2.2.0-dev.1

USDZ export

CHANGELOG.md

@@ -3,8 +3,29 @@ All notable changes to this project will be documented in this file, following t
 
 Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
 
+
 ## [Unreleased]
 
+- Add `tubularHelices` parameter to Cartoon representation
+- Add `SdfFormat` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
+- Fix mononucleotides detected as polymer components (#229)
+- Set default outline scale back to 1
+- Improved DCD reader cell angle handling (intepret near 0 angles as 90 deg)
+- Handle more residue/atom names commonly used in force-fields
+- Add USDZ support to ``geo-export`` extension.
+
+## [v2.1.0] - 2021-07-05
+
+- Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
+- Add backbone representation
+- Fix outline in orthographic mode and set default scale to 2.
+
+## [v2.0.7] - 2021-06-23
+
+- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
+- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
+- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
+
 ## [v2.0.6] - 2021-06-01
 
 - Add glTF (GLB) and STL support to ``geo-export`` extension.

package-lock.json

@@ -1,11 +1,11 @@
 {
   "name": "molstar",
-  "version": "2.0.6",
+  "version": "2.2.0-dev.1",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "version": "2.0.6",
+      "version": "2.0.7",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^1.0.38",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.6",
+  "version": "2.2.0-dev.1",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/apps/viewer/embedded.html

@@ -38,19 +38,6 @@
             viewer.loadPdb('7bv2');
             viewer.loadEmdb('EMD-30210', { detail: 6 });
 
-            // viewer.loadVolumeFromUrl({
-            //     url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
-            //     format: 'dscif',
-            //     isBinary: true 
-            // }, [{
-            //     type: 'relative',
-            //     value: 1,
-            //     color: 0x3377aa
-            // }], {
-            //     entryId: 'EMD-30210',
-            //     isLazy: true
-            // });
-
             // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>

src/apps/viewer/index.ts

@@ -243,7 +243,46 @@ export class Viewer {
         }));
     }
 
-    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string, isLazy?: boolean }) {
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
         const plugin = this.plugin;
 
         if (!plugin.dataFormats.get(format)) {
@@ -257,26 +296,28 @@ export class Viewer {
                 format,
                 entryId: options?.entryId,
                 isBinary,
-                isovalues: isovalues.map(v => ({ alpha: 1, ...v }))
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
             });
             return update.commit();
         }
 
         return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary, label: options?.entryId }, { state: { isGhost: true } });
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
 
             const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
-            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
 
-            const repr = plugin.build().to(volume);
+            const repr = plugin.build();
             for (const iso of isovalues) {
-                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                    type: 'isosurface',
-                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                    color: 'uniform',
-                    colorParams: { value: iso.color }
-                }));
+                repr
+                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
             }
 
             await repr.commit();
@@ -296,5 +337,6 @@ export interface VolumeIsovalueInfo {
     type: 'absolute' | 'relative',
     value: number,
     color: Color,
-    alpha?: number
+    alpha?: number,
+    volumeIndex?: number
 }

src/extensions/dnatco/confal-pyramids/color.ts

@@ -181,6 +181,6 @@ export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramid
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ConfalPyramidsProvider.descriptor, false)
+        detach: (data) => data.structure && ConfalPyramidsProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/geo-export/controls.ts

@@ -5,6 +5,7 @@
  */
 
 import { getStyle } from '../../mol-gl/renderer';
+import { Box3D } from '../../mol-math/geometry';
 import { PluginComponent } from '../../mol-plugin-state/component';
 import { PluginContext } from '../../mol-plugin/context';
 import { Task } from '../../mol-task';
@@ -12,15 +13,17 @@ import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateSelection } from '../../mol-state';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { SetUtils } from '../../mol-util/set';
-import { ObjExporter } from './obj-exporter';
 import { GlbExporter } from './glb-exporter';
+import { ObjExporter } from './obj-exporter';
 import { StlExporter } from './stl-exporter';
+import { UsdzExporter } from './usdz-exporter';
 
 export const GeometryParams = {
     format: PD.Select('glb', [
         ['glb', 'glTF 2.0 Binary (.glb)'],
         ['stl', 'Stl (.stl)'],
-        ['obj', 'Wavefront (.obj)']
+        ['obj', 'Wavefront (.obj)'],
+        ['usdz', 'Universal Scene Description (.usdz)']
     ])
 };
 
@@ -43,17 +46,22 @@ export class GeometryControls extends PluginComponent {
                 const renderObjects = this.plugin.canvas3d?.getRenderObjects()!;
                 const filename = this.getFilename();
 
-                let renderObjectExporter: ObjExporter | GlbExporter | StlExporter;
+                const style = getStyle(this.plugin.canvas3d?.props.renderer.style!);
+                const boundingSphere = this.plugin.canvas3d?.boundingSphereVisible!;
+                const boundingBox = Box3D.fromSphere3D(Box3D(), boundingSphere);
+                let renderObjectExporter: GlbExporter | ObjExporter | StlExporter | UsdzExporter;
                 switch (this.behaviors.params.value.format) {
-                    case 'obj':
-                        renderObjectExporter = new ObjExporter(filename);
-                        break;
                     case 'glb':
-                        const style = getStyle(this.plugin.canvas3d?.props.renderer.style!);
-                        renderObjectExporter = new GlbExporter(style);
+                        renderObjectExporter = new GlbExporter(style, boundingBox);
+                        break;
+                    case 'obj':
+                        renderObjectExporter = new ObjExporter(filename, boundingBox);
                         break;
                     case 'stl':
-                        renderObjectExporter = new StlExporter();
+                        renderObjectExporter = new StlExporter(boundingBox);
+                        break;
+                    case 'usdz':
+                        renderObjectExporter = new UsdzExporter(style, boundingBox, boundingSphere.radius);
                         break;
                     default: throw new Error('Unsupported format.');
                 }

src/extensions/geo-export/glb-exporter.ts

@@ -8,6 +8,7 @@ import { BaseValues } from '../../mol-gl/renderable/schema';
 import { Style } from '../../mol-gl/renderer';
 import { asciiWrite } from '../../mol-io/common/ascii';
 import { IsNativeEndianLittle, flipByteOrder } from '../../mol-io/common/binary';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { PLUGIN_VERSION } from '../../mol-plugin/version';
 import { RuntimeContext } from '../../mol-task';
@@ -41,6 +42,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
     private bufferViews: Record<string, any>[] = [];
     private binaryBuffer: ArrayBuffer[] = [];
     private byteOffset = 0;
+    private centerTransform: Mat4;
 
     private static vec3MinMax(a: NumberArray) {
         const min: number[] = [Infinity, Infinity, Infinity];
@@ -252,16 +254,17 @@ export class GlbExporter extends MeshExporter<GlbData> {
             }
 
             // node
-            const node: Record<string, any> = {
-                mesh: meshIndex!
-            };
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
-            if (!Mat4.isIdentity(t)) node.matrix = t.slice();
+            Mat4.mul(t, this.centerTransform, t);
+            const node: Record<string, any> = {
+                mesh: meshIndex!,
+                matrix: t.slice()
+            };
             this.nodes.push(node);
         }
     }
 
-    getData() {
+    async getData() {
         const binaryBufferLength = this.byteOffset;
 
         const gltf = {
@@ -331,10 +334,14 @@ export class GlbExporter extends MeshExporter<GlbData> {
     }
 
     async getBlob(ctx: RuntimeContext) {
-        return new Blob([this.getData().glb], { type: 'model/gltf-binary' });
+        return new Blob([(await this.getData()).glb], { type: 'model/gltf-binary' });
     }
 
-    constructor(private style: Style) {
+    constructor(private style: Style, boundingBox: Box3D) {
         super();
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
     }
 }

src/extensions/geo-export/mesh-exporter.ts

@@ -4,6 +4,7 @@
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  */
 
+import { sort, arraySwap } from '../../mol-data/util';
 import { GraphicsRenderObject } from '../../mol-gl/render-object';
 import { MeshValues } from '../../mol-gl/renderable/mesh';
 import { LinesValues } from '../../mol-gl/renderable/lines';
@@ -22,6 +23,7 @@ import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { sizeDataFactor } from '../../mol-geo/geometry/size-data';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../mol-task';
+import { Color } from '../../mol-util/color/color';
 import { decodeFloatRGB } from '../../mol-util/float-packing';
 import { RenderObjectExporter, RenderObjectExportData } from './render-object-exporter';
 
@@ -111,6 +113,70 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
         return interpolated.array;
     }
 
+    protected static quantizeColors(colorArray: Uint8Array, vertexCount: number) {
+        if (vertexCount <= 1024) return;
+        const rgb = Vec3();
+        const min = Vec3();
+        const max = Vec3();
+        const sum = Vec3();
+        const colorMap = new Map<Color, Color>();
+        const colorComparers = [
+            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[0] - Color.toVec3(rgb, colors[j])[0]),
+            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[1] - Color.toVec3(rgb, colors[j])[1]),
+            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[2] - Color.toVec3(rgb, colors[j])[2]),
+        ];
+
+        const medianCut = (colors: Color[], l: number, r: number, depth: number) => {
+            if (l > r) return;
+            if (l === r || depth >= 10) {
+                // Find the average color.
+                Vec3.set(sum, 0, 0, 0);
+                for (let i = l; i <= r; ++i) {
+                    Color.toVec3(rgb, colors[i]);
+                    Vec3.add(sum, sum, rgb);
+                }
+                Vec3.round(rgb, Vec3.scale(rgb, sum, 1 / (r - l + 1)));
+                const averageColor = Color.fromArray(rgb, 0);
+                for (let i = l; i <= r; ++i) colorMap.set(colors[i], averageColor);
+                return;
+            }
+
+            // Find the color channel with the greatest range.
+            Vec3.set(min, 255, 255, 255);
+            Vec3.set(max, 0, 0, 0);
+            for (let i = l; i <= r; ++i) {
+                Color.toVec3(rgb, colors[i]);
+                for (let j = 0; j < 3; ++j) {
+                    Vec3.min(min, min, rgb);
+                    Vec3.max(max, max, rgb);
+                }
+            }
+            let k = 0;
+            if (max[1] - min[1] > max[k] - min[k]) k = 1;
+            if (max[2] - min[2] > max[k] - min[k]) k = 2;
+
+            sort(colors, l, r + 1, colorComparers[k], arraySwap);
+
+            const m = (l + r) >> 1;
+            medianCut(colors, l, m, depth + 1);
+            medianCut(colors, m + 1, r, depth + 1);
+        };
+
+        // Create an array of unique colors and use the median cut algorithm.
+        const colorSet = new Set<Color>();
+        for (let i = 0; i < vertexCount; ++i) {
+            colorSet.add(Color.fromArray(colorArray, i * 3));
+        }
+        const colors = Array.from(colorSet);
+        medianCut(colors, 0, colors.length - 1, 0);
+
+        // Map actual colors to quantized colors.
+        for (let i = 0; i < vertexCount; ++i) {
+            const color = colorMap.get(Color.fromArray(colorArray, i * 3));
+            Color.toArray(color!, colorArray, i * 3);
+        }
+    }
+
     protected static getInstance(input: AddMeshInput, instanceIndex: number) {
         const { mesh, meshes } = input;
         if (mesh !== undefined) {
@@ -278,7 +344,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
         }
     }
 
-    abstract getData(): D;
+    abstract getData(ctx: RuntimeContext): Promise<D>;
 
     abstract getBlob(ctx: RuntimeContext): Promise<Blob>;
 }

src/extensions/geo-export/obj-exporter.ts

@@ -4,8 +4,8 @@
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  */
 
-import { sort, arraySwap } from '../../mol-data/util';
 import { asciiWrite } from '../../mol-io/common/ascii';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat3, Mat4 } from '../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../mol-task';
 import { StringBuilder } from '../../mol-util';
@@ -35,6 +35,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
     private currentColor: Color | undefined;
     private currentAlpha: number | undefined;
     private materialSet = new Set<string>();
+    private centerTransform: Mat4;
 
     private updateMaterial(color: Color, alpha: number) {
         if (this.currentColor === color && this.currentAlpha === alpha) return;
@@ -67,70 +68,6 @@ export class ObjExporter extends MeshExporter<ObjData> {
         }
     }
 
-    private static quantizeColors(colorArray: Uint8Array, vertexCount: number) {
-        if (vertexCount <= 1024) return;
-        const rgb = Vec3();
-        const min = Vec3();
-        const max = Vec3();
-        const sum = Vec3();
-        const colorMap = new Map<Color, Color>();
-        const colorComparers = [
-            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[0] - Color.toVec3(rgb, colors[j])[0]),
-            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[1] - Color.toVec3(rgb, colors[j])[1]),
-            (colors: Color[], i: number, j: number) => (Color.toVec3(rgb, colors[i])[2] - Color.toVec3(rgb, colors[j])[2]),
-        ];
-
-        const medianCut = (colors: Color[], l: number, r: number, depth: number) => {
-            if (l > r) return;
-            if (l === r || depth >= 10) {
-                // Find the average color.
-                Vec3.set(sum, 0, 0, 0);
-                for (let i = l; i <= r; ++i) {
-                    Color.toVec3(rgb, colors[i]);
-                    Vec3.add(sum, sum, rgb);
-                }
-                Vec3.round(rgb, Vec3.scale(rgb, sum, 1 / (r - l + 1)));
-                const averageColor = Color.fromArray(rgb, 0);
-                for (let i = l; i <= r; ++i) colorMap.set(colors[i], averageColor);
-                return;
-            }
-
-            // Find the color channel with the greatest range.
-            Vec3.set(min, 255, 255, 255);
-            Vec3.set(max, 0, 0, 0);
-            for (let i = l; i <= r; ++i) {
-                Color.toVec3(rgb, colors[i]);
-                for (let j = 0; j < 3; ++j) {
-                    Vec3.min(min, min, rgb);
-                    Vec3.max(max, max, rgb);
-                }
-            }
-            let k = 0;
-            if (max[1] - min[1] > max[k] - min[k]) k = 1;
-            if (max[2] - min[2] > max[k] - min[k]) k = 2;
-
-            sort(colors, l, r + 1, colorComparers[k], arraySwap);
-
-            const m = (l + r) >> 1;
-            medianCut(colors, l, m, depth + 1);
-            medianCut(colors, m + 1, r, depth + 1);
-        };
-
-        // Create an array of unique colors and use the median cut algorithm.
-        const colorSet = new Set<Color>();
-        for (let i = 0; i < vertexCount; ++i) {
-            colorSet.add(Color.fromArray(colorArray, i * 3));
-        }
-        const colors = Array.from(colorSet);
-        medianCut(colors, 0, colors.length - 1, 0);
-
-        // Map actual colors to quantized colors.
-        for (let i = 0; i < vertexCount; ++i) {
-            const color = colorMap.get(Color.fromArray(colorArray, i * 3));
-            Color.toArray(color!, colorArray, i * 3);
-        }
-    }
-
     protected async addMeshWithColors(input: AddMeshInput) {
         const { mesh, values, isGeoTexture, webgl, ctx } = input;
 
@@ -163,6 +100,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
             const { vertices, normals, indices, groups, vertexCount, drawCount } = ObjExporter.getInstance(input, instanceIndex);
 
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
+            Mat4.mul(t, this.centerTransform, t);
             mat3directionTransform(n, t);
 
             // position
@@ -253,7 +191,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
         }
     }
 
-    getData() {
+    async getData() {
         return {
             obj: StringBuilder.getString(this.obj),
             mtl: StringBuilder.getString(this.mtl)
@@ -261,7 +199,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
     }
 
     async getBlob(ctx: RuntimeContext) {
-        const { obj, mtl } = this.getData();
+        const { obj, mtl } = await this.getData();
         const objData = new Uint8Array(obj.length);
         asciiWrite(objData, obj);
         const mtlData = new Uint8Array(mtl.length);
@@ -273,8 +211,12 @@ export class ObjExporter extends MeshExporter<ObjData> {
         return new Blob([await zip(ctx, zipDataObj)], { type: 'application/zip' });
     }
 
-    constructor(private filename: string) {
+    constructor(private filename: string, boundingBox: Box3D) {
         super();
         StringBuilder.writeSafe(this.obj, `mtllib ${filename}.mtl\n`);
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
     }
 }

src/extensions/geo-export/render-object-exporter.ts

@@ -9,12 +9,12 @@ import { WebGLContext } from '../../mol-gl/webgl/context';
 import { RuntimeContext } from '../../mol-task';
 
 export type RenderObjectExportData = {
-    [k: string]: string | Uint8Array | undefined
+    [k: string]: string | Uint8Array | ArrayBuffer | undefined
 }
 
 export interface RenderObjectExporter<D extends RenderObjectExportData> {
     readonly fileExtension: string
     add(renderObject: GraphicsRenderObject, webgl: WebGLContext, ctx: RuntimeContext): Promise<void> | undefined
-    getData(): D
+    getData(ctx: RuntimeContext): Promise<D>
     getBlob(ctx: RuntimeContext): Promise<Blob>
 }

src/extensions/geo-export/stl-exporter.ts

@@ -5,6 +5,7 @@
  */
 
 import { asciiWrite } from '../../mol-io/common/ascii';
+import { Box3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { PLUGIN_VERSION } from '../../mol-plugin/version';
 import { RuntimeContext } from '../../mol-task';
@@ -26,6 +27,7 @@ export class StlExporter extends MeshExporter<StlData> {
     readonly fileExtension = 'stl';
     private triangleBuffers: ArrayBuffer[] = [];
     private triangleCount = 0;
+    private centerTransform: Mat4;
 
     protected async addMeshWithColors(input: AddMeshInput) {
         const { values, isGeoTexture, ctx } = input;
@@ -46,6 +48,7 @@ export class StlExporter extends MeshExporter<StlData> {
             const { vertices, indices, vertexCount, drawCount } = StlExporter.getInstance(input, instanceIndex);
 
             Mat4.fromArray(t, aTransform, instanceIndex * 16);
+            Mat4.mul(t, this.centerTransform, t);
 
             // position
             const vertexArray = new Float32Array(vertexCount * 3);
@@ -86,7 +89,7 @@ export class StlExporter extends MeshExporter<StlData> {
         }
     }
 
-    getData() {
+    async getData() {
         const stl = new Uint8Array(84 + 50 * this.triangleCount);
 
         asciiWrite(stl, `Exported from Mol* ${PLUGIN_VERSION}`);
@@ -103,6 +106,14 @@ export class StlExporter extends MeshExporter<StlData> {
     }
 
     async getBlob(ctx: RuntimeContext) {
-        return new Blob([this.getData().stl], { type: 'model/stl' });
+        return new Blob([(await this.getData()).stl], { type: 'model/stl' });
+    }
+
+    constructor(boundingBox: Box3D) {
+        super();
+        const tmpV = Vec3();
+        Vec3.add(tmpV, boundingBox.min, boundingBox.max);
+        Vec3.scale(tmpV, tmpV, -0.5);
+        this.centerTransform = Mat4.fromTranslation(Mat4(), tmpV);
     }
 }

src/extensions/geo-export/ui.tsx

@@ -7,7 +7,7 @@
 import { merge } from 'rxjs';
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 import { Button } from '../../mol-plugin-ui/controls/common';
-import { GetAppSvg, CubeSendSvg } from '../../mol-plugin-ui/controls/icons';
+import { GetAppSvg, CubeScanSvg, CubeSendSvg } from '../../mol-plugin-ui/controls/icons';
 import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
 import { download } from '../../mol-util/download';
 import { GeometryParams, GeometryControls } from './controls';
@@ -18,6 +18,7 @@ interface State {
 
 export class GeometryExporterUI extends CollapsableControls<{}, State> {
     private _controls: GeometryControls | undefined;
+    private isARSupported: boolean | undefined;
 
     get controls() {
         return this._controls || (this._controls = new GeometryControls(this.plugin));
@@ -32,6 +33,9 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
     }
 
     protected renderControls(): JSX.Element {
+        if (this.isARSupported === undefined) {
+            this.isARSupported = !!document.createElement('a').relList?.supports?.('ar');
+        }
         const ctrl = this.controls;
         return <>
             <ParameterControls
@@ -45,6 +49,13 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
                 disabled={this.state.busy || !this.plugin.canvas3d?.reprCount.value}>
                 Save
             </Button>
+            {this.isARSupported && ctrl.behaviors.params.value.format === 'usdz' &&
+                <Button icon={CubeScanSvg}
+                    onClick={this.viewInAR} style={{ marginTop: 1 }}
+                    disabled={this.state.busy || !this.plugin.canvas3d?.reprCount.value}>
+                    View in AR
+                </Button>
+            }
         </>;
     }
 
@@ -75,4 +86,22 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
             this.setState({ busy: false });
         }
     }
+
+    viewInAR = async () => {
+        try {
+            this.setState({ busy: true });
+            const data = await this.controls.exportGeometry();
+            this.setState({ busy: false });
+            const a = document.createElement('a');
+            a.rel = 'ar';
+            a.href = URL.createObjectURL(data.blob);
+            // For in-place viewing of USDZ on iOS, the link must contain a single child that is either an img or picture.
+            // https://webkit.org/blog/8421/viewing-augmented-reality-assets-in-safari-for-ios/
+            a.appendChild(document.createElement('img'));
+            setTimeout(() => URL.revokeObjectURL(a.href), 4E4); // 40s
+            setTimeout(() => a.dispatchEvent(new MouseEvent('click')));
+        } catch {
+            this.setState({ busy: false });
+        }
+    }
 }

src/extensions/geo-export/usdz-exporter.ts

@@ -0,0 +1,262 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ */
+
+import { Style } from '../../mol-gl/renderer';
+import { asciiWrite } from '../../mol-io/common/ascii';
+import { Box3D } from '../../mol-math/geometry';
+import { Vec3, Mat3, Mat4 } from '../../mol-math/linear-algebra';
+import { PLUGIN_VERSION } from '../../mol-plugin/version';
+import { RuntimeContext } from '../../mol-task';
+import { StringBuilder } from '../../mol-util';
+import { Color } from '../../mol-util/color/color';
+import { zip } from '../../mol-util/zip/zip';
+import { MeshExporter, AddMeshInput } from './mesh-exporter';
+
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3fromArray = Vec3.fromArray;
+const v3transformMat4 = Vec3.transformMat4;
+const v3transformMat3 = Vec3.transformMat3;
+const mat3directionTransform = Mat3.directionTransform;
+
+// https://graphics.pixar.com/usd/docs/index.html
+
+export type UsdzData = {
+    usdz: ArrayBuffer
+}
+
+export class UsdzExporter extends MeshExporter<UsdzData> {
+    readonly fileExtension = 'usdz';
+    private meshes: string[] = [];
+    private materials: string[] = [];
+    private materialSet = new Set<number>();
+    private centerTransform: Mat4;
+
+    private static getMaterialKey(color: Color, alpha: number) {
+        return color * 256 + Math.round(alpha * 255);
+    }
+
+    private addMaterial(color: Color, alpha: number) {
+        const materialKey = UsdzExporter.getMaterialKey(color, alpha);
+        if (this.materialSet.has(materialKey)) return;
+        this.materialSet.add(materialKey);
+        const [r, g, b] = Color.toRgbNormalized(color);
+        this.materials.push(`
+def Material "material${materialKey}"
+{
+    token outputs:surface.connect = </material${materialKey}/shader.outputs:surface>
+    def Shader "shader"
+    {
+        uniform token info:id = "UsdPreviewSurface"
+        color3f inputs:diffuseColor = (${r},${g},${b})
+        float inputs:opacity = ${alpha}
+        float inputs:metallic = ${this.style.metalness}
+        float inputs:roughness = ${this.style.roughness}
+        token outputs:surface
+    }
+}
+`);
+    }
+
+    protected async addMeshWithColors(input: AddMeshInput) {
+        const { mesh, values, isGeoTexture, webgl, ctx } = input;
+
+        const t = Mat4();
+        const n = Mat3();
+        const tmpV = Vec3();
+        const stride = isGeoTexture ? 4 : 3;
+
+        const groupCount = values.uGroupCount.ref.value;
+        const colorType = values.dColorType.ref.value;
+        const tColor = values.tColor.ref.value.array;
+        const uAlpha = values.uAlpha.ref.value;
+        const dTransparency = values.dTransparency.ref.value;
+        const tTransparency = values.tTransparency.ref.value;
+        const aTransform = values.aTransform.ref.value;
+        const instanceCount = values.uInstanceCount.ref.value;
+
+        let interpolatedColors: Uint8Array;
+        if (colorType === 'volume' || colorType === 'volumeInstance') {
+            interpolatedColors = UsdzExporter.getInterpolatedColors(mesh!.vertices, mesh!.vertexCount, values, stride, colorType, webgl!);
+            UsdzExporter.quantizeColors(interpolatedColors, mesh!.vertexCount);
+        }
+
+        await ctx.update({ isIndeterminate: false, current: 0, max: instanceCount });
+
+        for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
+            if (ctx.shouldUpdate) await ctx.update({ current: instanceIndex + 1 });
+
+            const { vertices, normals, indices, groups, vertexCount, drawCount } = UsdzExporter.getInstance(input, instanceIndex);
+
+            Mat4.fromArray(t, aTransform, instanceIndex * 16);
+            Mat4.mul(t, this.centerTransform, t);
+            mat3directionTransform(n, t);
+
+            const vertexBuilder = StringBuilder.create();
+            const normalBuilder = StringBuilder.create();
+            const indexBuilder = StringBuilder.create();
+
+            // position
+            for (let i = 0; i < vertexCount; ++i) {
+                v3transformMat4(tmpV, v3fromArray(tmpV, vertices, i * stride), t);
+                StringBuilder.writeSafe(vertexBuilder, (i === 0) ? '(' : ',(');
+                StringBuilder.writeFloat(vertexBuilder, tmpV[0], 10000);
+                StringBuilder.writeSafe(vertexBuilder, ',');
+                StringBuilder.writeFloat(vertexBuilder, tmpV[1], 10000);
+                StringBuilder.writeSafe(vertexBuilder, ',');
+                StringBuilder.writeFloat(vertexBuilder, tmpV[2], 10000);
+                StringBuilder.writeSafe(vertexBuilder, ')');
+            }
+
+            // normal
+            for (let i = 0; i < vertexCount; ++i) {
+                v3transformMat3(tmpV, v3fromArray(tmpV, normals, i * stride), n);
+                StringBuilder.writeSafe(normalBuilder, (i === 0) ? '(' : ',(');
+                StringBuilder.writeFloat(normalBuilder, tmpV[0], 100);
+                StringBuilder.writeSafe(normalBuilder, ',');
+                StringBuilder.writeFloat(normalBuilder, tmpV[1], 100);
+                StringBuilder.writeSafe(normalBuilder, ',');
+                StringBuilder.writeFloat(normalBuilder, tmpV[2], 100);
+                StringBuilder.writeSafe(normalBuilder, ')');
+            }
+
+            // face
+            for (let i = 0; i < drawCount; ++i) {
+                const v = isGeoTexture ? i : indices![i];
+                if (i > 0) StringBuilder.writeSafe(indexBuilder, ',');
+                StringBuilder.writeInteger(indexBuilder, v);
+            }
+
+            // color
+            const faceIndicesByMaterial = new Map<number, number[]>();
+            for (let i = 0; i < drawCount; i += 3) {
+                let color: Color;
+                switch (colorType) {
+                    case 'uniform':
+                        color = Color.fromNormalizedArray(values.uColor.ref.value, 0);
+                        break;
+                    case 'instance':
+                        color = Color.fromArray(tColor, instanceIndex * 3);
+                        break;
+                    case 'group': {
+                        const group = isGeoTexture ? UsdzExporter.getGroup(groups, i) : groups[indices![i]];
+                        color = Color.fromArray(tColor, group * 3);
+                        break;
+                    }
+                    case 'groupInstance': {
+                        const group = isGeoTexture ? UsdzExporter.getGroup(groups, i) : groups[indices![i]];
+                        color = Color.fromArray(tColor, (instanceIndex * groupCount + group) * 3);
+                        break;
+                    }
+                    case 'vertex':
+                        color = Color.fromArray(tColor, indices![i] * 3);
+                        break;
+                    case 'vertexInstance':
+                        color = Color.fromArray(tColor, (instanceIndex * vertexCount + indices![i]) * 3);
+                        break;
+                    case 'volume':
+                        color = Color.fromArray(interpolatedColors!, (isGeoTexture ? i : indices![i]) * 3);
+                        break;
+                    case 'volumeInstance':
+                        color = Color.fromArray(interpolatedColors!, (instanceIndex * vertexCount + (isGeoTexture ? i : indices![i])) * 3);
+                        break;
+                    default: throw new Error('Unsupported color type.');
+                }
+
+                let alpha = uAlpha;
+                if (dTransparency) {
+                    const group = isGeoTexture ? UsdzExporter.getGroup(groups, i) : groups[indices![i]];
+                    const transparency = tTransparency.array[instanceIndex * groupCount + group] / 255;
+                    alpha *= 1 - transparency;
+                }
+
+                this.addMaterial(color, alpha);
+
+                const materialKey = UsdzExporter.getMaterialKey(color, alpha);
+                let faceIndices = faceIndicesByMaterial.get(materialKey);
+                if (faceIndices === undefined) {
+                    faceIndices = [];
+                    faceIndicesByMaterial.set(materialKey, faceIndices);
+                }
+                faceIndices.push(i / 3);
+            }
+
+            // If this mesh uses only one material, bind it to the material directly.
+            // Otherwise, use GeomSubsets to bind it to multiple materials.
+            let materialBinding: string;
+            if (faceIndicesByMaterial.size === 1) {
+                const materialKey = faceIndicesByMaterial.keys().next().value;
+                materialBinding = `rel material:binding = </material${materialKey}>`;
+            } else {
+                const geomSubsets: string[] = [];
+                faceIndicesByMaterial.forEach((faceIndices: number[], materialKey: number) => {
+                    geomSubsets.push(`
+    def GeomSubset "g${materialKey}"
+    {
+        uniform token elementType = "face"
+        uniform token familyName = "materialBind"
+        int[] indices = [${faceIndices.join(',')}]
+        rel material:binding = </material${materialKey}>
+    }
+`);
+                });
+                materialBinding = geomSubsets.join('');
+            }
+
+            this.meshes.push(`
+def Mesh "mesh${this.meshes.length}"
+{
+    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
+    int[] faceVertexIndices = [${StringBuilder.getString(indexBuilder)}]
+    point3f[] points = [${StringBuilder.getString(vertexBuilder)}]
+    normal3f[] primvars:normals = [${StringBuilder.getString(normalBuilder)}] (
+        interpolation = "vertex"
+    )
+    uniform token subdivisionScheme = "none"
+    ${materialBinding}
+}
+`);
+        }
+    }
+
+    async getData(ctx: RuntimeContext) {
+        const header = `#usda 1.0
+(
+    customLayerData = {
+        string creator = "Mol* ${PLUGIN_VERSION}"
+    }
+    metersPerUnit = 1
+)
+`;
+        const usda = [header, ...this.materials, ...this.meshes].join('');
+        const usdaData = new Uint8Array(usda.length);
+        asciiWrite(usdaData, usda);
+        const zipDataObj = {
+            ['model.usda']: usdaData
+        };
+        return {
+            usdz: await zip(ctx, zipDataObj, true)
+        };
+    }
+
+    async getBlob(ctx: RuntimeContext) {
+        const { usdz } = await this.getData(ctx);
+        return new Blob([usdz], { type: 'model/vnd.usdz+zip' });
+    }
+
+    constructor(private style: Style, boundingBox: Box3D, radius: number) {
+        super();
+        const t = Mat4();
+        // scale the model so that it fits within 1 meter
+        Mat4.fromUniformScaling(t, Math.min(1 / (radius * 2), 1));
+        // translate the model so that it sits on the ground plane (y = 0)
+        Mat4.translate(t, t, Vec3.create(
+            -(boundingBox.min[0] + boundingBox.max[0]) / 2,
+            -boundingBox.min[1],
+            -(boundingBox.min[2] + boundingBox.max[2]) / 2
+        ));
+        this.centerTransform = t;
+    }
+}

src/extensions/pdbe/structure-quality-report/color.ts

@@ -115,6 +115,6 @@ export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Param
     isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(StructureQualityReportProvider.descriptor, false)
+        detach: (data) => data.structure && StructureQualityReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/assembly-symmetry/color.ts

@@ -109,6 +109,6 @@ export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<Asse
     isApplicable: (ctx: ThemeDataContext) => AssemblySymmetry.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AssemblySymmetryProvider.descriptor, false)
+        detach: (data) => data.structure && AssemblySymmetryProvider.ref(data.structure, false)
     }
 };

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -77,6 +77,6 @@ export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationRep
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -115,6 +115,6 @@ export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQua
     isApplicable: (ctx: ThemeDataContext) => ValidationReport.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -68,6 +68,6 @@ export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}, Validati
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromNmr(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/mol-canvas3d/camera.ts

@@ -364,8 +364,9 @@ function updateClip(camera: Camera) {
         near = Math.max(Math.min(radiusMax, 5), near);
         far = Math.max(5, far);
     } else {
-        near = Math.max(0, near);
-        far = Math.max(0, far);
+        // not too close to 0 as it causes issues with outline rendering
+        near = Math.max(Math.min(radiusMax, 5), near);
+        far = Math.max(5, far);
     }
 
     if (near === far) {

src/mol-canvas3d/canvas3d.ts

@@ -242,6 +242,7 @@ interface Canvas3D {
     requestCameraReset(options?: { durationMs?: number, snapshot?: Camera.SnapshotProvider }): void
     readonly camera: Camera
     readonly boundingSphere: Readonly<Sphere3D>
+    readonly boundingSphereVisible: Readonly<Sphere3D>
     setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
     getImagePass(props: Partial<ImageProps>): ImagePass
     getRenderObjects(): GraphicsRenderObject[]
@@ -717,6 +718,7 @@ namespace Canvas3D {
             },
             camera,
             boundingSphere: scene.boundingSphere,
+            boundingSphereVisible: scene.boundingSphereVisible,
             get notifyDidDraw() { return notifyDidDraw; },
             set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,

src/mol-canvas3d/passes/draw.ts

@@ -290,7 +290,7 @@ export class DrawPass {
         renderer.setViewport(x, y, width, height);
         renderer.update(camera);
 
-        if (transparentBackground) {
+        if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
             renderer.clear(false);
         }

src/mol-canvas3d/passes/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -103,7 +103,9 @@ export class ImagePass {
         } else {
             this.webgl.readPixels(viewport.x, height - viewport.y - viewport.height, w, h, array);
         }
-        PixelData.flipY({ array, width: w, height: h });
+        const pixelData = PixelData.create(array, w, h);
+        PixelData.flipY(pixelData);
+        PixelData.divideByAlpha(pixelData);
         return new ImageData(new Uint8ClampedArray(array), w, h);
     }
 }

src/mol-canvas3d/passes/postprocessing.ts

@@ -306,7 +306,8 @@ export class PostprocessingPass {
         this.nSamples = 1;
         this.blurKernelSize = 1;
 
-        this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'nearest');
+        // needs to be linear for anti-aliasing pass
+        this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
 
         this.outlinesTarget = webgl.createRenderTarget(width, height, false);
         this.outlinesRenderable = getOutlinesRenderable(webgl, depthTexture);
@@ -433,8 +434,12 @@ export class PostprocessingPass {
         }
 
         if (props.outline.name === 'on') {
-            const factor = Math.pow(1000, props.outline.params.threshold) / 1000;
-            const maxPossibleViewZDiff = factor * (camera.far - camera.near);
+            let { threshold } = props.outline.params;
+            // orthographic needs lower threshold
+            if (camera.state.mode === 'orthographic') threshold /= 5;
+            const factor = Math.pow(1000, threshold) / 1000;
+            // use radiusMax for stable outlines when zooming
+            const maxPossibleViewZDiff = factor * camera.state.radiusMax;
             const outlineScale = props.outline.params.scale - 1;
 
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
@@ -442,7 +447,6 @@ export class PostprocessingPass {
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
 
             ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
-            ValueCell.updateIfChanged(this.renderable.values.uOutlineThreshold, props.outline.params.threshold);
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
             ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
         }

src/mol-geo/geometry/mesh/builder/cylinder.ts

@@ -31,6 +31,7 @@ function setCylinderMat(m: Mat4, start: Vec3, dir: Vec3, length: number, matchDi
     // ensure the direction used to create the rotation is always pointing in the same
     // direction so the triangles of adjacent cylinder will line up
     if (matchDir) Vec3.matchDirection(tmpUp, up, tmpCylinderMatDir);
+    else Vec3.copy(tmpUp, up);
     Mat4.fromScaling(tmpCylinderMatScale, Vec3.set(tmpCylinderScale, 1, length, 1));
     Vec3.makeRotation(tmpCylinderMatRot, tmpUp, tmpCylinderMatDir);
     Mat4.mul(m, tmpCylinderMatRot, tmpCylinderMatScale);

src/mol-gl/shader/postprocessing.frag.ts

@@ -26,9 +26,6 @@ uniform bool uTransparentBackground;
 uniform float uOcclusionBias;
 uniform float uOcclusionRadius;
 
-uniform float uOutlineScale;
-uniform float uOutlineThreshold;
-
 uniform float uMaxPossibleViewZDiff;
 
 const vec3 occlusionColor = vec3(0.0);

src/mol-gl/webgl/texture.ts

@@ -186,6 +186,7 @@ export interface Texture {
     readonly format: number
     readonly internalFormat: number
     readonly type: number
+    readonly filter: number
 
     getWidth: () => number
     getHeight: () => number
@@ -326,6 +327,7 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
         format,
         internalFormat,
         type,
+        filter,
 
         getWidth: () => width,
         getHeight: () => height,
@@ -415,6 +417,7 @@ export function createNullTexture(gl?: GLRenderingContext): Texture {
         format: 0,
         internalFormat: 0,
         type: 0,
+        filter: 0,
 
         getWidth: () => 0,
         getHeight: () => 0,

src/mol-io/reader/_spec/sdf.spec.ts

@@ -22,8 +22,8 @@ M  END
 > <DATABASE_NAME>
 drugbank
 
-> <SMILES>
-[O-]P([O-])([O-])=O
+> 5225 <TEST_FIELD>
+whatever
 
 > <INCHI_IDENTIFIER>
 InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
@@ -362,22 +362,25 @@ describe('sdf reader', () => {
         expect(bonds.atomIdxB.value(3)).toBe(5);
         expect(bonds.order.value(3)).toBe(1);
 
-        expect(dataItems.dataHeader.value(0)).toBe('DATABASE_ID');
+        expect(dataItems.dataHeader.value(0)).toBe('<DATABASE_ID>');
         expect(dataItems.data.value(0)).toBe('0');
 
-        expect(dataItems.dataHeader.value(1)).toBe('DATABASE_NAME');
+        expect(dataItems.dataHeader.value(1)).toBe('<DATABASE_NAME>');
         expect(dataItems.data.value(1)).toBe('drugbank');
 
-        expect(dataItems.dataHeader.value(31)).toBe('SYNONYMS');
+        expect(dataItems.dataHeader.value(2)).toBe('5225 <TEST_FIELD>');
+        expect(dataItems.data.value(2)).toBe('whatever');
+
+        expect(dataItems.dataHeader.value(31)).toBe('<SYNONYMS>');
         expect(dataItems.data.value(31)).toBe('Orthophosphate; Phosphate');
 
         expect(compound1.dataItems.data.value(0)).toBe('0');
         expect(compound2.dataItems.data.value(0)).toBe('1');
 
-        expect(compound3.dataItems.dataHeader.value(2)).toBe('PUBCHEM_CONFORMER_DIVERSEORDER');
+        expect(compound3.dataItems.dataHeader.value(2)).toBe('<PUBCHEM_CONFORMER_DIVERSEORDER>');
         expect(compound3.dataItems.data.value(2)).toBe('1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2');
 
-        expect(compound3.dataItems.dataHeader.value(21)).toBe('PUBCHEM_COORDINATE_TYPE');
+        expect(compound3.dataItems.dataHeader.value(21)).toBe('<PUBCHEM_COORDINATE_TYPE>');
         expect(compound3.dataItems.data.value(21)).toBe('2\n5\n10');
     });
 });

src/mol-io/reader/sdf/parser.ts

@@ -13,16 +13,20 @@ import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
 
 /** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 */
-export interface SdfFile {
-    readonly compounds: {
-        readonly molFile: MolFile,
-        readonly dataItems: {
-            readonly dataHeader: Column<string>,
-            readonly data: Column<string>
-        }
-    }[]
+
+export interface SdfFileCompound {
+    readonly molFile: MolFile,
+    readonly dataItems: {
+        readonly dataHeader: Column<string>,
+        readonly data: Column<string>
+    }
 }
 
+export interface SdfFile {
+    readonly compounds: SdfFileCompound[]
+}
+
+
 const delimiter = '$$$$';
 function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, data: Column<string> } {
     const dataHeader = TokenBuilder.create(tokenizer.data, 32);
@@ -33,8 +37,8 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
         if (line.startsWith(delimiter)) break;
         if (!line) continue;
 
-        if (line.startsWith('> <')) {
-            TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
+        if (line.startsWith('> ')) {
+            TokenBuilder.add(dataHeader, tokenizer.tokenStart + 2, tokenizer.tokenEnd);
 
             Tokenizer.markLine(tokenizer);
             const start = tokenizer.tokenStart;
@@ -42,7 +46,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
             let added = false;
             while (tokenizer.position < tokenizer.length) {
                 const line2 = Tokenizer.readLine(tokenizer);
-                if (!line2 || line2.startsWith(delimiter) || line2.startsWith('> <')) {
+                if (!line2 || line2.startsWith(delimiter) || line2.startsWith('> ')) {
                     TokenBuilder.add(data, start, end);
                     added = true;
                     break;

src/mol-io/writer/_spec/cif.spec.ts

@@ -3,7 +3,10 @@ import { CifWriter } from '../cif';
 import { decodeMsgPack } from '../../common/msgpack/decode';
 import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
 import { Field } from '../../reader/cif/binary/field';
+import { TextEncoder } from '../cif/encoder/text';
 import * as C from '../cif/encoder';
+import { Column, Database, Table } from '../../../mol-data/db';
+import { parseCifText } from '../../reader/cif/text/parser';
 
 const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
 const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
@@ -38,6 +41,30 @@ const encoding_aware_encoder = CifWriter.createEncoder({
     ])
 });
 
+test('cif writer value escaping', async () => {
+    const values = ['1', ' ', '  ', ` ' `, `a'`, `b"`, `"`, '  a  ', `"'"`, `'"`, `\na`];
+    const table = Table.ofArrays({ values: Column.Schema.str }, { values });
+
+    const encoder = new TextEncoder();
+    C.Encoder.writeDatabase(encoder, 'test', Database.ofTables('test', { test: table._schema }, { test: table }));
+    encoder.encode();
+    const data = encoder.getData();
+
+    const result = await parseCifText(data).run();
+    if (result.isError) {
+        expect(false).toBe(true);
+        return;
+    }
+
+    const cat = result.result.blocks[0].categories['test'];
+    const parsed = cat.getField('values')?.toStringArray();
+
+    expect(values.length).toBe(parsed?.length);
+    for (let i = 0; i < values.length; i++) {
+        expect(values[i]).toBe(parsed?.[i]);
+    }
+});
+
 describe('encoding-config', () => {
     const decoded = process(encoding_aware_encoder);
 

src/mol-io/writer/cif/encoder/text.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Adapted from CIFTools.js (https://github.com/dsehnal/CIFTools.js)
  *
@@ -208,55 +208,61 @@ function writeChecked(builder: StringBuilder, val: string) {
         return false;
     }
 
-    let escape = val.charCodeAt(0) === 95 /* _ */, escapeCharStart = '\'', escapeCharEnd = '\' ';
-    let hasWhitespace = false;
-    let hasSingle = false;
-    let hasDouble = false;
-    for (let i = 0, _l = val.length - 1; i < _l; i++) {
+    const fst = val.charCodeAt(0);
+    let escape = false;
+    let escapeKind = 0; // 0 => ', 1 => "
+    let hasSingleQuote = false, hasDoubleQuote = false;
+    for (let i = 0, _l = val.length - 1; i <= _l; i++) {
         const c = val.charCodeAt(i);
 
         switch (c) {
-            case 9: hasWhitespace = true; break; // \t
+            case 9: // \t
+                escape = true;
+                break;
             case 10: // \n
                 writeMultiline(builder, val);
                 return true;
-            case 32: hasWhitespace = true; break; // ' '
+            case 32: // ' '
+                escape = true;
+                break;
             case 34: // "
-                if (hasSingle) {
+                // no need to escape quote if it's the last char and the length is > 1
+                if (i && i === _l) break;
+
+                if (hasSingleQuote) {
+                    // the string already has a " => use multiline value
                     writeMultiline(builder, val);
                     return true;
                 }
 
-                hasDouble = true;
+                hasDoubleQuote = true;
                 escape = true;
-                escapeCharStart = '\'';
-                escapeCharEnd = '\' ';
+                escapeKind = 0;
                 break;
             case 39: // '
-                if (hasDouble) {
+                // no need to escape quote if it's the last char and the length is > 1
+                if (i && i === _l) break;
+
+                if (hasDoubleQuote) {
                     writeMultiline(builder, val);
                     return true;
                 }
 
+                hasSingleQuote = true;
                 escape = true;
-                hasSingle = true;
-                escapeCharStart = '"';
-                escapeCharEnd = '" ';
+                escapeKind = 1;
                 break;
         }
     }
 
-    const fst = val.charCodeAt(0);
-    if (!escape && (fst === 35 /* # */|| fst === 36 /* $ */ || fst === 59 /* ; */ || fst === 91 /* [ */ || fst === 93 /* ] */ || hasWhitespace)) {
-        escapeCharStart = '\'';
-        escapeCharEnd = '\' ';
+    if (!escape && (fst === 35 /* # */ || fst === 36 /* $ */ || fst === 59 /* ; */ || fst === 91 /* [ */ || fst === 93 /* ] */ || fst === 95 /* _ */)) {
         escape = true;
     }
 
     if (escape) {
-        StringBuilder.writeSafe(builder, escapeCharStart);
+        StringBuilder.writeSafe(builder, escapeKind ? '"' : '\'');
         StringBuilder.writeSafe(builder, val);
-        StringBuilder.writeSafe(builder, escapeCharEnd);
+        StringBuilder.writeSafe(builder, escapeKind ? '" ' : '\' ');
     } else {
         StringBuilder.writeSafe(builder, val);
         StringBuilder.writeSafe(builder, ' ');

src/mol-math/linear-algebra/3d/vec3.ts

@@ -474,7 +474,9 @@ namespace Vec3 {
 
     /** Computes the angle between 2 vectors, reports in radians. */
     export function angle(a: Vec3, b: Vec3) {
-        const theta = dot(a, b) / Math.sqrt(squaredMagnitude(a) * squaredMagnitude(b));
+        const denominator = Math.sqrt(squaredMagnitude(a) * squaredMagnitude(b));
+        if (denominator === 0) return Math.PI / 2;
+        const theta = dot(a, b) / denominator;
         return Math.acos(clamp(theta, -1, 1)); // clamp to avoid numerical problems
     }
 

src/mol-model-formats/structure/common/component.ts

@@ -13,21 +13,26 @@ import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-e
 type Component = Table.Row<Pick<mmCIF_chemComp_schema, 'id' | 'name' | 'type'>>
 
 const ProteinAtomIdsList = [
-    new Set([ 'CA' ]),
-    new Set([ 'C' ]),
-    new Set([ 'N' ])
+    new Set(['CA']),
+    new Set(['C']),
+    new Set(['N'])
 ];
 const RnaAtomIdsList = [
-    new Set([ 'P', 'O3\'', 'O3*' ]),
-    new Set([ 'C4\'', 'C4*' ]),
-    new Set([ 'O2\'', 'O2*', 'F2\'', 'F2*' ])
+    new Set(['P', 'O3\'', 'O3*']),
+    new Set(['C4\'', 'C4*']),
+    new Set(['O2\'', 'O2*', 'F2\'', 'F2*'])
 ];
 const DnaAtomIdsList = [
-    new Set([ 'P', 'O3\'', 'O3*' ]),
-    new Set([ 'C3\'', 'C3*' ]),
-    new Set([ 'O2\'', 'O2*', 'F2\'', 'F2*' ])
+    new Set(['P', 'O3\'', 'O3*']),
+    new Set(['C3\'', 'C3*']),
+    new Set(['O2\'', 'O2*', 'F2\'', 'F2*'])
 ];
 
+/** Used to reduce false positives for atom name-based type guessing */
+const NonPolymerNames = new Set([
+    'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
+]);
+
 const StandardComponents = (function() {
     const map = new Map<string, Component>();
     const components: Component[] = [
@@ -151,9 +156,11 @@ export class ComponentBuilder {
                 this.set(StandardComponents.get(compId)!);
             } else if (WaterNames.has(compId)) {
                 this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
+            } else if (NonPolymerNames.has(compId)) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             } else {
                 const atomIds = this.getAtomIds(index);
-                if (CharmmIonComponents.has(compId) && atomIds.size === 1) {
+                if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {
                     this.set(CharmmIonComponents.get(compId)!);
                 } else {
                     const type = this.getType(atomIds);

src/mol-model-formats/structure/dcd.ts

@@ -11,6 +11,7 @@ import { Vec3 } from '../../mol-math/linear-algebra';
 import { degToRad, halfPI } from '../../mol-math/misc';
 import { Cell } from '../../mol-math/geometry/spacegroup/cell';
 import { Mutable } from '../../mol-util/type-helpers';
+import { EPSILON, equalEps } from '../../mol-math/linear-algebra/3d/common';
 
 const charmmTimeUnitFactor = 20.45482949774598;
 
@@ -38,6 +39,8 @@ export function coordinatesFromDcd(dcdFile: DcdFile): Task<Coordinates> {
                 x: dcdFrame.x,
                 y: dcdFrame.y,
                 z: dcdFrame.z,
+
+                xyzOrdering: { isIdentity: true }
             };
 
             if (dcdFrame.cell) {
@@ -64,7 +67,12 @@ export function coordinatesFromDcd(dcdFile: DcdFile): Task<Coordinates> {
                 } else {
                     frame.cell = Cell.create(
                         Vec3.create(c[0], c[2], c[5]),
-                        Vec3.create(degToRad(c[1]), degToRad(c[3]), degToRad(c[4]))
+                        // interpret angles very close to 0 as 90 deg
+                        Vec3.create(
+                            degToRad(equalEps(c[1], 0, EPSILON) ? 90 : c[1]),
+                            degToRad(equalEps(c[3], 0, EPSILON) ? 90 : c[3]),
+                            degToRad(equalEps(c[4], 0, EPSILON) ? 90 : c[4])
+                        )
                     );
                 }
             }

src/mol-model-formats/structure/mol.ts

@@ -17,7 +17,7 @@ import { ModelFormat } from '../format';
 import { IndexPairBonds } from './property/bonds/index-pair';
 import { Trajectory } from '../../mol-model/structure';
 
-async function getModels(mol: MolFile, ctx: RuntimeContext) {
+export async function getMolModels(mol: MolFile, format: ModelFormat<any> | undefined, ctx: RuntimeContext) {
     const { atoms, bonds } = mol;
 
     const MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
@@ -61,7 +61,7 @@ async function getModels(mol: MolFile, ctx: RuntimeContext) {
         atom_site
     });
 
-    const models = await createModels(basics, MolFormat.create(mol), ctx);
+    const models = await createModels(basics, format ?? MolFormat.create(mol), ctx);
 
     if (models.frameCount > 0) {
         const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
@@ -91,5 +91,5 @@ namespace MolFormat {
 }
 
 export function trajectoryFromMol(mol: MolFile): Task<Trajectory> {
-    return Task.create('Parse MOL', ctx => getModels(mol, ctx));
+    return Task.create('Parse MOL', ctx => getMolModels(mol, void 0, ctx));
 }

src/mol-model-formats/structure/mol2.ts

@@ -6,7 +6,7 @@
 
 import { Column, Table } from '../../mol-data/db';
 import { Model } from '../../mol-model/structure/model';
-import { MoleculeType } from '../../mol-model/structure/model/types';
+import { BondType, MoleculeType } from '../../mol-model/structure/model/types';
 import { RuntimeContext, Task } from '../../mol-task';
 import { createModels } from './basic/parser';
 import { BasicSchema, createBasic } from './basic/schema';
@@ -74,8 +74,33 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
         if (_models.frameCount > 0) {
             const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
             const indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, x => x - 1, Int32Array));
-            const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => x === 'ar' ? 1 : parseInt(x), Int8Array));
-            const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: atoms.count });
+            const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => {
+                switch (x) {
+                    case 'ar': // aromatic
+                    case 'am': // amide
+                    case 'un': // unknown
+                        return 1;
+                    case 'du': // dummy
+                    case 'nc': // not connected
+                        return 0;
+                    default:
+                        return parseInt(x);
+                }
+            }, Int8Array));
+            const flag = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => {
+                switch (x) {
+                    case 'ar': // aromatic
+                        return BondType.Flag.Aromatic | BondType.Flag.Covalent;
+                    case 'du': // dummy
+                    case 'nc': // not connected
+                        return BondType.Flag.None;
+                    case 'am': // amide
+                    case 'un': // unknown
+                    default:
+                        return BondType.Flag.Covalent;
+                }
+            }, Int8Array));
+            const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order, flag }, count: atoms.count });
 
             const first = _models.representative;
             IndexPairBonds.Provider.set(first, pairBonds);

src/mol-model-formats/structure/sdf.ts

@@ -0,0 +1,29 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { SdfFileCompound } from '../../mol-io/reader/sdf/parser';
+import { Trajectory } from '../../mol-model/structure';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+import { getMolModels } from './mol';
+
+export { SdfFormat };
+
+type SdfFormat = ModelFormat<SdfFileCompound>
+
+namespace SdfFormat {
+    export function is(x?: ModelFormat): x is SdfFormat {
+        return x?.kind === 'sdf';
+    }
+
+    export function create(mol: SdfFileCompound): SdfFormat {
+        return { kind: 'sdf', name: mol.molFile.title, data: mol };
+    }
+}
+
+export function trajectoryFromSdf(mol: SdfFileCompound): Task<Trajectory> {
+    return Task.create('Parse SDF', ctx => getMolModels(mol.molFile, SdfFormat.create(mol), ctx));
+}

src/mol-model-formats/structure/util.ts

@@ -61,6 +61,14 @@ export function guessElementSymbolString(str: string) {
         ) return str;
     }
 
+    if (l === 3) { // three chars
+        if (str === 'SOD') return 'NA';
+        if (str === 'POT') return 'K';
+        if (str === 'CES') return 'CS';
+        if (str === 'CAL') return 'CA';
+        if (str === 'CLA') return 'CL';
+    }
+
     const c = str[0];
     if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S') return c;
 

src/mol-model-formats/structure/xtc.ts

@@ -30,6 +30,7 @@ export function coordinatesFromXtc(file: XtcFile): Task<Coordinates> {
                 x: file.frames[i].x,
                 y: file.frames[i].y,
                 z: file.frames[i].z,
+                xyzOrdering: { isIdentity: true },
                 time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
             });
         }

src/mol-model-props/computed/helix-orientation.ts

@@ -0,0 +1,31 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Model } from '../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
+import { CustomModelProperty } from '../common/custom-model-property';
+import { calcHelixOrientation, HelixOrientation } from './helix-orientation/helix-orientation';
+
+export const HelixOrientationParams = { };
+export type HelixOrientationParams = typeof HelixOrientationParams
+export type HelixOrientationProps = PD.Values<HelixOrientationParams>
+
+export type HelixOrientationValue = HelixOrientation;
+
+export const HelixOrientationProvider: CustomModelProperty.Provider<HelixOrientationParams, HelixOrientationValue> = CustomModelProperty.createProvider({
+    label: 'Helix Orientation',
+    descriptor: CustomPropertyDescriptor({
+        name: 'molstar_helix_orientation'
+    }),
+    type: 'dynamic',
+    defaultParams: {},
+    getParams: () => ({}),
+    isApplicable: (data: Model) => true,
+    obtain: async (ctx, data) => {
+        return { value: calcHelixOrientation(data) };
+    }
+});

src/mol-model-props/computed/helix-orientation/helix-orientation.ts

@@ -0,0 +1,138 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ElementIndex } from '../../../mol-model/structure';
+import { Segmentation } from '../../../mol-data/int/segmentation';
+import { SortedRanges } from '../../../mol-data/int/sorted-ranges';
+import { OrderedSet } from '../../../mol-data/int';
+import { Model } from '../../../mol-model/structure/model';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+
+export interface HelixOrientation {
+    centers: ArrayLike<number>
+}
+
+/** Usees same definition as GROMACS' helixorient */
+export function calcHelixOrientation(model: Model): HelixOrientation {
+    const { x, y, z } = model.atomicConformation;
+    const { polymerType, traceElementIndex } = model.atomicHierarchy.derived.residue;
+    const n = polymerType.length;
+
+    const elements = OrderedSet.ofBounds(0, model.atomicConformation.atomId.rowCount) as OrderedSet<ElementIndex>;
+    const polymerIt = SortedRanges.transientSegments(model.atomicRanges.polymerRanges, elements);
+    const residueIt = Segmentation.transientSegments(model.atomicHierarchy.residueAtomSegments, elements);
+
+    const centers = new Float32Array(n * 3);
+    const axes = new Float32Array(n * 3);
+
+    let i = 0;
+    let j = -1;
+    let s = -1;
+
+    const a1 = Vec3();
+    const a2 = Vec3();
+    const a3 = Vec3();
+    const a4 = Vec3();
+
+    const r12 = Vec3();
+    const r23 = Vec3();
+    const r34 = Vec3();
+
+    const v1 = Vec3();
+    const v2 = Vec3();
+    const vt = Vec3();
+
+    const diff13 = Vec3();
+    const diff24 = Vec3();
+
+    const axis = Vec3();
+    const prevAxis = Vec3();
+
+    while (polymerIt.hasNext) {
+        const ps = polymerIt.move();
+        residueIt.setSegment(ps);
+        i = -1;
+        s = -1;
+        while (residueIt.hasNext) {
+            i += 1;
+            const { index } = residueIt.move();
+            if (i === 0) s = index;
+
+            j = (index - 2);
+            const j3 = j * 3;
+
+            Vec3.copy(a1, a2);
+            Vec3.copy(a2, a3);
+            Vec3.copy(a3, a4);
+
+            const eI = traceElementIndex[index];
+            Vec3.set(a4, x[eI], y[eI], z[eI]);
+
+            if (i < 3) continue;
+
+            Vec3.sub(r12, a2, a1);
+            Vec3.sub(r23, a3, a2);
+            Vec3.sub(r34, a4, a3);
+
+            Vec3.sub(diff13, r12, r23);
+            Vec3.sub(diff24, r23, r34);
+
+            Vec3.cross(axis, diff13, diff24);
+            Vec3.normalize(axis, axis);
+            Vec3.toArray(axis, axes, j3);
+
+            const tmp = Math.cos(Vec3.angle(diff13, diff24));
+
+            const diff13Length = Vec3.magnitude(diff13);
+            const diff24Length = Vec3.magnitude(diff24);
+
+            const r = (
+                Math.sqrt(diff24Length * diff13Length) /
+                // clamp, to avoid numerical instabilities for when
+                // angle between diff13 and diff24 is close to 0
+                Math.max(2.0, 2.0 * (1.0 - tmp))
+            );
+
+            Vec3.scale(v1, diff13, r / diff13Length);
+            Vec3.sub(v1, a2, v1);
+            Vec3.toArray(v1, centers, j3);
+
+            Vec3.scale(v2, diff24, r / diff24Length);
+            Vec3.sub(v2, a3, v2);
+            Vec3.toArray(v2, centers, j3 + 3);
+
+            Vec3.copy(prevAxis, axis);
+        }
+
+        // calc axis as dir of second and third center pos
+        // project first trace atom onto axis to get first center pos
+        const s3 = s * 3;
+        Vec3.fromArray(v1, centers, s3 + 3);
+        Vec3.fromArray(v2, centers, s3 + 6);
+        Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
+        const sI = traceElementIndex[s];
+        Vec3.set(a1, x[sI], y[sI], z[sI]);
+        Vec3.copy(vt, a1);
+        Vec3.projectPointOnVector(vt, vt, axis, v1);
+        Vec3.toArray(vt, centers, s3);
+
+        // calc axis as dir of n-1 and n-2 center pos
+        // project last traceAtom onto axis to get last center pos
+        const e = j + 2;
+        const e3 = e * 3;
+        Vec3.fromArray(v1, centers, e3 - 3);
+        Vec3.fromArray(v2, centers, e3 - 6);
+        Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
+        const eI = traceElementIndex[e];
+        Vec3.set(a1, x[eI], y[eI], z[eI]);Vec3.copy(vt, a1);
+        Vec3.projectPointOnVector(vt, vt, axis, v1);
+        Vec3.toArray(vt, centers, e3);
+    }
+
+    return {
+        centers
+    };
+}

src/mol-model-props/computed/themes/accessible-surface-area.ts

@@ -83,6 +83,6 @@ export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<Access
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AccessibleSurfaceAreaProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AccessibleSurfaceAreaProvider.descriptor, false)
+        detach: (data) => data.structure && AccessibleSurfaceAreaProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/computed/themes/interaction-type.ts

@@ -117,6 +117,6 @@ export const InteractionTypeColorThemeProvider: ColorTheme.Provider<InteractionT
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? InteractionsProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(InteractionsProvider.descriptor, false)
+        detach: (data) => data.structure && InteractionsProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/integrative/cross-link-restraint/color.ts

@@ -70,6 +70,6 @@ export const CrossLinkColorThemeProvider: ColorTheme.Provider<CrossLinkColorThem
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && CrossLinkRestraint.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? CrossLinkRestraintProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(CrossLinkRestraintProvider.descriptor, false)
+        detach: (data) => data.structure && CrossLinkRestraintProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/sequence/best-database-mapping.ts

@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
@@ -92,4 +92,4 @@ namespace BestDatabaseSequenceMapping {
 
         return { dbName, accession, num, residue };
     }
-}
+}

src/mol-model-props/sequence/themes/best-database-mapping.ts

@@ -98,7 +98,7 @@ export const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<
         detach: (data) => {
             if (!data.structure) return;
             for (const m of data.structure.models) {
-                m.customProperties.reference(BestDatabaseSequenceMapping.Provider.descriptor, false);
+                BestDatabaseSequenceMapping.Provider.ref(m, false);
             }
         }
     }

src/mol-model/sequence/constants.ts

@@ -39,6 +39,18 @@ const ProteinOneLetterCodes: { [name: string]: AminoAlphabet }  = {
 
     'SEC': 'U',  // as per IUPAC definition
     'PYL': 'O',  // as per IUPAC definition
+
+    // charmm ff
+    'HSD': 'H', 'HSE': 'H', 'HSP': 'H',
+    'LSN': 'K',
+    'ASPP': 'D',
+    'GLUP': 'E',
+
+    // amber ff
+    'HID': 'H', 'HIE': 'H', 'HIP': 'H',
+    'LYN': 'K',
+    'ASH': 'D',
+    'GLH': 'E',
 };
 
 const DnaOneLetterCodes: { [name: string]: NuclecicAlphabet } = {

src/mol-model/structure/coordinates/coordinates.ts

@@ -1,10 +1,11 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { UUID } from '../../../mol-util';
+import { arrayEqual, UUID } from '../../../mol-util';
 import { Cell } from '../../../mol-math/geometry/spacegroup/cell';
 import { AtomicConformation } from '../model/properties/atomic';
 import { Column } from '../../../mol-data/db';
@@ -34,6 +35,12 @@ export interface Frame {
         readonly fy: ArrayLike<number>
         readonly fz: ArrayLike<number>
     }
+
+    readonly xyzOrdering: {
+        isIdentity: boolean,
+        frozen?: boolean,
+        index?: ArrayLike<number>,
+    }
 }
 
 //
@@ -85,41 +92,106 @@ namespace Coordinates {
             hasVelocities,
             hasForces,
             deltaTime,
-            timeOffset
+            timeOffset,
         };
     }
 
-    export function getAtomicConformation(frame: Frame, atomId: Column<number>): AtomicConformation {
+    /**
+     * Only use ordering if it's not identity.
+     */
+    export function getAtomicConformation(frame: Frame, atomId: Column<number>, ordering?: ArrayLike<number>): AtomicConformation {
+        let { x, y, z } = frame;
+
+        if (frame.xyzOrdering.frozen) {
+            if (ordering) {
+                if (frame.xyzOrdering.isIdentity) {
+                    // simple list reordering
+                    x = getOrderedCoords(x, ordering);
+                    y = getOrderedCoords(y, ordering);
+                    z = getOrderedCoords(z, ordering);
+                } else if (!arrayEqual(frame.xyzOrdering.index! as any, ordering as any)) {
+                    x = getSourceOrderedCoords(x, frame.xyzOrdering.index!, ordering);
+                    y = getSourceOrderedCoords(y, frame.xyzOrdering.index!, ordering);
+                    z = getSourceOrderedCoords(z, frame.xyzOrdering.index!, ordering);
+                }
+            } else if (!frame.xyzOrdering.isIdentity) {
+                x = getInvertedCoords(x, frame.xyzOrdering.index!);
+                y = getInvertedCoords(y, frame.xyzOrdering.index!);
+                z = getInvertedCoords(z, frame.xyzOrdering.index!);
+            }
+        } else if (ordering) {
+            if (frame.xyzOrdering.isIdentity) {
+                frame.xyzOrdering.isIdentity = false;
+                frame.xyzOrdering.index = ordering;
+                reorderCoordsInPlace(x as unknown as number[], ordering);
+                reorderCoordsInPlace(y as unknown as number[], ordering);
+                reorderCoordsInPlace(z as unknown as number[], ordering);
+            } else {
+                // is current ordering is not the same as requested?
+                //   => copy the conformations into a new array
+                if (!arrayEqual(frame.xyzOrdering.index! as any, ordering as any)) {
+                    x = getSourceOrderedCoords(x, frame.xyzOrdering.index!, ordering);
+                    y = getSourceOrderedCoords(y, frame.xyzOrdering.index!, ordering);
+                    z = getSourceOrderedCoords(z, frame.xyzOrdering.index!, ordering);
+                }
+            }
+        }
+
+        // once the conformation has been accessed at least once, freeze it.
+        //   => any other request to the frame with different ordering will result in a copy.
+        frame.xyzOrdering.frozen = true;
+
         return {
             id: UUID.create22(),
             atomId,
             occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
             B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
             xyzDefined: true,
-            x: frame.x,
-            y: frame.y,
-            z: frame.z,
+            x,
+            y,
+            z,
         };
     }
 
-    function reorderCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
-        const ret = new Float32Array(xs.length);
+    const _reorderBuffer = [0.123];
+    function reorderCoordsInPlace(xs: number[], index: ArrayLike<number>) {
+        const buffer = _reorderBuffer;
+
         for (let i = 0, _i = xs.length; i < _i; i++) {
-            ret[i] = xs[index[i]];
+            buffer[i] = xs[index[i]];
         }
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            xs[i] = buffer[i];
+        }
+    }
+
+    function getSourceOrderedCoords(xs: ArrayLike<number>, srcIndex: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[i] = xs[srcIndex[index[i]]];
+        }
+
         return ret;
     }
 
-    export function getAtomicConformationReordered(frame: Frame, atomId: Column<number>, srcIndex: ArrayLike<number>): AtomicConformation {
-        return {
-            id: UUID.create22(),
-            atomId,
-            occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
-            B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
-            xyzDefined: true,
-            x: reorderCoords(frame.x, srcIndex),
-            y: reorderCoords(frame.y, srcIndex),
-            z: reorderCoords(frame.z, srcIndex)
-        };
+    function getOrderedCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[i] = xs[index[i]];
+        }
+
+        return ret;
+    }
+
+    function getInvertedCoords(xs: ArrayLike<number>, index: ArrayLike<number>) {
+        const ret = new Float32Array(xs.length);
+
+        for (let i = 0, _i = xs.length; i < _i; i++) {
+            ret[index[i]] = xs[i];
+        }
+
+        return ret;
     }
 }

src/mol-model/structure/model/model.ts

@@ -105,9 +105,7 @@ export namespace Model {
                 ...model,
                 id: UUID.create22(),
                 modelNum: i,
-                atomicConformation: isIdentity
-                    ? Coordinates.getAtomicConformation(f, model.atomicConformation.atomId)
-                    : Coordinates.getAtomicConformationReordered(f, model.atomicConformation.atomId, srcIndexArray!),
+                atomicConformation: Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray),
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
                 customProperties: new CustomProperties(),

src/mol-model/structure/model/properties/utils/guess-element.ts

@@ -1,33 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-const elm1 = [ 'H', 'C', 'O', 'N', 'S', 'P' ];
-const elm2 = [ 'NA', 'CL', 'FE' ];
-
-function charAtIsNumber(str: string, index: number) {
-    const code = str.charCodeAt(index);
-    return code >= 48 && code <= 57;
-}
-
-export function guessElement(str: string) {
-    let at = str.trim().toUpperCase();
-
-    if (charAtIsNumber(at, 0)) at = at.substr(1);
-    // parse again to check for a second integer
-    if (charAtIsNumber(at, 0)) at = at.substr(1);
-    const n = at.length;
-
-    if (n === 0) return '';
-    if (n === 1) return at;
-    if (n === 2) {
-        if (elm2.indexOf(at) !== -1) return at;
-        if (elm1.indexOf(at[0]) !== -1) return at[0];
-    }
-    if (n >= 3) {
-        if (elm1.indexOf(at[0]) !== -1) return at[0];
-    }
-    return '';
-}

src/mol-model/structure/model/types.ts

@@ -99,7 +99,7 @@ export const PolymerTypeAtomRoleId: { [k in PolymerType]: { [k in AtomRole]: Set
     [PolymerType.Protein]: {
         trace: new Set(['CA']),
         directionFrom: new Set(['C']),
-        directionTo: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT']),
+        directionTo: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT', 'OT1']),
         backboneStart: new Set(['N']),
         backboneEnd: new Set(['C']),
         // CA1 is used e.g. in GFP chromophores
@@ -246,8 +246,13 @@ export const AminoAcidNamesL = new Set([
     'HIS', 'ARG', 'LYS', 'ILE', 'PHE', 'LEU', 'TRP', 'ALA', 'MET', 'PRO', 'CYS',
     'ASN', 'VAL', 'GLY', 'SER', 'GLN', 'TYR', 'ASP', 'GLU', 'THR', 'SEC', 'PYL',
     'UNK', // unknown amino acid from CCD
-    'MSE', 'SEP', 'TPO', 'PTR', 'PCA' // common
+    'MSE', 'SEP', 'TPO', 'PTR', 'PCA', // common from CCD
 
+    // charmm ff
+    'HSD', 'HSE', 'HSP', 'LSN', 'ASPP', 'GLUP',
+
+    // amber ff
+    'HID', 'HIE', 'HIP', 'LYN', 'ASH', 'GLH',
 ]);
 export const AminoAcidNamesD = new Set([
     'DAL', // D-ALANINE
@@ -586,7 +591,13 @@ export const MaxAsa = {
     'THR': 163.0,
     'TRP': 264.0,
     'TYR': 255.0,
-    'VAL': 165.0
+    'VAL': 165.0,
+
+    // charmm ff
+    'HSD': 216.0, 'HSE': 216.0, 'HSP': 216.0,
+
+    // amber ff
+    'HID': 216.0, 'HIE': 216.0, 'HIP': 216.0, 'ASH': 187.0, 'GLH': 214.0,
 };
 export const DefaultMaxAsa = 121.0;
 
@@ -620,9 +631,9 @@ export namespace BondType {
         'covalent': Flag.Covalent,
         'metal-coordination': Flag.MetallicCoordination,
         'hydrogen-bond': Flag.HydrogenBond,
-        'disulfide': Flag.HydrogenBond,
-        'aromatic': Flag.HydrogenBond,
-        'computed': Flag.HydrogenBond,
+        'disulfide': Flag.Disulfide,
+        'aromatic': Flag.Aromatic,
+        'computed': Flag.Computed,
     };
     export type Names = keyof typeof Names
 
@@ -680,6 +691,12 @@ export const ResidueHydrophobicity = {
     'THR': [0.14, 0.25, 0.11],
     'TRP': [-1.85, -2.09, -0.24],
     'TYR': [-0.94, -0.71, 0.23],
-    'VAL': [0.07, -0.46, -0.53]
+    'VAL': [0.07, -0.46, -0.53],
+
+    // charmm ff
+    'HSD': [0.17, 0.11, -0.06], 'HSE': [0.17, 0.11, -0.06], 'HSP': [0.96, 2.33, 1.37],
+
+    // amber ff
+    'HID': [0.17, 0.11, -0.06], 'HIE': [0.17, 0.11, -0.06], 'HIP': [0.96, 2.33, 1.37],
 };
 export const DefaultResidueHydrophobicity = [0.00, 0.00, 0.00];

src/mol-model/structure/query/queries/filters.ts

@@ -278,7 +278,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
 
             for (let li = 0; li < buCount; li++) {
                 const lu = bondedUnits[li];
-                const bUnit = structure.unitMap.get(lu.unitB) as Unit.Atomic;
+                const bUnit = input.unitMap.get(lu.unitB) as Unit.Atomic;
                 const bElements = bUnit.elements;
                 const bonds = lu.getEdges(inputIndex);
                 for (let bi = 0, _bi = bonds.length; bi < _bi; bi++) {

src/mol-model/structure/structure/structure.ts

@@ -368,13 +368,16 @@ class Structure {
 
     private _child: Structure | undefined;
     private _target: Structure | undefined;
+    private _proxy: Structure | undefined;
 
     /**
      * For `structure` with `parent` this returns a proxy that
      * targets `parent` and has `structure` attached as a child.
      */
     asParent(): Structure {
-        return this.parent ? new Structure(this.parent.units, this.parent.unitMap, this.parent.unitIndexMap, this.parent.state, { child: this, target: this.parent }) : this;
+        if (this._proxy) return this._proxy;
+        this._proxy = this.parent ? new Structure(this.parent.units, this.parent.unitMap, this.parent.unitIndexMap, this.parent.state, { child: this, target: this.parent }) : this;
+        return this._proxy;
     }
 
     get child(): Structure | undefined {

src/mol-model/structure/structure/unit/rings.ts

@@ -117,7 +117,6 @@ namespace UnitRing {
                 // comes e.g. from `chem_comp_bond.pdbx_aromatic_flag`
                 if (BondType.is(BondType.Flag.Aromatic, flags[j])) {
                     if (SortedArray.has(ring, b[j])) aromaticBondCount += 1;
-
                 }
             }
         }

src/mol-plugin-state/formats/volume.ts

@@ -191,6 +191,9 @@ export const CubeProvider = DataFormatProvider({
     }
 });
 
+
+type DsCifParams = { entryId?: string | string[] };
+
 export const DscifProvider = DataFormatProvider({
     label: 'DensityServer CIF',
     description: 'DensityServer CIF',
@@ -200,7 +203,7 @@ export const DscifProvider = DataFormatProvider({
     isApplicable: (info, data) => {
         return guessCifVariant(info, data) === 'dscif' ? true : false;
     },
-    parse: async (plugin, data, params?: Params) => {
+    parse: async (plugin, data, params?: DsCifParams) => {
         const cifCell = await plugin.build().to(data).apply(StateTransforms.Data.ParseCif).commit();
         const b = plugin.build().to(cifCell);
         const blocks = cifCell.obj!.data.blocks.slice(1); // zero block contains query meta-data
@@ -208,8 +211,11 @@ export const DscifProvider = DataFormatProvider({
         if (blocks.length !== 1 && blocks.length !== 2) throw new Error('unknown number of blocks');
 
         const volumes: StateObjectSelector<PluginStateObject.Volume.Data>[] = [];
+        let i = 0;
         for (const block of blocks) {
-            volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: params?.entryId }).selector);
+            const entryId = Array.isArray(params?.entryId) ? params?.entryId[i] : params?.entryId;
+            volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId }).selector);
+            i++;
         }
 
         await b.commit();

src/mol-plugin-state/objects.ts

@@ -125,12 +125,13 @@ export namespace PluginStateObject {
             url: string | Asset.Url,
             isBinary: boolean,
             format: string,
-            entryId?: string,
+            entryId?: string | string[],
             isovalues: {
                 type: 'absolute' | 'relative',
                 value: number,
                 color: Color,
-                alpha?: number
+                alpha?: number,
+                volumeIndex?: number,
             }[]
         }
 

src/mol-plugin-state/transforms/data.ts

@@ -455,18 +455,20 @@ const LazyVolume = PluginStateTransform.BuiltIn({
         url: PD.Url(''),
         isBinary: PD.Boolean(false),
         format: PD.Text('ccp4'), // TODO: use Select based on available formats
-        entryId: PD.Text(''),
+        entryId: PD.Value<string | string[]>('', { isHidden: true }),
         isovalues: PD.ObjectList({
             type: PD.Text<'absolute' | 'relative'>('relative'), // TODO: Select
             value: PD.Numeric(0),
             color: PD.Color(ColorNames.black),
-            alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 })
+            alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+            volumeIndex: PD.Numeric(0),
         }, e => `${e.type} ${e.value}`)
     }
 })({
     apply({ a, params }) {
         return Task.create('Lazy Volume', async ctx => {
-            return new SO.Volume.Lazy(params, { label: `${params.entryId || params.url}`, description: 'Lazy Volume' });
+            const entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
+            return new SO.Volume.Lazy(params, { label: `${entryId || params.url}`, description: 'Lazy Volume' });
         });
     }
 });

src/mol-plugin-state/transforms/model.ts

@@ -40,6 +40,7 @@ import { coordinatesFromXtc } from '../../mol-model-formats/structure/xtc';
 import { parseXyz } from '../../mol-io/reader/xyz/parser';
 import { trajectoryFromXyz } from '../../mol-model-formats/structure/xyz';
 import { parseSdf } from '../../mol-io/reader/sdf/parser';
+import { trajectoryFromSdf } from '../../mol-model-formats/structure/sdf';
 
 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
@@ -308,8 +309,8 @@ const TrajectoryFromSDF = PluginStateTransform.BuiltIn({
 
             const models: Model[] = [];
 
-            for (const { molFile } of parsed.result.compounds) {
-                const traj = await trajectoryFromMol(molFile).runInContext(ctx);
+            for (const compound of parsed.result.compounds) {
+                const traj = await trajectoryFromSdf(compound).runInContext(ctx);
                 for (let i = 0; i < traj.frameCount; i++) {
                     models.push(await Task.resolveInContext(traj.getFrameAtIndex(i), ctx));
                 }

src/mol-plugin-ui/controls/icons.tsx

@@ -41,6 +41,9 @@ export function MoleculeSvg() { return _Molecule; }
 const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z" /></svg>;
 export function CubeOutlineSvg() { return _CubeOutline; }
 
+const _CubeScan = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z" /></svg>;
+export function CubeScanSvg() { return _CubeScan; }
+
 const _CubeSend = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M16,4L9,8.04V15.96L16,20L23,15.96V8.04M16,6.31L19.8,8.5L16,10.69L12.21,8.5M0,7V9H7V7M11,10.11L15,12.42V17.11L11,14.81M21,10.11V14.81L17,17.11V12.42M2,11V13H7V11M4,15V17H7V15" /></svg>;
 export function CubeSendSvg() { return _CubeSend; }
 

src/mol-plugin-ui/structure/volume.tsx

@@ -205,19 +205,21 @@ export class VolumeSourceControls extends CollapsableControls<{}, VolumeSourceCo
         try {
             const plugin = this.plugin;
             await plugin.dataTransaction(async () => {
-                const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
+                const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
                 const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
-                const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-                if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+                const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+                if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
 
-                const repr = plugin.build().to(volume);
+                const repr = plugin.build();
                 for (const iso of isovalues) {
-                    repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                        type: 'isosurface',
-                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                        color: 'uniform',
-                        colorParams: { value: iso.color }
-                    }));
+                    repr
+                        .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                        .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                            type: 'isosurface',
+                            typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                            color: 'uniform',
+                            colorParams: { value: iso.color }
+                        }));
                 }
 
                 await repr.commit();

src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts

@@ -276,10 +276,12 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         // TODO: is this correct behavior?
         if (!channel) return StateTransformer.UpdateResult.Unchanged;
 
+        const visible = b.data.repr.state.visible;
         const params = createVolumeProps(a.data, newParams.channel);
         const props = { ...b.data.repr.props, ...params.type.params };
         b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
         await b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx);
+        b.data.repr.setState({ visible });
         b.data.sourceData = channel.data;
 
         // TODO: set the transform here as well in case the structure moves?

src/mol-repr/structure/complex-visual.ts

@@ -118,6 +118,11 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
             updateState.createGeometry = true;
         }
 
+        if (currentStructure.child !== newStructure.child) {
+            // console.log('new child');
+            updateState.createGeometry = true;
+        }
+
         if (updateState.updateSize && !('uSize' in renderObject.values)) {
             updateState.createGeometry = true;
         }

src/mol-repr/structure/registry.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -21,6 +21,7 @@ import { PuttyRepresentationProvider } from './representation/putty';
 import { SpacefillRepresentationProvider } from './representation/spacefill';
 import { LineRepresentationProvider } from './representation/line';
 import { GaussianVolumeRepresentationProvider } from './representation/gaussian-volume';
+import { BackboneRepresentationProvider } from './representation/backbone';
 
 export class StructureRepresentationRegistry extends RepresentationRegistry<Structure, StructureRepresentationState> {
     constructor() {
@@ -35,6 +36,7 @@ export class StructureRepresentationRegistry extends RepresentationRegistry<Stru
 export namespace StructureRepresentationRegistry {
     export const BuiltIn = {
         'cartoon': CartoonRepresentationProvider,
+        'backbone': BackboneRepresentationProvider,
         'ball-and-stick': BallAndStickRepresentationProvider,
         'carbohydrate': CarbohydrateRepresentationProvider,
         'ellipsoid': EllipsoidRepresentationProvider,

src/mol-repr/structure/representation/backbone.ts

@@ -1,29 +1,57 @@
-// /**
-//  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-//  *
-//  * @author Alexander Rose <alexander.rose@weirdbyte.de>
-//  */
+/**
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
 
-// import { PolymerBackboneVisual, PolymerBackboneParams } from '../visual/polymer-backbone-cylinder';
-// import { ParamDefinition as PD } from 'mol-util/param-definition';
-// import { UnitsRepresentation } from '../units-representation';
-// import { StructureRepresentation } from '../representation';
-// import { Representation } from 'mol-repr/representation';
-// import { ThemeRegistryContext } from 'mol-theme/theme';
-// import { Structure } from 'mol-model/structure';
+import { PolymerBackboneCylinderVisual, PolymerBackboneCylinderParams } from '../visual/polymer-backbone-cylinder';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsRepresentation } from '../units-representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
+import { ThemeRegistryContext } from '../../../mol-theme/theme';
+import { Structure } from '../../../mol-model/structure';
+import { PolymerBackboneSphereParams, PolymerBackboneSphereVisual } from '../visual/polymer-backbone-sphere';
+import { PolymerGapParams, PolymerGapVisual } from '../visual/polymer-gap-cylinder';
 
-// export const BackboneParams = {
-//     ...PolymerBackboneParams,
-// }
-// export function getBackboneParams(ctx: ThemeRegistryContext, structure: Structure) {
-//     return BackboneParams // TODO return copy
-// }
-// export type BackboneProps = PD.DefaultValues<typeof BackboneParams>
+const BackboneVisuals = {
+    'polymer-backbone-cylinder': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerBackboneCylinderParams>) => UnitsRepresentation('Polymer backbone cylinder', ctx, getParams, PolymerBackboneCylinderVisual),
+    'polymer-backbone-sphere': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerBackboneSphereParams>) => UnitsRepresentation('Polymer backbone sphere', ctx, getParams, PolymerBackboneSphereVisual),
+    'polymer-gap': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerGapParams>) => UnitsRepresentation('Polymer gap cylinder', ctx, getParams, PolymerGapVisual),
+};
 
-// export type BackboneRepresentation = StructureRepresentation<BackboneProps>
+export const BackboneParams = {
+    ...PolymerBackboneSphereParams,
+    ...PolymerBackboneCylinderParams,
+    ...PolymerGapParams,
+    sizeAspectRatio: PD.Numeric(1, { min: 0.1, max: 3, step: 0.1 }),
+    visuals: PD.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], PD.objectToOptions(BackboneVisuals))
+};
+export type BackboneParams = typeof BackboneParams
+export function getBackboneParams(ctx: ThemeRegistryContext, structure: Structure) {
+    const params = PD.clone(BackboneParams);
+    let hasGaps = false;
+    structure.units.forEach(u => {
+        if (!hasGaps && u.gapElements.length) hasGaps = true;
+    });
+    params.visuals.defaultValue = ['polymer-backbone-cylinder', 'polymer-backbone-sphere'];
+    if (hasGaps) params.visuals.defaultValue.push('polymer-gap');
+    return params;
+}
 
-// export function BackboneRepresentation(defaultProps: BackboneProps): BackboneRepresentation {
-//     return Representation.createMulti('Backbone', defaultProps, [
-//         UnitsRepresentation('Polymer backbone cylinder', defaultProps, PolymerBackboneVisual)
-//     ])
-// }
+export type BackboneRepresentation = StructureRepresentation<BackboneParams>
+export function BackboneRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, BackboneParams>): BackboneRepresentation {
+    return Representation.createMulti('Backbone', ctx, getParams, StructureRepresentationStateBuilder, BackboneVisuals as unknown as Representation.Def<Structure, BackboneParams>);
+}
+
+export const BackboneRepresentationProvider = StructureRepresentationProvider({
+    name: 'backbone',
+    label: 'Backbone',
+    description: 'Displays polymer backbone with cylinders and spheres.',
+    factory: BackboneRepresentation,
+    getParams: getBackboneParams,
+    defaultValues: PD.getDefaultValues(BackboneParams),
+    defaultColorTheme: { name: 'chain-id' },
+    defaultSizeTheme: { name: 'uniform' },
+    isApplicable: (structure: Structure) => structure.polymerResidueCount > 0,
+});

src/mol-repr/structure/representation/cartoon.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -17,6 +17,7 @@ import { PolymerGapParams, PolymerGapVisual } from '../visual/polymer-gap-cylind
 import { PolymerTraceParams, PolymerTraceVisual } from '../visual/polymer-trace-mesh';
 import { SecondaryStructureProvider } from '../../../mol-model-props/computed/secondary-structure';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { HelixOrientationProvider } from '../../../mol-model-props/computed/helix-orientation';
 
 const CartoonVisuals = {
     'polymer-trace': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerTraceParams>) => UnitsRepresentation('Polymer trace mesh', ctx, getParams, PolymerTraceVisual),
@@ -67,7 +68,17 @@ export const CartoonRepresentationProvider = StructureRepresentationProvider({
     defaultSizeTheme: { name: 'uniform' },
     isApplicable: (structure: Structure) => structure.polymerResidueCount > 0,
     ensureCustomProperties: {
-        attach: (ctx: CustomProperty.Context, structure: Structure) => SecondaryStructureProvider.attach(ctx, structure, void 0, true),
-        detach: (data) => SecondaryStructureProvider.ref(data, false)
+        attach: async (ctx: CustomProperty.Context, structure: Structure) => {
+            await SecondaryStructureProvider.attach(ctx, structure, void 0, true);
+            for (const m of structure.models) {
+                await HelixOrientationProvider.attach(ctx, m, void 0, true);
+            }
+        },
+        detach: (data) => {
+            SecondaryStructureProvider.ref(data, false);
+            for (const m of data.models) {
+                HelixOrientationProvider.ref(m, false);
+            }
+        }
     }
 });

src/mol-repr/structure/units-representation.ts

@@ -66,7 +66,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
                     visuals.set(group.hashCode, { visual, group });
                     if (runtime.shouldUpdate) await runtime.update({ message: 'Creating or updating UnitsVisual', current: i, max: _groups.length });
                 }
-            } else if (structure && !Structure.areUnitIdsAndIndicesEqual(structure, _structure)) {
+            } else if (structure && (!Structure.areUnitIdsAndIndicesEqual(structure, _structure) || structure.child !== _structure.child)) {
                 // console.log(label, 'structures not equivalent');
                 // Tries to re-use existing visuals for the groups of the new structure.
                 // Creates additional visuals if needed, destroys left-over visuals.

src/mol-repr/structure/units-visual.ts

@@ -120,6 +120,11 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
             updateState.updateColor = true;
         }
 
+        if (currentStructureGroup.structure.child !== newStructureGroup.structure.child) {
+            // console.log('new child');
+            updateState.createGeometry = true;
+        }
+
         if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) {
             // console.log('new unitKinds');
             updateState.createGeometry = true;

src/mol-repr/structure/visual/aromatic-ring-mesh.ts

@@ -1 +0,0 @@
-// TODO

src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts

@@ -11,7 +11,7 @@ import { Theme } from '../../../mol-theme/theme';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { BitFlags, arrayEqual } from '../../../mol-util';
-import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkStyle } from './util/link';
+import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkBuilderProps, LinkStyle } from './util/link';
 import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual, ComplexCylindersParams, ComplexCylindersVisual } from '../complex-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
@@ -34,22 +34,20 @@ function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, inde
 
 const tmpRef = Vec3();
 
-function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme, props: PD.Values<InterUnitBondCylinderParams>) {
+function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme, props: PD.Values<InterUnitBondCylinderParams>): LinkBuilderProps {
     const locE = StructureElement.Location.create(structure);
     const locB = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
 
     const bonds = structure.interUnitBonds;
     const { edgeCount, edges } = bonds;
-    const { sizeFactor, sizeAspectRatio, adjustCylinderLength } = props;
+    const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds } = props;
 
     const delta = Vec3();
 
     let stub: undefined | ((edgeIndex: number) => boolean);
 
-    if (props.includeParent) {
-        const { child } = structure;
-        if (!child) throw new Error('expected child to exist');
-
+    const { child } = structure;
+    if (props.includeParent && child) {
         stub = (edgeIndex: number) => {
             const b = edges[edgeIndex];
             const childUnitA = child.unitMap.get(b.unitA);
@@ -137,13 +135,15 @@ function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme
             if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
                 // show metall coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
-            } else if (o === 2) {
-                return LinkStyle.Double;
             } else if (o === 3) {
                 return LinkStyle.Triple;
-            } else {
-                return LinkStyle.Solid;
+            } else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
+                return LinkStyle.Aromatic;
+            } else if (o === 2) {
+                return LinkStyle.Double;
             }
+
+            return LinkStyle.Solid;
         },
         radius: (edgeIndex: number) => {
             return radius(edgeIndex) * sizeAspectRatio;
@@ -205,6 +205,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>) => {
             state.createGeometry = (
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

src/mol-repr/structure/visual/bond-inter-unit-line.ts

@@ -10,7 +10,7 @@ import { Structure, StructureElement, Bond, Unit } from '../../../mol-model/stru
 import { Theme } from '../../../mol-theme/theme';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { BitFlags, arrayEqual } from '../../../mol-util';
-import { LinkStyle, createLinkLines } from './util/link';
+import { LinkStyle, createLinkLines, LinkBuilderProps } from './util/link';
 import { ComplexVisual, ComplexLinesVisual, ComplexLinesParams } from '../complex-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
@@ -32,14 +32,14 @@ function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, inde
 function createInterUnitBondLines(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitBondLineParams>, lines?: Lines) {
     const bonds = structure.interUnitBonds;
     const { edgeCount, edges } = bonds;
-    const { sizeFactor } = props;
+    const { sizeFactor, aromaticBonds } = props;
 
     if (!edgeCount) return Lines.createEmpty(lines);
 
     const ref = Vec3();
     const loc = StructureElement.Location.create();
 
-    const builderProps = {
+    const builderProps: LinkBuilderProps = {
         linkCount: edgeCount,
         referencePosition: (edgeIndex: number) => {
             const b = edges[edgeIndex];
@@ -73,13 +73,15 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
             if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
                 // show metall coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
-            } else if (o === 2) {
-                return LinkStyle.Double;
             } else if (o === 3) {
                 return LinkStyle.Triple;
-            } else {
-                return LinkStyle.Solid;
+            }else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
+                return LinkStyle.Aromatic;
+            } else if (o === 2) {
+                return LinkStyle.Double;
             }
+
+            return LinkStyle.Solid;
         },
         radius: (edgeIndex: number) => {
             const b = edges[edgeIndex];

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -12,7 +12,7 @@ import { Theme } from '../../../mol-theme/theme';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { arrayEqual } from '../../../mol-util';
-import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkStyle } from './util/link';
+import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkBuilderProps, LinkStyle } from './util/link';
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
@@ -22,16 +22,17 @@ import { IntAdjacencyGraph } from '../../../mol-math/graph';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
 import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
 import { SortedArray } from '../../../mol-data/int';
+import { arrayIntersectionSize } from '../../../mol-util/array';
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const isBondType = BondType.is;
 
-function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Structure, theme: Theme, props: PD.Values<IntraUnitBondCylinderParams>) {
+function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Structure, theme: Theme, props: PD.Values<IntraUnitBondCylinderParams>): LinkBuilderProps {
     const elements = unit.elements;
     const bonds = unit.bonds;
     const { edgeCount, a, b, edgeProps, offset } = bonds;
     const { order: _order, flags: _flags } = edgeProps;
-    const { sizeFactor, sizeAspectRatio, adjustCylinderLength } = props;
+    const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds } = props;
 
     const vRef = Vec3(), delta = Vec3();
     const pos = unit.conformation.invariantPosition;
@@ -41,9 +42,8 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
     const locE = StructureElement.Location.create(structure, unit);
     const locB = Bond.Location(structure, unit, undefined, structure, unit, undefined);
 
-    if (props.includeParent) {
-        const { child } = structure;
-        if (!child) throw new Error('expected child to exist');
+    const { child } = structure;
+    if (props.includeParent && child) {
         const childUnit = child.unitMap.get(unit.id);
         if (!childUnit) throw new Error('expected childUnit to exist');
 
@@ -70,6 +70,8 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
         return theme.size.size(locE) * sizeFactor;
     };
 
+    const { elementRingIndices, elementAromaticRingIndices } = unit.rings;
+
     return {
         linkCount: edgeCount * 2,
         referencePosition: (edgeIndex: number) => {
@@ -77,17 +79,28 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
 
             if (aI > bI) [aI, bI] = [bI, aI];
             if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
-            // TODO prefer reference atoms within rings
+
+            const aR = elementRingIndices.get(aI);
+            let maxSize = 0;
 
             for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 const _bI = b[i];
-                if (_bI !== bI && _bI !== aI) return pos(elements[_bI], vRef);
+                if (_bI !== bI && _bI !== aI) {
+                    if (aR) {
+                        const _bR = elementRingIndices.get(_bI);
+                        if (!_bR) continue;
+
+                        const size = arrayIntersectionSize(aR, _bR);
+                        if (size > maxSize) {
+                            maxSize = size;
+                            pos(elements[_bI], vRef);
+                        }
+                    } else {
+                        return pos(elements[_bI], vRef);
+                    }
+                }
             }
-            for (let i = offset[bI], il = offset[bI + 1]; i < il; ++i) {
-                const _aI = a[i];
-                if (_aI !== aI && _aI !== bI) return pos(elements[_aI], vRef);
-            }
-            return null;
+            return maxSize > 0 ? vRef : null;
         },
         position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
             pos(elements[a[edgeIndex]], posA);
@@ -111,13 +124,24 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
             if (isBondType(f, BondType.Flag.MetallicCoordination) || isBondType(f, BondType.Flag.HydrogenBond)) {
                 // show metall coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
-            } else if (o === 2) {
-                return LinkStyle.Double;
             } else if (o === 3) {
                 return LinkStyle.Triple;
-            } else {
-                return LinkStyle.Solid;
+            } else if (aromaticBonds) {
+                const aI = a[edgeIndex], bI = b[edgeIndex];
+                const aR = elementAromaticRingIndices.get(aI);
+                const bR = elementAromaticRingIndices.get(bI);
+                const arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
+
+                if (arCount || isBondType(f, BondType.Flag.Aromatic)) {
+                    if (arCount === 2) {
+                        return LinkStyle.MirroredAromatic;
+                    } else {
+                        return LinkStyle.Aromatic;
+                    }
+                }
             }
+
+            return o === 2 ? LinkStyle.Double : LinkStyle.Solid;
         },
         radius: (edgeIndex: number) => {
             return radius(edgeIndex) * sizeAspectRatio;
@@ -187,6 +211,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondCylinderParams>, currentProps: PD.Values<IntraUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
             state.createGeometry = (
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
@@ -197,7 +222,8 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
                 newProps.stubCap !== currentProps.stubCap ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                 !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
-                newProps.adjustCylinderLength !== currentProps.adjustCylinderLength
+                newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
+                newProps.aromaticBonds !== currentProps.aromaticBonds
             );
 
             const newUnit = newStructureGroup.group.units[0];
@@ -239,7 +265,8 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
                 newProps.stubCap !== currentProps.stubCap ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                 !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
-                newProps.adjustCylinderLength !== currentProps.adjustCylinderLength
+                newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
+                newProps.aromaticBonds !== currentProps.aromaticBonds
             );
 
             const newUnit = newStructureGroup.group.units[0];

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -10,7 +10,7 @@ import { Unit, Structure, StructureElement } from '../../../mol-model/structure'
 import { Theme } from '../../../mol-theme/theme';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { arrayEqual } from '../../../mol-util';
-import { LinkStyle, createLinkLines } from './util/link';
+import { LinkStyle, createLinkLines, LinkBuilderProps } from './util/link';
 import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual, StructureGroup } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
@@ -18,6 +18,7 @@ import { BondIterator, BondLineParams, getIntraBondLoci, eachIntraBond, makeIntr
 import { Sphere3D } from '../../../mol-math/geometry';
 import { Lines } from '../../../mol-geo/geometry/lines/lines';
 import { IntAdjacencyGraph } from '../../../mol-math/graph';
+import { arrayIntersectionSize } from '../../../mol-util/array';
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const isBondType = BondType.is;
@@ -29,41 +30,50 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
     const childUnit = child?.unitMap.get(unit.id);
     if (child && !childUnit) return Lines.createEmpty(lines);
 
-    if (props.includeParent) {
-        if (!child) throw new Error('expected child to exist');
-    }
-
     const location = StructureElement.Location.create(structure, unit);
 
     const elements = unit.elements;
     const bonds = unit.bonds;
     const { edgeCount, a, b, edgeProps, offset } = bonds;
     const { order: _order, flags: _flags } = edgeProps;
-    const { sizeFactor } = props;
+    const { sizeFactor, aromaticBonds } = props;
 
     if (!edgeCount) return Lines.createEmpty(lines);
 
     const vRef = Vec3();
     const pos = unit.conformation.invariantPosition;
 
-    const builderProps = {
+    const { elementRingIndices, elementAromaticRingIndices } = unit.rings;
+
+    const builderProps: LinkBuilderProps = {
         linkCount: edgeCount * 2,
         referencePosition: (edgeIndex: number) => {
             let aI = a[edgeIndex], bI = b[edgeIndex];
 
             if (aI > bI) [aI, bI] = [bI, aI];
             if (offset[aI + 1] - offset[aI] === 1) [aI, bI] = [bI, aI];
-            // TODO prefer reference atoms within rings
+
+            const aR = elementRingIndices.get(aI);
+            let maxSize = 0;
 
             for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 const _bI = b[i];
-                if (_bI !== bI && _bI !== aI) return pos(elements[_bI], vRef);
+                if (_bI !== bI && _bI !== aI) {
+                    if (aR) {
+                        const _bR = elementRingIndices.get(_bI);
+                        if (!_bR) continue;
+
+                        const size = arrayIntersectionSize(aR, _bR);
+                        if (size > maxSize) {
+                            maxSize = size;
+                            pos(elements[_bI], vRef);
+                        }
+                    } else {
+                        return pos(elements[_bI], vRef);
+                    }
+                }
             }
-            for (let i = offset[bI], il = offset[bI + 1]; i < il; ++i) {
-                const _aI = a[i];
-                if (_aI !== aI && _aI !== bI) return pos(elements[_aI], vRef);
-            }
-            return null;
+            return maxSize > 0 ? vRef : null;
         },
         position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
             pos(elements[a[edgeIndex]], posA);
@@ -75,13 +85,24 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
             if (isBondType(f, BondType.Flag.MetallicCoordination) || isBondType(f, BondType.Flag.HydrogenBond)) {
                 // show metall coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
-            } else if (o === 2) {
-                return LinkStyle.Double;
             } else if (o === 3) {
                 return LinkStyle.Triple;
-            } else {
-                return LinkStyle.Solid;
+            } else if (aromaticBonds) {
+                const aI = a[edgeIndex], bI = b[edgeIndex];
+                const aR = elementAromaticRingIndices.get(aI);
+                const bR = elementAromaticRingIndices.get(bI);
+                const arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
+
+                if (arCount || isBondType(f, BondType.Flag.Aromatic)) {
+                    if (arCount === 2) {
+                        return LinkStyle.MirroredAromatic;
+                    } else {
+                        return LinkStyle.Aromatic;
+                    }
+                }
             }
+
+            return o === 2 ? LinkStyle.Double : LinkStyle.Solid;
         },
         radius: (edgeIndex: number) => {
             location.element = elements[a[edgeIndex]];
@@ -123,7 +144,8 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
-                !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes)
+                !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
+                newProps.aromaticBonds !== currentProps.aromaticBonds
             );
 
             const newUnit = newStructureGroup.group.units[0];

src/mol-repr/structure/visual/polymer-backbone-cylinder.ts

@@ -1,34 +1,102 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { VisualContext } from '../../visual';
-import { Unit, Structure } from '../../../mol-model/structure';
+import { Unit, Structure, StructureElement, ElementIndex } from '../../../mol-model/structure';
 import { Theme } from '../../../mol-theme/theme';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
-import { PolymerBackboneIterator } from './util/polymer';
-import { OrderedSet } from '../../../mol-data/int';
+import { eachPolymerElement, getPolymerElementLoci, NucleicShift, PolymerLocationIterator, StandardShift } from './util/polymer';
 import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
-import { ElementIterator, getElementLoci, eachElement } from './util/element';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsCylindersVisual, UnitsCylindersParams, StructureGroup } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { isNucleic, MoleculeType } from '../../../mol-model/structure/model/types';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
+import { CylindersBuilder } from '../../../mol-geo/geometry/cylinders/cylinders-builder';
+import { eachPolymerBackboneLink } from './util/polymer/backbone';
+
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3scale = Vec3.scale;
+const v3add = Vec3.add;
+const v3sub = Vec3.sub;
 
 export const PolymerBackboneCylinderParams = {
+    ...UnitsMeshParams,
+    ...UnitsCylindersParams,
     sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
     radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
+    tryUseImpostor: PD.Boolean(true),
 };
-export const DefaultPolymerBackboneCylinderProps = PD.getDefaultValues(PolymerBackboneCylinderParams);
-export type PolymerBackboneCylinderProps = typeof DefaultPolymerBackboneCylinderProps
+export type PolymerBackboneCylinderParams = typeof PolymerBackboneCylinderParams
+
+export function PolymerBackboneCylinderVisual(materialId: number, structure: Structure, props: PD.Values<PolymerBackboneCylinderParams>, webgl?: WebGLContext) {
+    return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
+        ? PolymerBackboneCylinderImpostorVisual(materialId)
+        : PolymerBackboneCylinderMeshVisual(materialId);
+}
+
+interface PolymerBackboneCylinderProps {
+    radialSegments: number,
+    sizeFactor: number,
+}
+
+function createPolymerBackboneCylinderImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneCylinderProps, cylinders?: Cylinders) {
+    const polymerElementCount = unit.polymerElements.length;
+    if (!polymerElementCount) return Cylinders.createEmpty(cylinders);
+
+    const cylindersCountEstimate = polymerElementCount * 2;
+    const builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
+
+    const pos = unit.conformation.invariantPosition;
+    const pA = Vec3();
+    const pB = Vec3();
+    const pM = Vec3();
+
+    const add = function(indexA: ElementIndex, indexB: ElementIndex, groupA: number, groupB: number, moleculeType: MoleculeType) {
+        pos(indexA, pA);
+        pos(indexB, pB);
+
+        const isNucleicType = isNucleic(moleculeType);
+        const shift = isNucleicType ? NucleicShift : 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, groupA);
+        builder.add(pM[0], pM[1], pM[2], pB[0], pB[1], pB[2], 1, false, false, groupB);
+    };
+
+    eachPolymerBackboneLink(unit, add);
+
+    const c = builder.getCylinders();
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    c.setBoundingSphere(sphere);
+
+    return c;
+}
+
+export function PolymerBackboneCylinderImpostorVisual(materialId: number): UnitsVisual<PolymerBackboneCylinderParams> {
+    return UnitsCylindersVisual<PolymerBackboneCylinderParams>({
+        defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
+        createGeometry: createPolymerBackboneCylinderImpostor,
+        createLocationIterator: PolymerLocationIterator.fromGroup,
+        getLoci: getPolymerElementLoci,
+        eachLocation: eachPolymerElement,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneCylinderParams>, currentProps: PD.Values<PolymerBackboneCylinderParams>) => { },
+        mustRecreate: (structureGroup: StructureGroup, props: PD.Values<PolymerBackboneCylinderParams>, webgl?: WebGLContext) => {
+            return !props.tryUseImpostor || !webgl;
+        }
+    }, materialId);
+}
 
-// TODO do group id based on polymer index not element index
 function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
     const polymerElementCount = unit.polymerElements.length;
     if (!polymerElementCount) return Mesh.createEmpty(mesh);
@@ -38,26 +106,34 @@ function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, struc
     const vertexCountEstimate = radialSegments * 2 * polymerElementCount * 2;
     const builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 10, mesh);
 
-    const { elements } = unit;
     const pos = unit.conformation.invariantPosition;
-    const pA = Vec3.zero();
-    const pB = Vec3.zero();
+    const pA = Vec3();
+    const pB = Vec3();
     const cylinderProps: CylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments };
 
-    const polymerBackboneIt = PolymerBackboneIterator(structure, unit);
-    while (polymerBackboneIt.hasNext) {
-        const { centerA, centerB } = polymerBackboneIt.move();
+    const centerA = StructureElement.Location.create(structure, unit);
+    const centerB = StructureElement.Location.create(structure, unit);
+
+    const add = function(indexA: ElementIndex, indexB: ElementIndex, groupA: number, groupB: number, moleculeType: MoleculeType) {
+        centerA.element = indexA;
+        centerB.element = indexB;
+
         pos(centerA.element, pA);
         pos(centerB.element, pB);
 
+        const isNucleicType = isNucleic(moleculeType);
+        const shift = isNucleicType ? NucleicShift : StandardShift;
+
         cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerA) * sizeFactor;
-        builderState.currentGroup = OrderedSet.indexOf(elements, centerA.element);
-        addCylinder(builderState, pA, pB, 0.5, cylinderProps);
+        builderState.currentGroup = groupA;
+        addCylinder(builderState, pA, pB, shift, cylinderProps);
 
         cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerB) * sizeFactor;
-        builderState.currentGroup = OrderedSet.indexOf(elements, centerB.element);
-        addCylinder(builderState, pB, pA, 0.5, cylinderProps);
-    }
+        builderState.currentGroup = groupB;
+        addCylinder(builderState, pB, pA, 1 - shift, cylinderProps);
+    };
+
+    eachPolymerBackboneLink(unit, add);
 
     const m = MeshBuilder.getMesh(builderState);
 
@@ -67,25 +143,21 @@ function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, struc
     return m;
 }
 
-export const PolymerBackboneParams = {
-    ...UnitsMeshParams,
-    ...PolymerBackboneCylinderParams,
-};
-export type PolymerBackboneParams = typeof PolymerBackboneParams
-
-export function PolymerBackboneVisual(materialId: number): UnitsVisual<PolymerBackboneParams> {
-    return UnitsMeshVisual<PolymerBackboneParams>({
-        defaultProps: PD.getDefaultValues(PolymerBackboneParams),
+export function PolymerBackboneCylinderMeshVisual(materialId: number): UnitsVisual<PolymerBackboneCylinderParams> {
+    return UnitsMeshVisual<PolymerBackboneCylinderParams>({
+        defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderMesh,
-        // TODO create a specialized location iterator
-        createLocationIterator: ElementIterator.fromGroup,
-        getLoci: getElementLoci,
-        eachLocation: eachElement,
-        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneParams>, currentProps: PD.Values<PolymerBackboneParams>) => {
+        createLocationIterator: PolymerLocationIterator.fromGroup,
+        getLoci: getPolymerElementLoci,
+        eachLocation: eachPolymerElement,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneCylinderParams>, currentProps: PD.Values<PolymerBackboneCylinderParams>) => {
             state.createGeometry = (
                 newProps.sizeFactor !== currentProps.sizeFactor ||
                 newProps.radialSegments !== currentProps.radialSegments
             );
+        },
+        mustRecreate: (structureGroup: StructureGroup, props: PD.Values<PolymerBackboneCylinderParams>, webgl?: WebGLContext) => {
+            return props.tryUseImpostor && !!webgl;
         }
     }, materialId);
 }

src/mol-repr/structure/visual/polymer-backbone-sphere.ts

@@ -1 +1,131 @@
-// TODO
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { VisualContext } from '../../visual';
+import { Unit, Structure, ElementIndex, StructureElement } from '../../../mol-model/structure';
+import { Theme } from '../../../mol-theme/theme';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { eachPolymerElement, getPolymerElementLoci, PolymerLocationIterator } from './util/polymer';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsSpheresVisual, UnitsSpheresParams, StructureGroup } from '../units-visual';
+import { VisualUpdateState } from '../../util';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
+import { sphereVertexCount } from '../../../mol-geo/primitive/sphere';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Spheres } from '../../../mol-geo/geometry/spheres/spheres';
+import { SpheresBuilder } from '../../../mol-geo/geometry/spheres/spheres-builder';
+import { eachPolymerBackboneElement } from './util/polymer/backbone';
+
+export const PolymerBackboneSphereParams = {
+    ...UnitsMeshParams,
+    ...UnitsSpheresParams,
+    sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
+    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
+    tryUseImpostor: PD.Boolean(true),
+};
+export type PolymerBackboneSphereParams = typeof PolymerBackboneSphereParams
+
+export function PolymerBackboneSphereVisual(materialId: number, structure: Structure, props: PD.Values<PolymerBackboneSphereParams>, webgl?: WebGLContext) {
+    return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
+        ? PolymerBackboneSphereImpostorVisual(materialId)
+        : PolymerBackboneSphereMeshVisual(materialId);
+}
+
+interface PolymerBackboneSphereProps {
+    detail: number,
+    sizeFactor: number,
+}
+
+function createPolymerBackboneSphereImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneSphereProps, spheres?: Spheres) {
+    const polymerElementCount = unit.polymerElements.length;
+    if (!polymerElementCount) return Spheres.createEmpty(spheres);
+
+    const builder = SpheresBuilder.create(polymerElementCount, polymerElementCount / 2, spheres);
+
+    const pos = unit.conformation.invariantPosition;
+    const p = Vec3();
+
+    const add = (index: ElementIndex, group: number) => {
+        pos(index, p);
+        builder.add(p[0], p[1], p[2], group);
+    };
+
+    eachPolymerBackboneElement(unit, add);
+
+    const s = builder.getSpheres();
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    s.setBoundingSphere(sphere);
+
+    return s;
+}
+
+export function PolymerBackboneSphereImpostorVisual(materialId: number): UnitsVisual<PolymerBackboneSphereParams> {
+    return UnitsSpheresVisual<PolymerBackboneSphereParams>({
+        defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
+        createGeometry: createPolymerBackboneSphereImpostor,
+        createLocationIterator: PolymerLocationIterator.fromGroup,
+        getLoci: getPolymerElementLoci,
+        eachLocation: eachPolymerElement,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneSphereParams>, currentProps: PD.Values<PolymerBackboneSphereParams>) => { },
+        mustRecreate: (structureGroup: StructureGroup, props: PD.Values<PolymerBackboneSphereParams>, webgl?: WebGLContext) => {
+            return !props.tryUseImpostor || !webgl;
+        }
+    }, materialId);
+}
+
+function createPolymerBackboneSphereMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneSphereProps, mesh?: Mesh) {
+    const polymerElementCount = unit.polymerElements.length;
+    if (!polymerElementCount) return Mesh.createEmpty(mesh);
+
+    const { detail, sizeFactor } = props;
+
+    const vertexCount = polymerElementCount * sphereVertexCount(detail);
+    const builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
+
+    const pos = unit.conformation.invariantPosition;
+    const p = Vec3();
+    const center = StructureElement.Location.create(structure, unit);
+
+    const add = (index: ElementIndex, group: number) => {
+        center.element = index;
+        pos(center.element, p);
+        builderState.currentGroup = group;
+        addSphere(builderState, p, theme.size.size(center) * sizeFactor, detail);
+    };
+
+    eachPolymerBackboneElement(unit, add);
+
+    const m = MeshBuilder.getMesh(builderState);
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    m.setBoundingSphere(sphere);
+
+    return m;
+}
+
+export function PolymerBackboneSphereMeshVisual(materialId: number): UnitsVisual<PolymerBackboneSphereParams> {
+    return UnitsMeshVisual<PolymerBackboneSphereParams>({
+        defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
+        createGeometry: createPolymerBackboneSphereMesh,
+        createLocationIterator: PolymerLocationIterator.fromGroup,
+        getLoci: getPolymerElementLoci,
+        eachLocation: eachPolymerElement,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneSphereParams>, currentProps: PD.Values<PolymerBackboneSphereParams>) => {
+            state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.detail !== currentProps.detail
+            );
+        },
+        mustRecreate: (structureGroup: StructureGroup, props: PD.Values<PolymerBackboneSphereParams>, webgl?: WebGLContext) => {
+            return props.tryUseImpostor && !!webgl;
+        }
+    }, materialId);
+}

src/mol-repr/structure/visual/polymer-trace-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -27,6 +27,7 @@ export const PolymerTraceMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
     aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
     arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }),
+    tubularHelices: PD.Boolean(false),
     detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo)
@@ -40,7 +41,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
     const polymerElementCount = unit.polymerElements.length;
 
     if (!polymerElementCount) return Mesh.createEmpty(mesh);
-    const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor } = props;
+    const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor, tubularHelices } = props;
 
     const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2;
     const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
@@ -50,7 +51,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
     const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
 
     let i = 0;
-    const polymerTraceIt = PolymerTraceIterator(unit, structure);
+    const polymerTraceIt = PolymerTraceIterator(unit, structure, { ignoreSecondaryStructure: false, useHelixOrientation: tubularHelices });
     while (polymerTraceIt.hasNext) {
         const v = polymerTraceIt.move();
         builderState.currentGroup = i;
@@ -58,7 +59,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
         const isNucleicType = isNucleic(v.moleculeType);
         const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta);
         const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix);
-        const tension = isHelix ? HelixTension : StandardTension;
+        const tension = isHelix && !tubularHelices ? HelixTension : StandardTension;
         const shift = isNucleicType ? NucleicShift : StandardShift;
 
         interpolateCurveSegment(state, v, tension, shift);
@@ -112,9 +113,19 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
         } else {
             let h0: number, h1: number, h2: number;
             if (isHelix && !v.isCoarseBackbone) {
-                h0 = w0 * aspectRatio;
-                h1 = w1 * aspectRatio;
-                h2 = w2 * aspectRatio;
+                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 && !v.isCoarseBackbone) {
                 h0 = w0 * aspectRatio;
                 h1 = w1 * aspectRatio;
@@ -172,6 +183,7 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
             state.createGeometry = (
                 newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.tubularHelices !== currentProps.tubularHelices ||
                 newProps.detail !== currentProps.detail ||
                 newProps.linearSegments !== currentProps.linearSegments ||
                 newProps.radialSegments !== currentProps.radialSegments ||

src/mol-repr/structure/visual/polymer-tube-mesh.ts

@@ -46,7 +46,7 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
     const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
 
     let i = 0;
-    const polymerTraceIt = PolymerTraceIterator(unit, structure, true);
+    const polymerTraceIt = PolymerTraceIterator(unit, structure, { ignoreSecondaryStructure: true });
     while (polymerTraceIt.hasNext) {
         const v = polymerTraceIt.move();
         builderState.currentGroup = i;

src/mol-repr/structure/visual/util/bond.ts

@@ -20,6 +20,7 @@ export const BondParams = {
     includeTypes: PD.MultiSelect(ObjectKeys(BondType.Names), PD.objectToOptions(BondType.Names)),
     excludeTypes: PD.MultiSelect([] as BondType.Names[], PD.objectToOptions(BondType.Names)),
     ignoreHydrogens: PD.Boolean(false),
+    aromaticBonds: PD.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
 };
 export const DefaultBondProps = PD.getDefaultValues(BondParams);
 export type BondProps = typeof DefaultBondProps

src/mol-repr/structure/visual/util/element.ts

@@ -46,7 +46,7 @@ export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: E
     const childUnit = child?.unitMap.get(unit.id);
     if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');
 
-    if (!child && ((!ignoreHydrogens && !traceOnly) || traceOnly)) return;
+    if (!child && !ignoreHydrogens && !traceOnly) return;
 
     return (element: ElementIndex) => {
         return (

src/mol-repr/structure/visual/util/link.ts

@@ -18,7 +18,7 @@ import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
 import { CylindersBuilder } from '../../../../mol-geo/geometry/cylinders/cylinders-builder';
 
 export const LinkCylinderParams = {
-    linkScale: PD.Numeric(0.4, { min: 0, max: 1, step: 0.1 }),
+    linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
     linkCap: PD.Boolean(false),
     dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
@@ -84,7 +84,9 @@ export const enum LinkStyle {
     Dashed = 1,
     Double = 2,
     Triple = 3,
-    Disk = 4
+    Disk = 4,
+    Aromatic = 5,
+    MirroredAromatic = 6,
 }
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
@@ -133,6 +135,8 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
         const [topCap, bottomCap] = (v3dot(tmpV12, up) > 0) ? [linkStub, linkCap] : [linkCap, linkStub];
         builderState.currentGroup = edgeIndex;
 
+        const aromaticOffsetFactor = 4.5;
+
         if (linkStyle === LinkStyle.Solid) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
             cylinderProps.topCap = topCap;
@@ -144,20 +148,41 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
 
             addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
-        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple) {
-            const order = linkStyle === LinkStyle.Double ? 2 : 3;
+        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+            const order = linkStyle === LinkStyle.Double ? 2 :
+                linkStyle === LinkStyle.Triple ? 3 : 1.5;
             const multiRadius = linkRadius * (linkScale / (0.5 * order));
             const absOffset = (linkRadius - multiRadius) * linkSpacing;
 
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            v3setMagnitude(vShift, vShift, absOffset);
 
-            cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
             cylinderProps.topCap = topCap;
             cylinderProps.bottomCap = bottomCap;
 
-            if (order === 3) addCylinder(builderState, va, vb, 0.5, cylinderProps);
-            addDoubleCylinder(builderState, va, vb, 0.5, vShift, cylinderProps);
+            if (linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+                cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
+                addCylinder(builderState, va, vb, 0.5, cylinderProps);
+
+                cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
+                cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
+                v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+                v3sub(va, va, vShift);
+                v3sub(vb, vb, vShift);
+                addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+
+                if (linkStyle === LinkStyle.MirroredAromatic) {
+                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                    v3add(va, va, vShift);
+                    v3add(vb, vb, vShift);
+                    addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+                }
+            } else {
+                v3setMagnitude(vShift, vShift, absOffset);
+
+                cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
+                if (order === 3) addCylinder(builderState, va, vb, 0.5, cylinderProps);
+                addDoubleCylinder(builderState, va, vb, 0.5, vShift, cylinderProps);
+            }
         } else if (linkStyle === LinkStyle.Disk) {
             v3scale(tmpV12, tmpV12, 0.475);
             v3add(va, va, tmpV12);
@@ -190,12 +215,17 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
 
     const va = Vec3();
     const vb = Vec3();
+    const vm = Vec3();
     const vShift = Vec3();
 
     // automatically adjust length for evenly spaced dashed cylinders
     const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
 
+    const aromaticSegmentCount = 3;
+    const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
+    const aromaticOffsetFactor = 4.5;
+
     for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex)) continue;
 
@@ -206,24 +236,45 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
         const linkStub = stubCap && (stub ? stub(edgeIndex) : false);
 
         if (linkStyle === LinkStyle.Solid) {
-            v3scale(vb, v3add(vb, va, vb), 0.5);
-            builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], 1, linkCap, linkStub, edgeIndex);
+            v3scale(vm, v3add(vm, va, vb), 0.5);
+            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         } else if (linkStyle === LinkStyle.Dashed) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
-        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple) {
-            v3scale(vb, v3add(vb, va, vb), 0.5);
-            const order = linkStyle === LinkStyle.Double ? 2 : 3;
+        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+            const order = linkStyle === LinkStyle.Double ? 2 :
+                linkStyle === LinkStyle.Triple ? 3 : 1.5;
             const multiScale = linkScale / (0.5 * order);
             const absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
 
+            v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            v3setMagnitude(vShift, vShift, absOffset);
 
-            if (order === 3) builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], multiScale, linkCap, false, edgeIndex);
-            builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vb[0] + vShift[0], vb[1] + vShift[1], vb[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
-            builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vb[0] - vShift[0], vb[1] - vShift[1], vb[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
+            if (linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
+                v3sub(vb, vb, tmpV12);
+
+                v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+                v3sub(va, va, vShift);
+                v3sub(vb, vb, vShift);
+                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+
+                if (linkStyle === LinkStyle.MirroredAromatic) {
+                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                    v3add(va, va, vShift);
+                    v3add(vb, vb, vShift);
+                    builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+                }
+            } else {
+                v3setMagnitude(vShift, vShift, absOffset);
+
+                if (order === 3) builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, false, edgeIndex);
+                builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
+                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
+            }
         } else if (linkStyle === LinkStyle.Disk) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);
@@ -252,12 +303,17 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
 
     const va = Vec3();
     const vb = Vec3();
+    const vm = Vec3();
     const vShift = Vec3();
 
     // automatically adjust length for evenly spaced dashed lines
     const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
 
+    const aromaticSegmentCount = 3;
+    const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
+    const aromaticOffsetFactor = 4.5;
+
     for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex)) continue;
 
@@ -266,24 +322,45 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
         const linkStyle = style ? style(edgeIndex) : LinkStyle.Solid;
 
         if (linkStyle === LinkStyle.Solid) {
-            v3scale(vb, v3add(vb, va, vb), 0.5);
-            builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], edgeIndex);
+            v3scale(vm, v3add(vm, va, vb), 0.5);
+            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
         } else if (linkStyle === LinkStyle.Dashed) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
-        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple) {
-            v3scale(vb, v3add(vb, va, vb), 0.5);
-            const order = linkStyle === LinkStyle.Double ? 2 : 3;
+        } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+            const order = linkStyle === LinkStyle.Double ? 2 :
+                linkStyle === LinkStyle.Triple ? 3 : 1.5;
             const multiRadius = 1 * (linkScale / (0.5 * order));
             const absOffset = (1 - multiRadius) * linkSpacing;
 
+            v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            v3setMagnitude(vShift, vShift, absOffset);
 
-            if (order === 3) builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], edgeIndex);
-            builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vb[0] + vShift[0], vb[1] + vShift[1], vb[2] + vShift[2], edgeIndex);
-            builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vb[0] - vShift[0], vb[1] - vShift[1], vb[2] - vShift[2], edgeIndex);
+            if (linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
+                v3sub(vb, vb, tmpV12);
+
+                v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+                v3sub(va, va, vShift);
+                v3sub(vb, vb, vShift);
+                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
+
+                if (linkStyle === LinkStyle.MirroredAromatic) {
+                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                    v3add(va, va, vShift);
+                    v3add(vb, vb, vShift);
+                    builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
+                }
+            } else {
+                v3setMagnitude(vShift, vShift, absOffset);
+
+                if (order === 3) builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+                builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
+                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
+            }
         } else if (linkStyle === LinkStyle.Disk) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);

src/mol-repr/structure/visual/util/polymer.ts

@@ -14,7 +14,7 @@ import { PickingId } from '../../../../mol-geo/geometry/picking';
 import { StructureGroup } from '../../../structure/units-visual';
 import { getResidueLoci } from './common';
 
-export * from './polymer/backbone-iterator';
+export * from './polymer/backbone';
 export * from './polymer/gap-iterator';
 export * from './polymer/trace-iterator';
 export * from './polymer/curve-segment';

src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts

@@ -1,134 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Unit, Structure, StructureElement, ElementIndex, ResidueIndex } from '../../../../../mol-model/structure';
-import { Segmentation } from '../../../../../mol-data/int';
-import { Iterator } from '../../../../../mol-data/iterator';
-import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
-import { getPolymerRanges } from '../polymer';
-
-/** Iterates over consecutive pairs of residues/coarse elements in polymers */
-export function PolymerBackboneIterator(structure: Structure, unit: Unit): Iterator<PolymerBackbonePair> {
-    switch (unit.kind) {
-        case Unit.Kind.Atomic: return new AtomicPolymerBackboneIterator(structure, unit);
-        case Unit.Kind.Spheres:
-        case Unit.Kind.Gaussians:
-            return new CoarsePolymerBackboneIterator(structure, unit);
-    }
-}
-
-interface PolymerBackbonePair {
-    centerA: StructureElement.Location
-    centerB: StructureElement.Location
-}
-
-function createPolymerBackbonePair (structure: Structure, unit: Unit) {
-    return {
-        centerA: StructureElement.Location.create(structure, unit),
-        centerB: StructureElement.Location.create(structure, unit),
-    };
-}
-
-const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextResidue, cycle }
-
-export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePair> {
-    private traceElementIndex: ArrayLike<ElementIndex>
-    private value: PolymerBackbonePair
-    private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
-    private residueIt: Segmentation.SegmentIterator<ResidueIndex>
-    private state: AtomicPolymerBackboneIteratorState = AtomicPolymerBackboneIteratorState.nextPolymer
-    private residueSegment: Segmentation.Segment<ResidueIndex>
-    hasNext: boolean = false;
-
-    move() {
-        if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
-            while (this.polymerIt.hasNext) {
-                this.residueIt.setSegment(this.polymerIt.move());
-                if (this.residueIt.hasNext) {
-                    this.residueSegment = this.residueIt.move();
-                    this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-                    this.state = AtomicPolymerBackboneIteratorState.nextResidue;
-                    break;
-                }
-            }
-        }
-
-        if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
-            this.residueSegment = this.residueIt.move();
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-            if (!this.residueIt.hasNext) {
-                if (this.unit.model.atomicRanges.cyclicPolymerMap.has(this.residueSegment.index)) {
-                    this.state = AtomicPolymerBackboneIteratorState.cycle;
-                } else {
-                    // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-                    this.state = AtomicPolymerBackboneIteratorState.nextPolymer;
-                }
-            }
-        } else if (this.state === AtomicPolymerBackboneIteratorState.cycle) {
-            const { cyclicPolymerMap } = this.unit.model.atomicRanges;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[cyclicPolymerMap.get(this.residueSegment.index)!];
-            // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-            this.state = AtomicPolymerBackboneIteratorState.nextPolymer;
-        }
-
-        this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext || this.state === AtomicPolymerBackboneIteratorState.cycle;
-        return this.value;
-    }
-
-    constructor(structure: Structure, private unit: Unit.Atomic) {
-        this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex>; // can assume it won't be -1 for polymer residues
-        this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
-        this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext;
-    }
-}
-
-const enum CoarsePolymerBackboneIteratorState { nextPolymer, nextElement }
-
-export class CoarsePolymerBackboneIterator implements Iterator<PolymerBackbonePair> {
-    private value: PolymerBackbonePair
-    private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
-    private polymerSegment: Segmentation.Segment<ResidueIndex>
-    private state: CoarsePolymerBackboneIteratorState = CoarsePolymerBackboneIteratorState.nextPolymer
-    private elementIndex: number
-    hasNext: boolean = false;
-
-    move() {
-        if (this.state === CoarsePolymerBackboneIteratorState.nextPolymer) {
-            if (this.polymerIt.hasNext) {
-                this.polymerSegment = this.polymerIt.move();
-                this.elementIndex = this.polymerSegment.start;
-                if (this.elementIndex + 1 < this.polymerSegment.end) {
-                    this.value.centerB.element = this.unit.elements[this.elementIndex];
-                    this.state = CoarsePolymerBackboneIteratorState.nextElement;
-                } else {
-                    this.state = CoarsePolymerBackboneIteratorState.nextPolymer;
-                }
-            }
-        }
-
-        if (this.state === CoarsePolymerBackboneIteratorState.nextElement) {
-            this.elementIndex += 1;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.unit.elements[this.elementIndex];
-            if (this.elementIndex + 1 >= this.polymerSegment.end) {
-                this.state = CoarsePolymerBackboneIteratorState.nextPolymer;
-            }
-        }
-
-        this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || this.polymerIt.hasNext;
-        return this.value;
-    }
-
-    constructor(structure: Structure, private unit: Unit.Spheres | Unit.Gaussians) {
-        this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.polymerIt.hasNext;
-    }
-}

src/mol-repr/structure/visual/util/polymer/backbone.ts

@@ -0,0 +1,126 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Segmentation } from '../../../../../mol-data/int';
+import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
+import { ElementIndex, ResidueIndex, Unit } from '../../../../../mol-model/structure';
+import { MoleculeType } from '../../../../../mol-model/structure/model/types';
+import { getPolymerRanges } from '../polymer';
+
+export type PolymerBackboneLinkCallback = (indexA: ElementIndex, indexB: ElementIndex, groupA: number, groupB: number, moleculeType: MoleculeType) => void
+
+export function eachPolymerBackboneLink(unit: Unit, callback: PolymerBackboneLinkCallback) {
+    switch (unit.kind) {
+        case Unit.Kind.Atomic: return eachAtomicPolymerBackboneLink(unit, callback);
+        case Unit.Kind.Spheres:
+        case Unit.Kind.Gaussians:
+            return eachCoarsePolymerBackboneLink(unit, callback);
+    }
+}
+
+function eachAtomicPolymerBackboneLink(unit: Unit.Atomic, callback: PolymerBackboneLinkCallback) {
+    const cyclicPolymerMap = unit.model.atomicRanges.cyclicPolymerMap;
+    const polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
+    const residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+    const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex>; // can assume it won't be -1 for polymer residues
+    const { moleculeType } = unit.model.atomicHierarchy.derived.residue;
+
+    let indexA = -1 as ResidueIndex;
+    let indexB = -1 as ResidueIndex;
+    let isFirst = true;
+    let firstGroup = -1;
+    let i = 0;
+    while (polymerIt.hasNext) {
+        isFirst = true;
+        firstGroup = i;
+        residueIt.setSegment(polymerIt.move());
+        while (residueIt.hasNext) {
+            if (isFirst) {
+                const index_1 = residueIt.move().index;
+                ++i;
+                if (!residueIt.hasNext)
+                    continue;
+                isFirst = false;
+                indexB = index_1;
+            }
+            const index = residueIt.move().index;
+            indexA = indexB;
+            indexB = index;
+            callback(traceElementIndex[indexA], traceElementIndex[indexB], i - 1, i, moleculeType[indexA]);
+            ++i;
+        }
+        if (cyclicPolymerMap.has(indexB)) {
+            indexA = indexB;
+            indexB = cyclicPolymerMap.get(indexA)!;
+            callback(traceElementIndex[indexA], traceElementIndex[indexB], i - 1, firstGroup, moleculeType[indexA]);
+        }
+    }
+}
+
+function eachCoarsePolymerBackboneLink(unit: Unit.Spheres | Unit.Gaussians, callback: PolymerBackboneLinkCallback) {
+    const polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
+    const { elements } = unit;
+
+    let isFirst = true;
+    let i = 0;
+    while (polymerIt.hasNext) {
+        isFirst = true;
+        const _a = polymerIt.move(), start = _a.start, end = _a.end;
+        for (let j = start, jl = end; j < jl; ++j) {
+            if (isFirst) {
+                ++j;
+                ++i;
+                if (j > jl)
+                    continue;
+                isFirst = false;
+            }
+            callback(elements[j - 1], elements[j], i - 1, i, 0 /* Unknown */);
+            ++i;
+        }
+    }
+}
+
+//
+
+export type PolymerBackboneElementCallback = (index: ElementIndex, group: number) => void
+
+export function eachPolymerBackboneElement(unit: Unit, callback: PolymerBackboneElementCallback) {
+    switch (unit.kind) {
+        case Unit.Kind.Atomic: return eachAtomicPolymerBackboneElement(unit, callback);
+        case Unit.Kind.Spheres:
+        case Unit.Kind.Gaussians:
+            return eachCoarsePolymerBackboneElement(unit, callback);
+    }
+}
+
+export function eachAtomicPolymerBackboneElement(unit: Unit.Atomic, callback: PolymerBackboneElementCallback) {
+    const polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
+    const residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+    const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex>; // can assume it won't be -1 for polymer residues
+
+    let i = 0;
+    while (polymerIt.hasNext) {
+        residueIt.setSegment(polymerIt.move());
+        while (residueIt.hasNext) {
+            const index = residueIt.move().index;
+            callback(traceElementIndex[index], i);
+            ++i;
+        }
+    }
+}
+
+function eachCoarsePolymerBackboneElement(unit: Unit.Spheres | Unit.Gaussians, callback: PolymerBackboneElementCallback) {
+    const polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
+    const { elements } = unit;
+
+    let i = 0;
+    while (polymerIt.hasNext) {
+        const _a = polymerIt.move(), start = _a.start, end = _a.end;
+        for (let j = start, jl = end; j < jl; ++j) {
+            callback(elements[j], i);
+            ++i;
+        }
+    }
+}

src/mol-repr/structure/visual/util/polymer/curve-segment.ts

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Vec3 } from '../../../../../mol-math/linear-algebra';
 import { NumberArray } from '../../../../../mol-util/type-helpers';
-import { lerp } from '../../../../../mol-math/interpolate';
+import { lerp, smoothstep } from '../../../../../mol-math/interpolate';
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const v3fromArray = Vec3.fromArray;
@@ -19,6 +19,8 @@ const v3copy = Vec3.copy;
 const v3cross = Vec3.cross;
 const v3orthogonalize = Vec3.orthogonalize;
 const v3matchDirection = Vec3.matchDirection;
+const v3scale = Vec3.scale;
+const v3add = Vec3.add;
 
 export interface CurveSegmentState {
     curvePoints: NumberArray,
@@ -92,6 +94,7 @@ const tangentVec = Vec3();
 const normalVec = Vec3();
 const binormalVec = Vec3();
 const prevNormal = Vec3();
+const nextNormal = Vec3();
 const firstTangentVec = Vec3();
 const lastTangentVec = Vec3();
 const firstNormalVec = Vec3();
@@ -116,8 +119,10 @@ export function interpolateNormals(state: CurveSegmentState, controls: CurveSegm
 
     v3copy(prevNormal, firstNormalVec);
 
+    const n1 = n - 1;
     for (let i = 0; i < n; ++i) {
-        const t = i === 0 ? 0 : 1 / (n - i);
+        const j = smoothstep(0, n1, i) * n1;
+        const t = i === 0 ? 0 : 1 / (n - j);
 
         v3fromArray(tangentVec, tangentVectors, i * 3);
 
@@ -129,6 +134,19 @@ export function interpolateNormals(state: CurveSegmentState, controls: CurveSegm
         v3normalize(binormalVec, v3cross(binormalVec, tangentVec, normalVec));
         v3toArray(binormalVec, binormalVectors, i * 3);
     }
+
+    for (let i = 1; i < n1; ++i) {
+        v3fromArray(prevNormal, normalVectors, (i - 1) * 3);
+        v3fromArray(normalVec, normalVectors, i * 3);
+        v3fromArray(nextNormal, normalVectors, (i + 1) * 3);
+
+        v3scale(normalVec, v3add(normalVec, prevNormal, v3add(normalVec, nextNormal, normalVec)), 1 / 3);
+        v3toArray(normalVec, normalVectors, i * 3);
+
+        v3fromArray(tangentVec, tangentVectors, i * 3);
+        v3normalize(binormalVec, v3cross(binormalVec, tangentVec, normalVec));
+        v3toArray(binormalVec, binormalVectors, i * 3);
+    }
 }
 
 export function interpolateSizes(state: CurveSegmentState, w0: number, w1: number, w2: number, h0: number, h1: number, h2: number, shift: number) {

src/mol-repr/structure/visual/util/polymer/trace-iterator.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,14 +14,31 @@ import { CoarseSphereConformation, CoarseGaussianConformation } from '../../../.
 import { getPolymerRanges } from '../polymer';
 import { AtomicConformation } from '../../../../../mol-model/structure/model/properties/atomic';
 import { SecondaryStructureProvider } from '../../../../../mol-model-props/computed/secondary-structure';
+import { HelixOrientationProvider } from '../../../../../mol-model-props/computed/helix-orientation';
+import { SecondaryStructure } from '../../../../../mol-model/structure/model/properties/seconday-structure';
+
+function isHelixSS(ss: SecondaryStructureType.Flag) {
+    return SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Helix);
+}
+
+function isSheetSS(ss: SecondaryStructureType.Flag) {
+    return SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta);
+}
+
+//
+
+type PolymerTraceIteratorOptions = {
+    ignoreSecondaryStructure?: boolean,
+    useHelixOrientation?: boolean
+}
 
 /**
  * Iterates over individual residues/coarse elements in polymers of a unit while
  * providing information about the neighbourhood in the underlying model for drawing splines
  */
-export function PolymerTraceIterator(unit: Unit, structure: Structure, ignoreSecondaryStructure = false): Iterator<PolymerTraceElement> {
+export function PolymerTraceIterator(unit: Unit, structure: Structure, options: PolymerTraceIteratorOptions = {}): Iterator<PolymerTraceElement> {
     switch (unit.kind) {
-        case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit, structure, ignoreSecondaryStructure);
+        case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit, structure, options);
         case Unit.Kind.Spheres:
         case Unit.Kind.Gaussians:
             return new CoarsePolymerTraceIterator(unit, structure);
@@ -91,6 +108,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
     private directionToElementIndex: ArrayLike<ElementIndex | -1>
     private moleculeType: ArrayLike<MoleculeType>
     private atomicConformation: AtomicConformation
+    private secondaryStructure: SecondaryStructure | undefined
+    private helixOrientationCenters: ArrayLike<number> | undefined
 
     private p0 = Vec3()
     private p1 = Vec3()
@@ -107,7 +126,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
 
     hasNext: boolean = false;
 
-    private pos(target: Vec3, index: number) {
+    private atomicPos(target: Vec3, index: ElementIndex | -1) {
         if (index !== -1) {
             target[0] = this.atomicConformation.x[index];
             target[1] = this.atomicConformation.y[index];
@@ -115,6 +134,15 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         }
     }
 
+    private pos(target: Vec3, residueIndex: ResidueIndex, ss: SecondaryStructureType.Flag) {
+        const index = this.traceElementIndex[residueIndex];
+        if (this.helixOrientationCenters && isHelixSS(ss)) {
+            Vec3.fromArray(target, this.helixOrientationCenters, residueIndex * 3);
+        } else {
+            this.atomicPos(target, index);
+        }
+    }
+
     private updateResidueSegmentRange(polymerSegment: Segmentation.Segment<number>) {
         const { index } = this.residueAtomSegments;
         this.residueSegmentMin = index[this.polymerRanges[polymerSegment.index * 2]];
@@ -140,23 +168,31 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         return residueIndex as ResidueIndex;
     }
 
-    private getSecStruc: (residueIndex: ResidueIndex) => SecondaryStructureType.Flag
+    private getSecStruc(residueIndex: ResidueIndex): SecondaryStructureType.Flag {
+        if (this.secondaryStructure) {
+            const { type, getIndex } = this.secondaryStructure;
+            const ss = type[getIndex(residueIndex)];
+            // normalize helix-type
+            return isHelixSS(ss) ? SecondaryStructureType.Flag.Helix : ss;
+        } else {
+            return SecStrucTypeNA;
+        }
+    }
 
-    private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
-        const ss =  this.getSecStruc(residueIndex);
-        if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
+    private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, ss: SecondaryStructureType.Flag) {
+        if (isSheetSS(ss) || (this.helixOrientationCenters && isHelixSS(ss))) {
             Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p3, Vec3.add(out, p2, p2))), 1 / 4);
         } else {
             Vec3.copy(out, p2);
         }
     }
 
-    private setFromToVector(out: Vec3, residueIndex: ResidueIndex) {
-        if (this.value.isCoarseBackbone) {
+    private setFromToVector(out: Vec3, residueIndex: ResidueIndex, ss: SecondaryStructureType.Flag) {
+        if (this.value.isCoarseBackbone || (this.helixOrientationCenters && isHelixSS(ss))) {
             Vec3.set(out, 1, 0, 0);
         } else {
-            this.pos(tmpVecA, this.directionFromElementIndex[residueIndex]);
-            this.pos(tmpVecB, this.directionToElementIndex[residueIndex]);
+            this.atomicPos(tmpVecA, this.directionFromElementIndex[residueIndex]);
+            this.atomicPos(tmpVecB, this.directionToElementIndex[residueIndex]);
             Vec3.sub(out, tmpVecB, tmpVecA);
         }
     }
@@ -203,7 +239,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
 
             this.prevCoarseBackbone = this.currCoarseBackbone;
             this.currCoarseBackbone = this.nextCoarseBackbone;
-            this.nextCoarseBackbone = residueIndex === residueIndexNext1 ? false : (this.directionFromElementIndex[residueIndexNext1] === -1 || this.directionToElementIndex[residueIndexNext1] === -1);
+            this.nextCoarseBackbone = this.directionFromElementIndex[residueIndexNext1] === -1 || this.directionToElementIndex[residueIndexNext1] === -1;
 
             value.secStrucType = this.currSecStrucType;
             value.secStrucFirst = this.prevSecStrucType !== this.currSecStrucType;
@@ -214,7 +250,6 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
             value.first = residueIndex === this.residueSegmentMin;
             value.last = residueIndex === this.residueSegmentMax;
             value.moleculeType = this.moleculeType[residueIndex];
-            value.isCoarseBackbone = this.directionFromElementIndex[residueIndex] === -1 || this.directionToElementIndex[residueIndex] === -1;
 
             value.initial = residueIndex === residueIndexPrev1;
             value.final = residueIndex === residueIndexNext1;
@@ -223,53 +258,132 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
             value.center.element = this.traceElementIndex[residueIndex];
             value.centerNext.element = this.traceElementIndex[residueIndexNext1];
 
-            this.pos(this.p0, this.traceElementIndex[residueIndexPrev3]);
-            this.pos(this.p1, this.traceElementIndex[residueIndexPrev2]);
-            this.pos(this.p2, this.traceElementIndex[residueIndexPrev1]);
-            this.pos(this.p3, this.traceElementIndex[residueIndex]);
-            this.pos(this.p4, this.traceElementIndex[residueIndexNext1]);
-            this.pos(this.p5, this.traceElementIndex[residueIndexNext2]);
-            this.pos(this.p6, this.traceElementIndex[residueIndexNext3]);
+            const ssPrev3 = this.getSecStruc(residueIndexPrev3);
+            const ssPrev2 = this.getSecStruc(residueIndexPrev2);
+            const ssPrev1 = this.getSecStruc(residueIndexPrev1);
+            const ss = this.getSecStruc(residueIndex);
+            const ssNext1 = this.getSecStruc(residueIndexNext1);
+            const ssNext2 = this.getSecStruc(residueIndexNext2);
+            const ssNext3 = this.getSecStruc(residueIndexNext3);
 
-            this.setFromToVector(this.d01, residueIndexPrev1);
-            this.setFromToVector(this.d12, residueIndex);
-            this.setFromToVector(this.d23, residueIndexNext1);
-            this.setFromToVector(this.d34, residueIndexNext2);
+            this.pos(this.p0, residueIndexPrev3, ssPrev3);
+            this.pos(this.p1, residueIndexPrev2, ssPrev2);
+            this.pos(this.p2, residueIndexPrev1, ssPrev1);
+            this.pos(this.p3, residueIndex, ss);
+            this.pos(this.p4, residueIndexNext1, ssNext1);
+            this.pos(this.p5, residueIndexNext2, ssNext2);
+            this.pos(this.p6, residueIndexNext3, ssNext3);
+
+            const isHelixPrev3 = isHelixSS(ssPrev3);
+            const isHelixPrev2 = isHelixSS(ssPrev2);
+            const isHelixPrev1 = isHelixSS(ssPrev1);
+            const isHelix = isHelixSS(ss);
+            const isHelixNext1 = isHelixSS(ssNext1);
+            const isHelixNext2 = isHelixSS(ssNext2);
+            const isHelixNext3 = isHelixSS(ssNext3);
+
+            // handle positions for tubular helices
+            if (this.helixOrientationCenters) {
+                if (isHelix !== isHelixPrev1) {
+                    if (isHelix) {
+                        Vec3.copy(this.p0, this.p3);
+                        Vec3.copy(this.p1, this.p3);
+                        Vec3.copy(this.p2, this.p3);
+                    } else if(isHelixPrev1) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p2, this.p3), 2);
+                        Vec3.add(this.p2, this.p3, tmpDir);
+                        Vec3.add(this.p1, this.p2, tmpDir);
+                        Vec3.add(this.p0, this.p1, tmpDir);
+                    }
+                } else if (isHelix !== isHelixPrev2) {
+                    if (isHelix) {
+                        Vec3.copy(this.p0, this.p2);
+                        Vec3.copy(this.p1, this.p2);
+                    } else if(isHelixPrev2) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p1, this.p2), 2);
+                        Vec3.add(this.p1, this.p2, tmpDir);
+                        Vec3.add(this.p0, this.p1, tmpDir);
+                    }
+                } else if (isHelix !== isHelixPrev3) {
+                    if (isHelix) {
+                        Vec3.copy(this.p0, this.p1);
+                    } else if(isHelixPrev3) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p0, this.p1), 2);
+                        Vec3.add(this.p0, this.p1, tmpDir);
+                    }
+                }
+
+                if (isHelix !== isHelixNext1) {
+                    if (isHelix) {
+                        Vec3.copy(this.p4, this.p3);
+                        Vec3.copy(this.p5, this.p3);
+                        Vec3.copy(this.p6, this.p3);
+                    } else if(isHelixNext1) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p4, this.p3), 2);
+                        Vec3.add(this.p4, this.p3, tmpDir);
+                        Vec3.add(this.p5, this.p4, tmpDir);
+                        Vec3.add(this.p6, this.p5, tmpDir);
+                    }
+                } else if (isHelix !== isHelixNext2) {
+                    if (isHelix) {
+                        Vec3.copy(this.p5, this.p4);
+                        Vec3.copy(this.p6, this.p4);
+                    } else if(isHelixNext2) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p5, this.p4), 2);
+                        Vec3.add(this.p5, this.p4, tmpDir);
+                        Vec3.add(this.p6, this.p5, tmpDir);
+                    }
+                } else if (isHelix !== isHelixNext3) {
+                    if (isHelix) {
+                        Vec3.copy(this.p6, this.p5);
+                    } else if(isHelixNext3) {
+                        Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p6, this.p5), 2);
+                        Vec3.add(this.p6, this.p5, tmpDir);
+                    }
+                }
+            }
+
+            this.setFromToVector(this.d01, residueIndexPrev1, ssPrev1);
+            this.setFromToVector(this.d12, residueIndex, ss);
+            this.setFromToVector(this.d23, residueIndexNext1, ssNext1);
+            this.setFromToVector(this.d34, residueIndexNext2, ssNext2);
+
+            const helixFlag = isHelix && this.helixOrientationCenters;
 
             // extend termini
-            const f = 0.5;
-            if (residueIndex === residueIndexPrev1) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p3, this.p4), f);
+            const f = 1.5;
+            if (residueIndex === residueIndexPrev1 || (ss !== ssPrev1 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p3, this.p4), f);
                 Vec3.add(this.p2, this.p3, tmpDir);
                 Vec3.add(this.p1, this.p2, tmpDir);
                 Vec3.add(this.p0, this.p1, tmpDir);
-            } else if (residueIndexPrev1 === residueIndexPrev2) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p2, this.p3), f);
+            } else if (residueIndexPrev1 === residueIndexPrev2 || (ss !== ssPrev2 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p2, this.p3), f);
                 Vec3.add(this.p1, this.p2, tmpDir);
                 Vec3.add(this.p0, this.p1, tmpDir);
-            } else if (residueIndexPrev2 === residueIndexPrev3) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p1, this.p2), f);
+            } else if (residueIndexPrev2 === residueIndexPrev3 || (ss !== ssPrev3 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p1, this.p2), f);
                 Vec3.add(this.p0, this.p1, tmpDir);
             }
-            if (residueIndex === residueIndexNext1) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p3, this.p2), f);
+            if (residueIndex === residueIndexNext1 || (ss !== ssNext1 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p3, this.p2), f);
                 Vec3.add(this.p4, this.p3, tmpDir);
                 Vec3.add(this.p5, this.p4, tmpDir);
                 Vec3.add(this.p6, this.p5, tmpDir);
-            } else if (residueIndexNext1 === residueIndexNext2) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p4, this.p3), f);
+            } else if (residueIndexNext1 === residueIndexNext2 || (ss !== ssNext2 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p4, this.p3), f);
                 Vec3.add(this.p5, this.p4, tmpDir);
                 Vec3.add(this.p6, this.p5, tmpDir);
-            } else if (residueIndexNext2 === residueIndexNext3) {
-                Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p5, this.p4), f);
+            } else if (residueIndexNext2 === residueIndexNext3 || (ss !== ssNext3 && helixFlag)) {
+                Vec3.setMagnitude(tmpDir, Vec3.sub(tmpDir, this.p5, this.p4), f);
                 Vec3.add(this.p6, this.p5, tmpDir);
             }
 
-            this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndexPrev2);
-            this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndexPrev1);
-            this.setControlPoint(value.p2, this.p2, this.p3, this.p4, residueIndex);
-            this.setControlPoint(value.p3, this.p3, this.p4, this.p5, residueIndexNext1);
-            this.setControlPoint(value.p4, this.p4, this.p5, this.p6, residueIndexNext2);
+            this.setControlPoint(value.p0, this.p0, this.p1, this.p2, ssPrev2);
+            this.setControlPoint(value.p1, this.p1, this.p2, this.p3, ssPrev1);
+            this.setControlPoint(value.p2, this.p2, this.p3, this.p4, ss);
+            this.setControlPoint(value.p3, this.p3, this.p4, this.p5, ssNext1);
+            this.setControlPoint(value.p4, this.p4, this.p5, this.p6, ssNext2);
 
             this.setDirection(value.d12, this.d01, this.d12, this.d23);
             this.setDirection(value.d23, this.d12, this.d23, this.d34);
@@ -284,7 +398,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         return this.value;
     }
 
-    constructor(private unit: Unit.Atomic, structure: Structure, ignoreSecondaryStructure = false) {
+    constructor(private unit: Unit.Atomic, structure: Structure, options: PolymerTraceIteratorOptions = {}) {
         this.atomicConformation = unit.model.atomicConformation;
         this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments;
         this.polymerRanges = unit.model.atomicRanges.polymerRanges;
@@ -298,12 +412,15 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         this.value = createPolymerTraceElement(structure, unit);
         this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext;
 
-        const secondaryStructure = !ignoreSecondaryStructure && SecondaryStructureProvider.get(structure).value?.get(unit.invariantId);
-        if (secondaryStructure) {
-            const { type, getIndex } = secondaryStructure;
-            this.getSecStruc = (residueIndex: ResidueIndex) => type[getIndex(residueIndex as ResidueIndex)];
-        } else {
-            this.getSecStruc = (residueIndex: ResidueIndex) => SecStrucTypeNA;
+        if (!options.ignoreSecondaryStructure) {
+            this.secondaryStructure = SecondaryStructureProvider.get(structure).value?.get(unit.invariantId);
+        }
+
+        if (options.useHelixOrientation) {
+            const helixOrientation = HelixOrientationProvider.get(unit.model).value;
+            if (!helixOrientation) throw new Error('missing helix-orientation');
+
+            this.helixOrientationCenters = helixOrientation.centers;
         }
     }
 }

src/mol-theme/color/secondary-structure.ts

@@ -123,6 +123,6 @@ export const SecondaryStructureColorThemeProvider: ColorTheme.Provider<Secondary
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? SecondaryStructureProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(SecondaryStructureProvider.descriptor, false)
+        detach: (data) => data.structure && SecondaryStructureProvider.ref(data.structure, false)
     }
 };

src/mol-util/array.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -105,6 +105,29 @@ export function arraySetRemove<T>(xs: T[], x: T) {
     return true;
 }
 
+/**
+ * Caution, O(n^2) complexity. Only use for small input sizes.
+ * For larger inputs consider using `SortedArray`.
+ */
+export function arrayAreIntersecting<T>(xs: T[], ys: T[]) {
+    for (let i = 0, il = xs.length; i < il; ++i) {
+        if (ys.includes(xs[i])) return true;
+    }
+    return false;
+}
+
+/**
+ * Caution, O(n^2) complexity. Only use for small input sizes.
+ * For larger inputs consider using `SortedArray`.
+ */
+export function arrayIntersectionSize<T>(xs: T[], ys: T[]) {
+    let count = 0;
+    for (let i = 0, il = xs.length; i < il; ++i) {
+        if (ys.includes(xs[i])) count += 1;
+    }
+    return count;
+}
+
 export function arrayEqual<T>(xs?: ArrayLike<T>, ys?: ArrayLike<T>) {
     if (!xs || xs.length === 0) return !ys || ys.length === 0;
     if (!ys) return false;

src/mol-util/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -32,4 +32,16 @@ namespace PixelData {
         }
         return pixelData;
     }
+
+    /** to undo pre-multiplied alpha */
+    export function divideByAlpha(pixelData: PixelData): PixelData {
+        const { array } = pixelData;
+        for (let i = 0, il = array.length; i < il; i += 4) {
+            const a = array[i + 3] / 255;
+            array[i] /= a;
+            array[i + 1] /= a;
+            array[i + 2] /= a;
+        }
+        return pixelData;
+    }
 }