molstar 3.3.1 → 3.6.0

package/lib/commonjs/mol-model/structure/model/types.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 Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -62,32 +62,33 @@ export declare const PolymerTypeAtomRoleId: {
 };
 export declare const ProteinBackboneAtoms: Set<string>;
 export declare const NucleicBackboneAtoms: Set<string>;
+declare type ChemCompType = mmCIF_chemComp_schema['type']['T'];
 /** Chemical component type names for D-linked protein */
-export declare const DProteinComponentTypeNames: Set<string>;
+export declare const DProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for L-linked protein */
-export declare const LProteinComponentTypeNames: Set<string>;
+export declare const LProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
-export declare const GammaProteinComponentTypeNames: Set<string>;
+export declare const GammaProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
-export declare const BetaProteinComponentTypeNames: Set<string>;
+export declare const BetaProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
-export declare const ProteinTerminusComponentTypeNames: Set<string>;
+export declare const ProteinTerminusComponentTypeNames: Set<"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">;
 /** Chemical component type names for peptide-like protein */
-export declare const OtherProteinComponentTypeNames: Set<string>;
+export declare const OtherProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for protein */
-export declare const ProteinComponentTypeNames: Set<string>;
+export declare const ProteinComponentTypeNames: Set<"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">;
 /** Chemical component type names for DNA */
-export declare const DNAComponentTypeNames: Set<string>;
+export declare const DNAComponentTypeNames: Set<"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">;
 /** Chemical component type names for RNA */
-export declare const RNAComponentTypeNames: Set<string>;
+export declare const RNAComponentTypeNames: Set<"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">;
 /** Chemical component type names for saccharide */
 export declare const SaccharideComponentTypeNames: Set<string>;
 /** Chemical component type names for other */
-export declare const OtherComponentTypeNames: Set<string>;
+export declare const OtherComponentTypeNames: Set<"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">;
 /** Chemical component type names for ion (extension to mmcif) */
-export declare const IonComponentTypeNames: Set<string>;
+export declare const IonComponentTypeNames: Set<"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">;
 /** Chemical component type names for lipid (extension to mmcif) */
-export declare const LipidComponentTypeNames: Set<string>;
+export declare const LipidComponentTypeNames: Set<"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">;
 /** Common names for water molecules */
 export declare const WaterNames: Set<string>;
 export declare const AminoAcidNamesL: Set<string>;
@@ -103,12 +104,12 @@ export declare const isPurineBase: (compId: string) => boolean;
 export declare const isPyrimidineBase: (compId: string) => boolean;
 export declare const PolymerNames: Set<string>;
 /** get the molecule type from component type and id */
-export declare function getMoleculeType(compType: string, compId: string): MoleculeType;
-export declare function getPolymerType(compType: string, molType: MoleculeType): PolymerType;
-export declare function getComponentType(compId: string): mmCIF_chemComp_schema['type']['T'];
+export declare function getMoleculeType(compType: ChemCompType, compId: string): MoleculeType;
+export declare function getPolymerType(compType: ChemCompType, molType: MoleculeType): PolymerType;
+export declare function getComponentType(compId: string): ChemCompType;
 export declare function getDefaultChemicalComponent(compId: string): ChemicalComponent;
 export declare function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'];
-export declare function getEntitySubtype(compId: string, compType: string): EntitySubtype;
+export declare function getEntitySubtype(compId: string, compType: ChemCompType): EntitySubtype;
 export declare function isPolymer(moleculeType: MoleculeType): boolean;
 export declare function isNucleic(moleculeType: MoleculeType): boolean;
 export declare function isProtein(moleculeType: MoleculeType): boolean;
@@ -259,3 +260,4 @@ export declare const ResidueHydrophobicity: {
     HIP: number[];
 };
 export declare const DefaultResidueHydrophobicity: number[];
+export {};

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/model.js

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -166,14 +166,12 @@ function findPairBonds(unitA, unitB, props, builder) {
     }
     builder.finishUnitPair();
 }
-var DefaultInterBondComputationProps = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
+var DefaultInterBondComputationProps = tslib_1.__assign(tslib_1.__assign({}, common_1.DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
 function findBonds(structure, props) {
     var builder = new inter_unit_graph_1.InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return index_pair_1.IndexPairBonds.Provider.get(m); });
-    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) {
@@ -186,8 +184,8 @@ function findBonds(structure, props) {
     return new data_1.InterUnitBonds(builder.getMap());
 }
 function computeInterUnitBonds(structure, props) {
-    var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultInterBondComputationProps), props);
-    return findBonds(structure, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
+    var p = tslib_1.__assign(tslib_1.__assign({}, DefaultInterBondComputationProps), props);
+    return findBonds(structure, tslib_1.__assign(tslib_1.__assign({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
             var mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&

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

@@ -223,10 +223,8 @@ function findBonds(unit, props) {
     return getGraph(atomA, atomB, order, flags, atomCount, canRemap);
 }
 function computeIntraUnitBonds(unit, props) {
-    var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, common_1.DefaultBondComputationProps), props);
-    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
+    var p = tslib_1.__assign(tslib_1.__assign({}, common_1.DefaultBondComputationProps), props);
+    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/bonds.js

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

package/lib/commonjs/mol-model/structure/structure/unit/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;
     }