molstar 4.2.0 → 4.3.0

package/lib/extensions/sb-ncbr/tunnels/actions.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateAction } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+export declare const TunnelDownloadServer: {
+    channelsdb: PD.Group<PD.Normalize<unknown>>;
+};
+export declare const DownloadTunnels: StateAction<PluginStateObject.Root, void, PD.Normalize<{
+    source: PD.NamedParams<PD.Normalize<{
+        url: any;
+    }>, "url"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "pdb">;
+}>>;

package/lib/extensions/sb-ncbr/tunnels/actions.js

@@ -0,0 +1,86 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { StateAction } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { TunnelsServerConfig } from './props';
+import { TunnelsFromRawData, SelectTunnel, TunnelShapeProvider } from './representation';
+export const TunnelDownloadServer = {
+    'channelsdb': PD.EmptyGroup({ label: 'ChannelsDB' })
+};
+export const DownloadTunnels = StateAction.build({
+    display: { name: 'Download Tunnels', description: 'Load a tunnels from the provided source and create theirs representations' },
+    from: PluginStateObject.Root,
+    params: (_, plugin) => {
+        return {
+            source: PD.MappedStatic('pdb', {
+                'pdb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' }),
+                }, { isFlat: true, label: 'PDB' }),
+                'alphafolddb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' })
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'url': PD.Group({
+                    url: PD.Url(''),
+                }, { isFlat: true, label: 'URL' })
+            })
+        };
+    }
+})(({ params, state }, plugin) => Task.create('Download Tunnels', async (ctx) => {
+    plugin.behaviors.layout.leftPanelTabName.next('data');
+    const src = params.source;
+    let downloadParams;
+    switch (src.name) {
+        case 'url':
+            downloadParams = [{ url: src.params.url }];
+            break;
+        case 'pdb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/pdb/${src.params.provider.id}` }]
+                : assertUnreachable(src);
+            break;
+        case 'alphafolddb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/alphafill/${src.params.provider.id.toLowerCase()}` }]
+                : assertUnreachable(src);
+            break;
+        default: assertUnreachable(src);
+    }
+    await state.transaction(async () => {
+        var _a;
+        const update = plugin.build();
+        const webgl = (_a = plugin.canvas3dContext) === null || _a === void 0 ? void 0 : _a.webgl;
+        for (const download of downloadParams) {
+            const response = await (await fetch(download.url.toString())).json();
+            const tunnels = [];
+            Object.entries(response.Channels).forEach(([key, values]) => {
+                if (values.length > 0) {
+                    values.forEach((item) => {
+                        tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+                    });
+                }
+            });
+            update
+                .toRoot()
+                .apply(TunnelsFromRawData, { data: tunnels })
+                .apply(SelectTunnel)
+                .apply(TunnelShapeProvider, {
+                webgl,
+            })
+                .apply(StateTransforms.Representation.ShapeRepresentation3D);
+            await update.commit();
+        }
+    }).runInContext(ctx);
+}));

package/lib/extensions/sb-ncbr/tunnels/algorithm.d.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Shape } from '../../../mol-model/shape';
+import { Color } from '../../../mol-util/color';
+import { Tunnel } from './data-model';
+export declare function createSpheresShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    showRadii: boolean;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;
+export declare function createTunnelShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    webgl: WebGLContext | undefined;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;

package/lib/extensions/sb-ncbr/tunnels/algorithm.js

@@ -0,0 +1,469 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { OrderedSet } from '../../../mol-data/int';
+import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
+import { Sphere3D, Box3D, GridLookup3D, fillGridDim } from '../../../mol-math/geometry';
+import { getBoundary } from '../../../mol-math/geometry/boundary';
+import { DefaultMolecularSurfaceCalculationProps } from '../../../mol-math/geometry/molecular-surface';
+import { lerp, spline } from '../../../mol-math/interpolate';
+import { Vec3, Tensor, Mat4 } from '../../../mol-math/linear-algebra';
+import { Shape } from '../../../mol-model/shape';
+import { ensureReasonableResolution } from '../../../mol-repr/structure/visual/util/common';
+import { Task } from '../../../mol-task';
+import { ValueCell } from '../../../mol-util';
+import { Color } from '../../../mol-util/color';
+export async function createSpheresShape(options) {
+    var _a;
+    const builder = MeshBuilder.createState(512, 512, (_a = options.prev) === null || _a === void 0 ? void 0 : _a.geometry);
+    const tunnel = options.tunnel;
+    const processedData = interpolateTunnel(tunnel.data, options.sampleRate);
+    if (options.showRadii) {
+        for (let i = 0; i < processedData.length; i += 1) {
+            const p = processedData[i];
+            builder.currentGroup = i;
+            const center = [p.X, p.Y, p.Z];
+            addSphere(builder, center, p.Radius, options.resolution);
+        }
+    }
+    else {
+        for (let i = 0; i < processedData.length; i += 1) {
+            const p = processedData[i];
+            builder.currentGroup = 0;
+            const center = [p.X, p.Y, p.Z];
+            addSphere(builder, center, p.Radius, options.resolution);
+        }
+    }
+    const mesh = MeshBuilder.getMesh(builder);
+    const name = tunnel.props.highlight_label ?
+        tunnel.props.highlight_label :
+        tunnel.props.type && tunnel.props.id ?
+            `${tunnel.props.type} ${tunnel.props.id}` :
+            'Tunnel';
+    if (options.showRadii)
+        return Shape.create(name, tunnel.props, mesh, () => Color(options.color), () => 1, (i) => `[${processedData[i].X.toFixed(3)}, ${processedData[i].Y.toFixed(3)}, ${processedData[i].Z.toFixed(3)}] - radius: ${processedData[i].Radius.toFixed(3)}`);
+    return Shape.create(name, tunnel.props, mesh, () => Color(options.color), () => 1, () => name);
+}
+export async function createTunnelShape(options) {
+    var _a;
+    const tunnel = options.tunnel;
+    const mesh = await createTunnelMesh(tunnel.data, {
+        detail: options.resolution,
+        sampleRate: options.sampleRate,
+        webgl: options.webgl,
+        prev: (_a = options.prev) === null || _a === void 0 ? void 0 : _a.geometry
+    });
+    const name = tunnel.props.highlight_label ?
+        tunnel.props.highlight_label :
+        tunnel.props.type && tunnel.props.id ?
+            `${tunnel.props.type} ${tunnel.props.id}` :
+            'Tunnel';
+    return Shape.create(name, tunnel.props, mesh, () => Color(options.color), () => 1, () => name);
+}
+function profileToVec3(profile) {
+    return Vec3.create(profile.X, profile.Y, profile.Z);
+}
+// Centripetal Catmull–Rom spline interpolation
+function interpolateTunnel(profile, sampleRate) {
+    const interpolatedProfiles = [];
+    if (profile.length < 4)
+        return profile; // Ensuring there are enough points to interpolate
+    interpolatedProfiles.push(profile[0]);
+    let lastPoint = profileToVec3(profile[0]);
+    let currentDistance = 0;
+    const pointInterval = 1 / sampleRate;
+    for (let i = 1; i < profile.length - 2; i++) {
+        const P0 = profile[i - 1];
+        const P1 = profile[i];
+        const P2 = profile[i + 1];
+        const P3 = profile[i + 2];
+        for (let t = 0; t <= 1; t += 0.05) {
+            const interpolatedX = spline(P0.X, P1.X, P2.X, P3.X, t, 0.5);
+            const interpolatedY = spline(P0.Y, P1.Y, P2.Y, P3.Y, t, 0.5);
+            const interpolatedZ = spline(P0.Z, P1.Z, P2.Z, P3.Z, t, 0.5);
+            const interpolatedPoint = Vec3.create(interpolatedX, interpolatedY, interpolatedZ);
+            const distanceToAdd = Vec3.distance(lastPoint, interpolatedPoint);
+            currentDistance += distanceToAdd;
+            if (currentDistance >= pointInterval) {
+                interpolatedProfiles.push({
+                    X: interpolatedX,
+                    Y: interpolatedY,
+                    Z: interpolatedZ,
+                    Radius: spline(P0.Radius, P1.Radius, P2.Radius, P3.Radius, t, 0.5),
+                    Charge: lerp(P1.Charge, P2.Charge, t),
+                    FreeRadius: spline(P0.FreeRadius, P1.FreeRadius, P2.FreeRadius, P3.FreeRadius, t, 0.5),
+                    T: lerp(P1.T, P2.T, t),
+                    Distance: lerp(P1.Distance, P2.Distance, t)
+                });
+                lastPoint = interpolatedPoint;
+                currentDistance -= pointInterval;
+            }
+        }
+    }
+    // Ensuring the last profile point is included
+    interpolatedProfiles.push(profile[profile.length - 1]);
+    return interpolatedProfiles;
+}
+function convertToPositionData(profile, probeRadius) {
+    let position = {};
+    const x = [];
+    const y = [];
+    const z = [];
+    const indices = [];
+    const radius = [];
+    let maxRadius = Number.MIN_SAFE_INTEGER;
+    let sphereCounter = 0;
+    for (const sphere of profile) {
+        x.push(sphere.X);
+        y.push(sphere.Y);
+        z.push(sphere.Z);
+        indices.push(sphereCounter);
+        radius.push(sphere.Radius + probeRadius);
+        if (sphere.Radius > maxRadius)
+            maxRadius = sphere.Radius;
+        sphereCounter++;
+    }
+    position = { x, y, z, indices: OrderedSet.ofSortedArray(indices), radius, id: indices };
+    return position;
+}
+async function createTunnelMesh(data, options) {
+    const props = {
+        ...DefaultMolecularSurfaceCalculationProps,
+    };
+    const preprocessedData = interpolateTunnel(data, options.sampleRate);
+    const positions = convertToPositionData(preprocessedData, props.probeRadius);
+    const bounds = getBoundary(positions);
+    let maxR = 0;
+    for (let i = 0; i < positions.radius.length; ++i) {
+        const r = positions.radius[i];
+        if (maxR < r)
+            maxR = r;
+    }
+    const p = ensureReasonableResolution(bounds.box, props);
+    const { field, transform, /* resolution,*/ maxRadius, /* idField */ } = await computeTunnelSurface({
+        positions,
+        boundary: bounds,
+        maxRadius: maxR,
+        box: bounds.box,
+        props: p
+    }).run();
+    const params = {
+        isoLevel: p.probeRadius,
+        scalarField: field,
+    };
+    const surface = await computeMarchingCubesMesh(params, options.prev).run();
+    const iterations = Math.ceil(2 / 1);
+    Mesh.smoothEdges(surface, { iterations, maxNewEdgeLength: Math.sqrt(2) });
+    Mesh.transform(surface, transform);
+    if (options.webgl && !options.webgl.isWebGL2) {
+        Mesh.uniformTriangleGroup(surface);
+        ValueCell.updateIfChanged(surface.varyingGroup, false);
+    }
+    else {
+        ValueCell.updateIfChanged(surface.varyingGroup, true);
+    }
+    const sphere = Sphere3D.expand(Sphere3D(), bounds.sphere, maxRadius);
+    surface.setBoundingSphere(sphere);
+    surface.meta.resolution = options.detail;
+    return surface;
+}
+function normalToLine(out, p) {
+    out[0] = out[1] = out[2] = 1.0;
+    if (p[0] !== 0) {
+        out[0] = (p[1] + p[2]) / -p[0];
+    }
+    else if (p[1] !== 0) {
+        out[1] = (p[0] + p[2]) / -p[1];
+    }
+    else if (p[2] !== 0) {
+        out[2] = (p[0] + p[1]) / -p[2];
+    }
+    return out;
+}
+function computeTunnelSurface(surfaceData) {
+    return Task.create('Tunnel Surface', async (ctx) => {
+        return await calcTunnelSurface(ctx, surfaceData);
+    });
+}
+function getAngleTables(probePositions) {
+    let theta = 0.0;
+    const step = 2 * Math.PI / probePositions;
+    const cosTable = new Float32Array(probePositions);
+    const sinTable = new Float32Array(probePositions);
+    for (let i = 0; i < probePositions; i++) {
+        cosTable[i] = Math.cos(theta);
+        sinTable[i] = Math.sin(theta);
+        theta += step;
+    }
+    return { cosTable, sinTable };
+}
+// From '../../../\mol-math\geometry\molecular-surface.ts'
+async function calcTunnelSurface(ctx, surfaceData) {
+    // Field generation method adapted from AstexViewer (Mike Hartshorn) by Fred Ludlow.
+    // Other parts based heavily on NGL (Alexander Rose) EDT Surface class
+    let lastClip = -1;
+    /**
+     * Is the point at x,y,z obscured by any of the atoms specifeid by indices in neighbours.
+     * Ignore indices a and b (these are the relevant atoms in projectPoints/Torii)
+     *
+     * Cache the last clipped atom (as very often the same one in subsequent calls)
+     *
+     * `a` and `b` must be resolved indices
+     */
+    function obscured(x, y, z, a, b) {
+        if (lastClip !== -1) {
+            const ai = lastClip;
+            if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
+                return ai;
+            }
+            else {
+                lastClip = -1;
+            }
+        }
+        for (let j = 0, jl = neighbours.count; j < jl; ++j) {
+            const ai = OrderedSet.getAt(indices, neighbours.indices[j]);
+            if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
+                lastClip = ai;
+                return ai;
+            }
+        }
+        return -1;
+    }
+    /**
+     * `ai` must be a resolved index
+     */
+    function singleAtomObscures(ai, x, y, z) {
+        const r = radius[ai];
+        const dx = px[ai] - x;
+        const dy = py[ai] - y;
+        const dz = pz[ai] - z;
+        const dSq = dx * dx + dy * dy + dz * dz;
+        return dSq < (r * r);
+    }
+    /**
+     * For each atom:
+     *     Iterate over a subsection of the grid, for each point:
+     *         If current value < 0.0, unvisited, set positive
+     *
+     *         In any case: Project this point onto surface of the atomic sphere
+     *         If this projected point is not obscured by any other atom
+     *             Calculate delta distance and set grid value to minimum of
+     *             itself and delta
+     */
+    function projectPointsRange(begI, endI) {
+        for (let i = begI; i < endI; ++i) {
+            const j = OrderedSet.getAt(indices, i);
+            const vx = px[j], vy = py[j], vz = pz[j];
+            const rad = radius[j];
+            const rSq = rad * rad;
+            lookup3d.find(vx, vy, vz, rad);
+            // Number of grid points, round this up...
+            const ng = Math.ceil(rad * scaleFactor);
+            // Center of the atom, mapped to grid points (take floor)
+            const iax = Math.floor(scaleFactor * (vx - minX));
+            const iay = Math.floor(scaleFactor * (vy - minY));
+            const iaz = Math.floor(scaleFactor * (vz - minZ));
+            // Extents of grid to consider for this atom
+            const begX = Math.max(0, iax - ng);
+            const begY = Math.max(0, iay - ng);
+            const begZ = Math.max(0, iaz - ng);
+            // Add two to these points:
+            // - iax are floor'd values so this ensures coverage
+            // - these are loop limits (exclusive)
+            const endX = Math.min(dimX, iax + ng + 2);
+            const endY = Math.min(dimY, iay + ng + 2);
+            const endZ = Math.min(dimZ, iaz + ng + 2);
+            for (let xi = begX; xi < endX; ++xi) {
+                const dx = gridx[xi] - vx;
+                const xIdx = xi * iuv;
+                for (let yi = begY; yi < endY; ++yi) {
+                    const dy = gridy[yi] - vy;
+                    const dxySq = dx * dx + dy * dy;
+                    const xyIdx = yi * iu + xIdx;
+                    for (let zi = begZ; zi < endZ; ++zi) {
+                        const dz = gridz[zi] - vz;
+                        const dSq = dxySq + dz * dz;
+                        if (dSq < rSq) {
+                            const idx = zi + xyIdx;
+                            // if unvisited, make positive
+                            if (data[idx] < 0.0)
+                                data[idx] *= -1;
+                            // Project on to the surface of the sphere
+                            // sp is the projected point ( dx, dy, dz ) * ( ra / d )
+                            const d = Math.sqrt(dSq);
+                            const ap = rad / d;
+                            const spx = dx * ap + vx;
+                            const spy = dy * ap + vy;
+                            const spz = dz * ap + vz;
+                            if (obscured(spx, spy, spz, j, -1) === -1) {
+                                const dd = rad - d;
+                                if (dd < data[idx]) {
+                                    data[idx] = dd;
+                                    idData[idx] = id[i];
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    async function projectPoints() {
+        for (let i = 0; i < n; i += updateChunk) {
+            projectPointsRange(i, Math.min(i + updateChunk, n));
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'projecting points', current: i, max: n });
+            }
+        }
+    }
+    // Vectors for Torus Projection
+    const atob = Vec3();
+    const mid = Vec3();
+    const n1 = Vec3();
+    const n2 = Vec3();
+    /**
+     * `a` and `b` must be resolved indices
+     */
+    function projectTorus(a, b) {
+        const rA = radius[a];
+        const rB = radius[b];
+        const dx = atob[0] = px[b] - px[a];
+        const dy = atob[1] = py[b] - py[a];
+        const dz = atob[2] = pz[b] - pz[a];
+        const dSq = dx * dx + dy * dy + dz * dz;
+        // This check now redundant as already done in AVHash.withinRadii
+        // if (dSq > ((rA + rB) * (rA + rB))) { return }
+        const d = Math.sqrt(dSq);
+        // Find angle between a->b vector and the circle
+        // of their intersection by cosine rule
+        const cosA = (rA * rA + d * d - rB * rB) / (2.0 * rA * d);
+        // distance along a->b at intersection
+        const dmp = rA * cosA;
+        Vec3.normalize(atob, atob);
+        // Create normal to line
+        normalToLine(n1, atob);
+        Vec3.normalize(n1, n1);
+        // Cross together for second normal vector
+        Vec3.cross(n2, atob, n1);
+        Vec3.normalize(n2, n2);
+        // r is radius of circle of intersection
+        const rInt = Math.sqrt(rA * rA - dmp * dmp);
+        Vec3.scale(n1, n1, rInt);
+        Vec3.scale(n2, n2, rInt);
+        Vec3.scale(atob, atob, dmp);
+        mid[0] = atob[0] + px[a];
+        mid[1] = atob[1] + py[a];
+        mid[2] = atob[2] + pz[a];
+        lastClip = -1;
+        for (let i = 0; i < probePositions; ++i) {
+            const cost = cosTable[i];
+            const sint = sinTable[i];
+            const px = mid[0] + cost * n1[0] + sint * n2[0];
+            const py = mid[1] + cost * n1[1] + sint * n2[1];
+            const pz = mid[2] + cost * n1[2] + sint * n2[2];
+            if (obscured(px, py, pz, a, b) === -1) {
+                const iax = Math.floor(scaleFactor * (px - minX));
+                const iay = Math.floor(scaleFactor * (py - minY));
+                const iaz = Math.floor(scaleFactor * (pz - minZ));
+                const begX = Math.max(0, iax - ngTorus);
+                const begY = Math.max(0, iay - ngTorus);
+                const begZ = Math.max(0, iaz - ngTorus);
+                const endX = Math.min(dimX, iax + ngTorus + 2);
+                const endY = Math.min(dimY, iay + ngTorus + 2);
+                const endZ = Math.min(dimZ, iaz + ngTorus + 2);
+                for (let xi = begX; xi < endX; ++xi) {
+                    const dx = px - gridx[xi];
+                    const xIdx = xi * iuv;
+                    for (let yi = begY; yi < endY; ++yi) {
+                        const dy = py - gridy[yi];
+                        const dxySq = dx * dx + dy * dy;
+                        const xyIdx = yi * iu + xIdx;
+                        for (let zi = begZ; zi < endZ; ++zi) {
+                            const dz = pz - gridz[zi];
+                            const dSq = dxySq + dz * dz;
+                            const idx = zi + xyIdx;
+                            const current = data[idx];
+                            if (current > 0.0 && dSq < (current * current)) {
+                                data[idx] = Math.sqrt(dSq);
+                                // Is this grid point closer to a or b?
+                                // Take dot product of atob and gridpoint->p (dx, dy, dz)
+                                const dp = dx * atob[0] + dy * atob[1] + dz * atob[2];
+                                idData[idx] = id[OrderedSet.indexOf(indices, dp < 0.0 ? b : a)];
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    function projectToriiRange(begI, endI) {
+        for (let i = begI; i < endI; ++i) {
+            const k = OrderedSet.getAt(indices, i);
+            lookup3d.find(px[k], py[k], pz[k], radius[k]);
+            for (let j = 0, jl = neighbours.count; j < jl; ++j) {
+                const l = OrderedSet.getAt(indices, neighbours.indices[j]);
+                if (k < l)
+                    projectTorus(k, l);
+            }
+        }
+    }
+    async function projectTorii() {
+        for (let i = 0; i < n; i += updateChunk) {
+            projectToriiRange(i, Math.min(i + updateChunk, n));
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'projecting torii', current: i, max: n });
+            }
+        }
+    }
+    // console.time('MolecularSurface')
+    // console.time('MolecularSurface createState')
+    const { resolution, probeRadius, probePositions } = surfaceData.props;
+    const scaleFactor = 1 / resolution;
+    const ngTorus = Math.max(5, 2 + Math.floor(probeRadius * scaleFactor));
+    const cellSize = Vec3.create(surfaceData.maxRadius, surfaceData.maxRadius, surfaceData.maxRadius);
+    Vec3.scale(cellSize, cellSize, 2);
+    const lookup3d = GridLookup3D(surfaceData.positions, surfaceData.boundary, cellSize);
+    const neighbours = lookup3d.result;
+    if (surfaceData.box === null)
+        surfaceData.box = lookup3d.boundary.box;
+    const { indices, x: px, y: py, z: pz, id, radius } = surfaceData.positions;
+    const n = OrderedSet.size(indices);
+    const pad = surfaceData.maxRadius + resolution;
+    const expandedBox = Box3D.expand(Box3D(), surfaceData.box, Vec3.create(pad, pad, pad));
+    const [minX, minY, minZ] = expandedBox.min;
+    const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor);
+    const dim = Box3D.size(Vec3(), scaledBox);
+    Vec3.ceil(dim, dim);
+    const [dimX, dimY, dimZ] = dim;
+    const iu = dimZ, iv = dimY, iuv = iu * iv;
+    const { cosTable, sinTable } = getAngleTables(probePositions);
+    const space = Tensor.Space(dim, [0, 1, 2], Float32Array);
+    const data = space.create();
+    const idData = space.create();
+    data.fill(-1001.0);
+    idData.fill(-1);
+    const gridx = fillGridDim(dimX, minX, resolution);
+    const gridy = fillGridDim(dimY, minY, resolution);
+    const gridz = fillGridDim(dimZ, minZ, resolution);
+    const updateChunk = Math.ceil(100000 / ((Math.pow(Math.pow(surfaceData.maxRadius, 3), 3) * scaleFactor)));
+    // console.timeEnd('MolecularSurface createState')
+    // console.time('MolecularSurface projectPoints')
+    await projectPoints();
+    // console.timeEnd('MolecularSurface projectPoints')
+    // console.time('MolecularSurface projectTorii')
+    await projectTorii();
+    // console.timeEnd('MolecularSurface projectTorii')
+    // console.timeEnd('MolecularSurface')
+    const field = Tensor.create(space, data);
+    const idField = Tensor.create(space, idData);
+    const transform = Mat4.identity();
+    Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
+    Mat4.setTranslation(transform, expandedBox.min);
+    // console.log({ field, idField, transform, updateChunk })
+    return { field, idField, transform, resolution, maxRadius: surfaceData.maxRadius };
+}

package/lib/extensions/sb-ncbr/tunnels/behavior.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginBehavior } from '../../../mol-plugin/behavior';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { Structure } from '../../../mol-model/structure';
+export declare const SbNcbrTunnels: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+    autoAttach: boolean;
+}>;
+export declare function isApplicable(structure?: Structure): boolean;
+export declare const TunnelsPreset: StructureRepresentationPresetProvider<{
+    serverType: "pdb";
+    serverUrl: string;
+    ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
+    ignoreLight: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: PD.Normalize<{
+        globalName: any;
+        globalColorParams: any;
+        carbonColor: any;
+        symmetryColor: any;
+        symmetryColorParams: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+    } | {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    } | undefined;
+    representations: {};
+}>;