2.0.0-dev.11

Surrounding Ligands query

README.md

@@ -5,15 +5,12 @@
 
 # Mol*
 
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as a basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open-source and available to anyone who wants to use it for developing visualization tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
 
-This particular project is the implementation of this technology (still under development).
 
-*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*
+## Project Structure Overview
 
-## Project Overview
-
-The core of Mol* currently consists of these modules (see under `src/`):
+The core of Mol* consists of these modules (see under `src/`):
 
 - `mol-task` Computation abstraction with progress tracking and cancellation support.
 - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
@@ -29,7 +26,6 @@ The core of Mol* currently consists of these modules (see under `src/`):
 - `mol-gl` A wrapper around WebGL.
 - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
 - `mol-state` State representation tree with state saving and automatic updates.
-- `mol-app` Components for building UIs.
 - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
 - `mol-plugin-state` State transformations, builders, and managers.
 - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
@@ -41,7 +37,7 @@ Moreover, the project contains the implementation of `servers`, including
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
 - `servers/plugin-state` A basic server to store Mol* Plugin states.
 
-The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -169,9 +165,6 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.
 
-## Roadmap
-Continually develop this prototype project. As individual modules become stable, make them into standalone libraries.
-
 ## Funding
 Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE

package-lock.json

@@ -1,11 +1,11 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.10",
+  "version": "2.0.0-dev.11",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "version": "2.0.0-dev.10",
+      "version": "2.0.0-dev.11",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^1.0.38",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.10",
+  "version": "2.0.0-dev.11",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/mol-canvas3d/canvas3d.ts

@@ -331,11 +331,13 @@ namespace Canvas3D {
                 changed = repr.mark(loci, action);
             } else {
                 changed = helper.handle.mark(loci, action);
+                changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
                 helper.handle.scene.update(void 0, true);
+                helper.camera.scene.update(void 0, true);
                 const prevPickDirty = pickHelper.dirty;
                 draw(true);
                 pickHelper.dirty = prevPickDirty; // marking does not change picking buffers

src/mol-canvas3d/helper/camera-helper.ts

@@ -1,10 +1,11 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import produce from 'immer';
+import { Interval } from '../../mol-data/int/interval';
 import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
 import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
@@ -17,7 +18,9 @@ import { Sphere3D } from '../../mol-math/geometry';
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
 import { Shape } from '../../mol-model/shape';
+import { Visual } from '../../mol-repr/visual';
 import { ColorNames } from '../../mol-util/color/names';
+import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera, ICamera } from '../camera';
 import { Viewport } from '../camera/util';
@@ -95,6 +98,26 @@ export class CameraHelper {
         return CameraAxesLoci(this, groupId, instanceId);
     }
 
+    private eachGroup = (loci: Loci, apply: (interval: Interval) => boolean): boolean => {
+        if (!this.renderObject) return false;
+        if (!isCameraAxesLoci(loci)) return false;
+        let changed = false;
+        const groupCount = this.renderObject.values.uGroupCount.ref.value;
+        const { elements } = loci;
+        for (const { groupId, instanceId } of elements) {
+            const idx = instanceId * groupCount + groupId;
+            if (apply(Interval.ofSingleton(idx))) changed = true;
+        }
+        return changed;
+    }
+
+    mark(loci: Loci, action: MarkerAction) {
+        if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
+        if (!isCameraAxesLoci(loci)) return false;
+        if (loci.data !== this) return false;
+        return Visual.mark(this.renderObject, loci, action, this.eachGroup);
+    }
+
     update(camera: ICamera) {
         if (!this.renderObject) return;
 

src/mol-canvas3d/util.ts

@@ -12,13 +12,13 @@ export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height:
 }
 
 /** Resize canvas to container element taking `devicePixelRatio` into account */
-export function resizeCanvas (canvas: HTMLCanvasElement, container: Element, scale = 1) {
+export function resizeCanvas (canvas: HTMLCanvasElement, container: HTMLElement, scale = 1) {
     let width = window.innerWidth;
     let height = window.innerHeight;
     if (container !== document.body) {
-        let bounds = container.getBoundingClientRect();
-        width = bounds.right - bounds.left;
-        height = bounds.bottom - bounds.top;
+        // fixes issue #molstar/molstar#147, offsetWidth/offsetHeight is correct size when css transform:scale is used
+        width = container.offsetWidth;
+        height = container.offsetHeight;
     }
     setCanvasSize(canvas, width, height, scale);
 }

src/mol-model-props/common/custom-element-property.ts

@@ -61,7 +61,7 @@ namespace CustomElementProperty {
             type: builder.type || 'dynamic',
             defaultParams: {},
             getParams: (data: Model) => ({}),
-            isApplicable: (data: Model) => !!builder.isApplicable?.(data),
+            isApplicable: (data: Model) => !builder.isApplicable || !!builder.isApplicable(data),
             obtain: async (ctx: CustomProperty.Context, data: Model) => {
                 return await builder.getData(data, ctx);
             }

src/mol-model/structure/model/properties/utils/residue-set.ts

@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureElement } from '../../../structure/element';
+import { StructureProperties } from '../../../structure/properties';
+
+export interface ResidueSetEntry {
+    label_asym_id: string,
+    label_comp_id: string,
+    label_seq_id: number,
+    label_alt_id: string,
+    ins_code: string,
+    // 1_555 by default
+    operator_name?: string
+}
+
+export class ResidueSet {
+    private index = new Map<string, Map<number, ResidueSetEntry[]>>();
+    private checkOperator: boolean = false;
+
+    add(entry: ResidueSetEntry) {
+        let root = this.index.get(entry.label_asym_id);
+        if (!root) {
+            root = new Map();
+            this.index.set(entry.label_asym_id, root);
+        }
+
+        let entries = root.get(entry.label_seq_id);
+        if (!entries) {
+            entries = [];
+            root.set(entry.label_seq_id, entries);
+        }
+
+        const exists = this._find(entry, entries);
+        if (!exists) {
+            entries.push(entry);
+            return true;
+        }
+
+        return false;
+    }
+
+    hasLabelAsymId(asym_id: string) {
+        return this.index.has(asym_id);
+    }
+
+    has(loc: StructureElement.Location) {
+        const asym_id = _asym_id(loc);
+        if (!this.index.has(asym_id)) return;
+        const root = this.index.get(asym_id)!;
+        const seq_id = _seq_id(loc);
+        if (!root.has(seq_id)) return;
+        const entries = root.get(seq_id)!;
+
+        const comp_id = _comp_id(loc);
+        const alt_id = _alt_id(loc);
+        const ins_code = _ins_code(loc);
+        const op_name = _op_name(loc) ?? '1_555';
+
+        for (const e of entries) {
+            if (e.label_comp_id !== comp_id || e.label_alt_id !== alt_id || e.ins_code !== ins_code) continue;
+            if (this.checkOperator && (e.operator_name ?? '1_555') !== op_name) continue;
+
+            return e;
+        }
+    }
+
+    static getLabel(entry: ResidueSetEntry, checkOperator = false) {
+        return `${entry.label_asym_id} ${entry.label_comp_id} ${entry.label_seq_id}:${entry.ins_code}:${entry.label_alt_id}${checkOperator ? ' ' + (entry.operator_name ?? '1_555') : ''}`;
+    }
+
+    static getEntryFromLocation(loc: StructureElement.Location): ResidueSetEntry {
+        return {
+            label_asym_id: _asym_id(loc),
+            label_comp_id: _comp_id(loc),
+            label_seq_id: _seq_id(loc),
+            label_alt_id: _alt_id(loc),
+            ins_code: _ins_code(loc),
+            operator_name: _op_name(loc) ?? '1_555'
+        };
+    }
+
+    private _find(entry: ResidueSetEntry, xs: ResidueSetEntry[]) {
+        for (const e of xs) {
+            if (e.label_comp_id !== entry.label_comp_id || e.label_alt_id !== entry.label_alt_id || e.ins_code !== entry.ins_code) continue;
+            if (this.checkOperator && (e.operator_name ?? '1_555') !== (entry.operator_name ?? '1_555')) continue;
+
+            return true;
+        }
+
+        return false;
+    }
+
+    constructor(options?: { checkOperator?: boolean }) {
+        this.checkOperator = options?.checkOperator ?? false;
+    }
+}
+
+const _asym_id = StructureProperties.chain.label_asym_id;
+const _seq_id = StructureProperties.residue.label_seq_id;
+const _comp_id = StructureProperties.atom.label_comp_id;
+const _alt_id = StructureProperties.atom.label_alt_id;
+const _ins_code = StructureProperties.residue.pdbx_PDB_ins_code;
+const _op_name = StructureProperties.unit.operator_name;

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

@@ -11,10 +11,14 @@ import { StructureSelection } from '../selection';
 import { UniqueStructuresBuilder } from '../utils/builders';
 import { StructureUniqueSubsetBuilder } from '../../structure/util/unique-subset-builder';
 import { QueryContext, QueryFn } from '../context';
-import { structureIntersect, structureSubtract } from '../utils/structure-set';
+import { structureIntersect, structureSubtract, structureUnion } from '../utils/structure-set';
 import { UniqueArray } from '../../../../mol-data/generic';
 import { StructureSubsetBuilder } from '../../structure/util/subset-builder';
 import { StructureElement } from '../../structure/element';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { ResidueSet, ResidueSetEntry } from '../../model/properties/utils/residue-set';
+import { StructureProperties } from '../../structure/properties';
+import { arraySetAdd } from '../../../../mol-util/array';
 
 function getWholeResidues(ctx: QueryContext, source: Structure, structure: Structure) {
     const builder = source.subsetBuilder(true);
@@ -435,4 +439,252 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
     return builder.getStructure();
 }
 
+export interface SurroundingLigandsParams {
+    query: StructureQuery,
+    radius: number,
+    includeWater: boolean
+}
+
+/**
+ * Includes expanded surrounding ligands based on radius from the source, struct_conn entries & pdbx_molecule entries.
+ */
+export function surroundingLigands({ query, radius, includeWater }: SurroundingLigandsParams): StructureQuery {
+    return function query_surroundingLigands(ctx) {
+
+        const inner = StructureSelection.unionStructure(query(ctx));
+        const surroundings = getWholeResidues(ctx, ctx.inputStructure, getIncludeSurroundings(ctx, ctx.inputStructure, inner, { radius }));
+
+        const prd = getPrdAsymIdx(ctx.inputStructure);
+        const graph = getStructConnInfo(ctx.inputStructure);
+
+        const l = StructureElement.Location.create(surroundings);
+
+        const includedPrdChains = new Map<string, string[]>();
+
+        const componentResidues = new ResidueSet({ checkOperator: true });
+
+        for (const unit of surroundings.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            l.unit = unit;
+
+            const { elements } = unit;
+            const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+            const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+            while (chainsIt.hasNext) {
+                const chainSegment = chainsIt.move();
+                l.element = elements[chainSegment.start];
+
+                const asym_id = StructureProperties.chain.label_asym_id(l);
+                const op_name = StructureProperties.unit.operator_name(l);
+
+                // check for PRD molecules
+                if (prd.has(asym_id)) {
+                    if (includedPrdChains.has(asym_id)) {
+                        arraySetAdd(includedPrdChains.get(asym_id)!, op_name);
+                    } else {
+                        includedPrdChains.set(asym_id, [op_name]);
+                    }
+                    continue;
+                }
+
+                const entityType = StructureProperties.entity.type(l);
+
+                // test entity and chain
+                if (entityType === 'water' || entityType === 'polymer') continue;
+
+                residuesIt.setSegment(chainSegment);
+                while (residuesIt.hasNext) {
+                    const residueSegment = residuesIt.move();
+                    l.element = elements[residueSegment.start];
+                    graph.addComponent(ResidueSet.getEntryFromLocation(l), componentResidues);
+                }
+            }
+
+            ctx.throwIfTimedOut();
+        }
+
+        // assemble the core structure
+
+        const builder = ctx.inputStructure.subsetBuilder(true);
+        for (const unit of ctx.inputStructure.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            l.unit = unit;
+            const { elements } = unit;
+            const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+            const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+            builder.beginUnit(unit.id);
+
+            while (chainsIt.hasNext) {
+                const chainSegment = chainsIt.move();
+                l.element = elements[chainSegment.start];
+
+                const asym_id = StructureProperties.chain.label_asym_id(l);
+                const op_name = StructureProperties.unit.operator_name(l);
+
+                if (includedPrdChains.has(asym_id) && includedPrdChains.get(asym_id)!.indexOf(op_name) >= 0) {
+                    builder.addElementRange(elements, chainSegment.start, chainSegment.end);
+                    continue;
+                }
+
+                if (!componentResidues.hasLabelAsymId(asym_id)) {
+                    continue;
+                }
+
+                residuesIt.setSegment(chainSegment);
+                while (residuesIt.hasNext) {
+                    const residueSegment = residuesIt.move();
+                    l.element = elements[residueSegment.start];
+
+                    if (!componentResidues.has(l)) continue;
+                    builder.addElementRange(elements, residueSegment.start, residueSegment.end);
+                }
+            }
+            builder.commitUnit();
+
+            ctx.throwIfTimedOut();
+        }
+
+        const components = structureUnion(ctx.inputStructure, [builder.getStructure(), inner]);
+
+        // add water
+        if (includeWater) {
+            const finalBuilder = new StructureUniqueSubsetBuilder(ctx.inputStructure);
+            const lookup = ctx.inputStructure.lookup3d;
+            for (const unit of components.units) {
+                const { x, y, z } = unit.conformation;
+                const elements = unit.elements;
+                for (let i = 0, _i = elements.length; i < _i; i++) {
+                    const e = elements[i];
+                    lookup.findIntoBuilderIf(x(e), y(e), z(e), radius, finalBuilder, testIsWater);
+                    finalBuilder.addToUnit(unit.id, e);
+                }
+
+                ctx.throwIfTimedOut();
+            }
+
+            return StructureSelection.Sequence(ctx.inputStructure, [finalBuilder.getStructure()]);
+        } else {
+            return StructureSelection.Sequence(ctx.inputStructure, [components]);
+        }
+    };
+}
+
+const _entity_type = StructureProperties.entity.type;
+function testIsWater(l: StructureElement.Location) {
+    return _entity_type(l) === 'water';
+}
+
+function getPrdAsymIdx(structure: Structure) {
+    const model = structure.models[0];
+    const ids = new Set<string>();
+    if (!MmcifFormat.is(model.sourceData)) return ids;
+    const { _rowCount, asym_id } = model.sourceData.data.db.pdbx_molecule;
+    for (let i = 0; i < _rowCount; i++) {
+        ids.add(asym_id.value(i));
+    }
+    return ids;
+}
+
+function getStructConnInfo(structure: Structure) {
+    const model = structure.models[0];
+    const graph = new StructConnGraph();
+
+    if (!MmcifFormat.is(model.sourceData)) return graph;
+
+    const struct_conn = model.sourceData.data.db.struct_conn;
+    const { conn_type_id } = struct_conn;
+    const { ptnr1_label_asym_id, ptnr1_label_comp_id, ptnr1_label_seq_id, ptnr1_symmetry, pdbx_ptnr1_label_alt_id, pdbx_ptnr1_PDB_ins_code } = struct_conn;
+    const { ptnr2_label_asym_id, ptnr2_label_comp_id, ptnr2_label_seq_id, ptnr2_symmetry, pdbx_ptnr2_label_alt_id, pdbx_ptnr2_PDB_ins_code } = struct_conn;
+
+    for (let i = 0; i < struct_conn._rowCount; i++) {
+        const bondType = conn_type_id.value(i);
+        if (bondType !== 'covale' && bondType !== 'metalc') continue;
+
+        const a: ResidueSetEntry = {
+            label_asym_id: ptnr1_label_asym_id.value(i),
+            label_comp_id: ptnr1_label_comp_id.value(i),
+            label_seq_id: ptnr1_label_seq_id.value(i),
+            label_alt_id: pdbx_ptnr1_label_alt_id.value(i),
+            ins_code: pdbx_ptnr1_PDB_ins_code.value(i),
+            operator_name: ptnr1_symmetry.value(i) ?? '1_555'
+        };
+
+        const b: ResidueSetEntry = {
+            label_asym_id: ptnr2_label_asym_id.value(i),
+            label_comp_id: ptnr2_label_comp_id.value(i),
+            label_seq_id: ptnr2_label_seq_id.value(i),
+            label_alt_id: pdbx_ptnr2_label_alt_id.value(i),
+            ins_code: pdbx_ptnr2_PDB_ins_code.value(i),
+            operator_name: ptnr2_symmetry.value(i) ?? '1_555'
+        };
+
+        graph.addEdge(a, b);
+    }
+
+    return graph;
+}
+
+class StructConnGraph {
+    vertices = new Map<string, ResidueSetEntry>();
+    edges = new Map<string, string[]>();
+
+    private addVertex(e: ResidueSetEntry, label: string) {
+        if (this.vertices.has(label)) return;
+        this.vertices.set(label, e);
+        this.edges.set(label, []);
+    }
+
+    addEdge(a: ResidueSetEntry, b: ResidueSetEntry) {
+        const al = ResidueSet.getLabel(a);
+        const bl = ResidueSet.getLabel(b);
+        this.addVertex(a, al);
+        this.addVertex(b, bl);
+        arraySetAdd(this.edges.get(al)!, bl);
+        arraySetAdd(this.edges.get(bl)!, al);
+    }
+
+    addComponent(start: ResidueSetEntry, set: ResidueSet) {
+        const startLabel = ResidueSet.getLabel(start);
+
+        if (!this.vertices.has(startLabel)) {
+            set.add(start);
+            return;
+        }
+
+        const visited = new Set<string>();
+        const added = new Set<string>();
+        const stack = [startLabel];
+
+        added.add(startLabel);
+        set.add(start);
+
+        while (stack.length > 0) {
+            const a = stack.pop()!;
+            visited.add(a);
+
+            const u = this.vertices.get(a)!;
+
+            for (const b of this.edges.get(a)!) {
+                if (visited.has(b)) continue;
+                stack.push(b);
+
+                if (added.has(b)) continue;
+                added.add(b);
+
+                const v = this.vertices.get(b)!;
+                if (u.operator_name === v.operator_name) {
+                    set.add({ ...v, operator_name: start.operator_name });
+                } else {
+                    set.add(v);
+                }
+
+            }
+        }
+    }
+}
+
 // TODO: unionBy (skip this one?), cluster

src/mol-model/structure/structure/util/lookup3d.ts

@@ -94,6 +94,36 @@ export class StructureLookup3D {
         }
     }
 
+    findIntoBuilderIf(x: number, y: number, z: number, radius: number, builder: StructureUniqueSubsetBuilder, test: (l: StructureElement.Location) => boolean) {
+        const { units } = this.structure;
+        const closeUnits = this.unitLookup.find(x, y, z, radius);
+        if (closeUnits.count === 0) return;
+
+        const loc = StructureElement.Location.create(this.structure);
+
+        for (let t = 0, _t = closeUnits.count; t < _t; t++) {
+            const unit = units[closeUnits.indices[t]];
+            Vec3.set(this.pivot, x, y, z);
+            if (!unit.conformation.operator.isIdentity) {
+                Vec3.transformMat4(this.pivot, this.pivot, unit.conformation.operator.inverse);
+            }
+            const unitLookup = unit.lookup3d;
+            const groupResult = unitLookup.find(this.pivot[0], this.pivot[1], this.pivot[2], radius);
+            if (groupResult.count === 0) continue;
+
+            const elements = unit.elements;
+            loc.unit = unit;
+            builder.beginUnit(unit.id);
+            for (let j = 0, _j = groupResult.count; j < _j; j++) {
+                loc.element = elements[groupResult.indices[j]];
+                if (test(loc)) {
+                    builder.addElement(loc.element);
+                }
+            }
+            builder.commitUnit();
+        }
+    }
+
     findIntoBuilderWithRadius(x: number, y: number, z: number, pivotR: number, maxRadius: number, radius: number, eRadius: StructureElement.Property<number>, builder: StructureUniqueSubsetBuilder) {
         const { units } = this.structure;
         const closeUnits = this.unitLookup.find(x, y, z, radius);

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -425,6 +425,18 @@ const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of
     referencesCurrent: true
 });
 
+const surroundingLigands = StructureSelectionQuery('Surrounding Ligands (5 \u212B) of Selection', MS.struct.modifier.union([
+    MS.struct.modifier.surroundingLigands({
+        0: MS.internal.generator.current(),
+        radius: 5,
+        'include-water': true
+    })
+]), {
+    description: 'Select ligand components within 5 \u212B of the current selection.',
+    category: StructureSelectionCategory.Manipulate,
+    referencesCurrent: true
+});
+
 const complement = StructureSelectionQuery('Inverse / Complement of Selection', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: MS.struct.generator.all(),
@@ -645,6 +657,7 @@ export const StructureSelectionQueries = {
     ring,
     aromaticRing,
     surroundings,
+    surroundingLigands,
     complement,
     covalentlyBonded,
     covalentlyOrMetallicBonded,

src/mol-plugin-state/transforms.ts

@@ -9,13 +9,15 @@ import * as Misc from './transforms/misc';
 import * as Model from './transforms/model';
 import * as Volume from './transforms/volume';
 import * as Representation from './transforms/representation';
+import * as Shape from './transforms/shape';
 
 export const StateTransforms = {
     Data,
     Misc,
     Model,
     Volume,
-    Representation
+    Representation,
+    Shape
 };
 
 export type StateTransforms = typeof StateTransforms

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

@@ -36,6 +36,10 @@ import { DihedralParams, DihedralRepresentation } from '../../mol-repr/shape/loc
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 import { Clipping } from '../../mol-theme/clipping';
 import { ObjectKeys } from '../../mol-util/type-helpers';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { getBoxMesh } from './shape';
+import { Shape } from '../../mol-model/shape';
+import { Box3D } from '../../mol-math/geometry';
 
 export { StructureRepresentation3D };
 export { ExplodeStructureRepresentation3D };
@@ -736,6 +740,41 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
     }
 });
 
+export { StructureBoundingBox3D };
+type StructureBoundingBox3D = typeof StructureBoundingBox3D
+const StructureBoundingBox3D = PluginStateTransform.BuiltIn({
+    name: 'structure-bounding-box-3d',
+    display: 'Bounding Box',
+    from: SO.Molecule.Structure,
+    to: SO.Shape.Representation3D,
+    params: {
+        radius: PD.Numeric(0.05, { min: 0.01, max: 4, step: 0.01 }, { isEssential: true }),
+        color: PD.Color(ColorNames.red, { isEssential: true }),
+        ...Mesh.Params,
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Bounding Box', async ctx => {
+            const repr = ShapeRepresentation((_, data: { box: Box3D, radius: number, color: Color }, __, shape) => {
+                const mesh = getBoxMesh(data.box, data.radius, shape?.geometry);
+                return Shape.create('Bouding Box', data, mesh, () => data.color, () => 1, () => 'Bounding Box');
+            }, Mesh.Utils);
+            await repr.createOrUpdate(params, { box: a.data.boundary.box, radius: params.radius, color: params.color }).runInContext(ctx);
+            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Bounding Box` });
+        });
+    },
+    update({ a, b, oldParams, newParams }, plugin: PluginContext) {
+        return Task.create('Bounding Box', async ctx => {
+            await b.data.repr.createOrUpdate(newParams, { box: a.data.boundary.box, radius: newParams.radius, color: newParams.color }).runInContext(ctx);
+            b.data.source = a;
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
+});
+
 export { StructureSelectionsDistance3D };
 type StructureSelectionsDistance3D = typeof StructureSelectionsDistance3D
 const StructureSelectionsDistance3D = PluginStateTransform.BuiltIn({

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

@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { BoxCage } from '../../mol-geo/primitive/box';
+import { Box3D, Sphere3D } from '../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { Shape } from '../../mol-model/shape';
+import { Task } from '../../mol-task';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginStateObject as SO, PluginStateTransform } from '../objects';
+
+export { BoxShape3D };
+type BoxShape3D = typeof BoxShape3D
+const BoxShape3D = PluginStateTransform.BuiltIn({
+    name: 'box-shape-3d',
+    display: 'Box Shape',
+    from: SO.Root,
+    to: SO.Shape.Provider,
+    params: {
+        bottomLeft: PD.Vec3(Vec3()),
+        topRight: PD.Vec3(Vec3.create(1, 1, 1)),
+        radius: PD.Numeric(0.15, { min: 0.01, max: 4, step: 0.01 }),
+        color: PD.Color(ColorNames.red)
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ params }) {
+        return Task.create('Shape Representation', async ctx => {
+            return new SO.Shape.Provider({
+                label: 'Box',
+                data: params,
+                params: Mesh.Params,
+                getShape: (_, data: typeof params) => {
+                    const mesh = getBoxMesh(Box3D.create(params.bottomLeft, params.topRight), params.radius);
+                    return Shape.create('Box', data, mesh, () => data.color, () => 1, () => 'Box');
+                },
+                geometryUtils: Mesh.Utils
+            }, { label: 'Box' });
+        });
+    }
+});
+
+export function getBoxMesh(box: Box3D, radius: number, oldMesh?: Mesh) {
+    const diag = Vec3.sub(Vec3(), box.max, box.min);
+    const translateUnit = Mat4.fromTranslation(Mat4(), Vec3.create(0.5, 0.5, 0.5));
+    const scale = Mat4.fromScaling(Mat4(), diag);
+    const translate = Mat4.fromTranslation(Mat4(), box.min);
+    const transform = Mat4.mul3(Mat4(), translate, scale, translateUnit);
+
+    // TODO: optimize?
+    const state = MeshBuilder.createState(256, 128, oldMesh);
+    state.currentGroup = 1;
+    MeshBuilder.addCage(state, transform, BoxCage(), radius, 2, 20);
+    const mesh = MeshBuilder.getMesh(state);
+
+    const center = Vec3.scaleAndAdd(Vec3(), box.min, diag, 0.5);
+    const sphereRadius = Vec3.distance(box.min, center);
+    mesh.setBoundingSphere(Sphere3D.create(center, sphereRadius));
+
+    return mesh;
+}

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

@@ -195,12 +195,27 @@ export class StructureSourceControls extends CollapsableControls<{}, StructureSo
     get presetActions() {
         const actions: ActionMenu.Item[] = [];
         const { trajectories } = this.plugin.managers.structure.hierarchy.selection;
-        if (trajectories.length !== 1) return actions;
+        if (trajectories.length === 0) return actions;
+
+        let providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[0].cell.obj);
+
+        if (trajectories.length > 1) {
+            const providerSet = new Set(providers);
+            for (let i = 1; i < trajectories.length; i++) {
+                const providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[i].cell.obj);
+                const current = new Set(providers);
+
+                for (const p of providers) {
+                    if (!current.has(p)) providerSet.delete(p);
+                }
+            }
+            providers = providers.filter(p => providerSet.has(p));
+        }
 
-        const providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[0].cell.obj);
         for (const p of providers) {
             actions.push(ActionMenu.Item(p.display.name, p, { description: p.display.description }));
         }
+
         return actions;
     }
 

src/mol-plugin/behavior/dynamic/camera.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -83,12 +83,22 @@ export const CameraAxisHelper = PluginBehavior.create<{}>({
                     lastPlane = CameraHelperAxis.None;
                     state = 0;
                     return;
-                } else if (axis >= CameraHelperAxis.X && axis <= CameraHelperAxis.Z) {
+                }
+
+                const { camera } = this.ctx.canvas3d;
+                let dir: Vec3, up: Vec3;
+
+                if (axis >= CameraHelperAxis.X && axis <= CameraHelperAxis.Z) {
                     lastPlane = CameraHelperAxis.None;
                     state = 0;
-                    const up = Vec3();
+
+                    const d = Vec3.sub(Vec3(), camera.target, camera.position);
+                    const c = Vec3.cross(Vec3(), d, camera.up);
+
+                    up = Vec3();
                     up[axis - 1] = 1;
-                    this.ctx.canvas3d.requestCameraReset({ snapshot: { up } });
+                    dir = Vec3.cross(Vec3(), up, c);
+                    if (Vec3.magnitude(dir) === 0) dir = d;
                 } else {
                     if (lastPlane === axis) {
                         state = (state + 1) % 2;
@@ -97,7 +107,6 @@ export const CameraAxisHelper = PluginBehavior.create<{}>({
                         state = 0;
                     }
 
-                    let up: Vec3, dir: Vec3;
                     if (axis === CameraHelperAxis.XY) {
                         up = state ? Vec3.unitX : Vec3.unitY;
                         dir = Vec3.negUnitZ;
@@ -108,11 +117,11 @@ export const CameraAxisHelper = PluginBehavior.create<{}>({
                         up = state ? Vec3.unitY : Vec3.unitZ;
                         dir = Vec3.negUnitX;
                     }
-
-                    this.ctx.canvas3d.requestCameraReset({
-                        snapshot: (scene, camera) => camera.getInvariantFocus(scene.boundingSphereVisible.center, scene.boundingSphereVisible.radius, up, dir)
-                    });
                 }
+
+                this.ctx.canvas3d.requestCameraReset({
+                    snapshot: (scene, camera) => camera.getInvariantFocus(scene.boundingSphereVisible.center, scene.boundingSphereVisible.radius, up, dir)
+                });
             });
         }
     },

src/mol-plugin/spec.ts

@@ -93,6 +93,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
         PluginSpec.Action(StateTransforms.Representation.StructureSelectionsLabel3D),
         PluginSpec.Action(StateTransforms.Representation.StructureSelectionsOrientation3D),
         PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureBoundingBox3D),
         PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),

src/mol-script/language/symbol-table/structure-query.ts

@@ -155,6 +155,12 @@ const modifier = {
         'as-whole-residues': Argument(Type.Bool, { isOptional: true })
     }), Types.ElementSelectionQuery, 'For each atom set in the selection, include all surrouding atoms/residues that are within the specified radius.'),
 
+    surroundingLigands: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        radius: Argument(Type.Num),
+        'include-water': Argument(Type.Bool, { isOptional: true, defaultValue: true })
+    }), Types.ElementSelectionQuery, 'Find all ligands components around the source query.'),
+
     includeConnected: symbol(Arguments.Dictionary({
         0: Argument(Types.ElementSelectionQuery),
         'bond-test': Argument(Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds' as any }),

src/mol-script/runtime/query/table.ts

@@ -258,6 +258,13 @@ const symbols = [
             elementRadius: xs['atom-radius']
         })(ctx);
     }),
+    D(MolScript.structureQuery.modifier.surroundingLigands, function structureQuery_modifier_includeSurroundingLigands(ctx, xs) {
+        return Queries.modifiers.surroundingLigands({
+            query: xs[0] as any,
+            radius: xs['radius'](ctx),
+            includeWater: !!(xs['include-water'] && xs['include-water'](ctx)),
+        })(ctx);
+    }),
     D(MolScript.structureQuery.modifier.wholeResidues, function structureQuery_modifier_wholeResidues(ctx, xs) { return Queries.modifiers.wholeResidues(xs[0] as any)(ctx); }),
     D(MolScript.structureQuery.modifier.union, function structureQuery_modifier_union(ctx, xs) { return Queries.modifiers.union(xs[0] as any)(ctx); }),
     D(MolScript.structureQuery.modifier.expandProperty, function structureQuery_modifier_expandProperty(ctx, xs) { return Queries.modifiers.expandProperty(xs[0] as any, xs['property'])(ctx); }),

src/mol-script/script/mol-script/symbols.ts

@@ -138,6 +138,7 @@ export const SymbolTable = [
             Alias(MolScript.structureQuery.modifier.union, 'sel.atom.union'),
             Alias(MolScript.structureQuery.modifier.cluster, 'sel.atom.cluster'),
             Alias(MolScript.structureQuery.modifier.includeSurroundings, 'sel.atom.include-surroundings'),
+            Alias(MolScript.structureQuery.modifier.surroundingLigands, 'sel.atom.surrounding-ligands'),
             Alias(MolScript.structureQuery.modifier.includeConnected, 'sel.atom.include-connected'),
             Alias(MolScript.structureQuery.modifier.expandProperty, 'sel.atom.expand-property'),
 

src/servers/model/CHANGELOG.md

@@ -1,3 +1,6 @@
+# 0.9.7
+* add Surrounding Ligands query
+
 # 0.9.6
 * optional download parameter
 

src/servers/model/server/api.ts

@@ -136,6 +136,13 @@ const AssemblyNameParam: QueryParamInfo = {
     description: 'Assembly name. If none is provided, crystal symmetry (where available) or deposited model is used.'
 };
 
+const OmitWaterParam: QueryParamInfo = {
+    name: 'omit_water',
+    type: QueryParamType.Boolean,
+    required: false,
+    defaultValue: false
+};
+
 function Q<Params = any>(definition: Partial<QueryDefinition<Params>>) {
     return definition;
 }
@@ -223,7 +230,28 @@ const QueryMap = {
         jsonParams: [ AtomSiteTestJsonParam, RadiusParam ],
         restParams: [ ...AtomSiteTestRestParams, RadiusParam ],
         filter: QuerySchemas.interaction
-    })
+    }),
+    'surroundingLigands': Q<{ atom_site: AtomSiteSchema, radius: number, assembly_name: string, omit_water: boolean }>({
+        niceName: 'Surrounding Ligands',
+        description: 'Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account.',
+        query(p) {
+            const tests = getAtomsTests(p.atom_site);
+            const center = Queries.combinators.merge(tests.map(test => Queries.generators.atoms({
+                ...test,
+                entityTest: test.entityTest
+                    ? ctx => test.entityTest!(ctx) && ctx.element.unit.conformation.operator.isIdentity
+                    : ctx => ctx.element.unit.conformation.operator.isIdentity
+            })));
+            return Queries.modifiers.surroundingLigands({ query: center, radius: p.radius !== void 0 ? p.radius : 5, includeWater: !p.omit_water });
+        },
+        structureTransform(p, s) {
+            if (p.assembly_name) return StructureSymmetry.buildAssembly(s, '' + p.assembly_name).run();
+            return StructureSymmetry.builderSymmetryMates(s, p.radius !== void 0 ? p.radius : 5).run();
+        },
+        jsonParams: [ AtomSiteTestJsonParam, RadiusParam, OmitWaterParam, AssemblyNameParam ],
+        restParams: [ ...AtomSiteTestRestParams, RadiusParam, OmitWaterParam, AssemblyNameParam ],
+        filter: QuerySchemas.interaction
+    }),
 };
 
 export type QueryName = keyof typeof QueryMap

src/servers/model/server/query.ts

@@ -248,6 +248,7 @@ async function resolveJobEntry(entry: JobEntry, structure: StructureWrapper, enc
 
         if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter(entry.queryDefinition.filter);
         if (result.length > 0) encode_mmCIF_categories(encoder, result, { copyAllCategories: entry.copyAllCategories });
+        else ConsoleLogger.logId(entry.job.id, 'Warning', `Empty result for Query ${entry.key}/${entry.queryDefinition.name}`);
         if (entry.transform && !Mat4.isIdentity(entry.transform)) GlobalModelTransformInfo.writeMmCif(encoder, entry.transform);
         if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter();
         perf.end('encode');

src/servers/model/version.ts

@@ -4,4 +4,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export const VERSION = '0.9.6';
+export const VERSION = '0.9.7';