molstar 3.3.0 → 3.3.1

package/lib/commonjs/extensions/rcsb/validation-report/representation.js

@@ -21,6 +21,7 @@ var complex_visual_1 = require("../../../mol-repr/structure/complex-visual");
 var color_1 = require("../../../mol-util/color");
 var marker_action_1 = require("../../../mol-util/marker-action");
 var centroid_helper_1 = require("../../../mol-math/geometry/centroid-helper");
+var geometry_1 = require("../../../mol-math/geometry");
 var label_1 = require("../../../mol-theme/label");
 var params_1 = require("../../../mol-repr/structure/params");
 //
@@ -44,7 +45,15 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
         style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return magnitude[edgeIndex] * sizeFactor; },
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 exports.IntraUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
 function IntraUnitClashVisual(materialId) {
@@ -137,7 +146,15 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
         style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return edges[edgeIndex].props.magnitude * sizeFactor; }
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 exports.InterUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
 function InterUnitClashVisual(materialId) {

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

@@ -283,7 +283,10 @@ var Structure = /** @class */ (function () {
                 this.state.interUnitBonds = new bonds_1.InterUnitBonds(new Map());
             }
             else {
-                this.state.interUnitBonds = (0, bonds_1.computeInterUnitBonds)(this, { ignoreWater: !this.dynamicBonds });
+                this.state.interUnitBonds = (0, bonds_1.computeInterUnitBonds)(this, {
+                    ignoreWater: !this.dynamicBonds,
+                    ignoreIon: !this.dynamicBonds,
+                });
             }
             return this.state.interUnitBonds;
         },

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts

@@ -11,6 +11,7 @@ import { InterUnitBonds } from './data';
 export interface InterBondComputationProps extends BondComputationProps {
     validUnitPair: (structure: Structure, unitA: Unit, unitB: Unit) => boolean;
     ignoreWater: boolean;
+    ignoreIon: boolean;
 }
 declare function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondComputationProps>): InterUnitBonds;
 export { computeInterUnitBonds };

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -166,7 +166,7 @@ function findPairBonds(unitA, unitB, props, builder) {
     }
     builder.finishUnitPair();
 }
-var DefaultInterBondComputationProps = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), { ignoreWater: true });
+var DefaultInterBondComputationProps = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
 function findBonds(structure, props) {
     var builder = new inter_unit_graph_1.InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return index_pair_1.IndexPairBonds.Provider.get(m); });
@@ -192,7 +192,9 @@ function computeInterUnitBonds(structure, props) {
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
                 (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
-            return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater);
+            var notIon = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
+                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
+            return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }
 exports.computeInterUnitBonds = computeInterUnitBonds;

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

@@ -24,8 +24,6 @@ var index_pair_1 = require("../../../mol-model-formats/structure/property/bonds/
 var element_set_intra_bond_cache_1 = require("./unit/bonds/element-set-intra-bond-cache");
 var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry");
 var resonance_1 = require("./unit/resonance");
-// avoiding namespace lookup improved performance in Chrome (Aug 2020)
-var v3add = linear_algebra_1.Vec3.add;
 var Unit;
 (function (Unit) {
     function isAtomic(u) { return u.kind === 0 /* Atomic */; }
@@ -158,22 +156,7 @@ var Unit;
                         ? undefined
                         : tryRemapBonds(this, this.props.bonds, model, dynamicBonds) });
                 if (!Unit.isSameConformation(this, model)) {
-                    var b = props.boundary;
-                    if (b) {
-                        var elements = this.elements;
-                        var pos = this.conformation.invariantPosition;
-                        var v = (0, linear_algebra_1.Vec3)();
-                        var center = (0, linear_algebra_1.Vec3)();
-                        for (var i = 0, il = elements.length; i < il; i++) {
-                            pos(elements[i], v);
-                            v3add(center, center, v);
-                        }
-                        linear_algebra_1.Vec3.scale(center, center, 1 / elements.length);
-                        // only invalidate boundary if sphere has changed too much
-                        if (linear_algebra_1.Vec3.distance(center, b.sphere.center) / b.sphere.radius >= 1.0) {
-                            props.boundary = undefined;
-                        }
-                    }
+                    props.boundary = undefined;
                     props.lookup3d = undefined;
                     props.principalAxes = undefined;
                 }

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js

@@ -76,9 +76,15 @@ function createInterUnitInteractionCylinderMesh(ctx, structure, theme, props, me
             return false;
         }
     };
-    var m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var child_1 = structure.child;
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child_1 !== null && child_1 !== void 0 ? child_1 : structure).boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
 exports.InteractionsInterUnitParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), dashCount: param_definition_1.ParamDefinition.Numeric(6, { min: 2, max: 10, step: 2 }), dashScale: param_definition_1.ParamDefinition.Numeric(0.4, { min: 0, max: 2, step: 0.1 }), includeParent: param_definition_1.ParamDefinition.Boolean(false) });

package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js

@@ -21,8 +21,8 @@ var interactions_2 = require("../interactions/interactions");
 var geometry_1 = require("../../../mol-math/geometry");
 function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, props, mesh) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var child, childUnit, location, interactions, features, contacts, x, y, z, members, offsets, edgeCount, a, b, flag, sizeFactor, builderProps, m, sphere;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        var child, childUnit, location, interactions, features, contacts, x, y, z, members, offsets, edgeCount, a, b, flag, sizeFactor, builderProps, _a, m, boundingSphere, sphere;
+        return (0, tslib_1.__generator)(this, function (_b) {
             if (!structure_1.Unit.isAtomic(unit))
                 return [2 /*return*/, mesh_1.Mesh.createEmpty(mesh)];
             child = structure.child;
@@ -66,9 +66,14 @@ function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, pr
                     return false;
                 }
             };
-            m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-            sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
-            m.setBoundingSphere(sphere);
+            _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+            if (boundingSphere) {
+                m.setBoundingSphere(boundingSphere);
+            }
+            else if (m.triangleCount > 0) {
+                sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
+                m.setBoundingSphere(sphere);
+            }
             return [2 /*return*/, m];
         });
     });

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js

@@ -18,6 +18,7 @@ var link_1 = require("../../../mol-repr/structure/visual/util/link");
 var complex_visual_1 = require("../../../mol-repr/structure/complex-visual");
 var representation_2 = require("../../../mol-repr/structure/representation");
 var property_1 = require("./property");
+var geometry_1 = require("../../../mol-math/geometry");
 function createCrossLinkRestraintCylinderMesh(ctx, structure, theme, props, mesh) {
     var crossLinks = property_1.CrossLinkRestraintProvider.get(structure).value;
     if (!crossLinks.count)
@@ -39,7 +40,15 @@ function createCrossLinkRestraintCylinderMesh(ctx, structure, theme, props, mesh
             return theme.size.size(location) * sizeFactor;
         },
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 exports.CrossLinkRestraintCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 10, step: 0.1 }) });
 function CrossLinkRestraintVisual(materialId) {

package/lib/commonjs/mol-plugin-state/helpers/root-structure.js

@@ -17,7 +17,7 @@ var symmetry_1 = require("../../mol-model/structure/model/properties/symmetry");
 var objects_1 = require("../objects");
 var symmetry_2 = require("../../mol-model-formats/structure/property/symmetry");
 var CommonStructureParams = {
-    dynamicBonds: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules.' })),
+    dynamicBonds: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules and ions.' })),
 };
 var RootStructureDefinition;
 (function (RootStructureDefinition) {

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -145,20 +145,30 @@ function createInterUnitBondCylinderImpostors(ctx, structure, theme, props, cyli
     if (!structure.interUnitBonds.edgeCount)
         return cylinders_1.Cylinders.createEmpty(cylinders);
     var builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
-    var m = (0, link_1.createLinkCylinderImpostors)(ctx, builderProps, props, cylinders);
-    var child = structure.child;
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
+    var _a = (0, link_1.createLinkCylinderImpostors)(ctx, builderProps, props, cylinders), c = _a.cylinders, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        c.setBoundingSphere(boundingSphere);
+    }
+    else if (c.cylinderCount > 0) {
+        var child = structure.child;
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
+        c.setBoundingSphere(sphere);
+    }
+    return c;
 }
 function createInterUnitBondCylinderMesh(ctx, structure, theme, props, mesh) {
     if (!structure.interUnitBonds.edgeCount)
         return mesh_1.Mesh.createEmpty(mesh);
     var builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
-    var m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-    var child = structure.child;
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var child = structure.child;
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
 exports.InterUnitBondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 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>
  */

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020-2021 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>
  */
@@ -99,10 +99,15 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
         },
         ignore: (0, bond_1.makeInterBondIgnoreTest)(structure, props)
     };
-    var l = (0, link_1.createLinkLines)(ctx, builderProps, props, lines);
-    var child = structure.child;
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    l.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkLines)(ctx, builderProps, props, lines), l = _a.lines, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        l.setBoundingSphere(boundingSphere);
+    }
+    else if (l.lineCount > 0) {
+        var child = structure.child;
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor);
+        l.setBoundingSphere(sphere);
+    }
     return l;
 }
 exports.InterUnitBondLineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });

package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -165,9 +165,14 @@ function createIntraUnitBondCylinderImpostors(ctx, unit, structure, theme, props
     if (child && !childUnit)
         return cylinders_1.Cylinders.createEmpty(cylinders);
     var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
-    var c = (0, link_1.createLinkCylinderImpostors)(ctx, builderProps, props, cylinders);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
-    c.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkCylinderImpostors)(ctx, builderProps, props, cylinders), c = _a.cylinders, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        c.setBoundingSphere(boundingSphere);
+    }
+    else if (c.cylinderCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
+        c.setBoundingSphere(sphere);
+    }
     return c;
 }
 function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mesh) {
@@ -180,9 +185,14 @@ function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mes
     if (child && !childUnit)
         return mesh_1.Mesh.createEmpty(mesh);
     var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
-    var m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
 exports.IntraUnitBondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });

package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -125,9 +125,14 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
         },
         ignore: (0, bond_1.makeIntraBondIgnoreTest)(structure, unit, props)
     };
-    var l = (0, link_1.createLinkLines)(ctx, builderProps, props, lines);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
-    l.setBoundingSphere(sphere);
+    var _b = (0, link_1.createLinkLines)(ctx, builderProps, props, lines), l = _b.lines, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        l.setBoundingSphere(boundingSphere);
+    }
+    else if (l.lineCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
+        l.setBoundingSphere(sphere);
+    }
     return l;
 }
 exports.IntraUnitBondLineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });

package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js

@@ -17,6 +17,7 @@ var units_visual_1 = require("../units-visual");
 var param_definition_1 = require("../../../mol-util/param-definition");
 var location_iterator_1 = require("../../../mol-geo/util/location-iterator");
 var common_1 = require("./util/common");
+var geometry_1 = require("../../../mol-math/geometry");
 function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh) {
     var _a = structure.carbohydrates, links = _a.links, elements = _a.elements;
     var linkSizeFactor = props.linkSizeFactor;
@@ -37,7 +38,15 @@ function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh)
             return theme.size.size(location) * linkSizeFactor;
         },
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    var _b = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * linkSizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 exports.CarbohydrateLinkParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 3, step: 0.01 }) });
 function CarbohydrateLinkVisual(materialId) {

package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js

@@ -18,6 +18,7 @@ var int_1 = require("../../../mol-data/int");
 var loci_1 = require("../../../mol-model/loci");
 var common_1 = require("../../../mol-model/structure/structure/unit/bonds/common");
 var common_2 = require("./util/common");
+var geometry_1 = require("../../../mol-math/geometry");
 function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props, mesh) {
     var _a = structure.carbohydrates, terminalLinks = _a.terminalLinks, elements = _a.elements;
     var terminalLinkSizeFactor = props.terminalLinkSizeFactor;
@@ -56,7 +57,15 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props
             return common_1.MetalsSet.has(beI) ? 1 /* Dashed */ : 0 /* Solid */;
         }
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    var _b = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * terminalLinkSizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 exports.CarbohydrateTerminalLinkParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { terminalLinkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 3, step: 0.01 }) });
 function CarbohydrateTerminalLinkVisual(materialId) {

package/lib/commonjs/mol-repr/structure/visual/element-point.d.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-repr/structure/visual/element-point.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,6 +14,8 @@ var points_builder_1 = require("../../../mol-geo/geometry/points/points-builder"
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var element_1 = require("./util/element");
 var geometry_1 = require("../../../mol-math/geometry");
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+var v3add = linear_algebra_1.Vec3.add;
 exports.ElementPointParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsPointsParams), { pointSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false) });
 // TODO size
 function createElementPoint(ctx, unit, structure, theme, props, points) {
@@ -27,23 +29,40 @@ function createElementPoint(ctx, unit, structure, theme, props, points) {
     var p = (0, linear_algebra_1.Vec3)();
     var pos = unit.conformation.invariantPosition;
     var ignore = (0, element_1.makeElementIgnoreTest)(structure, unit, props);
+    var center = (0, linear_algebra_1.Vec3)();
+    var count = 0;
     if (ignore) {
         for (var i = 0; i < n; ++i) {
             if (ignore(elements[i]))
                 continue;
             pos(elements[i], p);
+            v3add(center, center, p);
+            count += 1;
             builder.add(p[0], p[1], p[2], i);
         }
     }
     else {
         for (var i = 0; i < n; ++i) {
             pos(elements[i], p);
+            v3add(center, center, p);
+            count += 1;
             builder.add(p[0], p[1], p[2], i);
         }
     }
+    var oldBoundingSphere = points ? geometry_1.Sphere3D.clone(points.boundingSphere) : undefined;
     var pt = builder.getPoints();
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
-    pt.setBoundingSphere(sphere);
+    if (count === 0)
+        return pt;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, 1 * props.sizeFactor);
+    }
+    pt.setBoundingSphere(boundingSphere);
     return pt;
 }
 exports.createElementPoint = createElementPoint;

package/lib/commonjs/mol-repr/structure/visual/util/element.js

@@ -20,6 +20,8 @@ var spheres_1 = require("../../../../mol-geo/geometry/spheres/spheres");
 var spheres_builder_1 = require("../../../../mol-geo/geometry/spheres/spheres-builder");
 var common_1 = require("./common");
 var geometry_1 = require("../../../../mol-math/geometry");
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+var v3add = linear_algebra_1.Vec3.add;
 function makeElementIgnoreTest(structure, unit, props) {
     var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly;
     var atomicNumber = unit.model.atomicHierarchy.derived.atom.atomicNumber;
@@ -52,20 +54,36 @@ function createElementSphereMesh(ctx, unit, structure, theme, props, mesh) {
     var ignore = makeElementIgnoreTest(structure, unit, props);
     var l = structure_1.StructureElement.Location.create(structure, unit);
     var themeSize = theme.size.size;
+    var center = (0, linear_algebra_1.Vec3)();
     var maxSize = 0;
+    var count = 0;
     for (var i = 0; i < elementCount; i++) {
         if (ignore && ignore(elements[i]))
             continue;
         l.element = elements[i];
         pos(elements[i], v);
+        v3add(center, center, v);
+        count += 1;
         builderState.currentGroup = i;
         var size = themeSize(l);
         if (size > maxSize)
             maxSize = size;
         (0, sphere_2.addSphere)(builderState, v, size * sizeFactor, detail);
     }
+    var oldBoundingSphere = mesh ? geometry_1.Sphere3D.clone(mesh.boundingSphere) : undefined;
     var m = mesh_builder_1.MeshBuilder.getMesh(builderState);
-    m.setBoundingSphere(geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * sizeFactor + 0.05));
+    if (count === 0)
+        return m;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * sizeFactor + 0.05);
+    }
+    m.setBoundingSphere(boundingSphere);
     return m;
 }
 exports.createElementSphereMesh = createElementSphereMesh;
@@ -82,19 +100,35 @@ function createElementSphereImpostor(ctx, unit, structure, theme, props, spheres
     var ignore = makeElementIgnoreTest(structure, unit, props);
     var l = structure_1.StructureElement.Location.create(structure, unit);
     var themeSize = theme.size.size;
+    var center = (0, linear_algebra_1.Vec3)();
     var maxSize = 0;
+    var count = 0;
     for (var i = 0; i < elementCount; i++) {
         if (ignore === null || ignore === void 0 ? void 0 : ignore(elements[i]))
             continue;
         pos(elements[i], v);
         builder.add(v[0], v[1], v[2], i);
+        v3add(center, center, v);
+        count += 1;
         l.element = elements[i];
         var size = themeSize(l);
         if (size > maxSize)
             maxSize = size;
     }
+    var oldBoundingSphere = spheres ? geometry_1.Sphere3D.clone(spheres.boundingSphere) : undefined;
     var s = builder.getSpheres();
-    s.setBoundingSphere(geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * props.sizeFactor + 0.05));
+    if (count === 0)
+        return s;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * props.sizeFactor + 0.05);
+    }
+    s.setBoundingSphere(boundingSphere);
     return s;
 }
 exports.createElementSphereImpostor = createElementSphereImpostor;

package/lib/commonjs/mol-repr/structure/visual/util/link.d.ts

@@ -9,6 +9,7 @@ import { Mesh } from '../../../../mol-geo/geometry/mesh/mesh';
 import { VisualContext } from '../../../visual';
 import { Lines } from '../../../../mol-geo/geometry/lines/lines';
 import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
+import { Sphere3D } from '../../../../mol-math/geometry/primitives/sphere3d';
 export declare const LinkCylinderParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -75,14 +76,23 @@ export declare const enum LinkStyle {
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): Mesh;
+export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): {
+    mesh: Mesh;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): Cylinders;
+export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): {
+    cylinders: Cylinders;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): Lines;
+export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): {
+    lines: Lines;
+    boundingSphere?: Sphere3D;
+};