molstar 3.4.0 → 3.6.1

package/lib/mol-model-formats/structure/common/component.d.ts

@@ -19,7 +19,7 @@ export declare class ComponentBuilder {
     private getType;
     has(compId: string): boolean;
     get(compId: string): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
@@ -28,7 +28,7 @@ export declare class ComponentBuilder {
         pdbx_synonyms: Column.Schema.List<string>;
     }, "name" | "id" | "type">> | undefined;
     add(compId: string, index: number): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
@@ -37,7 +37,7 @@ export declare class ComponentBuilder {
         pdbx_synonyms: Column.Schema.List<string>;
     }, "name" | "id" | "type">>;
     getChemCompTable(): Table<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;

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

@@ -30,45 +30,45 @@ var NonPolymerNames = new Set([
 var StandardComponents = (function () {
     var map = new Map();
     var components = [
-        { id: 'HIS', name: 'HISTIDINE', type: 'L-peptide linking' },
-        { id: 'ARG', name: 'ARGININE', type: 'L-peptide linking' },
-        { id: 'LYS', name: 'LYSINE', type: 'L-peptide linking' },
-        { id: 'ILE', name: 'ISOLEUCINE', type: 'L-peptide linking' },
-        { id: 'PHE', name: 'PHENYLALANINE', type: 'L-peptide linking' },
-        { id: 'LEU', name: 'LEUCINE', type: 'L-peptide linking' },
-        { id: 'TRP', name: 'TRYPTOPHAN', type: 'L-peptide linking' },
-        { id: 'ALA', name: 'ALANINE', type: 'L-peptide linking' },
-        { id: 'MET', name: 'METHIONINE', type: 'L-peptide linking' },
-        { id: 'CYS', name: 'CYSTEINE', type: 'L-peptide linking' },
-        { id: 'ASN', name: 'ASPARAGINE', type: 'L-peptide linking' },
-        { id: 'VAL', name: 'VALINE', type: 'L-peptide linking' },
+        { id: 'HIS', name: 'HISTIDINE', type: 'l-peptide linking' },
+        { id: 'ARG', name: 'ARGININE', type: 'l-peptide linking' },
+        { id: 'LYS', name: 'LYSINE', type: 'l-peptide linking' },
+        { id: 'ILE', name: 'ISOLEUCINE', type: 'l-peptide linking' },
+        { id: 'PHE', name: 'PHENYLALANINE', type: 'l-peptide linking' },
+        { id: 'LEU', name: 'LEUCINE', type: 'l-peptide linking' },
+        { id: 'TRP', name: 'TRYPTOPHAN', type: 'l-peptide linking' },
+        { id: 'ALA', name: 'ALANINE', type: 'l-peptide linking' },
+        { id: 'MET', name: 'METHIONINE', type: 'l-peptide linking' },
+        { id: 'CYS', name: 'CYSTEINE', type: 'l-peptide linking' },
+        { id: 'ASN', name: 'ASPARAGINE', type: 'l-peptide linking' },
+        { id: 'VAL', name: 'VALINE', type: 'l-peptide linking' },
         { id: 'GLY', name: 'GLYCINE', type: 'peptide linking' },
-        { id: 'SER', name: 'SERINE', type: 'L-peptide linking' },
-        { id: 'GLN', name: 'GLUTAMINE', type: 'L-peptide linking' },
-        { id: 'TYR', name: 'TYROSINE', type: 'L-peptide linking' },
-        { id: 'ASP', name: 'ASPARTIC ACID', type: 'L-peptide linking' },
-        { id: 'GLU', name: 'GLUTAMIC ACID', type: 'L-peptide linking' },
-        { id: 'THR', name: 'THREONINE', type: 'L-peptide linking' },
-        { id: 'PRO', name: 'PROLINE', type: 'L-peptide linking' },
-        { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
-        { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
-        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'L-peptide linking' },
-        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'L-peptide linking' },
-        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'L-peptide linking' },
-        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'L-peptide linking' },
-        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'L-peptide linking' },
-        { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'G', name: 'GUANOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'I', name: 'INOSINIC ACID', type: 'RNA linking' },
-        { id: 'U', name: 'URIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'DA', name: '2\'-DEOXYADENOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DC', name: '2\'-DEOXYCYTIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DT', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DG', name: '2\'-DEOXYGUANOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DI', name: '2\'-DEOXYINOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DU', name: '2\'-DEOXYURIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
+        { id: 'SER', name: 'SERINE', type: 'l-peptide linking' },
+        { id: 'GLN', name: 'GLUTAMINE', type: 'l-peptide linking' },
+        { id: 'TYR', name: 'TYROSINE', type: 'l-peptide linking' },
+        { id: 'ASP', name: 'ASPARTIC ACID', type: 'l-peptide linking' },
+        { id: 'GLU', name: 'GLUTAMIC ACID', type: 'l-peptide linking' },
+        { id: 'THR', name: 'THREONINE', type: 'l-peptide linking' },
+        { id: 'PRO', name: 'PROLINE', type: 'l-peptide linking' },
+        { id: 'SEC', name: 'SELENOCYSTEINE', type: 'l-peptide linking' },
+        { id: 'PYL', name: 'PYRROLYSINE', type: 'l-peptide linking' },
+        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'l-peptide linking' },
+        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'l-peptide linking' },
+        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'l-peptide linking' },
+        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'l-peptide linking' },
+        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'l-peptide linking' },
+        { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'rna linking' },
+        { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'rna linking' },
+        { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'rna linking' },
+        { id: 'G', name: 'GUANOSINE-5\'-MONOPHOSPHATE', type: 'rna linking' },
+        { id: 'I', name: 'INOSINIC ACID', type: 'rna linking' },
+        { id: 'U', name: 'URIDINE-5\'-MONOPHOSPHATE', type: 'rna linking' },
+        { id: 'DA', name: '2\'-DEOXYADENOSINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
+        { id: 'DC', name: '2\'-DEOXYCYTIDINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
+        { id: 'DT', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
+        { id: 'DG', name: '2\'-DEOXYGUANOSINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
+        { id: 'DI', name: '2\'-DEOXYINOSINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
+        { id: 'DU', name: '2\'-DEOXYURIDINE-5\'-MONOPHOSPHATE', type: 'dna linking' },
     ];
     components.forEach(function (c) { return map.set(c.id, c); });
     return map;
@@ -76,12 +76,12 @@ var StandardComponents = (function () {
 var CharmmIonComponents = (function () {
     var map = new Map();
     var components = [
-        { id: 'ZN2', name: 'ZINC ION', type: 'Ion' },
-        { id: 'SOD', name: 'SODIUM ION', type: 'Ion' },
-        { id: 'CES', name: 'CESIUM ION', type: 'Ion' },
-        { id: 'CLA', name: 'CHLORIDE ION', type: 'Ion' },
-        { id: 'CAL', name: 'CALCIUM ION', type: 'Ion' },
-        { id: 'POT', name: 'POTASSIUM ION', type: 'Ion' },
+        { id: 'ZN2', name: 'ZINC ION', type: 'ion' },
+        { id: 'SOD', name: 'SODIUM ION', type: 'ion' },
+        { id: 'CES', name: 'CESIUM ION', type: 'ion' },
+        { id: 'CLA', name: 'CHLORIDE ION', type: 'ion' },
+        { id: 'CAL', name: 'CALCIUM ION', type: 'ion' },
+        { id: 'POT', name: 'POTASSIUM ION', type: 'ion' },
     ];
     components.forEach(function (c) { return map.set(c.id, c); });
     return map;
@@ -130,10 +130,10 @@ var ComponentBuilder = /** @class */ (function () {
             return 'peptide linking';
         }
         else if (this.hasAtomIds(atomIds, RnaAtomIdsList)) {
-            return 'RNA linking';
+            return 'rna linking';
         }
         else if (this.hasAtomIds(atomIds, DnaAtomIdsList)) {
-            return 'DNA linking';
+            return 'dna linking';
         }
         else {
             return 'other';

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -28,7 +28,7 @@ export declare function getAtomSiteTemplate(data: string, count: number): {
     label_entity_id: string[];
     partial_charge: import("../../../mol-io/reader/common/text/tokenizer").Tokens;
 };
-export declare function getAtomSite(sites: AtomSiteTemplate): {
+export declare function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): {
     [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField;
 };
 export declare function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number, isPdbqt: boolean): void;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -33,31 +33,96 @@ export function getAtomSiteTemplate(data, count) {
         partial_charge: ts(),
     };
 }
-export function getAtomSite(sites) {
+export function getAtomSite(sites, hasTer) {
+    var pdbx_PDB_model_num = CifField.ofStrings(sites.pdbx_PDB_model_num);
     var auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
+    var auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
     var auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
     var auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
+    var id = CifField.ofStrings(sites.id);
+    //
+    var currModelNum = pdbx_PDB_model_num.str(0);
+    var currAsymId = auth_asym_id.str(0);
+    var currSeqId = auth_seq_id.int(0);
+    var currLabelAsymId = currAsymId;
+    var asymIdCounts = new Map();
+    var atomIdCounts = new Map();
+    var labelAsymIds = [];
+    var labelAtomIds = [];
+    // ensure unique asym ids per model and unique atom ids per seq id
+    for (var i = 0, il = id.rowCount; i < il; ++i) {
+        var modelNum = pdbx_PDB_model_num.str(i);
+        var asymId = auth_asym_id.str(i);
+        var seqId = auth_seq_id.int(i);
+        var atomId = auth_atom_id.str(i);
+        var asymIdChanged = false;
+        if (modelNum !== currModelNum) {
+            asymIdCounts.clear();
+            atomIdCounts.clear();
+            currModelNum = modelNum;
+            currAsymId = asymId;
+            currSeqId = seqId;
+            asymIdChanged = true;
+            currLabelAsymId = asymId;
+        }
+        else if (currAsymId !== asymId) {
+            atomIdCounts.clear();
+            currAsymId = asymId;
+            currSeqId = seqId;
+            asymIdChanged = true;
+            currLabelAsymId = asymId;
+        }
+        else if (currSeqId !== seqId) {
+            atomIdCounts.clear();
+            currSeqId = seqId;
+        }
+        if (asymIdCounts.has(asymId)) {
+            // only change the chains name if there are TER records
+            // otherwise assume repeated chain name use is from interleaved chains
+            if (hasTer && asymIdChanged) {
+                var asymIdCount = asymIdCounts.get(asymId) + 1;
+                asymIdCounts.set(asymId, asymIdCount);
+                currLabelAsymId = "".concat(asymId, "_").concat(asymIdCount);
+            }
+        }
+        else {
+            asymIdCounts.set(asymId, 0);
+        }
+        labelAsymIds[i] = currLabelAsymId;
+        if (atomIdCounts.has(atomId)) {
+            var atomIdCount = atomIdCounts.get(atomId) + 1;
+            atomIdCounts.set(atomId, atomIdCount);
+            atomId = "".concat(atomId, "_").concat(atomIdCount);
+        }
+        else {
+            atomIdCounts.set(atomId, 0);
+        }
+        labelAtomIds[i] = atomId;
+    }
+    var labelAsymId = Column.ofStringArray(labelAsymIds);
+    var labelAtomId = Column.ofStringArray(labelAtomIds);
+    //
     return {
         auth_asym_id: auth_asym_id,
         auth_atom_id: auth_atom_id,
         auth_comp_id: auth_comp_id,
-        auth_seq_id: CifField.ofTokens(sites.auth_seq_id),
+        auth_seq_id: auth_seq_id,
         B_iso_or_equiv: CifField.ofTokens(sites.B_iso_or_equiv),
         Cartn_x: CifField.ofTokens(sites.Cartn_x),
         Cartn_y: CifField.ofTokens(sites.Cartn_y),
         Cartn_z: CifField.ofTokens(sites.Cartn_z),
         group_PDB: CifField.ofTokens(sites.group_PDB),
-        id: CifField.ofStrings(sites.id),
+        id: id,
         label_alt_id: CifField.ofTokens(sites.label_alt_id),
-        label_asym_id: auth_asym_id,
-        label_atom_id: auth_atom_id,
+        label_asym_id: CifField.ofColumn(labelAsymId),
+        label_atom_id: CifField.ofColumn(labelAtomId),
         label_comp_id: auth_comp_id,
         label_seq_id: CifField.ofUndefined(sites.index, Column.Schema.int),
         label_entity_id: CifField.ofStrings(sites.label_entity_id),
         occupancy: areTokensEmpty(sites.occupancy) ? CifField.ofUndefined(sites.index, Column.Schema.float) : CifField.ofTokens(sites.occupancy),
         type_symbol: CifField.ofTokens(sites.type_symbol),
         pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),
-        pdbx_PDB_model_num: CifField.ofStrings(sites.pdbx_PDB_model_num),
+        pdbx_PDB_model_num: pdbx_PDB_model_num,
         partial_charge: CifField.ofTokens(sites.partial_charge)
     };
 }

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

@@ -19,19 +19,19 @@ var HelixTypes = {
     // Left-handed gamma                           8
     // 2 - 7 ribbon/helix                          9
     // Polyproline                                10
-    1: 'HELX_RH_AL_P',
-    2: 'HELX_RH_OM_P',
-    3: 'HELX_RH_PI_P',
-    4: 'HELX_RH_GA_P',
-    5: 'HELX_RH_3T_P',
-    6: 'HELX_LH_AL_P',
-    7: 'HELX_LH_OM_P',
-    8: 'HELX_LH_GA_P',
-    9: 'HELX_RH_27_P',
-    10: 'HELX_RH_PP_P', // TODO or left-handed???
+    1: 'helx_rh_al_p',
+    2: 'helx_rh_om_p',
+    3: 'helx_rh_pi_p',
+    4: 'helx_rh_ga_p',
+    5: 'helx_rh_3t_p',
+    6: 'helx_lh_al_p',
+    7: 'helx_lh_om_p',
+    8: 'helx_lh_ga_p',
+    9: 'helx_rh_27_p',
+    10: 'helx_rh_pp_p', // TODO or left-handed???
 };
 function getStructConfTypeId(type) {
-    return HelixTypes[type] || 'HELX_P';
+    return HelixTypes[type] || 'helx_p';
 }
 export function parseHelix(lines, lineStart, lineEnd) {
     var helices = [];

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

@@ -21,7 +21,7 @@ import { parseConect } from './conect';
 import { isDebugMode } from '../../../mol-util/debug';
 export function pdbToMmCif(pdb) {
     return __awaiter(this, void 0, void 0, function () {
-        var lines, data, indices, tokenizer, isPdbqt, atomCount, anisotropicCount, i, _i, s, e, atomSite, anisotropic, entityBuilder, helperCategories, heteroNames, modelNum, modelStr, conectRange, i, _i, s, e, j, j, j, j, j, j, j, seqIds, atomIds, compIds, asymIds, componentBuilder, i, il, compId, moleculeType, atom_site, categories, _a, helperCategories_1, c;
+        var lines, data, indices, tokenizer, isPdbqt, atomCount, anisotropicCount, i, _i, s, e, atomSite, anisotropic, entityBuilder, helperCategories, heteroNames, modelNum, modelStr, conectRange, hasTer, i, _i, s, e, j, j, j, j, j, j, j, seqIds, atomIds, compIds, asymIds, componentBuilder, i, il, compId, moleculeType, atom_site, categories, _a, helperCategories_1, c;
         return __generator(this, function (_b) {
             lines = pdb.lines;
             data = lines.data, indices = lines.indices;
@@ -51,6 +51,7 @@ export function pdbToMmCif(pdb) {
             heteroNames = [];
             modelNum = 0, modelStr = '';
             conectRange = undefined;
+            hasTer = false;
             for (i = 0, _i = lines.count; i < _i; i++) {
                 s = indices[2 * i], e = indices[2 * i + 1];
                 switch (data[s]) {
@@ -186,6 +187,10 @@ export function pdbToMmCif(pdb) {
                         }
                         // TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
                         break;
+                    case 'T':
+                        if (substringStartsWith(data, s, e, 'TER')) {
+                            hasTer = true;
+                        }
                 }
             }
             seqIds = Column.ofIntTokens(atomSite.auth_seq_id);
@@ -200,7 +205,7 @@ export function pdbToMmCif(pdb) {
                 moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
                 atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
             }
-            atom_site = getAtomSite(atomSite);
+            atom_site = getAtomSite(atomSite, hasTer);
             if (!isPdbqt)
                 delete atom_site.partial_charge;
             if (conectRange) {

package/lib/mol-model-formats/structure/property/bonds/chem_comp.js

@@ -60,7 +60,7 @@ export var ComponentBond;
             var nameA = atom_id_1.value(i);
             var nameB = atom_id_2.value(i);
             var order = value_order.value(i);
-            var aromatic = pdbx_aromatic_flag.value(i) === 'Y';
+            var aromatic = pdbx_aromatic_flag.value(i) === 'y';
             if (entry.id !== id) {
                 entry = addEntry(id);
             }

package/lib/mol-model-formats/structure/property/bonds/struct_conn.js

@@ -115,7 +115,7 @@ export var StructConn;
             if (partnerA === undefined || partnerB === undefined)
                 continue;
             var type = conn_type_id.value(i);
-            var orderType = (pdbx_value_order.value(i) || '').toLowerCase();
+            var orderType = (pdbx_value_order.value(i) || '');
             var flags = 0 /* None */;
             var order = 1;
             switch (orderType) {

package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -25,6 +25,7 @@ export declare const InteractionsInterUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts

@@ -25,6 +25,7 @@ export declare const InteractionsIntraUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-model-props/computed/representations/interactions.d.ts

@@ -29,6 +29,7 @@ export declare const InteractionsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -114,6 +116,7 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -30,6 +30,7 @@ export declare const CrossLinkRestraintCylinderParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -72,6 +73,7 @@ export declare const CrossLinkRestraintParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -113,6 +115,7 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -155,6 +158,7 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        label: string; /** Precision data the server can show. */
+        /** Precision data the server can show. */
+        label: string;
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,7 +23,6 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js

@@ -68,7 +68,7 @@ export function getContourLevel(provider, plugin, taskCtx, emdbId) {
 }
 export function getContourLevelEmdb(plugin, taskCtx, emdbId) {
     return __awaiter(this, void 0, void 0, function () {
-        var emdbHeaderServer, header, contours, primaryContour, i, contourLevel;
+        var emdbHeaderServer, header, map, contours, primaryContour, i, contourLevel;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -76,7 +76,8 @@ export function getContourLevelEmdb(plugin, taskCtx, emdbId) {
                     return [4 /*yield*/, plugin.fetch({ url: "".concat(emdbHeaderServer, "/").concat(emdbId.toUpperCase(), "/header/").concat(emdbId.toLowerCase(), ".xml"), type: 'xml' }).runInContext(taskCtx)];
                 case 1:
                     header = _a.sent();
-                    contours = header.getElementsByTagName('contour');
+                    map = header.getElementsByTagName('map')[0];
+                    contours = map.getElementsByTagName('contour');
                     primaryContour = contours[0];
                     for (i = 1; i < contours.length; i++) {
                         if (contours[i].getAttribute('primary') === 'true') {
@@ -85,6 +86,7 @@ export function getContourLevelEmdb(plugin, taskCtx, emdbId) {
                         }
                     }
                     contourLevel = parseFloat(primaryContour.getElementsByTagName('level')[0].textContent);
+                    console.log({ contourLevel: contourLevel });
                     return [2 /*return*/, contourLevel];
             }
         });

package/lib/mol-plugin/commands.d.ts

@@ -331,6 +331,7 @@ export declare const PluginCommands: {
                         flipSided: any;
                         flatShaded: any;
                         xrayShaded: any;
+                        allowTransparentBackfaces: any;
                         bumpFrequency: any;
                         bumpAmplitude: any;
                         quality: any;

package/lib/mol-plugin/util/viewport-screenshot.d.ts

@@ -37,6 +37,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            allowTransparentBackfaces: boolean;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -69,6 +70,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 flipSided: boolean;
                 flatShaded: boolean;
                 xrayShaded: boolean;
+                allowTransparentBackfaces: boolean;
                 bumpFrequency: number;
                 bumpAmplitude: number;
                 quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -109,6 +111,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            allowTransparentBackfaces: boolean;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.4.0';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1647202245473);
+export var PLUGIN_VERSION = '3.6.1';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1648986596976);

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

@@ -26,6 +26,12 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
         isBinary: any;
         options: any;
     }>, "url"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
         provider: any;
         options: any;
     }>, "pdb"> | PD.NamedParams<PD.Normalize<{
@@ -37,12 +43,6 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
     }>, "swissmodel"> | PD.NamedParams<PD.Normalize<{
         id: any;
         options: any;
-    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
-        id: any;
-        options: any;
-    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
-        id: any;
-        options: any;
     }>, "pubchem">;
 }>>;
 export declare const UpdateTrajectory: StateAction<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, void, PD.Normalize<{

package/lib/mol-plugin-state/helpers/structure-selection-query.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-plugin-state/helpers/structure-selection-query.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-plugin-state/transforms/representation.d.ts

@@ -150,6 +150,7 @@ declare const ModelUnitcell3D: StateTransformer<SO.Molecule.Model, SO.Shape.Repr
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -172,6 +173,7 @@ declare const StructureBoundingBox3D: StateTransformer<SO.Molecule.Structure, SO
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -276,6 +278,7 @@ declare const StructureSelectionsAngle3D: StateTransformer<SO.Molecule.Structure
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     lineSizeAttenuation: boolean;
@@ -327,6 +330,7 @@ declare const StructureSelectionsDihedral3D: StateTransformer<SO.Molecule.Struct
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     lineSizeAttenuation: boolean;
@@ -384,6 +388,7 @@ declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Str
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
@@ -409,6 +414,7 @@ declare const StructureSelectionsPlane3D: StateTransformer<SO.Molecule.Structure
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;