molstar 2.4.0 → 2.4.1

package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts

@@ -23,16 +23,16 @@ export declare const mmCIF_chemCompBond_schema: {
     comp_id: Column.Schema.Str;
     value_order: Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     pdbx_ordinal: Column.Schema.Int;
-    pdbx_stereo_config: Column.Schema.Aliased<"E" | "Z" | "N">;
+    pdbx_stereo_config: Column.Schema.Aliased<"N" | "E" | "Z">;
     pdbx_aromatic_flag: Column.Schema.Aliased<"N" | "Y">;
 };
 /** Has `type` extended with 'Ion' and 'Lipid' */
 export declare const mmCIF_chemComp_schema: {
-    type: 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">;
+    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;
-    mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+    mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
     name: Column.Schema.Str;
     pdbx_synonyms: Column.Schema.List<string>;
 };

package/lib/mol-io/reader/cif/schema/mmcif.d.ts

@@ -478,7 +478,7 @@ export declare const mmCIF_Schema: {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        mon_nstd_flag: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * The full name of the component.
          */
@@ -489,7 +489,7 @@ export declare const mmCIF_Schema: {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: 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">;
+        type: 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">;
         /**
          * Synonym list for the component.
          */
@@ -534,7 +534,7 @@ export declare const mmCIF_Schema: {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Schema.Aliased<"E" | "Z" | "N">;
+        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
         /**
          * A flag indicating an aromatic bond.
          */
@@ -786,12 +786,12 @@ export declare const mmCIF_Schema: {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        nstd_linkage: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        nstd_monomer: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * The type of the polymer.
          */
@@ -885,7 +885,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -1886,7 +1886,7 @@ export declare const mmCIF_Schema: {
         /**
          * The identifying content type of the related entry.
          */
-        content_type: Schema.Aliased<"other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "split" | "re-refinement" | "complete structure" | "unspecified">;
+        content_type: Schema.Aliased<"split" | "other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "re-refinement" | "complete structure" | "unspecified">;
     };
     /**
      * The PDBX_ENTITY_NONPOLY category provides a mapping between
@@ -2660,7 +2660,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2779,7 +2779,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3083,7 +3083,7 @@ export declare const mmCIF_Schema: {
         /**
          * The primitive object used to model this segment.
          */
-        model_object_primitive: Schema.Aliased<"other" | "atomistic" | "sphere" | "gaussian">;
+        model_object_primitive: Schema.Aliased<"other" | "sphere" | "atomistic" | "gaussian">;
         /**
          * The identifier for the starting structural model.
          * This data item is a pointer to _ihm_starting_model_details.starting_model_id
@@ -3343,11 +3343,11 @@ export declare const mmCIF_Schema: {
         /**
          * The type of post modeling analysis being carried out.
          */
-        type: Schema.Aliased<"other" | "filter" | "cluster" | "rescore" | "validation" | "none">;
+        type: Schema.Aliased<"none" | "filter" | "other" | "cluster" | "rescore" | "validation">;
         /**
          * The parameter/feature used in the post modeling analysis.
          */
-        feature: Schema.Aliased<"other" | "none" | "energy/score" | "RMSD" | "dRMSD">;
+        feature: Schema.Aliased<"none" | "other" | "energy/score" | "RMSD" | "dRMSD">;
         /**
          * The number of models at the beginning of the post processing step.
          */
@@ -3566,7 +3566,7 @@ export declare const mmCIF_Schema: {
         /**
          * The application / utilization of the dataset group in modeling.
          */
-        application: Schema.Aliased<"other" | "filter" | "validation" | "restraint" | "representation" | "sampling">;
+        application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling">;
         /**
          * Additional details regarding the dataset group.
          */
@@ -4595,7 +4595,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of entity.
          */
-        entity_type: Schema.Aliased<"non-polymer" | "other" | "polymer" | "water">;
+        entity_type: Schema.Aliased<"other" | "non-polymer" | "polymer" | "water">;
     };
     /**
      * Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions

package/lib/mol-io/reader/ply/schema.d.ts

@@ -24,7 +24,7 @@ export declare const PlyTypeByteLength: {
 };
 export declare type PlyType = keyof typeof PlyTypeByteLength;
 export declare const PlyTypes: Set<string>;
-export declare function PlyType(str: string): "float32" | "int32" | "uint16" | "uint32" | "uint8" | "int8" | "int16" | "ushort" | "float" | "int" | "double" | "char" | "uchar" | "short" | "uint" | "float64";
+export declare function PlyType(str: string): "double" | "float" | "char" | "int" | "uint8" | "int8" | "uint16" | "int16" | "uint32" | "int32" | "float32" | "ushort" | "uchar" | "short" | "uint" | "float64";
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;

package/lib/mol-model/loci.d.ts

@@ -54,56 +54,56 @@ declare namespace Loci {
     export function getPrincipalAxes(loci: Loci): PrincipalAxes | undefined;
     const Granularity: {
         element: (loci: Loci) => Loci;
-        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
-        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | {
+        } | DataLoci<unknown, unknown>;
+        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-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 | {
+        } | DataLoci<unknown, unknown>;
+        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+        } | DataLoci<unknown, unknown>;
     };
     export type Granularity = keyof typeof Granularity;
-    export const GranularityOptions: ["residue" | "entity" | "model" | "structure" | "chain" | "element" | "operator" | "elementInstances" | "residueInstances" | "chainInstances", string][];
+    export const GranularityOptions: ["element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "residue" | "entity" | "model" | "structure" | "chain" | "element" | "operator" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): "element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances";
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies

package/lib/mol-model/shape/shape.d.ts

@@ -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<"text" | "spheres" | "mesh" | "points" | "cylinders" | "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" | "image" | "points" | "spheres" | "cylinders" | "lines" | "mesh" | "direct-volume" | "texture-mesh">;
     interface Loci {
         readonly kind: 'shape-loci';
         readonly shape: Shape;

package/lib/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<"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">;
+        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>;
@@ -68,7 +68,7 @@ declare const StructureProperties: {
         id: StructureElement.Property<number>;
         chainGroupId: StructureElement.Property<number>;
         multiChain: StructureElement.Property<boolean>;
-        object_primitive: StructureElement.Property<"atomistic" | "sphere" | "gaussian">;
+        object_primitive: StructureElement.Property<"sphere" | "atomistic" | "gaussian">;
         operator_name: StructureElement.Property<string>;
         model_index: StructureElement.Property<number>;
         model_label: StructureElement.Property<string>;

package/lib/mol-model/structure/structure/unit.d.ts

@@ -181,8 +181,8 @@ declare namespace Unit {
     export function areOperatorsEqual(a: Unit, b: Unit): boolean;
     export function areConformationsEqual(a: Unit, b: Unit): boolean;
     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 getModelConformationOfKind(kind: Unit.Kind, model: Model): import("../model/properties/atomic").AtomicConformation | CoarseSphereConformation | CoarseGaussianConformation;
+    export function getConformation(u: Unit): import("../model/properties/atomic").AtomicConformation | CoarseSphereConformation | CoarseGaussianConformation;
     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 {};

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

@@ -17,11 +17,11 @@ export declare const PlyShapeParams: {
         red: string;
         green: string;
         blue: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<{
+    }>, "material"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "material">>;
+    }>, "vertex">>;
     grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
     }>, "vertex">>;
@@ -31,7 +31,7 @@ export declare const PlyShapeParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type PlyShapeParams = typeof PlyShapeParams;
 export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapeProvider<PlyFile, Mesh, {
@@ -41,11 +41,11 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
         red: string;
         green: string;
         blue: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<{
+    }>, "material"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
-    }>, "material">>;
+    }>, "vertex">>;
     grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
     }>, "vertex">>;
@@ -55,5 +55,5 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 }>>;

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

@@ -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<"no" | "n" | "yes" | "y">;
-        nstd_monomer: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        nstd_linkage: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
+        nstd_monomer: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         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<"no" | "n" | "yes" | "y">;
+        hetero: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         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<"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">;
+        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;
-        mon_nstd_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        mon_nstd_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         name: import("../../../mol-data/db/column").Column.Schema.Str;
         pdbx_synonyms: import("../../../mol-data/db/column").Column.Schema.List<string>;
     };

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

@@ -19,29 +19,29 @@ export declare class ComponentBuilder {
     private getType;
     has(compId: string): boolean;
     get(compId: string): Table.Row<Pick<{
-        type: 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">;
+        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;
-        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
-    }, "id" | "name" | "type">> | undefined;
+    }, "name" | "id" | "type">> | undefined;
     add(compId: string, index: number): Table.Row<Pick<{
-        type: 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">;
+        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;
-        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
-    }, "id" | "name" | "type">>;
+    }, "name" | "id" | "type">>;
     getChemCompTable(): Table<{
-        type: 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">;
+        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;
-        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
+        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
     }>;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Fred Ludlow <Fred.Ludlow@astx.com>

package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Fred Ludlow <Fred.Ludlow@astx.com>
@@ -46,10 +46,7 @@ function addUnitHydrogenDonors(structure, unit, builder) {
     var totalH = getUnitValenceModel(structure, unit).totalH;
     var elements = unit.elements;
     var _a = unit.model.atomicConformation, x = _a.x, y = _a.y, z = _a.z;
-    var elementAromaticRingIndices = unit.rings.elementAromaticRingIndices;
     for (var i = 0, il = elements.length; i < il; ++i) {
-        if (elementAromaticRingIndices.has(i))
-            continue;
         var element = typeSymbol(unit, i);
         if ((
         // include both nitrogen atoms in histidine due to
@@ -100,13 +97,10 @@ function addUnitHydrogenAcceptors(structure, unit, builder) {
     var _a = getUnitValenceModel(structure, unit), charge = _a.charge, implicitH = _a.implicitH, idealGeometry = _a.idealGeometry;
     var elements = unit.elements;
     var _b = unit.model.atomicConformation, x = _b.x, y = _b.y, z = _b.z;
-    var elementAromaticRingIndices = unit.rings.elementAromaticRingIndices;
     var add = function (i) {
         builder.add(5 /* HydrogenAcceptor */, 0 /* None */, x[elements[i]], y[elements[i]], z[elements[i]], i);
     };
     for (var i = 0, il = elements.length; i < il; ++i) {
-        if (elementAromaticRingIndices.has(i))
-            continue;
         var element = typeSymbol(unit, i);
         if (element === "O" /* O */) {
             // Basically assume all oxygen atoms are acceptors!

package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js.map

@@ -1 +1 @@
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package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -19,14 +19,14 @@ export declare const InteractionsInterUnitParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionsInterUnitParams = typeof InteractionsInterUnitParams;
 export declare function InteractionsInterUnitVisual(materialId: number): ComplexVisual<InteractionsInterUnitParams>;

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

@@ -19,14 +19,14 @@ export declare const InteractionsIntraUnitParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams;
 export declare function InteractionsIntraUnitVisual(materialId: number): UnitsVisual<InteractionsIntraUnitParams>;

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

@@ -9,7 +9,7 @@ import { ThemeRegistryContext } from '../../../mol-theme/theme';
 import { Structure } from '../../../mol-model/structure';
 import { StructureRepresentation, StructureRepresentationProvider } from '../../../mol-repr/structure/representation';
 export declare const InteractionsParams: {
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"intra-unit" | "inter-unit">;
     dashCount: PD.Numeric;
@@ -30,11 +30,11 @@ export declare const InteractionsParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionsParams = typeof InteractionsParams;
 export declare function getInteractionParams(ctx: ThemeRegistryContext, structure: Structure): {
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"intra-unit" | "inter-unit">;
     dashCount: PD.Numeric;
@@ -55,12 +55,12 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionRepresentation = StructureRepresentation<InteractionsParams>;
 export declare function InteractionRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InteractionsParams>): InteractionRepresentation;
 export declare const InteractionsRepresentationProvider: StructureRepresentationProvider<{
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"intra-unit" | "inter-unit">;
     dashCount: PD.Numeric;
@@ -81,5 +81,5 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 }, "interactions">;