npm - molstar - Versions diffs - 3.2.0 → 3.4.0 - Mend

molstar 3.2.0 → 3.4.0

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Files changed (2448) hide show

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

@@ -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/mol-model/structure/model/types/saccharides.js ADDED Viewed

@@ -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 var 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/mol-model/structure/model/types.js CHANGED Viewed

@@ -601,4 +601,3 @@ export var ResidueHydrophobicity = {
     'HID': [0.17, 0.11, -0.06], 'HIE': [0.17, 0.11, -0.06], 'HIP': [0.96, 2.33, 1.37],
 };
 export var DefaultResidueHydrophobicity = [0.00, 0.00, 0.00];
-//# sourceMappingURL=types.js.map

package/lib/mol-model/structure/model/util.js CHANGED Viewed

@@ -44,4 +44,3 @@ export function getAsymIdCount(model) {
     });
     return { auth: auth.size, label: label.size };
 }
-//# sourceMappingURL=util.js.map

package/lib/mol-model/structure/model.js CHANGED Viewed

@@ -10,4 +10,3 @@ import { StructureSequence } from './model/properties/sequence';
 export * from './model/properties/custom/indexed';
 export * from './model/indexing';
 export { Model, Types, Symmetry, StructureSequence };
-//# sourceMappingURL=model.js.map

package/lib/mol-model/structure/query/context.js CHANGED Viewed

@@ -129,4 +129,3 @@ var QueryContextBondInfo = /** @class */ (function () {
     });
     return QueryContextBondInfo;
 }());
-//# sourceMappingURL=context.js.map

package/lib/mol-model/structure/query/predicates.js CHANGED Viewed

@@ -114,4 +114,3 @@ var Predicates;
     Predicates.or = or;
 })(Predicates || (Predicates = {}));
 export { Predicates };
-//# sourceMappingURL=predicates.js.map

package/lib/mol-model/structure/query/queries/combinators.js CHANGED Viewed

@@ -65,4 +65,3 @@ export function intersect(queries) {
     };
 }
 // TODO: distanceCluster
-//# sourceMappingURL=combinators.js.map

package/lib/mol-model/structure/query/queries/filters.js CHANGED Viewed

@@ -296,4 +296,3 @@ export function isConnectedTo(_a) {
         return ret.getSelection();
     };
 }
-//# sourceMappingURL=filters.js.map

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

@@ -337,4 +337,3 @@ export function bondedAtomicPairs(bondTest) {
         return ret.getSelection();
     };
 }
-//# sourceMappingURL=generators.js.map

package/lib/mol-model/structure/query/queries/internal.js CHANGED Viewed

@@ -117,4 +117,3 @@ export function bundleGenerator(elements) {
         return StructureSelection.Sequence(ctx.inputStructure, [Bundle.toStructure(bundle, ctx.inputStructure)]);
     };
 }
-//# sourceMappingURL=internal.js.map

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

@@ -599,4 +599,3 @@ var StructConnGraph = /** @class */ (function () {
     return StructConnGraph;
 }());
 // TODO: unionBy (skip this one?), cluster
-//# sourceMappingURL=modifiers.js.map

package/lib/mol-model/structure/query/query.js CHANGED Viewed

@@ -12,4 +12,3 @@ var StructureQuery;
     StructureQuery.run = run;
 })(StructureQuery || (StructureQuery = {}));
 export { StructureQuery };
-//# sourceMappingURL=query.js.map

package/lib/mol-model/structure/query/selection.js CHANGED Viewed

@@ -157,4 +157,3 @@ var StructureSelection;
     // TODO: spatial lookup?
 })(StructureSelection || (StructureSelection = {}));
 export { StructureSelection };
-//# sourceMappingURL=selection.js.map

package/lib/mol-model/structure/query/utils/builders.js CHANGED Viewed

@@ -80,4 +80,3 @@ var LinearGroupingBuilder = /** @class */ (function () {
     return LinearGroupingBuilder;
 }());
 export { LinearGroupingBuilder };
-//# sourceMappingURL=builders.js.map

package/lib/mol-model/structure/query/utils/structure-distance.js CHANGED Viewed

@@ -118,4 +118,3 @@ var MaxRadiusDist;
     }
     MaxRadiusDist.check = check;
 })(MaxRadiusDist || (MaxRadiusDist = {}));
-//# sourceMappingURL=structure-distance.js.map

package/lib/mol-model/structure/query/utils/structure-set.js CHANGED Viewed

@@ -127,4 +127,3 @@ export function structureSubtract(a, b) {
     }
     return Structure.create(units, { parent: a.parent || b.parent });
 }
-//# sourceMappingURL=structure-set.js.map

package/lib/mol-model/structure/query.js CHANGED Viewed

@@ -21,4 +21,3 @@ export var Queries = {
     internal: internal
 };
 export { StructureSelection, StructureQuery };
-//# sourceMappingURL=query.js.map

package/lib/mol-model/structure/structure/carbohydrates/compute.js CHANGED Viewed

@@ -383,4 +383,3 @@ function buildLookups(elements, links, terminalLinks) {
     }
     return { getElementIndices: getElementIndices, getLinkIndices: getLinkIndices, getTerminalLinkIndices: getTerminalLinkIndices };
 }
-//# sourceMappingURL=compute.js.map

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

@@ -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/mol-model/structure/structure/carbohydrates/constants.js CHANGED Viewed

@@ -1,11 +1,12 @@
 /**
- * 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>
  */
 var _a, _b;
 import { ColorMap } from '../../../../mol-util/color';
+import { SaccharideNames } from '../../model/types/saccharides';
 export var SaccharideColors = ColorMap({
     Blue: 0x0090bc,
     Green: 0x00a651,
@@ -262,11 +263,6 @@ 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
  */
@@ -309,9 +305,9 @@ export var SaccharideCompIdMap = (function () {
             }
         }
     }
-    for (var i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], UnknownSaccharideComponent);
-    }
+    SaccharideNames.forEach(function (name) {
+        if (!map.has(name))
+            map.set(name, UnknownSaccharideComponent);
+    });
     return map;
 })();
-//# sourceMappingURL=constants.js.map

package/lib/mol-model/structure/structure/carbohydrates/data.js CHANGED Viewed

@@ -13,4 +13,3 @@ export var EmptyCarbohydrates = {
     getLinkIndices: function () { return EmptyArray; },
     getTerminalLinkIndices: function () { return EmptyArray; },
 };
-//# sourceMappingURL=data.js.map

package/lib/mol-model/structure/structure/element/bundle.js CHANGED Viewed

@@ -241,4 +241,3 @@ export var Bundle;
     }
     Bundle.areEqual = areEqual;
 })(Bundle || (Bundle = {}));
-//# sourceMappingURL=bundle.js.map

package/lib/mol-model/structure/structure/element/element.js CHANGED Viewed

@@ -9,4 +9,3 @@ export * from './loci';
 export * from './bundle';
 export * from './stats';
 export * from './util';
-//# sourceMappingURL=element.js.map

package/lib/mol-model/structure/structure/element/location.js CHANGED Viewed

@@ -61,4 +61,3 @@ var Location;
     }
     Location.chainIndex = chainIndex;
 })(Location || (Location = {}));
-//# sourceMappingURL=location.js.map

package/lib/mol-model/structure/structure/element/loci.js CHANGED Viewed

@@ -716,4 +716,3 @@ export function Loci(structure, elements) {
             };
     }
 })(Loci || (Loci = {}));
-//# sourceMappingURL=loci.js.map

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

@@ -353,4 +353,3 @@ export var Stats;
     }
     Stats.add = add;
 })(Stats || (Stats = {}));
-//# sourceMappingURL=stats.js.map

package/lib/mol-model/structure/structure/element/util.js CHANGED Viewed

@@ -35,4 +35,3 @@ export function chainIndex(e) {
 export function entityIndex(l) {
     return StructureProperties.entity.key(l);
 }
-//# sourceMappingURL=util.js.map

package/lib/mol-model/structure/structure/element.js CHANGED Viewed

@@ -6,4 +6,3 @@
  */
 import * as StructureElement from './element/element';
 export { StructureElement };
-//# sourceMappingURL=element.js.map

package/lib/mol-model/structure/structure/properties.js CHANGED Viewed

@@ -171,4 +171,3 @@ var StructureProperties = {
     coarse: coarse
 };
 export { StructureProperties };
-//# sourceMappingURL=properties.js.map

package/lib/mol-model/structure/structure/structure.d.ts CHANGED Viewed

@@ -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/mol-model/structure/structure/structure.js CHANGED Viewed

@@ -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>
@@ -14,7 +14,7 @@ import { StructureElement } from './element';
 import { Unit } from './unit';
 import { StructureLookup3D } from './util/lookup3d';
 import { StructureSubsetBuilder } from './util/subset-builder';
-import { computeInterUnitBonds, Bond } from './unit/bonds';
+import { InterUnitBonds, computeInterUnitBonds, Bond } from './unit/bonds';
 import { StructureSymmetry } from './symmetry';
 import { StructureProperties } from './properties';
 import { computeCarbohydrates } from './carbohydrates/compute';
@@ -274,7 +274,17 @@ var Structure = /** @class */ (function () {
         get: function () {
             if (this.state.interUnitBonds)
                 return this.state.interUnitBonds;
-            this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+            if (this.parent && this.state.dynamicBonds === this.parent.state.dynamicBonds &&
+                this.parent.state.interUnitBonds && this.parent.state.interUnitBonds.edgeCount === 0) {
+                // no need to compute InterUnitBonds if parent's ones are empty
+                this.state.interUnitBonds = new InterUnitBonds(new Map());
+            }
+            else {
+                this.state.interUnitBonds = computeInterUnitBonds(this, {
+                    ignoreWater: !this.dynamicBonds,
+                    ignoreIon: !this.dynamicBonds,
+                });
+            }
             return this.state.interUnitBonds;
         },
         enumerable: false,
@@ -1383,4 +1393,3 @@ function getSerialMapping(structure) {
     Structure.getPrincipalAxes = getPrincipalAxes;
 })(Structure || (Structure = {}));
 export { Structure };
-//# sourceMappingURL=structure.js.map

package/lib/mol-model/structure/structure/symmetry.js CHANGED Viewed

@@ -331,4 +331,3 @@ function findMatesRadius(ctx, structure, radius) {
     });
 }
 export { StructureSymmetry };
-//# sourceMappingURL=symmetry.js.map

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

@@ -111,4 +111,3 @@ var H_ID = __ElementIndex['H'];
 export function isHydrogen(i) {
     return i === H_ID;
 }
-//# sourceMappingURL=common.js.map

package/lib/mol-model/structure/structure/unit/bonds/data.d.ts CHANGED Viewed

@@ -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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -13,6 +13,7 @@ declare type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
     readonly order: ArrayLike<number>;
     readonly flags: ArrayLike<BondType.Flag>;
 }, {
+    /** can remap even with dynamicBonds on, e.g., for water molecules */
     readonly canRemap?: boolean;
 }>;
 declare namespace IntraUnitBonds {

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

@@ -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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -38,4 +38,3 @@ var InterUnitBonds = /** @class */ (function (_super) {
     InterUnitBonds.UnitPairBonds = UnitPairBonds;
 })(InterUnitBonds || (InterUnitBonds = {}));
 export { IntraUnitBonds, InterUnitBonds };
-//# sourceMappingURL=data.js.map

package/lib/mol-model/structure/structure/unit/bonds/element-set-intra-bond-cache.js CHANGED Viewed

@@ -44,4 +44,3 @@ var ElementSetIntraBondCache = /** @class */ (function () {
     return ElementSetIntraBondCache;
 }());
 export { ElementSetIntraBondCache };
-//# sourceMappingURL=element-set-intra-bond-cache.js.map

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

@@ -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/mol-model/structure/structure/unit/bonds/inter-compute.js CHANGED Viewed

@@ -163,7 +163,7 @@ function findPairBonds(unitA, unitB, props, builder) {
     }
     builder.finishUnitPair();
 }
-var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputationProps), { ignoreWater: true });
+var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
 function findBonds(structure, props) {
     var builder = new InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return IndexPairBonds.Provider.get(m); });
@@ -189,8 +189,9 @@ function computeInterUnitBonds(structure, props) {
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
                 (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
-            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater);
+            var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
+                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
+            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }
 export { computeInterUnitBonds };
-//# sourceMappingURL=inter-compute.js.map

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

@@ -112,7 +112,7 @@ function findBonds(unit, props) {
     for (var _aI = 0; _aI < atomCount; _aI++) {
         var aI = atoms[_aI];
         var elemA = type_symbol.value(aI);
-        if (isWatery && (elemA !== 'H' || elemA !== 'O'))
+        if (isWatery && (elemA !== 'H' && elemA !== 'O'))
             isWatery = false;
         var structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
         var hasStructConn = false;
@@ -234,4 +234,3 @@ function computeIntraUnitBonds(unit, props) {
     }
 }
 export { computeIntraUnitBonds };
-//# sourceMappingURL=intra-compute.js.map

package/lib/mol-model/structure/structure/unit/bonds.js CHANGED Viewed

@@ -217,4 +217,3 @@ var Bond;
     Bond.getBoundingSphere = getBoundingSphere;
 })(Bond || (Bond = {}));
 export { Bond };
-//# sourceMappingURL=bonds.js.map

package/lib/mol-model/structure/structure/unit/resonance.d.ts ADDED Viewed

@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { SortedArray } from '../../../../mol-data/int/sorted-array';
+import { StructureElement } from '../element';
+import { Unit } from '../unit';
+export declare type UnitResonance = {
+    /**
+     * Lookup for triplets of atoms in delocalized bonds.
+     *
+     * Does not include triplets that are part of aromatic rings.
+     */
+    readonly delocalizedTriplets: {
+        /** Return 3rd element in triplet or undefined if `a` and `b` are not part of a triplet */
+        readonly getThirdElement: (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex) => StructureElement.UnitIndex | undefined;
+        /** Return index into `triplets` or undefined if `a` is not part of any triplet */
+        readonly getTripletIndices: (a: StructureElement.UnitIndex) => number[] | undefined;
+        readonly triplets: SortedArray<StructureElement.UnitIndex>[];
+    };
+};
+export declare function getResonance(unit: Unit.Atomic): UnitResonance;

package/lib/mol-model/structure/structure/unit/resonance.js ADDED Viewed

@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { SortedArray } from '../../../../mol-data/int/sorted-array';
+import { sortedCantorPairing } from '../../../../mol-data/util';
+import { BondType } from '../../model/types';
+export function getResonance(unit) {
+    return {
+        delocalizedTriplets: getDelocalizedTriplets(unit)
+    };
+}
+function getDelocalizedTriplets(unit) {
+    var bonds = unit.bonds;
+    var b = bonds.b, edgeProps = bonds.edgeProps, offset = bonds.offset;
+    var _order = edgeProps.order, _flags = edgeProps.flags;
+    var elementAromaticRingIndices = unit.rings.elementAromaticRingIndices;
+    var triplets = [];
+    var thirdElementMap = new Map();
+    var indicesMap = new Map();
+    var add = function (a, b, c) {
+        var index = triplets.length;
+        triplets.push(SortedArray.ofUnsortedArray([a, b, c]));
+        thirdElementMap.set(sortedCantorPairing(a, b), c);
+        if (indicesMap.has(a))
+            indicesMap.get(a).push(index);
+        else
+            indicesMap.set(a, [index]);
+    };
+    for (var i = 0; i < unit.elements.length; i++) {
+        if (elementAromaticRingIndices.has(i))
+            continue;
+        var count = offset[i + 1] - offset[i] + 1;
+        if (count < 2)
+            continue;
+        var deloBonds = [];
+        for (var t = offset[i], _t = offset[i + 1]; t < _t; t++) {
+            var f = _flags[t];
+            if (!BondType.is(f, 16 /* Aromatic */))
+                continue;
+            deloBonds.push(b[t]);
+        }
+        if (deloBonds.length >= 2) {
+            add(i, deloBonds[0], deloBonds[1]);
+            for (var j = 1, jl = deloBonds.length; j < jl; j++) {
+                add(i, deloBonds[j], deloBonds[0]);
+            }
+        }
+    }
+    return {
+        getThirdElement: function (a, b) {
+            return thirdElementMap.get(sortedCantorPairing(a, b));
+        },
+        getTripletIndices: function (a) {
+            return indicesMap.get(a);
+        },
+        triplets: triplets,
+    };
+}