molstar 3.3.0 → 3.5.0

package/lib/commonjs/mol-math/graph/inter-unit-graph.js

@@ -30,7 +30,7 @@ var InterUnitGraph = /** @class */ (function () {
                             vertexKeyIndex.set(vertexKey, [edges.length]);
                         else
                             e.push(edges.length);
-                        edges.push((0, tslib_1.__assign)((0, tslib_1.__assign)({}, edgeInfo), { indexA: indexA, unitA: unitA, unitB: unitB }));
+                        edges.push(tslib_1.__assign(tslib_1.__assign({}, edgeInfo), { indexA: indexA, unitA: unitA, unitB: unitB }));
                     });
                 });
             });

package/lib/commonjs/mol-math/graph.js

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./graph/int-adjacency-graph"), exports);
+tslib_1.__exportStar(require("./graph/int-adjacency-graph"), exports);

package/lib/commonjs/mol-math/linear-algebra.js

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./linear-algebra/3d"), exports);
-(0, tslib_1.__exportStar)(require("./linear-algebra/tensor"), exports);
+tslib_1.__exportStar(require("./linear-algebra/3d"), exports);
+tslib_1.__exportStar(require("./linear-algebra/tensor"), exports);

package/lib/commonjs/mol-model/sequence/alignment/alignment.js

@@ -15,7 +15,7 @@ var DefaultAlignmentOptions = {
 };
 function align(seqA, seqB, options) {
     if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultAlignmentOptions), options);
+    var o = tslib_1.__assign(tslib_1.__assign({}, DefaultAlignmentOptions), options);
     var alignment = new Alignment(seqA, seqB, o);
     alignment.calculate();
     return alignment.trace();

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

@@ -9,6 +9,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.Sequence = void 0;
 var constants_1 = require("./constants");
 var db_1 = require("../../mol-data/db");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 var Sequence;
 (function (Sequence) {
     function getSequenceString(seq) {
@@ -43,7 +44,7 @@ var Sequence;
             case "generic" /* Generic */:
                 code = function () { return 'X'; };
                 break;
-            default: throw new Error("unknown kind '".concat(kind, "'"));
+            default: (0, type_helpers_1.assertUnreachable)(kind);
         }
         if (map && map.size > 0) {
             return function (name) {

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./sequence/sequence"), exports);
+tslib_1.__exportStar(require("./sequence/sequence"), exports);

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./shape/shape"), exports);
+tslib_1.__exportStar(require("./shape/shape"), exports);

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./coordinates/coordinates"), exports);
+tslib_1.__exportStar(require("./coordinates/coordinates"), exports);

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

@@ -38,7 +38,7 @@ function compare_ssr(x, y) {
     return a.sheet_id < b.sheet_id ? -1 : a.sheet_id === b.sheet_id ? x.start.element - y.start.element : 1;
 }
 ;
-var struct_conf_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+var struct_conf_fields = function () { return tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([
     CifField.str('conf_type_id', function (i, data) { return data[i].element.type_id; }),
     CifField.str('id', function (i, data, idx) { return "".concat(data[i].element.type_id).concat(idx + 1); })
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
@@ -48,7 +48,7 @@ var struct_conf_fields = function () { return (0, tslib_1.__spreadArray)((0, tsl
     }),
     CifField.int('pdbx_PDB_helix_length', function (i, data) { return data[i].length; })
 ], false); };
-var struct_sheet_range_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+var struct_sheet_range_fields = function () { return tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([
     CifField.str('sheet_id', function (i, data) { return data[i].element.sheet_id; }),
     CifField.index('id')
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [

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

@@ -33,7 +33,7 @@ var Model;
         var coarseGrained = isCoarseGrained(model);
         for (var i = 0, il = frames.length; i < il; ++i) {
             var f = frames[i];
-            var m = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, model), { id: uuid_1.UUID.create22(), modelNum: i, atomicConformation: coordinates_1.Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
+            var m = tslib_1.__assign(tslib_1.__assign({}, model), { id: uuid_1.UUID.create22(), modelNum: i, atomicConformation: coordinates_1.Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
                 customProperties: new custom_property_1.CustomProperties(), _staticPropertyData: Object.create(null), _dynamicPropertyData: Object.create(null) });
@@ -53,9 +53,9 @@ var Model;
     Model.trajectoryFromModelAndCoordinates = trajectoryFromModelAndCoordinates;
     function trajectoryFromTopologyAndCoordinates(topology, coordinates) {
         var _this = this;
-        return mol_task_1.Task.create('Create Trajectory', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Create Trajectory', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, model, trajectory, bondData, indexPairBonds, coarseGrained, index, _a, trajectory_2, m;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, (0, parser_1.createModels)(topology.basic, topology.sourceData, ctx)];
                     case 1:

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

@@ -6,6 +6,6 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./atomic/conformation"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/hierarchy"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/measures"), exports);
+tslib_1.__exportStar(require("./atomic/conformation"), exports);
+tslib_1.__exportStar(require("./atomic/hierarchy"), exports);
+tslib_1.__exportStar(require("./atomic/measures"), exports);

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

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./coarse/conformation"), exports);
-(0, tslib_1.__exportStar)(require("./coarse/hierarchy"), exports);
+tslib_1.__exportStar(require("./coarse/conformation"), exports);
+tslib_1.__exportStar(require("./coarse/hierarchy"), exports);

package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+export declare const SaccharideNames: Set<string>;

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

@@ -0,0 +1,11 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SaccharideNames = void 0;
+exports.SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KTU', 'L1L', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);

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

@@ -9,11 +9,11 @@ exports.StructureSequence = exports.Symmetry = exports.Types = exports.Model = v
 var tslib_1 = require("tslib");
 var model_1 = require("./model/model");
 Object.defineProperty(exports, "Model", { enumerable: true, get: function () { return model_1.Model; } });
-var Types = (0, tslib_1.__importStar)(require("./model/types"));
+var Types = tslib_1.__importStar(require("./model/types"));
 exports.Types = Types;
 var symmetry_1 = require("./model/properties/symmetry");
 Object.defineProperty(exports, "Symmetry", { enumerable: true, get: function () { return symmetry_1.Symmetry; } });
 var sequence_1 = require("./model/properties/sequence");
 Object.defineProperty(exports, "StructureSequence", { enumerable: true, get: function () { return sequence_1.StructureSequence; } });
-(0, tslib_1.__exportStar)(require("./model/properties/custom/indexed"), exports);
-(0, tslib_1.__exportStar)(require("./model/indexing"), exports);
+tslib_1.__exportStar(require("./model/properties/custom/indexed"), exports);
+tslib_1.__exportStar(require("./model/indexing"), exports);

package/lib/commonjs/mol-model/structure/query/queries/generators.js

@@ -19,9 +19,9 @@ var none = function (ctx) { return selection_1.StructureSelection.Sequence(ctx.i
 exports.none = none;
 var all = function (ctx) { return selection_1.StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure); };
 exports.all = all;
-function residues(params) { return atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }
+function residues(params) { return atoms(tslib_1.__assign(tslib_1.__assign({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }
 exports.residues = residues;
-function chains(params) { return atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.chain.key(ctx.element); } })); }
+function chains(params) { return atoms(tslib_1.__assign(tslib_1.__assign({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.chain.key(ctx.element); } })); }
 exports.chains = chains;
 function _true(ctx) { return true; }
 function _zero(ctx) { return 0; }

package/lib/commonjs/mol-model/structure/query/queries/modifiers.js

@@ -129,7 +129,7 @@ function includeSurroundings(query, params) {
     return function query_includeSurroundings(ctx) {
         var inner = query(ctx);
         if (params.elementRadius) {
-            var prms = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { elementRadius: params.elementRadius, elementRadiusClosure: createElementRadiusFn(ctx, params.elementRadius), sourceMaxRadius: findStructureRadius(ctx, params.elementRadius) });
+            var prms = tslib_1.__assign(tslib_1.__assign({}, params), { elementRadius: params.elementRadius, elementRadiusClosure: createElementRadiusFn(ctx, params.elementRadius), sourceMaxRadius: findStructureRadius(ctx, params.elementRadius) });
             if (selection_1.StructureSelection.isSingleton(inner)) {
                 var surr = getIncludeSurroundingsWithRadius(ctx, ctx.inputStructure, inner.structure, prms);
                 var ret = selection_1.StructureSelection.Singletons(ctx.inputStructure, surr);
@@ -600,7 +600,7 @@ var StructConnGraph = /** @class */ (function () {
                 added.add(b);
                 var v = this.vertices.get(b);
                 if (u.operator_name === v.operator_name) {
-                    set.add((0, tslib_1.__assign)((0, tslib_1.__assign)({}, v), { operator_name: start.operator_name }));
+                    set.add(tslib_1.__assign(tslib_1.__assign({}, v), { operator_name: start.operator_name }));
                 }
                 else {
                     set.add(v);

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

@@ -11,12 +11,12 @@ var selection_1 = require("./query/selection");
 Object.defineProperty(exports, "StructureSelection", { enumerable: true, get: function () { return selection_1.StructureSelection; } });
 var query_1 = require("./query/query");
 Object.defineProperty(exports, "StructureQuery", { enumerable: true, get: function () { return query_1.StructureQuery; } });
-(0, tslib_1.__exportStar)(require("./query/context"), exports);
-var generators = (0, tslib_1.__importStar)(require("./query/queries/generators"));
-var modifiers = (0, tslib_1.__importStar)(require("./query/queries/modifiers"));
-var filters = (0, tslib_1.__importStar)(require("./query/queries/filters"));
-var combinators = (0, tslib_1.__importStar)(require("./query/queries/combinators"));
-var internal = (0, tslib_1.__importStar)(require("./query/queries/internal"));
+tslib_1.__exportStar(require("./query/context"), exports);
+var generators = tslib_1.__importStar(require("./query/queries/generators"));
+var modifiers = tslib_1.__importStar(require("./query/queries/modifiers"));
+var filters = tslib_1.__importStar(require("./query/queries/filters"));
+var combinators = tslib_1.__importStar(require("./query/queries/combinators"));
+var internal = tslib_1.__importStar(require("./query/queries/internal"));
 var predicates_1 = require("./query/predicates");
 exports.Queries = {
     generators: generators,

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

@@ -304,7 +304,7 @@ function computeCarbohydrates(structure) {
             });
         });
     }
-    return (0, tslib_1.__assign)({ links: links, terminalLinks: terminalLinks, elements: elements, partialElements: partialElements }, buildLookups(elements, links, terminalLinks));
+    return tslib_1.__assign({ links: links, terminalLinks: terminalLinks, elements: elements, partialElements: partialElements }, buildLookups(elements, links, terminalLinks));
 }
 exports.computeCarbohydrates = computeCarbohydrates;
 function buildLookups(elements, links, terminalLinks) {

package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -9,6 +9,7 @@ var _a, _b;
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SaccharideCompIdMap = exports.MonosaccharidesColorTable = exports.SaccharidesSnfgMap = exports.UnknownSaccharideComponent = exports.getSaccharideShape = exports.getSaccharideName = exports.SaccharideColors = void 0;
 var color_1 = require("../../../../mol-util/color");
+var saccharides_1 = require("../../model/types/saccharides");
 exports.SaccharideColors = (0, color_1.ColorMap)({
     Blue: 0x0090bc,
     Green: 0x00a651,
@@ -267,11 +268,6 @@ var CommonSaccharideNames = {
     Sor: ['SOE', 'UEA'],
     Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };
-var UnknownSaccharideNames = [
-    'NGZ',
-    'LAT',
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
 /**
  * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
  */
@@ -314,8 +310,9 @@ exports.SaccharideCompIdMap = (function () {
             }
         }
     }
-    for (var i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], exports.UnknownSaccharideComponent);
-    }
+    saccharides_1.SaccharideNames.forEach(function (name) {
+        if (!map.has(name))
+            map.set(name, exports.UnknownSaccharideComponent);
+    });
     return map;
 })();

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

@@ -7,8 +7,8 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./location"), exports);
-(0, tslib_1.__exportStar)(require("./loci"), exports);
-(0, tslib_1.__exportStar)(require("./bundle"), exports);
-(0, tslib_1.__exportStar)(require("./stats"), exports);
-(0, tslib_1.__exportStar)(require("./util"), exports);
+tslib_1.__exportStar(require("./location"), exports);
+tslib_1.__exportStar(require("./loci"), exports);
+tslib_1.__exportStar(require("./bundle"), exports);
+tslib_1.__exportStar(require("./stats"), exports);
+tslib_1.__exportStar(require("./util"), exports);

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

@@ -8,5 +8,5 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.StructureElement = void 0;
 var tslib_1 = require("tslib");
-var StructureElement = (0, tslib_1.__importStar)(require("./element/element"));
+var StructureElement = tslib_1.__importStar(require("./element/element"));
 exports.StructureElement = StructureElement;

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

@@ -283,7 +283,10 @@ var Structure = /** @class */ (function () {
                 this.state.interUnitBonds = new bonds_1.InterUnitBonds(new Map());
             }
             else {
-                this.state.interUnitBonds = (0, bonds_1.computeInterUnitBonds)(this, { ignoreWater: !this.dynamicBonds });
+                this.state.interUnitBonds = (0, bonds_1.computeInterUnitBonds)(this, {
+                    ignoreWater: !this.dynamicBonds,
+                    ignoreIon: !this.dynamicBonds,
+                });
             }
             return this.state.interUnitBonds;
         },
@@ -511,7 +514,7 @@ var Structure = /** @class */ (function () {
         if (this.parent) {
             var p = this.parent.coordinateSystem.isIdentity ? this.parent : Structure.transform(this.parent, this.parent.coordinateSystem.inverse);
             var s = this.coordinateSystem.isIdentity ? p : Structure.transform(p, this.coordinateSystem.matrix);
-            this._proxy = new Structure(s.units, s.unitMap, s.unitIndexMap, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, s.state), { dynamicBonds: this.dynamicBonds }), { child: this, target: this.parent });
+            this._proxy = new Structure(s.units, s.unitMap, s.unitIndexMap, tslib_1.__assign(tslib_1.__assign({}, s.state), { dynamicBonds: this.dynamicBonds }), { child: this, target: this.parent });
         }
         else {
             this._proxy = this;
@@ -819,9 +822,9 @@ function getSerialMapping(structure) {
     }
     Structure.create = create;
     function ofTrajectory(trajectory, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var units, first, count, i, il, frame, structure, j, jl, u, invariantId, chainGroupId, newUnit;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (trajectory.frameCount === 0)
@@ -870,7 +873,7 @@ function getSerialMapping(structure) {
         var index = model.atomicHierarchy.index;
         var auth_asym_id = model.atomicHierarchy.chains.auth_asym_id;
         var atomicChainOperatorMappinng = model.atomicChainOperatorMappinng;
-        var builder = new StructureBuilder((0, tslib_1.__assign)({ label: model.label }, props));
+        var builder = new StructureBuilder(tslib_1.__assign({ label: model.label }, props));
         for (var c = 0; c < chains.count; c++) {
             var operator = atomicChainOperatorMappinng.get(c) || symmetry_operator_1.SymmetryOperator.Default;
             var start = chains.offsets[c];
@@ -1359,7 +1362,7 @@ function getSerialMapping(structure) {
     function getSize(structure, thresholds, residueCountFactor) {
         if (thresholds === void 0) { thresholds = {}; }
         if (residueCountFactor === void 0) { residueCountFactor = 1; }
-        var t = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, Structure.DefaultSizeThresholds), thresholds);
+        var t = tslib_1.__assign(tslib_1.__assign({}, Structure.DefaultSizeThresholds), thresholds);
         if (structure.polymerResidueCount >= t.largeResidueCount * residueCountFactor) {
             if (hasHighSymmetry(structure, t)) {
                 return Size.Huge;

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

@@ -23,9 +23,9 @@ var StructureSymmetry;
 (function (StructureSymmetry) {
     function buildAssembly(structure, asmName) {
         var _this = this;
-        return mol_task_1.Task.create('Build Assembly', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Build Assembly', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, assembly, coordinateSystem, assembler, queryCtx, _i, _a, g, selection, units, _b, _c, oper, _d, units_1, unit;
-            return (0, tslib_1.__generator)(this, function (_e) {
+            return tslib_1.__generator(this, function (_e) {
                 models = structure.models;
                 if (models.length !== 1)
                     throw new Error('Can only build assemblies from structures based on 1 model.');
@@ -61,9 +61,9 @@ var StructureSymmetry;
     StructureSymmetry.buildAssembly = buildAssembly;
     function buildSymmetryAssembly(structure, generators, symmetry) {
         var _this = this;
-        return mol_task_1.Task.create('Build Symmetry Assembly', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Build Symmetry Assembly', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, modelCenter, assembler, queryCtx, _i, generators_1, g, selector, selection, units, _a, _b, _c, index, _d, i, j, k, operators, _e, units_2, unit, _f, operators_1, op;
-            return (0, tslib_1.__generator)(this, function (_g) {
+            return tslib_1.__generator(this, function (_g) {
                 models = structure.models;
                 if (models.length !== 1)
                     throw new Error('Can only build symmetry assemblies from structures based on 1 model.');
@@ -231,9 +231,9 @@ function assembleOperators(structure, operators) {
     return assembler.getStructure();
 }
 function _buildNCS(ctx, structure) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var models, symmetry, operators;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             models = structure.models;
             if (models.length !== 1)
                 throw new Error('Can only build NCS from structures based on 1 model.');
@@ -248,9 +248,9 @@ function _buildNCS(ctx, structure) {
     });
 }
 function findSymmetryRange(ctx, structure, ijkMin, ijkMax) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var models, symmetry, spacegroup, modelCenter, operators;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             models = structure.models;
             if (models.length !== 1)
                 throw new Error('Can only build symmetries from structures based on 1 model.');
@@ -267,12 +267,12 @@ function findSymmetryRange(ctx, structure, ijkMin, ijkMax) {
     });
 }
 function findMatesRadius(ctx, structure, radius) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function hash(unit, oper) {
             return "".concat(unit.invariantId, "|").concat(oper.name);
         }
         var models, symmetry, spacegroup, modelCenter, operators, lookup, added, assembler, units, center, _i, operators_3, oper, _a, units_4, unit, boundingSphere, closeUnits, uI, _uI, closeUnit, h;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     models = structure.models;

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

@@ -17,7 +17,7 @@ var IntraUnitBonds;
 })(IntraUnitBonds || (IntraUnitBonds = {}));
 exports.IntraUnitBonds = IntraUnitBonds;
 var InterUnitBonds = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(InterUnitBonds, _super);
+    tslib_1.__extends(InterUnitBonds, _super);
     function InterUnitBonds() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
@@ -34,7 +34,7 @@ var InterUnitBonds = /** @class */ (function (_super) {
 exports.InterUnitBonds = InterUnitBonds;
 (function (InterUnitBonds) {
     var UnitPairBonds = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(UnitPairBonds, _super);
+        tslib_1.__extends(UnitPairBonds, _super);
         function UnitPairBonds() {
             return _super !== null && _super.apply(this, arguments) || this;
         }

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

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

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

@@ -166,7 +166,7 @@ function findPairBonds(unitA, unitB, props, builder) {
     }
     builder.finishUnitPair();
 }
-var DefaultInterBondComputationProps = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), { ignoreWater: true });
+var DefaultInterBondComputationProps = tslib_1.__assign(tslib_1.__assign({}, common_1.DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
 function findBonds(structure, props) {
     var builder = new inter_unit_graph_1.InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return index_pair_1.IndexPairBonds.Provider.get(m); });
@@ -186,13 +186,15 @@ function findBonds(structure, props) {
     return new data_1.InterUnitBonds(builder.getMap());
 }
 function computeInterUnitBonds(structure, props) {
-    var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultInterBondComputationProps), props);
-    return findBonds(structure, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
+    var p = tslib_1.__assign(tslib_1.__assign({}, DefaultInterBondComputationProps), props);
+    return findBonds(structure, tslib_1.__assign(tslib_1.__assign({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
             var mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
                 (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
-            return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater);
+            var notIon = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
+                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
+            return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }
 exports.computeInterUnitBonds = computeInterUnitBonds;

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

@@ -223,7 +223,7 @@ function findBonds(unit, props) {
     return getGraph(atomA, atomB, order, flags, atomCount, canRemap);
 }
 function computeIntraUnitBonds(unit, props) {
-    var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), props);
+    var p = tslib_1.__assign(tslib_1.__assign({}, common_1.DefaultBondComputationProps), props);
     if (p.noCompute || model_1.Model.isCoarseGrained(unit.model)) {
         // TODO add function that only adds bonds defined in structConn of chemCompBond
         //      and avoid using unit.lookup

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

@@ -12,9 +12,9 @@ var structure_1 = require("../../structure");
 var types_1 = require("../../model/types");
 var int_1 = require("../../../../mol-data/int");
 var centroid_helper_1 = require("../../../../mol-math/geometry/centroid-helper");
-(0, tslib_1.__exportStar)(require("./bonds/data"), exports);
-(0, tslib_1.__exportStar)(require("./bonds/intra-compute"), exports);
-(0, tslib_1.__exportStar)(require("./bonds/inter-compute"), exports);
+tslib_1.__exportStar(require("./bonds/data"), exports);
+tslib_1.__exportStar(require("./bonds/intra-compute"), exports);
+tslib_1.__exportStar(require("./bonds/inter-compute"), exports);
 var Bond;
 (function (Bond) {
     function Location(aStructure, aUnit, aIndex, bStructure, bUnit, bIndex) {

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

@@ -24,8 +24,6 @@ var index_pair_1 = require("../../../mol-model-formats/structure/property/bonds/
 var element_set_intra_bond_cache_1 = require("./unit/bonds/element-set-intra-bond-cache");
 var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry");
 var resonance_1 = require("./unit/resonance");
-// avoiding namespace lookup improved performance in Chrome (Aug 2020)
-var v3add = linear_algebra_1.Vec3.add;
 var Unit;
 (function (Unit) {
     function isAtomic(u) { return u.kind === 0 /* Atomic */; }
@@ -154,26 +152,11 @@ var Unit;
         Atomic.prototype.remapModel = function (model, dynamicBonds, props) {
             var _a, _b;
             if (!props) {
-                props = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.props), { bonds: dynamicBonds && !((_b = (_a = this.props.bonds) === null || _a === void 0 ? void 0 : _a.props) === null || _b === void 0 ? void 0 : _b.canRemap)
+                props = tslib_1.__assign(tslib_1.__assign({}, this.props), { bonds: dynamicBonds && !((_b = (_a = this.props.bonds) === null || _a === void 0 ? void 0 : _a.props) === null || _b === void 0 ? void 0 : _b.canRemap)
                         ? undefined
                         : tryRemapBonds(this, this.props.bonds, model, dynamicBonds) });
                 if (!Unit.isSameConformation(this, model)) {
-                    var b = props.boundary;
-                    if (b) {
-                        var elements = this.elements;
-                        var pos = this.conformation.invariantPosition;
-                        var v = (0, linear_algebra_1.Vec3)();
-                        var center = (0, linear_algebra_1.Vec3)();
-                        for (var i = 0, il = elements.length; i < il; i++) {
-                            pos(elements[i], v);
-                            v3add(center, center, v);
-                        }
-                        linear_algebra_1.Vec3.scale(center, center, 1 / elements.length);
-                        // only invalidate boundary if sphere has changed too much
-                        if (linear_algebra_1.Vec3.distance(center, b.sphere.center) / b.sphere.radius >= 1.0) {
-                            props.boundary = undefined;
-                        }
-                    }
+                    props.boundary = undefined;
                     props.lookup3d = undefined;
                     props.principalAxes = undefined;
                 }
@@ -353,7 +336,7 @@ var Unit;
             var coarseConformation = this.getCoarseConformation();
             var modelCoarseConformation = getCoarseConformation(this.kind, model);
             if (!props) {
-                props = (0, tslib_1.__assign)({}, this.props);
+                props = tslib_1.__assign({}, this.props);
                 if (!Unit.isSameConformation(this, model)) { // TODO get rid of casting
                     props.boundary = undefined;
                     props.lookup3d = undefined;
@@ -431,7 +414,7 @@ var Unit;
         return BaseProperties();
     }
     var Spheres = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Spheres, _super);
+        tslib_1.__extends(Spheres, _super);
         function Spheres() {
             return _super !== null && _super.apply(this, arguments) || this;
         }
@@ -439,7 +422,7 @@ var Unit;
     }(Coarse));
     Unit.Spheres = Spheres;
     var Gaussians = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Gaussians, _super);
+        tslib_1.__extends(Gaussians, _super);
         function Gaussians() {
             return _super !== null && _super.apply(this, arguments) || this;
         }