npm - molstar - Versions diffs - 2.3.3 → 2.3.5 - Mend

molstar 2.3.3 → 2.3.5

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Files changed (355) hide show

package/lib/mol-math/misc.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model/loci.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -54,61 +54,61 @@ declare namespace Loci {
     export function getPrincipalAxes(loci: Loci): PrincipalAxes | undefined;
     const Granularity: {
         element: (loci: Loci) => Loci;
-        residue: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
-            kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chain: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        entity: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        model: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        operator: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        structure: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci;
-        elementInstances: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        residueInstances: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chainInstances: (loci: Loci) => Volume.Isosurface.Loci | Volume.Loci | Volume.Cell.Loci | {
+        } | {
             kind: "empty-loci";
-        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "every-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        } | {
+            kind: "empty-loci";
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
     };
     export type Granularity = keyof typeof Granularity;
-    export const GranularityOptions: ["model" | "structure" | "residue" | "element" | "chain" | "entity" | "operator" | "elementInstances" | "residueInstances" | "chainInstances", string][];
+    export const GranularityOptions: ["residue" | "entity" | "model" | "chain" | "element" | "structure" | "operator" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "model" | "structure" | "residue" | "element" | "chain" | "entity" | "operator" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): "residue" | "entity" | "model" | "chain" | "element" | "structure" | "operator" | "elementInstances" | "residueInstances" | "chainInstances";
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies
      * granularity if given
      */
-    export function normalize(loci: Loci, granularity?: Granularity): Loci;
+    export function normalize(loci: Loci, granularity?: Granularity, alwaysConvertBonds?: boolean): Loci;
     export {};
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -297,8 +297,9 @@ var Loci;
      * Converts structure related loci to StructureElement.Loci and applies
      * granularity if given
      */
-    function normalize(loci, granularity) {
-        if (granularity !== 'element' && Bond.isLoci(loci)) {
+    function normalize(loci, granularity, alwaysConvertBonds) {
+        if (alwaysConvertBonds === void 0) { alwaysConvertBonds = false; }
+        if ((granularity !== 'element' || alwaysConvertBonds) && Bond.isLoci(loci)) {
             // convert Bond.Loci to a StructureElement.Loci so granularity can be applied
             loci = Bond.toStructureElementLoci(loci);
         }

package/lib/mol-model/loci.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model/shape/shape.d.ts CHANGED Viewed

@@ -38,7 +38,7 @@ export declare namespace Shape {
     function getTheme(shape: Shape): Theme;
     function groupIterator(shape: Shape): LocationIterator;
     function createTransform(transforms: Mat4[], transformData?: TransformData): TransformData;
-    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"points" | "mesh" | "spheres" | "cylinders" | "text" | "lines" | "direct-volume" | "image" | "texture-mesh">;
+    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"text" | "mesh" | "points" | "spheres" | "cylinders" | "lines" | "direct-volume" | "image" | "texture-mesh">;
     interface Loci {
         readonly kind: 'shape-loci';
         readonly shape: Shape;

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

@@ -10,60 +10,11 @@ export declare function checkStructureMinMaxDistance(ctx: QueryContext, a: Struc
 export declare function checkStructureMaxRadiusDistance(ctx: QueryContext, a: Structure, b: Structure, maxDist: number, elementRadius: QueryFn<number>): boolean | 0;
 declare namespace MinMaxDist {
     const enum Result {
-        BelowMin,
-        WithinMax,
-        Miss
-    }
-    const distVec = Vec3.zero();
-    function inUnit(ctx: QueryContext, unit: Unit, p: Vec3, eRadius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        const { elements, conformation: { position } } = unit, dV = distVec;
-        ctx.element.unit = unit;
-        let withinRange = false;
-        for (let i = 0, _i = elements.length; i < _i; i++) {
-            const e = elements[i];
-            ctx.element.element = e;
-            const d = Math.max(0, Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx));
-            if (d < minDist)
-                return Result.BelowMin;
-            if (d < maxDist)
-                withinRange = true;
-        }
-        return withinRange ? Result.WithinMax : Result.Miss;
-    }
-    function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        const { units } = s;
-        let withinRange = false;
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            const iu = inUnit(ctx, units[i], point, radius, minDist, maxDist, elementRadius);
-            if (iu === Result.BelowMin)
-                return Result.BelowMin;
-            if (iu === Result.WithinMax)
-                withinRange = true;
-        }
-        return withinRange ? Result.WithinMax : Result.Miss;
-    }
-    const distPivot = Vec3.zero();
-    function check(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        if (a.elementCount === 0 || b.elementCount === 0)
-            return 0;
-        const { units } = a;
-        let withinRange = false;
-        ctx.element.structure = a;
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            const unit = units[i];
-            const { elements, conformation: { position } } = unit;
-            ctx.element.unit = unit;
-            for (let i = 0, _i = elements.length; i < _i; i++) {
-                const e = elements[i];
-                ctx.element.element = e;
-                const tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
-                if (tp === Result.BelowMin)
-                    return Result.BelowMin;
-                if (tp === Result.WithinMax)
-                    withinRange = true;
-            }
-        }
-        return withinRange;
+        BelowMin = 0,
+        WithinMax = 1,
+        Miss = 2
     }
+    function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>): Result;
+    function check(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>): boolean | 0 | Result.BelowMin;
 }
 export {};

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

@@ -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<"non-polymer" | "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" | "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<"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" | "other" | "Ion" | "Lipid">;
     };
     chain: {
         key: StructureElement.Property<import("../model").ChainIndex>;
@@ -52,7 +52,7 @@ declare const StructureProperties: {
     entity: {
         key: StructureElement.Property<import("../model").EntityIndex>;
         id: StructureElement.Property<string>;
-        type: StructureElement.Property<"polymer" | "water" | "branched" | "non-polymer" | "macrolide">;
+        type: StructureElement.Property<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         src_method: StructureElement.Property<"nat" | "man" | "syn">;
         pdbx_description: StructureElement.Property<string[]>;
         formula_weight: StructureElement.Property<number>;
@@ -68,7 +68,7 @@ declare const StructureProperties: {
         id: StructureElement.Property<number>;
         chainGroupId: StructureElement.Property<number>;
         multiChain: StructureElement.Property<boolean>;
-        object_primitive: StructureElement.Property<"sphere" | "gaussian" | "atomistic">;
+        object_primitive: StructureElement.Property<"atomistic" | "sphere" | "gaussian">;
         operator_name: StructureElement.Property<string>;
         model_index: StructureElement.Property<number>;
         model_label: StructureElement.Property<string>;

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

@@ -66,7 +66,7 @@ function findIndexPairBonds(unit) {
             if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
-                orders[order.length] = order[i];
+                orders[orders.length] = order[i];
                 flags[flags.length] = flag[i];
             }
         }

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

	@@ -1 +1 @@
1	- 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package/lib/mol-model/structure/structure/unit/bonds.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -38,6 +38,7 @@ declare namespace Bond {
     function isLociEmpty(loci: Loci): boolean;
     function remapLoci(loci: Loci, structure: Structure): Loci;
     function toStructureElementLoci(loci: Loci): StructureElement.Loci;
+    function toFirstStructureElementLoci(loci: Loci): StructureElement.Loci;
     function getType(structure: Structure, location: Location<Unit.Atomic>): BondType;
     function getOrder(structure: Structure, location: Location<Unit.Atomic>): number;
     function getIntraUnitBondCount(structure: Structure): number;

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

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Unit, StructureElement } from '../../structure';
 import { BondType } from '../../model/types';
-import { SortedArray } from '../../../../mol-data/int';
+import { SortedArray, OrderedSet } from '../../../../mol-data/int';
 import { CentroidHelper } from '../../../../mol-math/geometry/centroid-helper';
 export * from './bonds/data';
 export * from './bonds/intra-compute';
@@ -115,6 +115,11 @@ var Bond;
         return StructureElement.Loci(loci.structure, elements);
     }
     Bond.toStructureElementLoci = toStructureElementLoci;
+    function toFirstStructureElementLoci(loci) {
+        var _a = loci.bonds[0], aUnit = _a.aUnit, aIndex = _a.aIndex;
+        return StructureElement.Loci(loci.structure, [{ unit: aUnit, indices: OrderedSet.ofSingleton(aIndex) }]);
+    }
+    Bond.toFirstStructureElementLoci = toFirstStructureElementLoci;
     function getType(structure, location) {
         if (location.aUnit === location.bUnit) {
             var bonds = location.aUnit.bonds;

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

	@@ -1 +1 @@
1	- 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package/lib/mol-model/structure/structure/unit.d.ts CHANGED Viewed

@@ -183,8 +183,8 @@ declare namespace Unit {
     export function isSameConformation(u: Unit, model: Model): boolean;
     export function getModelConformationOfKind(kind: Unit.Kind, model: Model): CoarseSphereConformation | CoarseGaussianConformation | import("../model/properties/atomic").AtomicConformation;
     export function getConformation(u: Unit): CoarseSphereConformation | CoarseGaussianConformation | import("../model/properties/atomic").AtomicConformation;
-    export function getModelHierarchyOfKind(kind: Unit.Kind, model: Model): CoarseElements | import("../model/properties/atomic").AtomicHierarchy;
-    export function getHierarchy(u: Unit): CoarseElements | import("../model/properties/atomic").AtomicHierarchy;
+    export function getModelHierarchyOfKind(kind: Unit.Kind, model: Model): import("../model/properties/atomic").AtomicHierarchy | CoarseElements;
+    export function getHierarchy(u: Unit): import("../model/properties/atomic").AtomicHierarchy | CoarseElements;
     export {};
 }
 export { Unit };

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

@@ -12,19 +12,19 @@ import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 export declare const PlyShapeParams: {
     coloring: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        color: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "material"> | PD.NamedParams<PD.Normalize<{
-        color: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+    }>, "vertex"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "vertex">>;
-    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    }>, "material">>;
+    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<unknown>, "none">>;
+    }>, "vertex">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -36,19 +36,19 @@ export declare const PlyShapeParams: {
 export declare type PlyShapeParams = typeof PlyShapeParams;
 export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapeProvider<PlyFile, Mesh, {
     coloring: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        color: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "material"> | PD.NamedParams<PD.Normalize<{
-        color: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+    }>, "vertex"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "vertex">>;
-    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    }>, "material">>;
+    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<unknown>, "none">>;
+    }>, "vertex">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;

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

@@ -60,7 +60,7 @@ export declare const BasicSchema: {
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
         src_method: import("../../../mol-data/db/column").Column.Schema.Aliased<"nat" | "man" | "syn">;
-        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"polymer" | "water" | "branched" | "non-polymer" | "macrolide">;
+        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: import("../../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_number_of_molecules: import("../../../mol-data/db/column").Column.Schema.Int;
         pdbx_mutation: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -69,8 +69,8 @@ export declare const BasicSchema: {
     };
     entity_poly: {
         entity_id: import("../../../mol-data/db/column").Column.Schema.Str;
-        nstd_linkage: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
-        nstd_monomer: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_linkage: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        nstd_monomer: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"other" | "polypeptide(D)" | "polypeptide(L)" | "polydeoxyribonucleotide" | "polyribonucleotide" | "polydeoxyribonucleotide/polyribonucleotide hybrid" | "cyclic-pseudo-peptide" | "peptide nucleic acid">;
         pdbx_strand_id: import("../../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_seq_one_letter_code: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -79,7 +79,7 @@ export declare const BasicSchema: {
     };
     entity_poly_seq: {
         entity_id: import("../../../mol-data/db/column").Column.Schema.Str;
-        hetero: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         mon_id: import("../../../mol-data/db/column").Column.Schema.Str;
         num: import("../../../mol-data/db/column").Column.Schema.Int;
     };
@@ -88,11 +88,11 @@ 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<"non-polymer" | "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" | "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<"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" | "other" | "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;
-        mon_nstd_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         name: import("../../../mol-data/db/column").Column.Schema.Str;
         pdbx_synonyms: import("../../../mol-data/db/column").Column.Schema.List<string>;
     };