molstar 2.4.0 → 2.4.1

package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js

@@ -33,24 +33,26 @@ var v3dot = linear_algebra_1.Vec3.dot;
 var v3unitX = linear_algebra_1.Vec3.unitX;
 var caAdd3 = util_1.ChunkedArray.add3;
 var CosSinCache = new Map();
-function getCosSin(radialSegments) {
-    if (!CosSinCache.has(radialSegments)) {
+function getCosSin(radialSegments, shift) {
+    var offset = shift ? 1 : 0;
+    var hash = (0, util_1.cantorPairing)(radialSegments, offset);
+    if (!CosSinCache.has(hash)) {
         var cos = [];
         var sin = [];
         for (var j = 0; j < radialSegments; ++j) {
-            var t = 2 * Math.PI * j / radialSegments;
+            var t = (j * 2 + offset) / radialSegments * Math.PI;
             cos[j] = Math.cos(t);
             sin[j] = Math.sin(t);
         }
-        CosSinCache.set(radialSegments, { cos: cos, sin: sin });
+        CosSinCache.set(hash, { cos: cos, sin: sin });
     }
-    return CosSinCache.get(radialSegments);
+    return CosSinCache.get(hash);
 }
 function addTube(state, controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, startCap, endCap, crossSection) {
     var currentGroup = state.currentGroup, vertices = state.vertices, normals = state.normals, indices = state.indices, groups = state.groups;
     var vertexCount = vertices.elementCount;
-    var _a = getCosSin(radialSegments), cos = _a.cos, sin = _a.sin;
-    var q1 = radialSegments / 4;
+    var _a = getCosSin(radialSegments, crossSection === 'rounded'), cos = _a.cos, sin = _a.sin;
+    var q1 = Math.round(radialSegments / 4);
     var q3 = q1 * 3;
     for (var i = 0; i <= linearSegments; ++i) {
         var i3 = i * 3;
@@ -67,7 +69,15 @@ function addTube(state, controlPoints, normalVectors, binormalVectors, linearSeg
                     ? (j < q1 || j >= q3) ? height - width : -height + width
                     : (j >= q1 && j < q3) ? -height + width : height - width;
                 v3scaleAndAdd(surfacePoint, surfacePoint, u, h);
-                add2AndScale2(normalVector, u, v, cos[j], sin[j]);
+                if (j === q1 || j === q1 - 1) {
+                    add2AndScale2(normalVector, u, v, 0, 1);
+                }
+                else if (j === q3 || j === q3 - 1) {
+                    add2AndScale2(normalVector, u, v, 0, -1);
+                }
+                else {
+                    add2AndScale2(normalVector, u, v, cos[j], sin[j]);
+                }
             }
             else {
                 add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);

package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts

@@ -63,7 +63,7 @@ export declare namespace Mesh {
         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">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Mesh, Params>;

package/lib/commonjs/mol-geo/geometry/points/points.d.ts

@@ -34,13 +34,13 @@ export declare namespace Points {
         fuzzy: string;
     };
     type StyleTypes = keyof typeof StyleTypes;
-    const StyleTypeNames: ("square" | "circle" | "fuzzy")[];
+    const StyleTypeNames: ("circle" | "square" | "fuzzy")[];
     const Params: {
         sizeFactor: PD.Numeric;
         pointSizeAttenuation: PD.BooleanParam;
-        pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+        pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
         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">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Points, Params>;

package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts

@@ -35,7 +35,7 @@ export declare namespace Spheres {
         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">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Spheres, Params>;

package/lib/commonjs/mol-geo/geometry/text/text.d.ts

@@ -59,7 +59,7 @@ export declare namespace Text {
         fontVariant: PD.Select<import("./font-atlas").FontVariant>;
         fontWeight: PD.Select<import("./font-atlas").FontWeight>;
         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">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Text, Params>;

package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts

@@ -46,7 +46,7 @@ export declare namespace TextureMesh {
         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">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<TextureMesh, Params>;

package/lib/commonjs/mol-gl/renderer.d.ts

@@ -59,13 +59,13 @@ export declare const RendererParams: {
     selectStrength: PD.Numeric;
     markerPriority: PD.Select<number>;
     xrayEdgeFalloff: PD.Numeric;
-    style: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<{
+    style: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<{
         lightIntensity: number;
         ambientIntensity: number;
         metalness: number;
         roughness: number;
         reflectivity: number;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">>;
+    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">>;
     clip: PD.Group<PD.Normalize<{
         variant: Clipping.Variant;
         objects: PD.Normalize<{

package/lib/commonjs/mol-gl/webgl/context.d.ts

@@ -17,7 +17,7 @@ import { ComputeRenderable } from '../renderable';
 export declare function getGLContext(canvas: HTMLCanvasElement, attribs?: WebGLContextAttributes & {
     preferWebGl1?: boolean;
 }): GLRenderingContext | null;
-export declare function getErrorDescription(gl: GLRenderingContext, error: number): "context lost" | "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "unknown error";
+export declare function getErrorDescription(gl: GLRenderingContext, error: number): "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "context lost" | "unknown error";
 export declare function checkError(gl: GLRenderingContext): void;
 export declare function readPixels(gl: GLRenderingContext, x: number, y: number, width: number, height: number, buffer: Uint8Array | Float32Array | Int32Array): void;
 declare function createStats(): {

package/lib/commonjs/mol-io/common/typed-array.d.ts

@@ -25,6 +25,6 @@ export interface TypedArrayBufferContext {
 }
 export declare function getElementByteSize(type: TypedArrayValueType): 1 | 2 | 4;
 export declare function makeTypedArray(type: TypedArrayValueType, buffer: ArrayBuffer, byteOffset?: number, length?: number): TypedArrayValueArray;
-export declare function createTypedArray(type: TypedArrayValueType, size: number): Float32Array | Uint16Array | Int8Array | Int16Array;
+export declare function createTypedArray(type: TypedArrayValueType, size: number): Int8Array | Int16Array | Uint16Array | Float32Array;
 export declare function createTypedArrayBufferContext(size: number, type: TypedArrayValueType): TypedArrayBufferContext;
 export declare function readTypedArray(ctx: TypedArrayBufferContext, file: FileHandle, position: number, byteCount: number, valueByteOffset: number, littleEndian?: boolean): Promise<TypedArrayValueArray>;

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

@@ -93,7 +93,7 @@ export declare const CCD_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.
          */
@@ -318,7 +318,7 @@ export declare const CCD_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.
          */

package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts

@@ -10,11 +10,11 @@ export declare const DensityServer_Header_Schema: {
         server_version: Schema.Str;
         datetime_utc: Schema.Str;
         guid: Schema.Str;
-        is_empty: Schema.Aliased<"y" | "no" | "n" | "yes">;
-        has_error: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        is_empty: Schema.Aliased<"y" | "yes" | "no" | "n">;
+        has_error: Schema.Aliased<"y" | "yes" | "no" | "n">;
         error: Schema.Str;
         query_source_id: Schema.Str;
-        query_type: Schema.Aliased<"box" | "cell">;
+        query_type: Schema.Aliased<"cell" | "box">;
         query_box_type: Schema.Aliased<"cartesian" | "fractional">;
         query_box_a: Schema.Tensor;
         query_box_b: Schema.Tensor;

package/lib/commonjs/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/commonjs/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/commonjs/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): "ushort" | "float" | "int" | "float32" | "int32" | "uint32" | "uint16" | "int8" | "int16" | "char" | "uchar" | "short" | "uint" | "double" | "uint8" | "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/commonjs/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/commonjs/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/commonjs/mol-model/structure/query/utils/structure-distance.d.ts

@@ -10,11 +10,60 @@ 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 = 0,
-        WithinMax = 1,
-        Miss = 2
+        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;
     }
-    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/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<"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/commonjs/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 {};