicType ? [binormalVectors, normalVectors] : [normalVectors, binormalVectors]; if (isNucleicType) { // TODO: find a cleaner way to swap normal and binormal for nucleic types for (let i = 0, il = normals.length; i < il; i++) normals[i] *= -1; } const profile = isNucleicType ? nucleicProfile : helixProfile; if (radialSegments === 2) { if (isNucleicType) { (0, ribbon_1.addRibbon)(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0); } else { (0, ribbon_1.addRibbon)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0); } } else if (radialSegments === 4) { (0, sheet_1.addSheet)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap); } else if (h1 === w1) { (0, tube_1.addTube)(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical', hasRoundCap); } else if (profile === 'square') { (0, sheet_1.addSheet)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap); } else { (0, tube_1.addTube)(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, profile); } } ++i; } 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; } exports.PolymerTraceParams = { ...units_visual_1.UnitsMeshParams, ...exports.PolymerTraceMeshParams }; function PolymerTraceVisual(materialId) { return (0, units_visual_1.UnitsMeshVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerTraceParams), createGeometry: createPolymerTraceMesh, createLocationIterator: (structureGroup) => polymer_1.PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }), getLoci: polymer_1.getPolymerElementLoci, eachLocation: polymer_1.eachPolymerElement, setUpdateState: (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) => { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.tubularHelices !== currentProps.tubularHelices || newProps.roundCap !== currentProps.roundCap || newProps.detail !== currentProps.detail || newProps.linearSegments !== currentProps.linearSegments || newProps.radialSegments !== currentProps.radialSegments || newProps.aspectRatio !== currentProps.aspectRatio || newProps.arrowFactor !== currentProps.arrowFactor || newProps.helixProfile !== currentProps.helixProfile || newProps.nucleicProfile !== currentProps.nucleicProfile); const secondaryStructureHash = secondary_structure_1.SecondaryStructureProvider.get(newStructureGroup.structure).version; if (state.info.secondaryStructureHash !== secondaryStructureHash) { if (state.info.secondaryStructureHash !== undefined) state.createGeometry = true; state.info.secondaryStructureHash = secondaryStructureHash; } }, initUpdateState: (state, newProps, newTheme, newStructureGroup) => { const secondaryStructureHash = secondary_structure_1.SecondaryStructureProvider.get(newStructureGroup.structure).version; state.info.secondaryStructureHash = secondaryStructureHash; } }, materialId); }