molstar 3.5.0 → 3.6.0

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -122,63 +122,65 @@ exports.NucleicBackboneAtoms = new Set([
 ]);
 /** Chemical component type names for D-linked protein */
 exports.DProteinComponentTypeNames = new Set([
-    'D-PEPTIDE LINKING', 'D-PEPTIDE NH3 AMINO TERMINUS',
-    'D-PEPTIDE COOH CARBOXY TERMINUS', 'D-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'D-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-peptide linking', 'd-peptide nh3 amino terminus',
+    'd-peptide cooh carboxy terminus', 'd-gamma-peptide, c-delta linking',
+    'd-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for L-linked protein */
 exports.LProteinComponentTypeNames = new Set([
-    'L-PEPTIDE LINKING', 'L-PEPTIDE NH3 AMINO TERMINUS',
-    'L-PEPTIDE COOH CARBOXY TERMINUS', 'L-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'l-peptide linking', 'l-peptide nh3 amino terminus',
+    'l-peptide cooh carboxy terminus', 'l-gamma-peptide, c-delta linking',
+    'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
 exports.GammaProteinComponentTypeNames = new Set([
-    'D-GAMMA-PEPTIDE, C-DELTA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING'
+    'd-gamma-peptide, c-delta linking', 'l-gamma-peptide, c-delta linking'
 ]);
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
 exports.BetaProteinComponentTypeNames = new Set([
-    'D-BETA-PEPTIDE, C-GAMMA LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-beta-peptide, c-gamma linking', 'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
 exports.ProteinTerminusComponentTypeNames = new Set([
-    'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE COOH CARBOXY TERMINUS',
-    'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE COOH CARBOXY TERMINUS'
+    'd-peptide nh3 amino terminus', 'd-peptide cooh carboxy terminus',
+    'l-peptide nh3 amino terminus', 'l-peptide cooh carboxy terminus'
 ]);
 /** Chemical component type names for peptide-like protein */
 exports.OtherProteinComponentTypeNames = new Set([
-    'PEPTIDE LINKING', 'PEPTIDE-LIKE',
+    'peptide linking', 'peptide-like',
 ]);
 /** Chemical component type names for protein */
 exports.ProteinComponentTypeNames = set_1.SetUtils.unionMany(exports.DProteinComponentTypeNames, exports.LProteinComponentTypeNames, exports.OtherProteinComponentTypeNames);
 /** Chemical component type names for DNA */
 exports.DNAComponentTypeNames = new Set([
-    'DNA LINKING', 'L-DNA LINKING', 'DNA OH 5 PRIME TERMINUS', 'DNA OH 3 PRIME TERMINUS',
+    'dna linking', 'l-dna linking', 'dna oh 5 prime terminus', 'dna oh 3 prime terminus',
 ]);
 /** Chemical component type names for RNA */
 exports.RNAComponentTypeNames = new Set([
-    'RNA LINKING', 'L-RNA LINKING', 'RNA OH 5 PRIME TERMINUS', 'RNA OH 3 PRIME TERMINUS',
+    'rna linking', 'l-rna linking', 'rna oh 5 prime terminus', 'rna oh 3 prime terminus',
 ]);
 /** Chemical component type names for saccharide */
-exports.SaccharideComponentTypeNames = new Set([
-    'D-SACCHARIDE, BETA LINKING', 'L-SACCHARIDE, BETA LINKING',
-    'D-SACCHARIDE, ALPHA LINKING', 'L-SACCHARIDE, ALPHA LINKING',
-    'L-SACCHARIDE', 'D-SACCHARIDE', 'SACCHARIDE',
-    // the following four are marked to be deprecated in the mmCIF dictionary
-    'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,4 LINKING',
-    'D-SACCHARIDE 1,4 AND 1,6 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING',
-]);
+exports.SaccharideComponentTypeNames = set_1.SetUtils.unionMany(new Set([
+    'd-saccharide, beta linking', 'l-saccharide, beta linking',
+    'd-saccharide, alpha linking', 'l-saccharide, alpha linking',
+    'l-saccharide', 'd-saccharide', 'saccharide',
+]), 
+// deprecated in the mmCIF dictionary, kept for backward compatibility
+new Set([
+    'd-saccharide 1,4 and 1,4 linking', 'l-saccharide 1,4 and 1,4 linking',
+    'd-saccharide 1,4 and 1,6 linking', 'l-saccharide 1,4 and 1,6 linking'
+]));
 /** Chemical component type names for other */
 exports.OtherComponentTypeNames = new Set([
-    'NON-POLYMER', 'OTHER'
+    'non-polymer', 'other'
 ]);
 /** Chemical component type names for ion (extension to mmcif) */
 exports.IonComponentTypeNames = new Set([
-    'ION'
+    'ion'
 ]);
 /** Chemical component type names for lipid (extension to mmcif) */
 exports.LipidComponentTypeNames = new Set([
-    'LIPID'
+    'lipid'
 ]);
 /** Common names for water molecules */
 exports.WaterNames = new Set([
@@ -237,7 +239,6 @@ exports.isPyrimidineBase = isPyrimidineBase;
 exports.PolymerNames = set_1.SetUtils.unionMany(exports.AminoAcidNames, exports.BaseNames);
 /** get the molecule type from component type and id */
 function getMoleculeType(compType, compId) {
-    compType = compType.toUpperCase();
     compId = compId.toUpperCase();
     if (exports.PeptideBaseNames.has(compId)) {
         return 8 /* PNA */;
@@ -265,7 +266,7 @@ function getMoleculeType(compType, compId) {
     }
     else if (exports.OtherComponentTypeNames.has(compType)) {
         if (constants_1.SaccharideCompIdMap.has(compId)) {
-            // trust our saccharide table more than given 'non-polymer' or 'other' component type
+            // trust our saccharide table more than given 'NON-POLYMER' or 'OTHER' component type
             return 9 /* Saccharide */;
         }
         else if (exports.AminoAcidNames.has(compId)) {
@@ -287,7 +288,6 @@ function getMoleculeType(compType, compId) {
 }
 exports.getMoleculeType = getMoleculeType;
 function getPolymerType(compType, molType) {
-    compType = compType.toUpperCase();
     if (molType === 5 /* Protein */) {
         if (exports.GammaProteinComponentTypeNames.has(compType)) {
             return 2 /* GammaProtein */;
@@ -322,10 +322,10 @@ function getComponentType(compId) {
         return 'peptide linking';
     }
     else if (exports.RnaBaseNames.has(compId)) {
-        return 'RNA linking';
+        return 'rna linking';
     }
     else if (exports.DnaBaseNames.has(compId)) {
-        return 'DNA linking';
+        return 'dna linking';
     }
     else if (constants_1.SaccharideCompIdMap.has(compId)) {
         return 'saccharide';
@@ -367,7 +367,6 @@ function getEntityType(compId) {
 exports.getEntityType = getEntityType;
 function getEntitySubtype(compId, compType) {
     compId = compId.toUpperCase();
-    compType = compType.toUpperCase();
     if (exports.LProteinComponentTypeNames.has(compType)) {
         return 'polypeptide(L)';
     }

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

@@ -330,7 +330,7 @@ function bondedAtomicPairs(bondTest) {
             atomicBond.a.unit = structure.unitMap.get(bond.unitA);
             atomicBond.a.element = atomicBond.a.unit.elements[bond.indexA];
             atomicBond.aIndex = bond.indexA;
-            atomicBond.b.unit = structure.unitMap.get(bond.unitA);
+            atomicBond.b.unit = structure.unitMap.get(bond.unitB);
             atomicBond.b.element = atomicBond.b.unit.elements[bond.indexB];
             atomicBond.bIndex = bond.indexB;
             atomicBond.order = bond.props.order;

package/lib/commonjs/mol-model/structure/structure/properties.d.ts

@@ -41,7 +41,7 @@ declare const StructureProperties: {
         microheterogeneityCompIds: StructureElement.Property<string[]>;
         secondary_structure_type: StructureElement.Property<SecondaryStructureType>;
         secondary_structure_key: StructureElement.Property<number>;
-        chem_comp_type: StructureElement.Property<"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">;
+        chem_comp_type: StructureElement.Property<"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">;
     };
     chain: {
         key: StructureElement.Property<import("../model").ChainIndex>;

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

@@ -170,10 +170,8 @@ var DefaultInterBondComputationProps = tslib_1.__assign(tslib_1.__assign({}, com
 function findBonds(structure, props) {
     var builder = new inter_unit_graph_1.InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return index_pair_1.IndexPairBonds.Provider.get(m); });
-    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds)) {
-        // TODO add function that only adds bonds defined in structConn and avoids using
-        //      structure.lookup and unit.lookup (expensive for large structure and not
-        //      needed for archival files or files with an MD topology)
+    var hasExhaustiveStructConn = structure.models.some(function (m) { return struct_conn_1.StructConn.isExhaustive(m); });
+    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds && !hasExhaustiveStructConn)) {
         return new data_1.InterUnitBonds(builder.getMap());
     }
     structure_1.Structure.eachUnitPair(structure, function (unitA, unitB) {

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

@@ -224,9 +224,7 @@ function findBonds(unit, props) {
 }
 function computeIntraUnitBonds(unit, props) {
     var p = tslib_1.__assign(tslib_1.__assign({}, common_1.DefaultBondComputationProps), props);
-    if (p.noCompute || model_1.Model.isCoarseGrained(unit.model)) {
-        // TODO add function that only adds bonds defined in structConn of chemCompBond
-        //      and avoid using unit.lookup
+    if (p.noCompute || (model_1.Model.isCoarseGrained(unit.model) && !index_pair_1.IndexPairBonds.Provider.get(unit.model) && !struct_conn_1.StructConn.isExhaustive(unit.model))) {
         return data_1.IntraUnitBonds.Empty;
     }
     if (!p.forceCompute && index_pair_1.IndexPairBonds.Provider.get(unit.model)) {

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

@@ -131,6 +131,9 @@ var UnitRing;
             return false;
         if (ring.length < 5)
             return false;
+        // no planarity-based aromaticity if any aromatic flags are present
+        if (aromaticBondCount > 0)
+            return false;
         var ma = principal_axes_1.PrincipalAxes.calculateMomentsAxes((0, util_1.getPositions)(unit, ring));
         return linear_algebra_1.Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;
     }

package/lib/commonjs/mol-model-formats/shape/ply.d.ts

@@ -30,6 +30,7 @@ export declare const PlyShapeParams: {
     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 shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-formats/structure/basic/entities.js

@@ -99,7 +99,7 @@ function getEntityData(data) {
                 var entityId = label_entity_id.value(i);
                 if (!entityIds.has(entityId)) {
                     var compId = label_comp_id.value(i);
-                    var compType = chemCompType.get(compId) || '';
+                    var compType = chemCompType.get(compId) || 'other';
                     subtypes[getEntityIndex(entityId)] = (0, types_1.getEntitySubtype)(compId, compType);
                     entityIds.add(entityId);
                 }

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

@@ -88,7 +88,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"oligosaccharide">;
     };
     chem_comp: {
-        type: import("../../../mol-data/db/column").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: import("../../../mol-data/db/column").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: import("../../../mol-data/db/column").Column.Schema.Str;
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -160,7 +160,7 @@ export declare const BasicSchema: {
     };
     pdbx_unobs_or_zero_occ_residues: {
         id: import("../../../mol-data/db/column").Column.Schema.Int;
-        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         occupancy_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"1" | "0">;
         PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         auth_asym_id: import("../../../mol-data/db/column").Column.Schema.Str;

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

@@ -33,45 +33,45 @@ 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;
@@ -79,12 +79,12 @@ 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;
@@ -133,10 +133,10 @@ 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/commonjs/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/commonjs/mol-model-formats/structure/pdb/atom-site.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -37,31 +37,96 @@ function getAtomSiteTemplate(data, count) {
     };
 }
 exports.getAtomSiteTemplate = getAtomSiteTemplate;
-function getAtomSite(sites) {
+function getAtomSite(sites, hasTer) {
+    var pdbx_PDB_model_num = cif_1.CifField.ofStrings(sites.pdbx_PDB_model_num);
     var auth_asym_id = cif_1.CifField.ofTokens(sites.auth_asym_id);
+    var auth_seq_id = cif_1.CifField.ofTokens(sites.auth_seq_id);
     var auth_atom_id = cif_1.CifField.ofTokens(sites.auth_atom_id);
     var auth_comp_id = cif_1.CifField.ofTokens(sites.auth_comp_id);
+    var id = cif_1.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 = db_1.Column.ofStringArray(labelAsymIds);
+    var labelAtomId = db_1.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: cif_1.CifField.ofTokens(sites.auth_seq_id),
+        auth_seq_id: auth_seq_id,
         B_iso_or_equiv: cif_1.CifField.ofTokens(sites.B_iso_or_equiv),
         Cartn_x: cif_1.CifField.ofTokens(sites.Cartn_x),
         Cartn_y: cif_1.CifField.ofTokens(sites.Cartn_y),
         Cartn_z: cif_1.CifField.ofTokens(sites.Cartn_z),
         group_PDB: cif_1.CifField.ofTokens(sites.group_PDB),
-        id: cif_1.CifField.ofStrings(sites.id),
+        id: id,
         label_alt_id: cif_1.CifField.ofTokens(sites.label_alt_id),
-        label_asym_id: auth_asym_id,
-        label_atom_id: auth_atom_id,
+        label_asym_id: cif_1.CifField.ofColumn(labelAsymId),
+        label_atom_id: cif_1.CifField.ofColumn(labelAtomId),
         label_comp_id: auth_comp_id,
         label_seq_id: cif_1.CifField.ofUndefined(sites.index, db_1.Column.Schema.int),
         label_entity_id: cif_1.CifField.ofStrings(sites.label_entity_id),
         occupancy: (0, token_1.areTokensEmpty)(sites.occupancy) ? cif_1.CifField.ofUndefined(sites.index, db_1.Column.Schema.float) : cif_1.CifField.ofTokens(sites.occupancy),
         type_symbol: cif_1.CifField.ofTokens(sites.type_symbol),
         pdbx_PDB_ins_code: cif_1.CifField.ofTokens(sites.pdbx_PDB_ins_code),
-        pdbx_PDB_model_num: cif_1.CifField.ofStrings(sites.pdbx_PDB_model_num),
+        pdbx_PDB_model_num: pdbx_PDB_model_num,
         partial_charge: cif_1.CifField.ofTokens(sites.partial_charge)
     };
 }

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

@@ -22,19 +22,19 @@ 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';
 }
 function parseHelix(lines, lineStart, lineEnd) {
     var helices = [];

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

@@ -24,7 +24,7 @@ var conect_1 = require("./conect");
 var debug_1 = require("../../../mol-util/debug");
 function pdbToMmCif(pdb) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             lines = pdb.lines;
             data = lines.data, indices = lines.indices;
@@ -54,6 +54,7 @@ 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]) {
@@ -189,6 +190,10 @@ function pdbToMmCif(pdb) {
                         }
                         // TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
                         break;
+                    case 'T':
+                        if ((0, string_1.substringStartsWith)(data, s, e, 'TER')) {
+                            hasTer = true;
+                        }
                 }
             }
             seqIds = db_1.Column.ofIntTokens(atomSite.auth_seq_id);
@@ -203,7 +208,7 @@ function pdbToMmCif(pdb) {
                 moleculeType = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
                 atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
             }
-            atom_site = (0, atom_site_1.getAtomSite)(atomSite);
+            atom_site = (0, atom_site_1.getAtomSite)(atomSite, hasTer);
             if (!isPdbqt)
                 delete atom_site.partial_charge;
             if (conectRange) {