molstar 3.0.0-dev.3 → 3.0.0-dev.7

package/lib/mol-math/linear-algebra/3d/quat.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -70,6 +70,14 @@ declare namespace Quat {
     function fromArray(a: Quat, array: NumberArray, offset: number): Quat;
     function copy(out: Quat, a: Quat): Quat;
     function set(out: Quat, x: number, y: number, z: number, w: number): Quat;
+    /**
+     * Returns whether or not the quaternions have exactly the same elements in the same position (when compared with ===)
+     */
+    function exactEquals(a: Quat, b: Quat): boolean;
+    /**
+     * Returns whether or not the quaternions have approximately the same elements in the same position.
+     */
+    function equals(a: Quat, b: Quat): boolean;
     function add(out: Quat, a: Quat, b: Quat): Quat;
     function normalize(out: Quat, a: Quat): Quat;
     function rotationTo(out: Quat, a: Vec3, b: Vec3): Quat;

package/lib/mol-math/linear-algebra/3d/quat.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -311,6 +311,25 @@ function Quat() {
         return out;
     }
     Quat.set = set;
+    /**
+     * Returns whether or not the quaternions have exactly the same elements in the same position (when compared with ===)
+     */
+    function exactEquals(a, b) {
+        return a[0] === b[0] && a[1] === b[1] && a[2] === b[2] && a[3] === b[3];
+    }
+    Quat.exactEquals = exactEquals;
+    /**
+     * Returns whether or not the quaternions have approximately the same elements in the same position.
+     */
+    function equals(a, b) {
+        var a0 = a[0], a1 = a[1], a2 = a[2], a3 = a[3];
+        var b0 = b[0], b1 = b[1], b2 = b[2], b3 = b[3];
+        return (Math.abs(a0 - b0) <= EPSILON * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
+            Math.abs(a1 - b1) <= EPSILON * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
+            Math.abs(a2 - b2) <= EPSILON * Math.max(1.0, Math.abs(a2), Math.abs(b2)) &&
+            Math.abs(a3 - b3) <= EPSILON * Math.max(1.0, Math.abs(a3), Math.abs(b3)));
+    }
+    Quat.equals = equals;
     function add(out, a, b) {
         out[0] = a[0] + b[0];
         out[1] = a[1] + b[1];

package/lib/mol-model/structure/model/model.d.ts

@@ -124,6 +124,7 @@ export declare namespace Model {
     function hasProtein(model: Model): boolean;
     function hasNucleic(model: Model): boolean;
     function isFromPdbArchive(model: Model): boolean;
+    function hasPdbId(model: Model): boolean;
     function hasSecondaryStructure(model: Model): boolean;
     function hasCrystalSymmetry(model: Model): boolean;
     function isFromXray(model: Model): boolean;

package/lib/mol-model/structure/model/model.js

@@ -201,13 +201,23 @@ export var Model;
         if (!MmcifFormat.is(model.sourceData))
             return false;
         var db = model.sourceData.data.db;
-        return (db.database_2.database_id.isDefined ||
-            // 4 character PDB id
-            model.entryId.match(/^[1-9][a-z0-9]{3,3}$/i) !== null ||
+        for (var i = 0, il = db.database_2.database_id.rowCount; i < il; ++i) {
+            if (db.database_2.database_id.value(i) === 'PDB')
+                return true;
+        }
+        return false;
+    }
+    Model.isFromPdbArchive = isFromPdbArchive;
+    function hasPdbId(model) {
+        if (!MmcifFormat.is(model.sourceData))
+            return false;
+        return (
+        // 4 character PDB id
+        model.entryId.match(/^[1-9][a-z0-9]{3,3}$/i) !== null ||
             // long PDB id
             model.entryId.match(/^pdb_[0-9]{4,4}[1-9][a-z0-9]{3,3}$/i) !== null);
     }
-    Model.isFromPdbArchive = isFromPdbArchive;
+    Model.hasPdbId = hasPdbId;
     function hasSecondaryStructure(model) {
         if (!MmcifFormat.is(model.sourceData))
             return false;
@@ -304,7 +314,7 @@ export var Model;
         var db = model.sourceData.data.db;
         return hasDensityMap(model) || (
         // check if from pdb archive but missing relevant meta data
-        isFromPdbArchive(model) && (!db.exptl.method.isDefined ||
+        hasPdbId(model) && (!db.exptl.method.isDefined ||
             (isFromXray(model) && (!db.pdbx_database_status.status_code_sf.isDefined ||
                 db.pdbx_database_status.status_code_sf.valueKind(0) === 2 /* Unknown */)) ||
             (isFromEm(model) && (!db.pdbx_database_related.db_name.isDefined))));

package/lib/mol-model/structure/model/properties/atomic/hierarchy.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -181,6 +181,11 @@ export interface AtomicIndex {
      * @returns first found index or -1 if none of the given atoms are present.
      */
     findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex;
+    /**
+     * Find element index of an atom on a given residue.
+     * @returns index or -1 if the atom is not present.
+     */
+    findElementOnResidue(residueIndex: ResidueIndex, type_symbol: ElementSymbol): ElementIndex;
 }
 export declare namespace AtomicIndex {
     interface ChainLabelKey {

package/lib/mol-model/structure/model/properties/atomic/hierarchy.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-model/structure/model/properties/utils/atomic-derived.d.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>
  */

package/lib/mol-model/structure/model/properties/utils/atomic-derived.js

@@ -1,10 +1,10 @@
 /**
- * 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 { AtomNumber } from '../atomic';
-import { getMoleculeType, getComponentType, getPolymerType } from '../../types';
+import { getMoleculeType, getComponentType, getPolymerType, isPolymer, ElementSymbol } from '../../types';
 import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
 import { isProductionMode } from '../../../../../mol-util/debug';
 export function getAtomicDerivedData(data, segments, index, chemicalComponentMap) {
@@ -54,6 +54,9 @@ export function getAtomicDerivedData(data, segments, index, chemicalComponentMap
         if (traceIndex === -1) {
             var coarseAtomId = getAtomIdForAtomRole(polyType, 'coarseBackbone');
             traceIndex = index.findAtomsOnResidue(i, coarseAtomId);
+            if (traceIndex === -1 && isPolymer(molType)) {
+                traceIndex = index.findElementOnResidue(i, ElementSymbol('C'));
+            }
         }
         traceElementIndex[i] = traceIndex;
         var directionFromAtomId = getAtomIdForAtomRole(polyType, 'directionFrom');

package/lib/mol-model/structure/model/properties/utils/atomic-index.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-model/structure/model/properties/utils/atomic-index.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -40,6 +40,7 @@ function createMapping(entities, data, segments) {
         label_atom_id: data.atoms.label_atom_id,
         auth_atom_id: data.atoms.auth_atom_id,
         label_alt_id: data.atoms.label_alt_id,
+        type_symbol: data.atoms.type_symbol,
         chain_index_entity_index: new Int32Array(data.chains._rowCount),
         entity_index_label_asym_id: new Map(),
         chain_index_label_seq_id: new Map(),
@@ -148,6 +149,9 @@ var Index = /** @class */ (function () {
     Index.prototype.findAtomsOnResidue = function (rI, label_atom_ids) {
         return findAtomByNames(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_ids);
     };
+    Index.prototype.findElementOnResidue = function (rI, type_symbol) {
+        return findAtomByElement(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.type_symbol, type_symbol);
+    };
     return Index;
 }());
 function findAtomByName(start, end, data, atomName) {
@@ -171,6 +175,13 @@ function findAtomByNameAndAltLoc(start, end, nameData, altLocData, atomName, alt
     }
     return -1;
 }
+function findAtomByElement(start, end, data, typeSymbol) {
+    for (var i = start; i < end; i++) {
+        if (data.value(i) === typeSymbol)
+            return i;
+    }
+    return -1;
+}
 export function getAtomicIndex(data, entities, segments) {
     var map = createMapping(entities, data, segments);
     var _a = data.residues, label_seq_id = _a.label_seq_id, auth_seq_id = _a.auth_seq_id, pdbx_PDB_ins_code = _a.pdbx_PDB_ins_code;

package/lib/mol-model/structure/model/types.js

@@ -261,6 +261,15 @@ export function getMoleculeType(compType, compId) {
             // trust our saccharide table more than given 'non-polymer' or 'other' component type
             return 9 /* Saccharide */;
         }
+        else if (AminoAcidNames.has(compId)) {
+            return 5 /* Protein */;
+        }
+        else if (RnaBaseNames.has(compId)) {
+            return 6 /* RNA */;
+        }
+        else if (DnaBaseNames.has(compId)) {
+            return 7 /* DNA */;
+        }
         else {
             return 1 /* Other */;
         }

package/lib/mol-model/structure/structure/unit/rings.js

@@ -125,6 +125,8 @@ var UnitRing;
             return true;
         if (!hasAromaticRingElement)
             return false;
+        if (ring.length < 5)
+            return false;
         var ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring));
         return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;
     }

package/lib/mol-model-formats/shape/ply.d.ts

@@ -30,11 +30,24 @@ export declare const PlyShapeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type PlyShapeParams = typeof PlyShapeParams;
@@ -58,10 +71,23 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 }>>;

package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -25,11 +25,24 @@ export declare const InteractionsInterUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type InteractionsInterUnitParams = typeof InteractionsInterUnitParams;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts

@@ -25,11 +25,24 @@ export declare const InteractionsIntraUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams;

package/lib/mol-model-props/computed/representations/interactions.d.ts

@@ -29,11 +29,24 @@ export declare const InteractionsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type InteractionsParams = typeof InteractionsParams;
@@ -58,11 +71,24 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type InteractionRepresentation = StructureRepresentation<InteractionsParams>;
@@ -88,10 +114,23 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 }, "interactions">;

package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -30,11 +30,24 @@ export declare const CrossLinkRestraintCylinderParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type CrossLinkRestraintCylinderParams = typeof CrossLinkRestraintCylinderParams;
@@ -59,11 +72,24 @@ export declare const CrossLinkRestraintParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type CrossLinkRestraintParams = typeof CrossLinkRestraintParams;
@@ -87,11 +113,24 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 export declare type CrossLinkRestraintRepresentation = StructureRepresentation<CrossLinkRestraintParams>;
@@ -116,10 +155,23 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 }, CrossLinkRestraint.Tag>;

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -7,6 +7,7 @@
 import { PluginBehavior } from '../../../behavior';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginContext } from '../../../context';
+import { Clip } from '../../../../mol-util/clip';
 declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     targetParams: PD.Group<PD.Normalize<{
@@ -24,6 +25,17 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
     }>>;
 };
 declare type StructureFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof StructureFocusRepresentationParams>>;

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -17,6 +17,7 @@ import { SizeTheme } from '../../../../mol-theme/size';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginCommands } from '../../../commands';
 import { Material } from '../../../../mol-util/material';
+import { Clip } from '../../../../mol-util/clip';
 var StructureFocusRepresentationParams = function (plugin) {
     var reprParams = StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
     return {
@@ -41,6 +42,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
         material: Material.getParam(),
+        clip: PD.Group(Clip.Params),
     };
 };
 var FocusComponents = ['target', 'surroundings', 'interactions'];
@@ -68,7 +70,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
         return __assign(__assign({}, this.params.targetParams), { type: {
                 name: reprParams.type.name,
-                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material })
+                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {

package/lib/mol-plugin/commands.d.ts

@@ -232,6 +232,7 @@ export declare const PluginCommands: {
                     outline: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         scale: any;
                         threshold: any;
+                        color: any;
                     }>, "on">;
                     antialiasing: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         edgeThreshold: any;
@@ -271,10 +272,6 @@ export declare const PluginCommands: {
                     }>[];
                     ambientColor: import("../mol-util/color").Color;
                     ambientIntensity: number;
-                    clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        variant: any;
-                        objects: any;
-                    }>;
                 }>>;
                 trackball: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     noScroll: boolean;
@@ -329,8 +326,11 @@ export declare const PluginCommands: {
                         flipSided: any;
                         flatShaded: any;
                         xrayShaded: any;
+                        bumpFrequency: any;
+                        bumpAmplitude: any;
                         quality: any;
                         material: any;
+                        clip: any;
                     }>, "on">;
                 }>>;
             }>> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void);

package/lib/mol-plugin/config.d.ts

@@ -16,6 +16,7 @@ export declare class PluginConfigItem<T = any> {
     constructor(key: string, defaultValue?: T | undefined);
 }
 declare function item<T>(key: string, defaultValue?: T): PluginConfigItem<T>;
+export declare function preferWebGl1(): boolean;
 export declare const PluginConfig: {
     item: typeof item;
     General: {
@@ -58,6 +59,7 @@ export declare const PluginConfig: {
             highSymmetryUnitCount: number;
             fiberResidueCount: number;
         }>;
+        DefaultRepresentationPreset: PluginConfigItem<string>;
         DefaultRepresentationPresetParams: PluginConfigItem<StructureRepresentationPresetProvider.CommonParams>;
     };
 };

package/lib/mol-plugin/config.js

@@ -16,12 +16,17 @@ var PluginConfigItem = /** @class */ (function () {
 }());
 export { PluginConfigItem };
 function item(key, defaultValue) { return new PluginConfigItem(key, defaultValue); }
-function preferWebGl1() {
+export function preferWebGl1() {
     if (typeof navigator === 'undefined' || typeof window === 'undefined')
         return false;
-    // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1 (but is working in Safari tech preview)
+    // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1, 15.2. It is working in Safari 15.4 tech preview, so disabling all versions before that.
     // prefer webgl 1 based on the userAgent substring
-    if (navigator.userAgent.indexOf('Version/15.1 Safari') > 0) {
+    var unpportedSafariVersions = [
+        'Version/15.1 Safari',
+        'Version/15.2 Safari',
+        'Version/15.3 Safari'
+    ];
+    if (unpportedSafariVersions.some(function (v) { return navigator.userAgent.indexOf(v) > 0; })) {
         return true;
     }
     // Check for iOS device which enabled WebGL2 recently but it doesn't seem
@@ -72,6 +77,7 @@ export var PluginConfig = {
     },
     Structure: {
         SizeThresholds: item('structure.size-thresholds', Structure.DefaultSizeThresholds),
+        DefaultRepresentationPreset: item('structure.default-representation-preset', 'auto'),
         DefaultRepresentationPresetParams: item('structure.default-representation-preset-params', {})
     }
 };

package/lib/mol-plugin/spec.js

@@ -67,6 +67,7 @@ export var DefaultPluginSpec = function () { return ({
         PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
         PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
+        PluginSpec.Action(StateTransforms.Representation.ClippingStructureRepresentation3DFromScript),
         PluginSpec.Action(StateTransforms.Representation.SubstanceStructureRepresentation3DFromScript),
         PluginSpec.Action(AssignColorVolume),
         PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),