molstar 3.0.0 → 3.2.0

package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -10,6 +10,8 @@ exports.Sphere3D = void 0;
 var tslib_1 = require("tslib");
 var linear_algebra_1 = require("../../linear-algebra");
 var int_1 = require("../../../mol-data/int");
+var axes3d_1 = require("./axes3d");
+var principal_axes_1 = require("../../linear-algebra/matrix/principal-axes");
 function Sphere3D() {
     return Sphere3D.zero();
 }
@@ -197,11 +199,22 @@ exports.Sphere3D = Sphere3D;
             return out;
         }
         if (hasExtrema(sphere)) {
+            var positions = new Float32Array(sphere.extrema.length * 3);
+            for (var i = 0; i < sphere.extrema.length; i++) {
+                linear_algebra_1.Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+            var axes_1 = principal_axes_1.PrincipalAxes.calculateMomentsAxes(positions);
+            axes3d_1.Axes3D.scale(axes_1, axes3d_1.Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
                 linear_algebra_1.Vec3.sub(tmpDir, e, sphere.center);
-                var dist = linear_algebra_1.Vec3.distance(sphere.center, e);
-                linear_algebra_1.Vec3.normalize(tmpDir, tmpDir);
-                return linear_algebra_1.Vec3.scaleAndAdd((0, linear_algebra_1.Vec3)(), sphere.center, tmpDir, dist + delta);
+                var out = linear_algebra_1.Vec3.clone(e);
+                var sA = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                var sB = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                var sC = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
+                return out;
             }));
         }
         return out;

package/lib/commonjs/mol-model/structure/export/categories/atom_site.js

@@ -8,6 +8,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.atomIdFields = exports.entityIdFields = exports.chainIdFields = exports.residueIdFields = exports._atom_site = void 0;
 var cif_1 = require("../../../../mol-io/writer/cif");
+var mmcif_1 = require("../../../../mol-model-formats/structure/mmcif");
+var sifts_mapping_1 = require("../../../../mol-model-props/sequence/sifts-mapping");
 var structure_1 = require("../../structure");
 var CifField = cif_1.CifWriter.Field;
 var E = cif_1.CifWriter.Encodings;
@@ -25,6 +27,61 @@ function atom_site_auth_asym_id(e) {
         return l;
     return l + suffix;
 }
+var atom_site_pdbx_label_index = {
+    shouldInclude: function (s) {
+        var _a;
+        return !!((_a = s.atom_site) === null || _a === void 0 ? void 0 : _a.pdbx_label_index.isDefined);
+    },
+    value: function (e, d) {
+        var srcIndex = d.sourceIndex.value(e.element);
+        return d.atom_site.pdbx_label_index.value(srcIndex);
+    },
+};
+var SIFTS = {
+    shouldInclude: function (s) {
+        return sifts_mapping_1.SIFTSMapping.isAvailable(s.structure.models[0]);
+    },
+    pdbx_sifts_xref_db_name: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_name.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_name.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_acc: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_acc.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_num: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_num.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_num.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_res: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_res.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_res.valueKind(srcIndex);
+        },
+    }
+};
 var atom_site_fields = function () { return cif_1.CifWriter.fields()
     .str('group_PDB', structure_1.StructureProperties.residue.group_PDB)
     .index('id')
@@ -56,6 +113,12 @@ var atom_site_fields = function () { return cif_1.CifWriter.fields()
     .int('auth_seq_id', structure_1.StructureProperties.residue.auth_seq_id, { encoder: E.deltaRLE })
     .str('auth_asym_id', atom_site_auth_asym_id)
     .int('pdbx_PDB_model_num', structure_1.StructureProperties.unit.model_num, { encoder: E.deltaRLE })
+    .int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
+    // SIFTS
+    .str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
+    .str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })
+    .str('pdbx_sifts_xref_db_num', SIFTS.pdbx_sifts_xref_db_num.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_num.valueKind })
+    .str('pdbx_sifts_xref_db_res', SIFTS.pdbx_sifts_xref_db_res.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_res.valueKind })
     // .str('operator_name', P.unit.operator_name, {
     //     shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
     // })
@@ -67,7 +130,11 @@ exports._atom_site = {
         return {
             fields: atom_site_fields(),
             source: structures.map(function (s) { return ({
-                data: s,
+                data: {
+                    structure: s,
+                    sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
+                    atom_site: mmcif_1.MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
+                },
                 rowCount: s.elementCount,
                 keys: function () { return s.elementLocations(); }
             }); })

package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js

@@ -62,13 +62,13 @@ function findElements(ctx, kind) {
     var key = secondaryStructure.key, elements = secondaryStructure.elements;
     var ssElements = [];
     var structure = ctx.structures[0];
-    for (var _i = 0, _a = structure.units; _i < _a.length; _i++) {
-        var unit = _a[_i];
-        // currently can only support this for "identity" operators.
-        if (!structure_1.Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity)
+    for (var _i = 0, _a = structure.unitSymmetryGroups; _i < _a.length; _i++) {
+        var units = _a[_i].units;
+        var u = units[0];
+        if (!structure_1.Unit.isAtomic(u))
             continue;
-        var segs = unit.model.atomicHierarchy.residueAtomSegments;
-        var residues = int_1.Segmentation.transientSegments(segs, unit.elements);
+        var segs = u.model.atomicHierarchy.residueAtomSegments;
+        var residues = int_1.Segmentation.transientSegments(segs, u.elements);
         var current = void 0, move = true;
         while (residues.hasNext) {
             if (move)
@@ -87,8 +87,8 @@ function findElements(ctx, kind) {
                 if (startIdx !== key[current.index]) {
                     move = false;
                     ssElements[ssElements.length] = {
-                        start: structure_1.StructureElement.Location.create(structure, unit, segs.offsets[start]),
-                        end: structure_1.StructureElement.Location.create(structure, unit, segs.offsets[prev]),
+                        start: structure_1.StructureElement.Location.create(structure, u, segs.offsets[start]),
+                        end: structure_1.StructureElement.Location.create(structure, u, segs.offsets[prev]),
                         length: prev - start + 1,
                         element: element
                     };

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 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>

package/lib/commonjs/mol-model/structure/model/properties/coarse/hierarchy.js

@@ -1,14 +1,36 @@
 "use strict";
 /**
- * Copyright (c) 2018 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CoarseHierarchy = void 0;
+var db_1 = require("../../../../../mol-data/db");
+var int_1 = require("../../../../../mol-data/int");
+var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
+var EmptyCoarseElements = {
+    chainKey: [],
+    entityKey: [],
+    findSequenceKey: function () { return -1; },
+    findChainKey: function () { return -1; },
+    getEntityFromChain: function () { return -1; },
+    count: 0,
+    entity_id: db_1.Column.Undefined(0, db_1.Column.Schema.str),
+    asym_id: db_1.Column.Undefined(0, db_1.Column.Schema.str),
+    seq_id_begin: db_1.Column.Undefined(0, db_1.Column.Schema.int),
+    seq_id_end: db_1.Column.Undefined(0, db_1.Column.Schema.int),
+    chainElementSegments: int_1.Segmentation.create([]),
+    polymerRanges: sorted_ranges_1.SortedRanges.ofSortedRanges([]),
+    gapRanges: sorted_ranges_1.SortedRanges.ofSortedRanges([]),
+};
 var CoarseHierarchy;
 (function (CoarseHierarchy) {
-    CoarseHierarchy.Empty = { isDefined: false };
+    CoarseHierarchy.Empty = {
+        isDefined: false,
+        spheres: EmptyCoarseElements,
+        gaussians: EmptyCoarseElements
+    };
 })(CoarseHierarchy = exports.CoarseHierarchy || (exports.CoarseHierarchy = {}));
 //# sourceMappingURL=hierarchy.js.map

package/lib/commonjs/mol-model/structure/structure/element/loci.d.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>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -491,7 +491,9 @@ exports.Loci = Loci;
             if (!elementIndices)
                 continue;
             var indices = getUnitIndices(unit.elements, elementIndices);
-            elements[elements.length] = { unit: unit, indices: indices };
+            if (int_1.OrderedSet.size(indices)) {
+                elements[elements.length] = { unit: unit, indices: indices };
+            }
         }
         return Loci(loci.structure, elements);
     }

package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
+import { Structure } from '../structure';
+export interface AlignmentResultEntry {
+    transform: MinimizeRmsd.Result;
+    pivot: number;
+    other: number;
+}
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[];
+    zeroOverlapPairs: [number, number][];
+    failedPairs: [number, number][];
+}
+export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
+    traceOnly?: boolean;
+}): AlignmentResult;

package/lib/commonjs/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js}

@@ -1,34 +1,46 @@
 "use strict";
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithBestDatabaseMapping = void 0;
+exports.alignAndSuperposeWithSIFTSMapping = void 0;
 var int_1 = require("../../../../mol-data/int");
-var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 var minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
-var best_database_mapping_1 = require("../../../../mol-model-props/sequence/best-database-mapping");
-function alignAndSuperposeWithBestDatabaseMapping(structures) {
+var sifts_mapping_1 = require("../../../../mol-model-props/sequence/sifts-mapping");
+function alignAndSuperposeWithSIFTSMapping(structures, options) {
+    var _a;
     var indexMap = new Map();
     for (var i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i);
+        buildIndex(structures[i], indexMap, i, (_a = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _a !== void 0 ? _a : true);
     }
     var index = Array.from(indexMap.values());
     // TODO: support non-first structure pivots
     var pairs = findPairs(structures.length, index);
-    var ret = [];
+    var zeroOverlapPairs = [];
+    var failedPairs = [];
+    var entries = [];
     for (var _i = 0, pairs_1 = pairs; _i < pairs_1.length; _i++) {
         var p = pairs_1[_i];
-        var _a = getPositionTables(index, p.i, p.j, p.count), a = _a[0], b = _a[1];
-        var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
-        console.log(linear_algebra_1.Mat4.makeTable(transform.bTransform), transform.rmsd);
-        ret.push({ transform: transform, pivot: p.i, other: p.j });
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        }
+        else {
+            var _b = getPositionTables(index, p.i, p.j, p.count), a = _b[0], b = _b[1];
+            var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            }
+            else {
+                entries.push({ transform: transform, pivot: p.i, other: p.j });
+            }
+        }
     }
-    return ret;
+    return { entries: entries, zeroOverlapPairs: zeroOverlapPairs, failedPairs: failedPairs };
 }
-exports.alignAndSuperposeWithBestDatabaseMapping = alignAndSuperposeWithBestDatabaseMapping;
+exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
 function getPositionTables(index, pivot, other, N) {
     var xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
     var ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
@@ -40,7 +52,6 @@ function getPositionTables(index, pivot, other, N) {
         if (!a || !b)
             continue;
         var l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // TODO: allow to use just backbone atoms?
         // TODO: check if residue types match?
         for (var i = 0; i < l; i++) {
             var eI = (a[1] + i);
@@ -94,19 +105,20 @@ function findPairs(N, index) {
     // }
     return ret;
 }
-function buildIndex(structure, index, sI) {
+function buildIndex(structure, index, sI, traceOnly) {
     var _a;
     for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
         var unit = _b[_i];
         if (unit.kind !== 0 /* Atomic */)
             continue;
         var elements = unit.elements, model = unit.model;
-        var map = best_database_mapping_1.BestDatabaseSequenceMapping.Provider.get(model).value;
+        var map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
         if (!map)
             return;
         var dbName = map.dbName, accession = map.accession, num = map.num;
         var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
         var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        var traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
         while (chainsIt.hasNext) {
             var chainSegment = chainsIt.move();
             residuesIt.setSegment(chainSegment);
@@ -115,8 +127,17 @@ function buildIndex(structure, index, sI) {
                 var rI = residueSegment.index;
                 if (!dbName[rI])
                     continue;
-                var start = elements[residueSegment.start];
-                var end = elements[residueSegment.end - 1] + 1;
+                var start = void 0, end = void 0;
+                if (traceOnly) {
+                    start = traceElementIndex[rI];
+                    if (start === -1)
+                        continue;
+                    end = start + 1;
+                }
+                else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1;
+                }
                 var key = "".concat(dbName[rI], "-").concat(accession[rI], "-").concat(num[rI]);
                 if (!index.has(key)) {
                     index.set(key, { key: key, pivots: (_a = {}, _a[sI] = [unit, start, end], _a) });
@@ -130,6 +151,5 @@ function buildIndex(structure, index, sI) {
             }
         }
     }
-    console.log(index);
 }
-//# sourceMappingURL=superposition-db-mapping.js.map
+//# sourceMappingURL=superposition-sifts-mapping.js.map

package/lib/commonjs/mol-model/volume/volume.d.ts

@@ -48,6 +48,13 @@ export declare namespace Volume {
         function toRelative(value: IsoValue, stats: Grid['stats']): Relative;
         function toString(value: IsoValue): string;
     }
+    function adjustedIsoValue(volume: Volume, value: number, kind: 'absolute' | 'relative'): Readonly<{
+        kind: "absolute";
+        absoluteValue: number;
+    }> | Readonly<{
+        kind: "relative";
+        relativeValue: number;
+    }>;
     function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']): PD.Conditioned<Readonly<{
         kind: "absolute";
         absoluteValue: number;

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

@@ -16,6 +16,7 @@ var common_1 = require("../../mol-math/linear-algebra/3d/common");
 var custom_property_1 = require("../custom-property");
 var param_definition_1 = require("../../mol-util/param-definition");
 var number_1 = require("../../mol-util/number");
+var density_server_1 = require("../../mol-model-formats/volume/density-server");
 var Volume;
 (function (Volume) {
     function is(x) {
@@ -60,6 +61,23 @@ var Volume;
         }
         IsoValue.toString = toString;
     })(IsoValue = Volume.IsoValue || (Volume.IsoValue = {}));
+    // Converts iso value to relative if using downsample VolumeServer data
+    function adjustedIsoValue(volume, value, kind) {
+        if (kind === 'relative')
+            return IsoValue.relative(value);
+        var absolute = IsoValue.absolute(value);
+        if (density_server_1.DscifFormat.is(volume.sourceData)) {
+            var stats = {
+                min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
+                max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
+                mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
+                sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
+            };
+            return Volume.IsoValue.toRelative(absolute, stats);
+        }
+        return absolute;
+    }
+    Volume.adjustedIsoValue = adjustedIsoValue;
     var defaultStats = { min: -1, max: 1, mean: 0, sigma: 0.1 };
     function createIsoValueParam(defaultValue, stats) {
         var sts = stats || defaultStats;

package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts

@@ -125,6 +125,11 @@ export declare const BasicSchema: {
         pdbx_PDB_ins_code: import("../../../mol-data/db/column").Column.Schema.Str;
         pdbx_PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         pdbx_formal_charge: import("../../../mol-data/db/column").Column.Schema.Int;
+        pdbx_label_index: import("../../../mol-data/db/column").Column.Schema.Int;
+        pdbx_sifts_xref_db_name: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_acc: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_num: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_res: import("../../../mol-data/db/column").Column.Schema.Str;
         ihm_model_id: import("../../../mol-data/db/column").Column.Schema.Int;
     };
     ihm_sphere_obj_site: {

package/lib/commonjs/mol-model-formats/structure/common/property.d.ts

@@ -1,7 +1,8 @@
 /**
- * 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>
  */
 import { Model } from '../../../mol-model/structure';
 import { ModelFormat } from '../../format';
@@ -24,5 +25,7 @@ interface FormatPropertyProvider<T> {
     delete(model: Model): void;
 }
 declare namespace FormatPropertyProvider {
-    function create<T>(descriptor: CustomPropertyDescriptor): FormatPropertyProvider<T>;
+    function create<T>(descriptor: CustomPropertyDescriptor, options?: {
+        asDynamic?: boolean;
+    }): FormatPropertyProvider<T>;
 }

package/lib/commonjs/mol-model-formats/structure/common/property.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FormatPropertyProvider = void 0;
@@ -31,7 +32,7 @@ var FormatRegistry = /** @class */ (function () {
 }());
 var FormatPropertyProvider;
 (function (FormatPropertyProvider) {
-    function create(descriptor) {
+    function create(descriptor, options) {
         var name = descriptor.name;
         var formatRegistry = new FormatRegistry();
         return {
@@ -41,22 +42,33 @@ var FormatPropertyProvider;
                 return formatRegistry.isApplicable(model);
             },
             get: function (model) {
-                if (model._staticPropertyData[name])
-                    return model._staticPropertyData[name];
+                var store = (options === null || options === void 0 ? void 0 : options.asDynamic) ? model._dynamicPropertyData : model._staticPropertyData;
+                if (store[name])
+                    return store[name];
                 if (model.customProperties.has(descriptor))
                     return;
                 var obtain = formatRegistry.get(model.sourceData.kind);
                 if (!obtain)
                     return;
-                model._staticPropertyData[name] = obtain(model);
+                store[name] = obtain(model);
                 model.customProperties.add(descriptor);
-                return model._staticPropertyData[name];
+                return store[name];
             },
             set: function (model, value) {
-                model._staticPropertyData[name] = value;
+                if (options === null || options === void 0 ? void 0 : options.asDynamic) {
+                    model._dynamicPropertyData[name] = value;
+                }
+                else {
+                    model._staticPropertyData[name] = value;
+                }
             },
             delete: function (model) {
-                delete model._staticPropertyData[name];
+                if (options === null || options === void 0 ? void 0 : options.asDynamic) {
+                    delete model._dynamicPropertyData[name];
+                }
+                else {
+                    delete model._staticPropertyData[name];
+                }
             }
         };
     }

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019-2022 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>
  */
 import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js

@@ -3,6 +3,7 @@
  * Copyright (c) 2019-2022 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.IndexPairBonds = void 0;
@@ -29,7 +30,7 @@ var IndexPairBonds;
     IndexPairBonds.Descriptor = {
         name: 'index_pair_bonds',
     };
-    IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor);
+    IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor, { asDynamic: true });
     IndexPairBonds.DefaultProps = {
         /**
          * If negative, test using element-based threshold, otherwise distance in Angstrom.

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 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>
  */

package/lib/commonjs/mol-model-props/computed/interactions/common.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 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>
  */
@@ -64,29 +64,21 @@ var InteractionsInterContacts = /** @class */ (function (_super) {
     (0, tslib_1.__extends)(InteractionsInterContacts, _super);
     function InteractionsInterContacts(map, unitsFeatures) {
         var _this = _super.call(this, map) || this;
-        var count = 0;
-        var elementKeyIndex = new Map();
-        var add = function (index, unitId) {
-            var vertexKey = _this.getElementKey(index, unitId);
-            var e = elementKeyIndex.get(vertexKey);
-            if (e === undefined)
-                elementKeyIndex.set(vertexKey, [count]);
-            else
-                e.push(count);
-        };
-        _this.map.forEach(function (pairEdgesArray) {
-            pairEdgesArray.forEach(function (_a) {
-                var unitA = _a.unitA, connectedIndices = _a.connectedIndices;
-                connectedIndices.forEach(function (indexA) {
-                    var _a = unitsFeatures.get(unitA), offsetsA = _a.offsets, membersA = _a.members;
-                    for (var j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
-                        add(membersA[j], unitA);
-                    }
-                    count += 1;
-                });
-            });
-        });
-        _this.elementKeyIndex = elementKeyIndex;
+        _this.elementKeyIndex = new Map();
+        for (var i = 0, il = _this.edges.length; i < il; ++i) {
+            var _a = _this.edges[i], unitA = _a.unitA, indexA = _a.indexA;
+            var _b = unitsFeatures.get(unitA), offsets = _b.offsets, members = _b.members;
+            for (var j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
+                var vertexKey = _this.getElementKey(members[j], unitA);
+                var e = _this.elementKeyIndex.get(vertexKey);
+                if (e === undefined) {
+                    _this.elementKeyIndex.set(vertexKey, [i]);
+                }
+                else {
+                    e.push(i);
+                }
+            }
+        }
         return _this;
     }
     InteractionsInterContacts.prototype.getContactIndicesForElement = function (index, unit) {

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.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>
  */