molstar 3.3.1 → 3.4.0

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

@@ -6,6 +6,7 @@
  */
 import { getProteinOneLetterCode, getRnaOneLetterCode, getDnaOneLetterCode } from './constants';
 import { Column } from '../../mol-data/db';
+import { assertUnreachable } from '../../mol-util/type-helpers';
 var Sequence;
 (function (Sequence) {
     function getSequenceString(seq) {
@@ -40,7 +41,7 @@ var Sequence;
             case "generic" /* Generic */:
                 code = function () { return 'X'; };
                 break;
-            default: throw new Error("unknown kind '".concat(kind, "'"));
+            default: assertUnreachable(kind);
         }
         if (map && map.size > 0) {
             return function (name) {

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

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

@@ -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
  */
@@ -309,8 +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;
 })();

package/lib/mol-model-formats/structure/basic/atomic.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/mol-model-formats/structure/basic/atomic.js

@@ -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>
@@ -37,14 +37,6 @@ function findHierarchyOffsets(atom_site) {
     }
     return { residues: residues, chains: chains };
 }
-function substUndefinedColumn(table, a, b) {
-    if (!table[a].isDefined) {
-        table[a] = table[b];
-    }
-    if (!table[b].isDefined) {
-        table[b] = table[a];
-    }
-}
 function createHierarchyData(atom_site, sourceIndex, offsets) {
     var atoms = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased(Column.Schema.str) }),
@@ -74,11 +66,6 @@ function createHierarchyData(atom_site, sourceIndex, offsets) {
     // Optimize the numeric columns
     Table.columnToArray(residues, 'label_seq_id', Int32Array);
     Table.columnToArray(residues, 'auth_seq_id', Int32Array);
-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
     return { atoms: atoms, residues: residues, chains: chains, atomSourceIndex: sourceIndex };
 }
 function getConformation(atom_site) {

package/lib/mol-model-formats/structure/basic/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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-model-formats/structure/basic/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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-model-formats/structure/basic/schema.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>
  */
@@ -196,4 +196,4 @@ export interface BasicData {
     pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues;
     pdbx_molecule: Molecule;
 }
-export declare function createBasic(data: Partial<BasicData>): BasicData;
+export declare function createBasic(data: Partial<BasicData>, normalize?: boolean): BasicData;

package/lib/mol-model-formats/structure/basic/schema.js

@@ -1,11 +1,12 @@
 /**
- * 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>
  */
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { getNormalizedAtomSite } from './util';
 export var BasicSchema = {
     entry: mmCIF_Schema.entry,
     struct: mmCIF_Schema.struct,
@@ -25,7 +26,8 @@ export var BasicSchema = {
     pdbx_unobs_or_zero_occ_residues: mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
     pdbx_molecule: mmCIF_Schema.pdbx_molecule,
 };
-export function createBasic(data) {
+export function createBasic(data, normalize) {
+    if (normalize === void 0) { normalize = false; }
     var basic = Object.create(null);
     for (var _i = 0, _a = Object.keys(BasicSchema); _i < _a.length; _i++) {
         var name_1 = _a[_i];
@@ -36,5 +38,8 @@ export function createBasic(data) {
             basic[name_1] = Table.ofUndefinedColumns(BasicSchema[name_1], 0);
         }
     }
+    if (normalize) {
+        basic.atom_site = getNormalizedAtomSite(basic.atom_site);
+    }
     return basic;
 }

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

@@ -1,8 +1,39 @@
 /**
- * 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>
  */
-import { BasicData } from './schema';
+import { AtomSite, BasicData } from './schema';
+import { Column, Table } from '../../../mol-data/db';
 export declare function getModelGroupName(model_id: number, data: BasicData): string;
+/** Fix possibly missing auth_/label_ columns */
+export declare function getNormalizedAtomSite(atom_site: AtomSite): Table<{
+    auth_asym_id: Column.Schema.Str;
+    auth_atom_id: Column.Schema.Str;
+    auth_comp_id: Column.Schema.Str;
+    auth_seq_id: Column.Schema.Int;
+    B_iso_or_equiv: Column.Schema.Float;
+    Cartn_x: Column.Schema.Coordinate;
+    Cartn_y: Column.Schema.Coordinate;
+    Cartn_z: Column.Schema.Coordinate;
+    group_PDB: Column.Schema.Aliased<"ATOM" | "HETATM">;
+    id: Column.Schema.Int;
+    label_alt_id: Column.Schema.Str;
+    label_asym_id: Column.Schema.Str;
+    label_atom_id: Column.Schema.Str;
+    label_comp_id: Column.Schema.Str;
+    label_entity_id: Column.Schema.Str;
+    label_seq_id: Column.Schema.Int;
+    occupancy: Column.Schema.Float;
+    type_symbol: Column.Schema.Str;
+    pdbx_PDB_ins_code: Column.Schema.Str;
+    pdbx_PDB_model_num: Column.Schema.Int;
+    pdbx_formal_charge: Column.Schema.Int;
+    pdbx_label_index: Column.Schema.Int;
+    pdbx_sifts_xref_db_name: Column.Schema.Str;
+    pdbx_sifts_xref_db_acc: Column.Schema.Str;
+    pdbx_sifts_xref_db_num: Column.Schema.Str;
+    pdbx_sifts_xref_db_res: Column.Schema.Str;
+    ihm_model_id: Column.Schema.Int;
+}>;

package/lib/mol-model-formats/structure/basic/util.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -15,3 +15,26 @@ export function getModelGroupName(model_id, data) {
     }
     return '';
 }
+//
+function hasPresentValues(column) {
+    for (var i = 0, il = column.rowCount; i < il; i++) {
+        if (column.valueKind(i) === 0 /* Present */)
+            return true;
+    }
+    return false;
+}
+function substUndefinedColumn(table, a, b) {
+    if (!table[a].isDefined || !hasPresentValues(table[a]))
+        table[a] = table[b];
+    if (!table[b].isDefined || !hasPresentValues(table[b]))
+        table[b] = table[a];
+}
+/** Fix possibly missing auth_/label_ columns */
+export function getNormalizedAtomSite(atom_site) {
+    var normalized = Table.ofColumns(atom_site._schema, atom_site);
+    substUndefinedColumn(normalized, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(normalized, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(normalized, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
+    return normalized;
+}

package/lib/mol-model-formats/structure/cif-core.js

@@ -41,7 +41,7 @@ function getSymmetry(db) {
 function getModels(db, format, ctx) {
     var _a;
     return __awaiter(this, void 0, void 0, function () {
-        var atomCount, MOL, A, seq_id, symmetry, m, _b, fract_x, fract_y, fract_z, x, y, z, v, i, _c, type_symbol, label, typeSymbol, formalCharge, element_symbol, formal_charge, i, ts, n, element_symbol, i, atom_site, name, entityBuilder, componentBuilder, basics, models, first, bondCount, labelIndexMap, label_1, i, il, bond_type, indexA, indexB, order, dist, flag, included, j, _d, atom_site_label_1, atom_site_label_2, valence, distance, i, iA, iB, id, t;
+        var atomCount, MOL, A, seq_id, symmetry, m, _b, fract_x, fract_y, fract_z, x, y, z, v, i, _c, type_symbol, label, typeSymbol, formalCharge, element_symbol, formal_charge, i, ts, n, element_symbol, i, atom_site, name, entityBuilder, componentBuilder, basic, models, first, bondCount, labelIndexMap, label_1, i, il, bond_type, indexA, indexB, order, dist, flag, included, j, _d, atom_site_label_1, atom_site_label_2, valence, distance, i, iA, iB, id, t;
         return __generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
@@ -96,7 +96,7 @@ function getModels(db, format, ctx) {
                         element_symbol = new Array(atomCount);
                         for (i = 0; i < atomCount; ++i) {
                             // TODO can take as is if type_symbol not given?
-                            element_symbol[i] = guessElementSymbolString(label.value(i));
+                            element_symbol[i] = guessElementSymbolString(label.value(i), '');
                         }
                         typeSymbol = Column.ofStringArray(element_symbol);
                         formalCharge = Column.Undefined(atomCount, Column.Schema.int);
@@ -132,12 +132,12 @@ function getModels(db, format, ctx) {
                     componentBuilder = new ComponentBuilder(seq_id, db.atom_site.type_symbol);
                     componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, format, ctx)];
+                    return [4 /*yield*/, createModels(basic, format, ctx)];
                 case 1:
                     models = _e.sent();
                     if (models.frameCount > 0) {

package/lib/mol-model-formats/structure/common/component.js

@@ -7,6 +7,7 @@ import { Table, Column } from '../../../mol-data/db';
 import { WaterNames, PolymerNames } from '../../../mol-model/structure/model/types';
 import { SetUtils } from '../../../mol-util/set';
 import { BasicSchema } from '../basic/schema';
+import { SaccharideCompIdMap } from '../../../mol-model/structure/structure/carbohydrates/constants';
 var ProteinAtomIdsList = [
     new Set(['CA']),
     new Set(['C']),
@@ -24,7 +25,7 @@ var DnaAtomIdsList = [
 ];
 /** Used to reduce false positives for atom name-based type guessing */
 var NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
 ]);
 var StandardComponents = (function () {
     var map = new Map();
@@ -151,6 +152,9 @@ var ComponentBuilder = /** @class */ (function () {
             else if (NonPolymerNames.has(compId.toUpperCase())) {
                 this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             }
+            else if (SaccharideCompIdMap.has(compId.toUpperCase())) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'saccharide' });
+            }
             else {
                 var atomIds = this.getAtomIds(index);
                 if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {

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

@@ -13,7 +13,7 @@ import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
 function getModels(cube, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics;
+        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basic;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -46,12 +46,12 @@ function getModels(cube, ctx) {
                     componentBuilder = new ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, MolFormat.create(cube), ctx)];
+                    return [4 /*yield*/, createModels(basic, MolFormat.create(cube), ctx)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
         });

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

@@ -21,6 +21,7 @@ function getBasic(atoms, modelNum) {
     var asymIds = new Array(atoms.count);
     var seqIds = new Uint32Array(atoms.count);
     var ids = new Uint32Array(atoms.count);
+    var typeSymbol = new Array(atoms.count);
     var entityBuilder = new EntityBuilder();
     var componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName);
     var currentEntityId = '';
@@ -50,6 +51,7 @@ function getBasic(atoms, modelNum) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var auth_asym_id = Column.ofStringArray(asymIds);
     var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -67,7 +69,7 @@ function getBasic(atoms, modelNum) {
         label_seq_id: Column.ofIntArray(seqIds),
         label_entity_id: Column.ofStringArray(entityIds),
         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, function (s) { return guessElementSymbolString(s); })),
+        type_symbol: Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: Column.ofConst(modelNum, atoms.count, Column.Schema.int),
     }, atoms.count);
     return createBasic({

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

@@ -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>
@@ -14,6 +14,7 @@ import { AtomSiteAnisotrop } from './property/anisotropic';
 import { ComponentBond } from './property/bonds/chem_comp';
 import { StructConn } from './property/bonds/struct_conn';
 import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
+import { createBasic } from './basic/schema';
 function modelSymmetryFromMmcif(model) {
     if (!MmcifFormat.is(model.sourceData))
         return;
@@ -85,5 +86,6 @@ var MmcifFormat;
 })(MmcifFormat || (MmcifFormat = {}));
 export function trajectoryFromMmCIF(frame) {
     var format = MmcifFormat.fromFrame(frame);
-    return Task.create('Create mmCIF Model', function (ctx) { return createModels(format.data.db, format, ctx); });
+    var basic = createBasic(format.data.db, true);
+    return Task.create('Create mmCIF Model', function (ctx) { return createModels(basic, format, ctx); });
 }

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

@@ -16,7 +16,7 @@ import { EntityBuilder } from './common/entity';
 import { IndexPairBonds } from './property/bonds/index-pair';
 export function getMolModels(mol, format, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basic, models, indexA, indexB, order, pairBonds;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -61,12 +61,12 @@ export function getMolModels(mol, format, ctx) {
                     componentBuilder = new ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
+                    return [4 /*yield*/, createModels(basic, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
                 case 1:
                     models = _a.sent();
                     if (models.frameCount > 0) {

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

@@ -19,7 +19,7 @@ import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
 import { Vec3 } from '../../mol-math/linear-algebra';
 function getModels(mol2, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        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;
+        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, basic, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
@@ -41,7 +41,7 @@ function getModels(mol2, ctx) {
                     for (i_2 = 0; i_2 < atoms.count; ++i_2) {
                         type_symbol[i_2] = hasAtomType
                             ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
-                            : guessElementSymbolString(atoms.atom_name.value(i_2));
+                            : guessElementSymbolString(atoms.atom_name.value(i_2), atoms.subst_name.value(i_2));
                     }
                     atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -68,12 +68,12 @@ function getModels(mol2, ctx) {
                     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 = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, Mol2Format.create(mol2), ctx)];
+                    return [4 /*yield*/, createModels(basic, Mol2Format.create(mol2), ctx)];
                 case 2:
                     _models = _b.sent();
                     if (_models.frameCount > 0) {

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

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Task } from '../../mol-task';
+import { NctrajFile } from '../../mol-io/reader/nctraj/parser';
+import { Coordinates } from '../../mol-model/structure/coordinates';
+export declare function coordinatesFromNctraj(file: NctrajFile): Task<Coordinates>;

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

@@ -0,0 +1,56 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Task } from '../../mol-task';
+import { Coordinates, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+export function coordinatesFromNctraj(file) {
+    var _this = this;
+    return Task.create('Parse NCTRAJ', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, c, elementCount, x, y, z, j, jl, frame, lengths, x_1, y_1, z_1;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
+                case 1:
+                    _a.sent();
+                    deltaTime = Time(file.deltaTime, 'step');
+                    offsetTime = Time(file.timeOffset, deltaTime.unit);
+                    frames = [];
+                    for (i = 0, il = file.coordinates.length; i < il; ++i) {
+                        c = file.coordinates[i];
+                        elementCount = c.length / 3;
+                        x = new Float32Array(elementCount);
+                        y = new Float32Array(elementCount);
+                        z = new Float32Array(elementCount);
+                        for (j = 0, jl = c.length; j < jl; j += 3) {
+                            x[j / 3] = c[j];
+                            y[j / 3] = c[j + 1];
+                            z[j / 3] = c[j + 2];
+                        }
+                        frame = {
+                            elementCount: elementCount,
+                            x: x,
+                            y: y,
+                            z: z,
+                            xyzOrdering: { isIdentity: true },
+                            time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        };
+                        // TODO: handle case where cell_lengths and cell_angles are set, i.e., angles not 90deg
+                        if (file.cell_lengths) {
+                            lengths = file.cell_lengths[i];
+                            x_1 = Vec3.scale(Vec3(), Vec3.unitX, lengths[0]);
+                            y_1 = Vec3.scale(Vec3(), Vec3.unitY, lengths[1]);
+                            z_1 = Vec3.scale(Vec3(), Vec3.unitZ, lengths[2]);
+                            frame.cell = Cell.fromBasis(x_1, y_1, z_1);
+                        }
+                        frames.push(frame);
+                    }
+                    return [2 /*return*/, Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,7 @@ import { MmcifFormat } from './mmcif';
 import { createModels } from './basic/parser';
 import { Column } from '../../mol-data/db';
 import { AtomPartialCharge } from './property/partial-charge';
+import { createBasic } from './basic/schema';
 export { PdbFormat };
 var PdbFormat;
 (function (PdbFormat) {
@@ -26,7 +27,7 @@ var PdbFormat;
 export function trajectoryFromPDB(pdb) {
     var _this = this;
     return Task.create('Parse PDB', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
-        var cif, format, models, partial_charge, first, srcIndex, isIdentity, srcIndexArray, q_1, partialCharge;
+        var cif, format, basic, models, partial_charge, first, srcIndex, isIdentity, srcIndexArray, q_1, partialCharge;
         var _a;
         return __generator(this, function (_b) {
             switch (_b.label) {
@@ -37,7 +38,8 @@ export function trajectoryFromPDB(pdb) {
                 case 2:
                     cif = _b.sent();
                     format = MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
-                    return [4 /*yield*/, createModels(format.data.db, format, ctx)];
+                    basic = createBasic(format.data.db, true);
+                    return [4 /*yield*/, createModels(basic, format, ctx)];
                 case 3:
                     models = _b.sent();
                     partial_charge = (_a = cif.categories['atom_site']) === null || _a === void 0 ? void 0 : _a.getField('partial_charge');

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

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { PrmtopFile } from '../../mol-io/reader/prmtop/parser';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+export { PrmtopFormat };
+declare type PrmtopFormat = ModelFormat<PrmtopFile>;
+declare namespace PrmtopFormat {
+    function is(x?: ModelFormat): x is PrmtopFormat;
+    function fromPrmtop(prmtop: PrmtopFile): PrmtopFormat;
+}
+export declare function topologyFromPrmtop(prmtop: PrmtopFile): Task<Topology>;