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@@ -16,14 +16,17 @@ import { BallAndStickRepresentation } from 'mol-geo/representation/structure/rep
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import { EveryLoci } from 'mol-model/loci';
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import { MarkerAction } from 'mol-geo/util/marker-data';
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import { labelFirst } from 'mol-view/label';
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-import { Queries as Q, StructureProperties as SP, StructureSelection, StructureQuery } from 'mol-model/structure';
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+// import { Queries as Q, StructureProperties as SP, StructureSelection, StructureQuery } from 'mol-model/structure';
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import { MeshBuilder } from 'mol-geo/mesh/mesh-builder';
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import { ShapeRepresentation } from 'mol-geo/representation/shape';
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-import { Vec3, Mat4 } from 'mol-math/linear-algebra';
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+import { /*Vec3, Mat4,*/ Tensor } from 'mol-math/linear-algebra';
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import { Shape } from 'mol-model/shape';
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import { Color } from 'mol-util/color';
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import { addSphere } from 'mol-geo/mesh/builder/sphere';
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-import { Box } from 'mol-geo/primitive/box';
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+// import { Box } from 'mol-geo/primitive/box';
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+import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
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+import { addCylinder } from 'mol-geo/mesh/builder/cylinder';
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+import { Table } from 'mol-data/db';
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const container = document.getElementById('container')
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if (!container) throw new Error('Can not find element with id "container".')
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@@ -84,11 +87,57 @@ async function getStructureFromModel(model: Model, assembly = '1') {
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}
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}
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+function getAxesShape(featureId: number, assemblySymmetry: AssemblySymmetry) {
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+ const f = assemblySymmetry.db.rcsb_assembly_symmetry_feature
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+ const feature = Table.pickRow(f, i => f.id.value(i) === featureId)
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+ if (!feature) return
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+
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+ const axes = assemblySymmetry.getAxes(featureId)
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+ if (!axes._rowCount) return
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+
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+ const vectorSpace = AssemblySymmetry.Schema.rcsb_assembly_symmetry_axis.start.space;
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+
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+ const colors: Color[] = []
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+ const labels: string[] = []
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+
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+ const radius = 0.4
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+ const cylinderProps = { radiusTop: radius, radiusBottom: radius }
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+ const meshBuilder = MeshBuilder.create(256, 128)
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+
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+ for (let i = 0, il = axes._rowCount; i < il; ++i) {
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+ const start = Tensor.toVec3(vectorSpace, axes.start.value(i))
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+ const end = Tensor.toVec3(vectorSpace, axes.end.value(i))
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+ meshBuilder.setGroup(i)
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+ addSphere(meshBuilder, start, radius, 2)
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+ addSphere(meshBuilder, end, radius, 2)
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+ addCylinder(meshBuilder, start, end, 1, cylinderProps)
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+ colors.push(Color(0xCCEE11))
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+ labels.push(`Axis ${i + 1} for ${feature.symmetry_value} ${feature.type.toLowerCase()} symmetry`)
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+ }
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+ const mesh = meshBuilder.getMesh()
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+ const shape = Shape.create('Axes', mesh, colors, labels)
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+ return shape
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+}
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+
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+function getClusterColorTheme(featureId: number, assemblySymmetry: AssemblySymmetry) {
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+ const f = assemblySymmetry.db.rcsb_assembly_symmetry_feature
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+ const feature = Table.pickRow(f, i => f.id.value(i) === featureId)
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+ if (!feature) return
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+
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+ const clusters = assemblySymmetry.getClusters(featureId)
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+ if (!clusters._rowCount) return
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+
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+ for (let i = 0, il = clusters._rowCount; i < il; ++i) {
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+ console.log(clusters.members.value(i), clusters.avg_rmsd.value(i), feature.stoichiometry_value, feature.stoichiometry_description)
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+ }
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+}
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+
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async function init() {
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- const cif = await getCifFromUrl('https://files.rcsb.org/download/1crn.cif')
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- const model = await getModelFromMmcif(cif)
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- const structure = await getStructureFromModel(model)
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+ const assembly = '1'
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+ const cif = await getCifFromUrl('https://files.rcsb.org/download/4hhb.cif')
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+ const model = await getModelFromMmcif(cif)
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+ const structure = await getStructureFromModel(model, assembly)
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viewer.center(structure.boundary.sphere.center)
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// cartoon for whole structure
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@@ -100,52 +149,85 @@ async function init() {
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}).run()
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viewer.add(cartoonRepr)
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- // create new structure via query
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- const q1 = Q.generators.atoms({
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- residueTest: qtx => SP.residue.label_seq_id(qtx.element) < 7
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- });
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- const newStructure = StructureSelection.unionStructure(await StructureQuery.run(q1, structure));
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-
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- // ball+stick for new structure
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+ // ball+stick for whole structure
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const ballStickRepr = BallAndStickRepresentation()
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- await ballStickRepr.create(newStructure, {
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+ await ballStickRepr.create(structure, {
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colorTheme: { name: 'element-symbol' },
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sizeTheme: { name: 'uniform', value: 0.1 },
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useFog: false // TODO fog not working properly
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}).run()
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viewer.add(ballStickRepr)
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- // create a mesh
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- const meshBuilder = MeshBuilder.create(256, 128)
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- const colors: Color[] = []
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- const labels: string[] = []
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- // red sphere
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- meshBuilder.setGroup(0)
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- colors[0] = Color(0xFF2233)
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- labels[0] = 'red sphere'
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- addSphere(meshBuilder, Vec3.create(0, 0, 0), 4, 2)
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- // green cube
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- meshBuilder.setGroup(1)
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- colors[1] = Color(0x2233FF)
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- labels[1] = 'blue cube'
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- const t = Mat4.identity()
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- Mat4.fromTranslation(t, Vec3.create(10, 0, 0))
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- Mat4.scale(t, t, Vec3.create(3, 3, 3))
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- meshBuilder.add(t, Box())
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- const mesh = meshBuilder.getMesh()
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+ // // create new structure via query
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+ // const q1 = Q.generators.atoms({
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+ // residueTest: qtx => SP.residue.label_seq_id(qtx.element) < 7
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+ // });
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+ // const newStructure = StructureSelection.unionStructure(await StructureQuery.run(q1, structure));
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+
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+ // // ball+stick for new structure
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+ // const newBallStickRepr = BallAndStickRepresentation()
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+ // await newBallStickRepr.create(newStructure, {
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+ // colorTheme: { name: 'element-symbol' },
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+ // sizeTheme: { name: 'uniform', value: 0.1 },
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+ // useFog: false // TODO fog not working properly
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+ // }).run()
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+ // viewer.add(newBallStickRepr)
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+
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+ // // create a mesh
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+ // const meshBuilder = MeshBuilder.create(256, 128)
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+ // const colors: Color[] = []
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+ // const labels: string[] = []
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+ // // red sphere
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+ // meshBuilder.setGroup(0)
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+ // colors[0] = Color(0xFF2233)
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+ // labels[0] = 'red sphere'
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+ // addSphere(meshBuilder, Vec3.create(0, 0, 0), 4, 2)
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+ // // green cube
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+ // meshBuilder.setGroup(1)
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+ // colors[1] = Color(0x2233FF)
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+ // labels[1] = 'blue cube'
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+ // const t = Mat4.identity()
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+ // Mat4.fromTranslation(t, Vec3.create(10, 0, 0))
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+ // Mat4.scale(t, t, Vec3.create(3, 3, 3))
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+ // meshBuilder.add(t, Box())
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+ // const mesh = meshBuilder.getMesh()
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// const mesh = getObjFromUrl('mesh.obj')
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- // create shape from mesh
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- const shape = Shape.create('myShape', mesh, colors, labels)
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-
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- // add representation from shape
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- const customRepr = ShapeRepresentation()
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- await customRepr.create(shape, {
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- colorTheme: { name: 'shape-group' },
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- // colorTheme: { name: 'uniform', value: Color(0xFFCC22) },
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- useFog: false // TODO fog not working properly
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- }).run()
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- viewer.add(customRepr)
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+ // // create shape from mesh
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+ // const shape = Shape.create('myShape', mesh, colors, labels)
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+
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+ // // add representation from shape
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+ // const customRepr = ShapeRepresentation()
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+ // await customRepr.create(shape, {
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+ // colorTheme: { name: 'shape-group' },
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+ // // colorTheme: { name: 'uniform', value: Color(0xFFCC22) },
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+ // useFog: false // TODO fog not working properly
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+ // }).run()
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+ // viewer.add(customRepr)
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+
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+
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+ await AssemblySymmetry.attachFromCifOrAPI(model)
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+ const assemblySymmetry = AssemblySymmetry.get(model)
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+ console.log(assemblySymmetry)
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+ if (assemblySymmetry) {
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+ const features = assemblySymmetry.getFeatures(assembly)
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+ if (features._rowCount) {
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+ const axesShape = getAxesShape(features.id.value(1), assemblySymmetry)
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+ console.log(axesShape)
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+ if (axesShape) {
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+ const customRepr = ShapeRepresentation()
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+ await customRepr.create(axesShape, {
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+ colorTheme: { name: 'shape-group' },
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+ // colorTheme: { name: 'uniform', value: Color(0xFFCC22) },
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+ useFog: false // TODO fog not working properly
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+ }).run()
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+ viewer.add(customRepr)
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+ }
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+
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+ getClusterColorTheme(features.id.value(0), assemblySymmetry)
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+ getClusterColorTheme(features.id.value(1), assemblySymmetry)
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+ }
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+ }
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// ensure the added representations get rendered, i.e. without mouse input
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viewer.requestDraw()
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Alexander Rose