3.0.2

Fix visual visibility edge case

CHANGELOG.md

@@ -6,6 +6,14 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.0.2] - 2022-01-30
+
+- Fix color smoothing of elongated structures (by fixing ``Sphere.expand`` for spheres with highly directional extrema)
+- Fix entity label not displayed when multiple instances of the same entity are highlighted
+- Fix empty elements created in ``StructureElement.Loci.extendToAllInstances``
+- Measurement options tweaks (allow larger ``textSize``; make ``customText`` essential)
+- Fix visual visibility sync edge case when changing state snapshots
+
 ## [v3.0.1] - 2022-01-27
 
 - Fix marking pass not working with ``transparentBackground``

CITATION.cff

@@ -0,0 +1,72 @@
+cff-version: 1.2.0
+title: >-
+  Mol* library
+message: >-
+  Please cite this software using the metadata from
+  'preferred-citation'.
+authors:
+  - given-names: Alexander S
+    family-names: Rose
+    orcid: 'https://orcid.org/0000-0002-0893-5551'
+  - given-names: David
+    family-names: Sehnal
+    orcid: 'https://orcid.org/0000-0002-0682-3089'
+  - given-names: Sebastian
+    family-names: Bittrich
+    orcid: 'https://orcid.org/0000-0003-3576-0387'
+  - given-names: Áron Samuel
+    family-names: Kovács
+  - given-names: Ludovic
+    family-names: Autin
+    orcid: 'https://orcid.org/0000-0002-2197-191X'
+  - given-names: Michal
+    family-names: Malý
+  - given-names: Jiří
+    family-names: Černý
+  - given-names: Panagiotis
+    family-names: Tourlas
+type: software
+doi: 10.5281/zenodo.3947306
+preferred-citation:
+  authors:
+    - given-names: David
+      family-names: Sehnal
+      orcid: 'https://orcid.org/0000-0002-0682-3089'
+    - given-names: Sebastian
+      family-names: Bittrich
+      orcid: 'https://orcid.org/0000-0003-3576-0387'
+    - given-names: Mandar
+      family-names: Deshpande
+      orcid: 'https://orcid.org/0000-0002-9043-7665'
+    - given-names: Radka
+      family-names: Svobodová
+      orcid: 'https://orcid.org/0000-0002-3840-8760'
+    - given-names: Karel
+      family-names: Berka
+      orcid: 'https://orcid.org/0000-0001-9472-2589'
+    - given-names: Václav
+      family-names: Bazgier
+      orcid: 'https://orcid.org/0000-0003-3393-3010'
+    - given-names: Sameer
+      family-names: Velankar
+      orcid: 'https://orcid.org/0000-0002-8439-5964'
+    - given-names: Stephen K
+      family-names: Burley
+      orcid: 'https://orcid.org/0000-0002-2487-9713'
+    - given-names: Jaroslav
+      family-names: Koča
+      orcid: 'https://orcid.org/0000-0002-2780-4901'
+    - given-names: Alexander S
+      family-names: Rose
+      orcid: 'https://orcid.org/0000-0002-0893-5551'
+  title: >-
+    Mol* Viewer: modern web app for 3D visualization
+    and analysis of large biomolecular structures
+  type: article
+  doi: 10.1093/nar/gkab314
+  journal: "Nucleic Acids Research"
+  issue: W1
+  volume: 49
+  year: 2021
+  month: 7
+  pages: "W431–W437"

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "3.0.1",
+  "version": "3.0.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "3.0.1",
+      "version": "3.0.2",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.10",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.1",
+  "version": "3.0.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/mol-math/geometry/primitives/sphere3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -11,6 +11,7 @@ import { OrderedSet } from '../../../mol-data/int';
 import { NumberArray, PickRequired } from '../../../mol-util/type-helpers';
 import { Box3D } from './box3d';
 import { Axes3D } from './axes3d';
+import { PrincipalAxes } from '../../linear-algebra/matrix/principal-axes';
 
 interface Sphere3D {
     center: Vec3,
@@ -202,11 +203,28 @@ namespace Sphere3D {
             return out;
         }
         if (hasExtrema(sphere)) {
+            const positions = new Float32Array(sphere.extrema.length * 3);
+            for (let i = 0; i < sphere.extrema.length; i++) {
+                Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+
+            const axes = PrincipalAxes.calculateMomentsAxes(positions);
+            Axes3D.scale(axes, Axes3D.normalize(axes, axes), delta);
+
             setExtrema(out, sphere.extrema.map(e => {
                 Vec3.sub(tmpDir, e, sphere.center);
-                const dist = Vec3.distance(sphere.center, e);
-                Vec3.normalize(tmpDir, tmpDir);
-                return Vec3.scaleAndAdd(Vec3(), sphere.center, tmpDir, dist + delta);
+                const out = Vec3.clone(e);
+
+                const sA = Vec3.dot(tmpDir, axes.dirA) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirA, sA);
+
+                const sB = Vec3.dot(tmpDir, axes.dirB) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirB, sB);
+
+                const sC = Vec3.dot(tmpDir, axes.dirC) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirC, sC);
+
+                return out;
             }));
         }
         return out;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -497,7 +497,9 @@ export namespace Loci {
             if (!elementIndices) continue;
 
             const indices = getUnitIndices(unit.elements, elementIndices);
-            elements[elements.length] = { unit, indices };
+            if (OrderedSet.size(indices)) {
+                elements[elements.length] = { unit, indices };
+            }
         }
 
         return Loci(loci.structure, elements);

src/mol-plugin/behavior/dynamic/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -212,11 +212,14 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
         private f = {
             label: (loci: Loci) => {
                 const label: string[] = [];
-                if (StructureElement.Loci.is(loci) && loci.elements.length === 1) {
-                    const { unit: u } = loci.elements[0];
-                    const l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
-                    const name = StructureProperties.entity.pdbx_description(l).join(', ');
-                    label.push(name);
+                if (StructureElement.Loci.is(loci)) {
+                    const entityNames = new Set<string>();
+                    for (const { unit: u } of loci.elements) {
+                        const l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                        const name = StructureProperties.entity.pdbx_description(l).join(', ');
+                        entityNames.add(name);
+                    }
+                    if (entityNames.size === 1) entityNames.forEach(name => label.push(name));
                 }
                 label.push(lociLabel(loci));
                 return label.filter(l => !!l).join('</br>');

src/mol-plugin/behavior/static/representation.ts

@@ -84,7 +84,7 @@ export function UpdateRepresentationVisibility(ctx: PluginContext) {
 }
 
 function updateVisibility(cell: StateObjectCell, r: Representation<any>) {
-    if (r.state.visible === cell.state.isHidden) {
+    if (r.state.visible === !!cell.state.isHidden) {
         r.setState({ visible: !cell.state.isHidden });
         return true;
     } else {

src/mol-repr/shape/loci/common.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
@@ -10,9 +10,9 @@ import { ColorNames } from '../../../mol-util/color/names';
 import { Text } from '../../../mol-geo/geometry/text/text';
 
 export const MeasurementRepresentationCommonTextParams = {
-    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.' }),
+    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.', isEssential: true }),
     textColor: PD.Color(ColorNames.black, { isEssential: true }),
-    textSize: PD.Numeric(0.5, { min: 0.1, max: 5, step: 0.1 }, { isEssential: true }),
+    textSize: PD.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
 };
 
 export const LociLabelTextParams = {

src/mol-repr/structure/visual/molecular-surface-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -57,7 +57,7 @@ async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, struct
     Mesh.transform(surface, transform);
     if (ctx.webgl && !ctx.webgl.isWebGL2) Mesh.uniformTriangleGroup(surface);
 
-    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius + getUnitExtraRadius(unit));
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, getUnitExtraRadius(unit));
     surface.setBoundingSphere(sphere);
     (surface.meta as MolecularSurfaceMeta).resolution = resolution;
 

src/mol-state/transform.ts

@@ -76,14 +76,23 @@ namespace Transform {
             const s = (b as any)[k], t = (a as any)[k];
             if (!!s === !!t) continue;
             changed = true;
-            (a as any)[k] = s;
+            if (s !== void 0) {
+                (a as any)[k] = s;
+            } else {
+                delete (a as any)[k];
+            }
         }
         for (const k of Object.keys(a)) {
             const s = (b as any)[k], t = (a as any)[k];
             if (!!s === !!t) continue;
             changed = true;
-            (a as any)[k] = s;
+            if (s !== void 0) {
+                (a as any)[k] = s;
+            } else {
+                delete (a as any)[k];
+            }
         }
+
         return changed;
     }