molstar 3.0.0-dev.8 → 3.0.2

package/lib/commonjs/mol-model-formats/structure/basic/parser.js

@@ -27,7 +27,7 @@ function createModels(data, format, ctx) {
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    properties = (0, properties_1.getProperties)(data);
+                    properties = getCommonProperties(data, format);
                     if (!(data.ihm_model_list._rowCount > 0)) return [3 /*break*/, 2];
                     return [4 /*yield*/, readIntegrative(ctx, data, properties, format)];
                 case 1:
@@ -48,6 +48,13 @@ function createModels(data, format, ctx) {
     });
 }
 exports.createModels = createModels;
+function getCommonProperties(data, format) {
+    return {
+        missingResidues: (0, properties_1.getMissingResidues)(data),
+        chemicalComponentMap: (0, properties_1.getChemicalComponentMap)(data),
+        saccharideComponentMap: (0, properties_1.getSaccharideComponentMap)(data)
+    };
+}
 /** Standard atomic model */
 function createStandardModel(data, atom_site, sourceIndex, entities, properties, format, previous) {
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
@@ -58,6 +65,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var coarse = coarse_1.EmptyCoarse;
     var sequence = (0, sequence_1.getSequence)(data, entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, entities, atomic.conformation, sequence);
+    var structAsymMap = (0, properties_1.getStructAsymMap)(atomic.hierarchy);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
@@ -73,7 +81,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         sourceData: format,
         modelNum: modelNum,
         parent: undefined,
-        entities: entities,
+        entities: (0, entities_1.getEntitiesWithPRD)(data, entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -81,7 +89,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -90,7 +98,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
 /** Integrative model with atomic/coarse parts */
 function createIntegrativeModel(data, ihm, properties, format) {
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    var coarse = (0, coarse_1.getCoarse)(ihm, properties);
+    var coarse = (0, coarse_1.getCoarse)(ihm, properties.chemicalComponentMap);
     var sequence = (0, sequence_1.getSequence)(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
     var entry = data.entry.id.valueKind(0) === 0 /* Present */
@@ -104,6 +112,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         label.push(ihm.model_name);
     if (ihm.model_group_name)
         label.push(ihm.model_group_name);
+    var structAsymMap = (0, properties_1.getStructAsymMap)(atomic.hierarchy, data);
     return {
         id: uuid_1.UUID.create22(),
         entryId: entry,
@@ -112,7 +121,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         sourceData: format,
         modelNum: ihm.model_id,
         parent: undefined,
-        entities: ihm.entities,
+        entities: (0, entities_1.getEntitiesWithPRD)(data, ihm.entities, structAsymMap),
         sequence: sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -120,7 +129,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: properties,
+        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -144,7 +153,7 @@ function readStandard(ctx, data, properties, format) {
                     models = [];
                     if (!data.atom_site) return [3 /*break*/, 3];
                     atomCount = data.atom_site.id.rowCount;
-                    entities = (0, entities_1.getEntities)(data, properties);
+                    entities = (0, entities_1.getEntityData)(data);
                     modelStart = 0;
                     _b.label = 1;
                 case 1:
@@ -184,7 +193,7 @@ function readIntegrative(ctx, data, properties, format) {
         return (0, tslib_1.__generator)(this, function (_c) {
             switch (_c.label) {
                 case 0:
-                    entities = (0, entities_1.getEntities)(data, properties);
+                    entities = (0, entities_1.getEntityData)(data);
                     atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
                         ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num;
                     atom_sites = splitTable(data.atom_site, atom_sites_modelColumn);

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

@@ -5,5 +5,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Model } from '../../../mol-model/structure/model/model';
+import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
+import { SaccharideComponentMap } from '../../../mol-model/structure/structure/carbohydrates/constants';
 import { BasicData } from './schema';
-export declare function getProperties(data: BasicData): Model['properties'];
+export declare function getMissingResidues(data: BasicData): Model['properties']['missingResidues'];
+export declare function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'];
+export declare function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap;
+export declare function getStructAsymMap(atomic: AtomicHierarchy, data?: BasicData): Model['properties']['structAsymMap'];

package/lib/commonjs/mol-model-formats/structure/basic/properties.js

@@ -6,11 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getProperties = void 0;
+exports.getStructAsymMap = exports.getSaccharideComponentMap = exports.getChemicalComponentMap = exports.getMissingResidues = void 0;
+var db_1 = require("../../../mol-data/db");
 var types_1 = require("../../../mol-model/structure/model/types");
 var constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
 var memoize_1 = require("../../../mol-util/memoize");
-var db_1 = require("../../../mol-data/db");
 function getMissingResidues(data) {
     var map = new Map();
     var getKey = function (model_num, asym_id, seq_id) {
@@ -31,6 +31,7 @@ function getMissingResidues(data) {
         size: map.size
     };
 }
+exports.getMissingResidues = getMissingResidues;
 function getChemicalComponentMap(data) {
     var map = new Map();
     if (data.chem_comp._rowCount > 0) {
@@ -47,6 +48,7 @@ function getChemicalComponentMap(data) {
     }
     return map;
 }
+exports.getChemicalComponentMap = getChemicalComponentMap;
 function getSaccharideComponentMap(data) {
     var map = new Map();
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -93,6 +95,7 @@ function getSaccharideComponentMap(data) {
     }
     return map;
 }
+exports.getSaccharideComponentMap = getSaccharideComponentMap;
 var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     var uniqueNames = new Set();
     var _a = data.atom_site, label_comp_id = _a.label_comp_id, auth_comp_id = _a.auth_comp_id;
@@ -102,20 +105,15 @@ var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     }
     return uniqueNames;
 });
-function getStructAsymMap(data) {
+function getStructAsymMap(atomic, data) {
     var map = new Map();
-    var _a = data.atom_site, label_asym_id = _a.label_asym_id, auth_asym_id = _a.auth_asym_id, label_entity_id = _a.label_entity_id;
-    for (var i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    var _a = atomic.chains, auth_asym_id = _a.auth_asym_id, label_asym_id = _a.label_asym_id, label_entity_id = _a.label_entity_id;
+    for (var i = 0, _i = atomic.chains._rowCount; i < _i; i++) {
         var id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id: id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id: id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
     }
-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data === null || data === void 0 ? void 0 : data.struct_asym._rowCount) {
         var _b = data.struct_asym, id = _b.id, entity_id = _b.entity_id;
         for (var i = 0, il = id.rowCount; i < il; ++i) {
             var _id = id.value(i);
@@ -130,13 +128,5 @@ function getStructAsymMap(data) {
     }
     return map;
 }
-function getProperties(data) {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
-}
-exports.getProperties = getProperties;
+exports.getStructAsymMap = getStructAsymMap;
 //# sourceMappingURL=properties.js.map

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

@@ -1,8 +1,9 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { MolFile } from '../../mol-io/reader/mol/parser';
 import { RuntimeContext, Task } from '../../mol-task';

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

@@ -1,31 +1,44 @@
 "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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.trajectoryFromMol = exports.MolFormat = exports.getMolModels = void 0;
 var tslib_1 = require("tslib");
 var db_1 = require("../../mol-data/db");
+var parser_1 = require("../../mol-io/reader/mol/parser");
 var mol_task_1 = require("../../mol-task");
-var parser_1 = require("./basic/parser");
+var parser_2 = require("./basic/parser");
 var schema_1 = require("./basic/schema");
 var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 var index_pair_1 = require("./property/bonds/index-pair");
 function getMolModels(mol, format, ctx) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, bonds, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    atoms = mol.atoms, bonds = mol.bonds;
+                    atoms = mol.atoms, bonds = mol.bonds, formalCharges = mol.formalCharges;
                     MOL = db_1.Column.ofConst('MOL', mol.atoms.count, db_1.Column.Schema.str);
                     A = db_1.Column.ofConst('A', mol.atoms.count, db_1.Column.Schema.str);
                     type_symbol = db_1.Column.asArrayColumn(atoms.type_symbol);
                     seq_id = db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int);
+                    computedFormalCharges = new Int32Array(mol.atoms.count);
+                    if (formalCharges.atomIdx.rowCount > 0) {
+                        for (i = 0; i < formalCharges.atomIdx.rowCount; i++) {
+                            computedFormalCharges[formalCharges.atomIdx.value(i) - 1] = formalCharges.charge.value(i);
+                        }
+                    }
+                    else {
+                        for (i = 0; i < mol.atoms.count; i++) {
+                            computedFormalCharges[i] = (0, parser_1.formalChargeMapper)(atoms.formal_charge.value(i));
+                        }
+                    }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
                         auth_atom_id: type_symbol,
@@ -43,6 +56,7 @@ function getMolModels(mol, format, ctx) {
                         occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
                         type_symbol: type_symbol,
                         pdbx_PDB_model_num: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int),
+                        pdbx_formal_charge: db_1.Column.ofIntArray(computedFormalCharges)
                     }, atoms.count);
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
@@ -55,7 +69,7 @@ function getMolModels(mol, format, ctx) {
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
+                    return [4 /*yield*/, (0, parser_2.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
                 case 1:
                     models = _a.sent();
                     if (models.frameCount > 0) {

package/lib/commonjs/mol-model-formats/structure/mol2.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-model-formats/structure/mol2.js

@@ -1,6 +1,6 @@
 "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>
  */
@@ -17,9 +17,12 @@ var index_pair_1 = require("./property/bonds/index-pair");
 var partial_charge_1 = require("./property/partial-charge");
 var structure_1 = require("../../mol-model/structure");
 var util_1 = require("./util");
+var symmetry_1 = require("./property/symmetry");
+var geometry_1 = require("../../mol-math/geometry");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function getModels(mol2, ctx) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, i, il, _a, atoms, bonds, molecule, A, type_symbol, i_1, atom_site, entityBuilder, componentBuilder, i_2, il_1, basics, _models, indexA, indexB, order, flag, pairBonds, first;
+        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basics, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
                 case 0:
@@ -28,11 +31,20 @@ function getModels(mol2, ctx) {
                     _b.label = 1;
                 case 1:
                     if (!(i < il)) return [3 /*break*/, 4];
-                    _a = mol2.structures[i], atoms = _a.atoms, bonds = _a.bonds, molecule = _a.molecule;
+                    _a = mol2.structures[i], molecule = _a.molecule, atoms = _a.atoms, bonds = _a.bonds, crysin = _a.crysin;
                     A = db_1.Column.ofConst('A', atoms.count, db_1.Column.Schema.str);
                     type_symbol = new Array(atoms.count);
+                    hasAtomType = false;
                     for (i_1 = 0; i_1 < atoms.count; ++i_1) {
-                        type_symbol[i_1] = (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_1));
+                        if (atoms.atom_type.value(i_1).includes('.')) {
+                            hasAtomType = true;
+                            break;
+                        }
+                    }
+                    for (i_2 = 0; i_2 < atoms.count; ++i_2) {
+                        type_symbol[i_2] = hasAtomType
+                            ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
+                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2));
                     }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -56,8 +68,8 @@ function getModels(mol2, ctx) {
                     entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
                     entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(atoms.subst_id, atoms.atom_name);
-                    for (i_2 = 0, il_1 = atoms.subst_name.rowCount; i_2 < il_1; ++i_2) {
-                        componentBuilder.add(atoms.subst_name.value(i_2), i_2);
+                    for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
+                        componentBuilder.add(atoms.subst_name.value(i_3), i_3);
                     }
                     basics = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
@@ -70,6 +82,7 @@ function getModels(mol2, ctx) {
                     if (_models.frameCount > 0) {
                         indexA = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.origin_atom_id, function (x) { return x - 1; }, Int32Array));
                         indexB = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.target_atom_id, function (x) { return x - 1; }, Int32Array));
+                        key = bonds.bond_id;
                         order = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.bond_type, function (x) {
                             switch (x) {
                                 case 'ar': // aromatic
@@ -96,13 +109,18 @@ function getModels(mol2, ctx) {
                                     return 1 /* Covalent */;
                             }
                         }, Int8Array));
-                        pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
+                        pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
                         first = _models.representative;
                         index_pair_1.IndexPairBonds.Provider.set(first, pairBonds);
                         partial_charge_1.AtomPartialCharge.Provider.set(first, {
                             data: atoms.charge,
                             type: molecule.charge_type
                         });
+                        if (crysin) {
+                            symmetry = getSymmetry(crysin);
+                            if (symmetry)
+                                symmetry_1.ModelSymmetry.Provider.set(first, symmetry);
+                        }
                         models.push(first);
                     }
                     _b.label = 3;
@@ -114,6 +132,18 @@ function getModels(mol2, ctx) {
         });
     });
 }
+function getSymmetry(crysin) {
+    // TODO handle `crysin.setting`
+    if (crysin.setting !== 1)
+        return;
+    var spaceCell = geometry_1.SpacegroupCell.create(crysin.spaceGroup, linear_algebra_1.Vec3.create(crysin.a, crysin.b, crysin.c), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180));
+    return {
+        spacegroup: geometry_1.Spacegroup.create(spaceCell),
+        assemblies: [],
+        isNonStandardCrystalFrame: false,
+        ncsOperators: []
+    };
+}
 var Mol2Format;
 (function (Mol2Format) {
     function is(x) {

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.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>
  */
@@ -10,6 +10,7 @@ import { FormatPropertyProvider } from '../../common/property';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { ElementIndex } from '../../../../mol-model/structure';
 export declare type IndexPairsProps = {
+    readonly key: ArrayLike<number>;
     readonly order: ArrayLike<number>;
     readonly distance: ArrayLike<number>;
     readonly flag: ArrayLike<BondType.Flag>;
@@ -26,13 +27,29 @@ export declare namespace IndexPairBonds {
         pairs: {
             indexA: Column<number>;
             indexB: Column<number>;
+            key?: Column<number>;
             order?: Column<number>;
+            /**
+             * Useful for bonds in periodic cells. That is, only bonds within the given
+             * distance are added. This allows for bond between periodic image but
+             * avoids unwanted bonds with wrong distances. If negative, test using the
+             * `maxDistance` option from `Props`.
+             */
             distance?: Column<number>;
             flag?: Column<BondType.Flag>;
         };
         count: number;
     };
     const DefaultProps: {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
         maxDistance: number;
     };
     type Props = typeof DefaultProps;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -9,19 +9,20 @@ exports.IndexPairBonds = void 0;
 var tslib_1 = require("tslib");
 var graph_1 = require("../../../../mol-math/graph");
 var property_1 = require("../../common/property");
-var common_1 = require("../../../../mol-model/structure/structure/unit/bonds/common");
 function getGraph(indexA, indexB, props, count) {
     var builder = new graph_1.IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
+    var key = new Int32Array(builder.slotCount);
     var order = new Int8Array(builder.slotCount);
     var distance = new Array(builder.slotCount);
     var flag = new Array(builder.slotCount);
     for (var i = 0, _i = builder.edgeCount; i < _i; i++) {
         builder.addNextEdge();
+        builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
         builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
     }
-    return builder.createGraph({ order: order, distance: distance, flag: flag });
+    return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
 }
 var IndexPairBonds;
 (function (IndexPairBonds) {
@@ -29,18 +30,30 @@ var IndexPairBonds;
         name: 'index_pair_bonds',
     };
     IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor);
-    IndexPairBonds.DefaultProps = { maxDistance: common_1.DefaultBondMaxRadius };
+    IndexPairBonds.DefaultProps = {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
+        maxDistance: -1
+    };
     function fromData(data, props) {
         if (props === void 0) { props = {}; }
         var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, IndexPairBonds.DefaultProps), props);
         var pairs = data.pairs, count = data.count;
         var indexA = pairs.indexA.toArray();
         var indexB = pairs.indexB.toArray();
+        var key = pairs.key && pairs.key.toArray();
         var order = pairs.order && pairs.order.toArray();
         var distance = pairs.distance && pairs.distance.toArray();
         var flag = pairs.flag && pairs.flag.toArray();
         return {
-            bonds: getGraph(indexA, indexB, { order: order, distance: distance, flag: flag }, count),
+            bonds: getGraph(indexA, indexB, { key: key, order: order, distance: distance, flag: flag }, count),
             maxDistance: p.maxDistance
         };
     }

package/lib/commonjs/mol-model-props/common/custom-property.d.ts

@@ -47,7 +47,7 @@ declare namespace CustomProperty {
             }>>;
         };
         setDefaultAutoAttach(name: string, value: boolean): void;
-        get(name: string): Provider<Data, any, any>;
+        get(name: string): Provider<Data, any, any> | undefined;
         register(provider: Provider<Data, any, any>, defaultAutoAttach: boolean): void;
         unregister(name: string): void;
     }

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>
  */