molstar 3.0.0-dev.8 → 3.0.0-dev.9

package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.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>
@@ -17,4 +17,5 @@ export declare const MetalsSet: Set<number>;
 export declare function getElementIdx(e: ElementSymbol): number;
 export declare function getElementPairThreshold(i: number, j: number): number;
 export declare function getElementThreshold(i: number): number;
+export declare function getPairingThreshold(elementIndexA: number, elementIndexB: number, thresholdA: number, thresholdB: number): number;
 export declare function isHydrogen(i: number): boolean;

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

@@ -1,12 +1,12 @@
 "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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isHydrogen = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
+exports.isHydrogen = exports.getPairingThreshold = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
 /** Default for atomic bonds */
 exports.DefaultBondMaxRadius = 4;
 exports.DefaultBondComputationProps = {
@@ -105,6 +105,15 @@ function getElementThreshold(i) {
     return r;
 }
 exports.getElementThreshold = getElementThreshold;
+function getPairingThreshold(elementIndexA, elementIndexB, thresholdA, thresholdB) {
+    var thresholdAB = getElementPairThreshold(elementIndexA, elementIndexB);
+    return thresholdAB > 0
+        ? thresholdAB
+        : elementIndexB < 0
+            ? thresholdA
+            : (thresholdA + thresholdB) / 1.95; // not sure if avg or min but max is too big
+}
+exports.getPairingThreshold = getPairingThreshold;
 var H_ID = __ElementIndex['H'];
 function isHydrogen(i) {
     return i === H_ID;

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.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/unit/bonds/inter-compute.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>
@@ -70,11 +70,26 @@ function findPairBonds(unitA, unitB, props, builder) {
                 var _bI = int_1.SortedArray.indexOf(unitB.elements, bI);
                 if (_bI < 0)
                     continue;
-                if (type_symbolA.value(aI) === 'H' && type_symbolB.value(bI) === 'H')
-                    continue;
+                var aeI_1 = (0, common_1.getElementIdx)(type_symbolA.value(aI));
+                var beI = (0, common_1.getElementIdx)(type_symbolA.value(bI));
                 var d = distance[i];
                 var dist = getDistance(unitA, aI, unitB, bI);
-                if ((d !== -1 && (0, common_2.equalEps)(dist, d, 0.5)) || dist < maxDistance) {
+                var add = false;
+                if (d >= 0) {
+                    add = (0, common_2.equalEps)(dist, d, 0.3);
+                }
+                else if (maxDistance >= 0) {
+                    add = dist < maxDistance;
+                }
+                else {
+                    var pairingThreshold = (0, common_1.getPairingThreshold)(aeI_1, beI, (0, common_1.getElementThreshold)(aeI_1), (0, common_1.getElementThreshold)(beI));
+                    add = dist < pairingThreshold;
+                    if ((0, common_1.isHydrogen)(aeI_1) && (0, common_1.isHydrogen)(beI)) {
+                        // TODO handle molecular hydrogen
+                        add = false;
+                    }
+                }
+                if (add) {
                     builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
                 }
             }
@@ -138,12 +153,7 @@ function findPairBonds(unitA, unitB, props, builder) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = (0, common_1.getElementPairThreshold)(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + (0, common_1.getElementThreshold)(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, thresholdA, (0, common_1.getElementThreshold)(beI));
             if (dist <= pairingThreshold) {
                 var atomIdB = label_atom_idB.value(bI);
                 var compIdB = label_comp_idB.value(residueIndexB[bI]);

package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.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/unit/bonds/intra-compute.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>
@@ -53,7 +53,8 @@ function findIndexPairBonds(unit) {
     var orders = [];
     for (var _aI = 0; _aI < atomCount; _aI++) {
         var aI = atoms[_aI];
-        var isHa = type_symbol.value(aI) === 'H';
+        var aeI = (0, common_1.getElementIdx)(type_symbol.value(aI));
+        var isHa = (0, common_1.isHydrogen)(aeI);
         var srcA = sourceIndex.value(aI);
         for (var i = offset[srcA], il = offset[srcA + 1]; i < il; ++i) {
             var bI = invertedIndex[b[i]];
@@ -62,11 +63,25 @@ function findIndexPairBonds(unit) {
             var _bI = int_1.SortedArray.indexOf(unit.elements, bI);
             if (_bI < 0)
                 continue;
-            if (isHa && type_symbol.value(bI) === 'H')
-                continue;
+            var beI = (0, common_1.getElementIdx)(type_symbol.value(bI));
             var d = distance[i];
             var dist = getDistance(unit, aI, bI);
-            if ((d !== -1 && (0, common_2.equalEps)(dist, d, 0.5)) || dist < maxDistance) {
+            var add = false;
+            if (d >= 0) {
+                add = (0, common_2.equalEps)(dist, d, 0.3);
+            }
+            else if (maxDistance >= 0) {
+                add = dist < maxDistance;
+            }
+            else {
+                var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, (0, common_1.getElementThreshold)(aeI), (0, common_1.getElementThreshold)(beI));
+                add = dist < pairingThreshold;
+                if (isHa && (0, common_1.isHydrogen)(beI)) {
+                    // TODO handle molecular hydrogen
+                    add = false;
+                }
+            }
+            if (add) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
@@ -190,12 +205,7 @@ function findBonds(unit, props) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = (0, common_1.getElementPairThreshold)(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + (0, common_1.getElementThreshold)(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = (0, common_1.getPairingThreshold)(aeI, beI, thresholdA, (0, common_1.getElementThreshold)(beI));
             if (dist <= pairingThreshold) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;

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-plugin/config.d.ts

@@ -47,7 +47,7 @@ export declare const PluginConfig: {
         ShowAnimation: PluginConfigItem<boolean>;
     };
     Download: {
-        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe">;
+        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe" | "pdbj">;
         DefaultEmdbProvider: PluginConfigItem<EmdbDownloadProvider>;
     };
     Structure: {

package/lib/commonjs/mol-plugin-state/actions/structure.d.ts

@@ -14,6 +14,7 @@ export declare const PdbDownloadProvider: {
     pdbe: PD.Group<PD.Normalize<{
         variant: "updated" | "updated-bcif" | "updtaed-bcif" | "archival";
     }>>;
+    pdbj: PD.Group<PD.Normalize<unknown>>;
 };
 export declare type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
 export { DownloadStructure };

package/lib/commonjs/mol-plugin-state/actions/structure.js

@@ -20,6 +20,7 @@ var model_1 = require("../transforms/model");
 var assets_1 = require("../../mol-util/assets");
 var config_1 = require("../../mol-plugin/config");
 var file_info_1 = require("../../mol-util/file-info");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 var DownloadModelRepresentationOptions = function (plugin) {
     var representationDefault = plugin.config.get(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.PresetStructureRepresentations.auto.id;
     return param_definition_1.ParamDefinition.Group({
@@ -36,6 +37,7 @@ exports.PdbDownloadProvider = {
     'pdbe': param_definition_1.ParamDefinition.Group({
         variant: param_definition_1.ParamDefinition.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']]),
     }, { label: 'PDBe', isFlat: true }),
+    'pdbj': param_definition_1.ParamDefinition.EmptyGroup({ label: 'PDBj' }),
 };
 var DownloadStructure = mol_state_1.StateAction.build({
     from: objects_1.PluginStateObject.Root,
@@ -110,14 +112,12 @@ var DownloadStructure = mol_state_1.StateAction.build({
                     format = src.params.format;
                     return [3 /*break*/, 15];
                 case 2: return [4 /*yield*/, (src.params.provider.server.name === 'pdbe'
-                        ? src.params.provider.server.params.variant === 'updated'
-                            ? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), "_updated.cif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, false)
-                            : src.params.provider.server.params.variant === 'updated-bcif'
-                                ? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/entry-files/download/".concat(id.toLowerCase(), ".bcif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, true)
-                                : getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBe: ".concat(id, " (cif)"); }, false)
-                        : src.params.provider.server.params.encoding === 'cif'
-                            ? getDownloadParams(src.params.provider.id, function (id) { return "https://files.rcsb.org/download/".concat(id.toUpperCase(), ".cif"); }, function (id) { return "RCSB: ".concat(id, " (cif)"); }, false)
-                            : getDownloadParams(src.params.provider.id, function (id) { return "https://models.rcsb.org/".concat(id.toUpperCase(), ".bcif"); }, function (id) { return "RCSB: ".concat(id, " (bcif)"); }, true))];
+                        ? getPdbeDownloadParams(src)
+                        : src.params.provider.server.name === 'pdbj'
+                            ? getPdbjDownloadParams(src)
+                            : src.params.provider.server.name === 'rcsb'
+                                ? getRcsbDownloadParams(src)
+                                : (0, type_helpers_1.assertUnreachable)(src))];
                 case 3:
                     downloadParams = _b.sent();
                     asTrajectory = !!src.params.options.asTrajectory;
@@ -270,6 +270,39 @@ function getDownloadParams(src, url, label, isBinary) {
         });
     });
 }
+function getPdbeDownloadParams(src) {
+    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return (0, tslib_1.__generator)(this, function (_a) {
+            if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbe')
+                throw new Error('expected pdbe');
+            return [2 /*return*/, src.params.provider.server.params.variant === 'updated'
+                    ? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), "_updated.cif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, false)
+                    : src.params.provider.server.params.variant === 'updated-bcif'
+                        ? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/entry-files/download/".concat(id.toLowerCase(), ".bcif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, true)
+                        : getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBe: ".concat(id, " (cif)"); }, false)];
+        });
+    });
+}
+function getPdbjDownloadParams(src) {
+    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return (0, tslib_1.__generator)(this, function (_a) {
+            if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbj')
+                throw new Error('expected pdbj');
+            return [2 /*return*/, getDownloadParams(src.params.provider.id, function (id) { return "https://data.pdbjbk1.pdbj.org/pub/pdb/data/structures/divided/mmCIF/".concat(id.toLowerCase().substring(1, 3), "/").concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBj: ".concat(id, " (cif)"); }, false)];
+        });
+    });
+}
+function getRcsbDownloadParams(src) {
+    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return (0, tslib_1.__generator)(this, function (_a) {
+            if (src.name !== 'pdb' || src.params.provider.server.name !== 'rcsb')
+                throw new Error('expected rcsb');
+            return [2 /*return*/, src.params.provider.server.params.encoding === 'cif'
+                    ? getDownloadParams(src.params.provider.id, function (id) { return "https://files.rcsb.org/download/".concat(id.toUpperCase(), ".cif"); }, function (id) { return "RCSB PDB: ".concat(id, " (cif)"); }, false)
+                    : getDownloadParams(src.params.provider.id, function (id) { return "https://models.rcsb.org/".concat(id.toUpperCase(), ".bcif"); }, function (id) { return "RCSB PDB: ".concat(id, " (bcif)"); }, true)];
+        });
+    });
+}
 exports.UpdateTrajectory = mol_state_1.StateAction.build({
     display: { name: 'Update Trajectory' },
     params: {

package/lib/mol-canvas3d/canvas3d.js

@@ -330,7 +330,7 @@ var Canvas3D;
                 return;
             }
             draw();
-            if (!camera.transition.inTransition && !controls.props.spin && !webgl.isContextLost) {
+            if (!camera.transition.inTransition && !webgl.isContextLost) {
                 interactionHelper.tick(currentTime);
             }
         }

package/lib/mol-io/reader/mol2/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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 Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-io/reader/mol2/parser.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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 Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -241,9 +241,38 @@ function handleBonds(state) {
         });
     });
 }
+function handleCrysin(state) {
+    var tokenizer = state.tokenizer;
+    while (tokenizer.position < tokenizer.data.length) {
+        var l = getTokenString(tokenizer);
+        if (l === '@<TRIPOS>MOLECULE') {
+            return;
+        }
+        else if (l === '@<TRIPOS>CRYSIN') {
+            break;
+        }
+        else {
+            markLine(tokenizer);
+        }
+    }
+    if (tokenizer.position >= tokenizer.data.length)
+        return;
+    markLine(tokenizer);
+    var values = getTokenString(tokenizer).trim().split(reWhitespace);
+    return {
+        a: parseFloat(values[0]),
+        b: parseFloat(values[1]),
+        c: parseFloat(values[2]),
+        alpha: parseFloat(values[3]),
+        beta: parseFloat(values[4]),
+        gamma: parseFloat(values[5]),
+        spaceGroup: parseInt(values[6], 10),
+        setting: parseInt(values[7], 10),
+    };
+}
 function parseInternal(ctx, data, name) {
     return __awaiter(this, void 0, void 0, function () {
-        var tokenizer, structures, state, atoms, bonds, result;
+        var tokenizer, structures, state, atoms, bonds, crysin, result;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -261,7 +290,8 @@ function parseInternal(ctx, data, name) {
                     return [4 /*yield*/, handleBonds(state)];
                 case 3:
                     bonds = _a.sent();
-                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds });
+                    crysin = handleCrysin(state);
+                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds, crysin: crysin });
                     skipWhitespace(tokenizer);
                     while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
                         markLine(tokenizer);

package/lib/mol-io/reader/mol2/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,10 +37,21 @@ export interface Mol2Bonds {
     bond_type: Column<string>;
     status_bits: Column<string>;
 }
+export interface Mol2Crysin {
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+    spaceGroup: number;
+    setting: number;
+}
 export interface Mol2Structure {
     molecule: Readonly<Mol2Molecule>;
     atoms: Readonly<Mol2Atoms>;
     bonds: Readonly<Mol2Bonds>;
+    crysin?: Readonly<Mol2Crysin>;
 }
 export interface Mol2File {
     name: string;

package/lib/mol-io/reader/mol2/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

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

@@ -49,6 +49,7 @@ export var Stats;
         }
         else if (size === 1) {
             if (Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+                // handled in `handleUnitChainsSimple`
                 return;
             }
             else {
@@ -174,6 +175,13 @@ export var Stats;
                     Location.set(stats.firstChainLoc, structure, unit, offsets[cI]);
                 }
             }
+            else if (size === 1) {
+                // need to handle here, skipped in `handleElement`
+                stats.elementCount += 1;
+                if (stats.elementCount === 1) {
+                    Location.set(stats.firstElementLoc, structure, unit, eI);
+                }
+            }
         }
     }
     function handleUnitChainsPartitioned(stats, structure, lociElements, start, end) {

package/lib/mol-model/structure/structure/unit/bonds/common.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>
@@ -17,4 +17,5 @@ export declare const MetalsSet: Set<number>;
 export declare function getElementIdx(e: ElementSymbol): number;
 export declare function getElementPairThreshold(i: number, j: number): number;
 export declare function getElementThreshold(i: number): number;
+export declare function getPairingThreshold(elementIndexA: number, elementIndexB: number, thresholdA: number, thresholdB: number): number;
 export declare function isHydrogen(i: number): boolean;