molstar 3.26.0 → 3.28.0

package/lib/commonjs/mol-gl/webgl/state.js

@@ -22,6 +22,20 @@ function createState(gl) {
     var currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
     var currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
     var currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
+    var currentStencilFunc = gl.getParameter(gl.STENCIL_FUNC);
+    var currentStencilValueMask = gl.getParameter(gl.STENCIL_VALUE_MASK);
+    var currentStencilRef = gl.getParameter(gl.STENCIL_REF);
+    var currentStencilBackFunc = gl.getParameter(gl.STENCIL_BACK_FUNC);
+    var currentStencilBackValueMask = gl.getParameter(gl.STENCIL_BACK_VALUE_MASK);
+    var currentStencilBackRef = gl.getParameter(gl.STENCIL_BACK_REF);
+    var currentStencilWriteMask = gl.getParameter(gl.STENCIL_WRITEMASK);
+    var currentStencilBackWriteMask = gl.getParameter(gl.STENCIL_BACK_WRITEMASK);
+    var currentStencilFail = gl.getParameter(gl.STENCIL_FAIL);
+    var currentStencilPassDepthPass = gl.getParameter(gl.STENCIL_PASS_DEPTH_PASS);
+    var currentStencilPassDepthFail = gl.getParameter(gl.STENCIL_PASS_DEPTH_FAIL);
+    var currentStencilBackFail = gl.getParameter(gl.STENCIL_BACK_FAIL);
+    var currentStencilBackPassDepthPass = gl.getParameter(gl.STENCIL_BACK_PASS_DEPTH_PASS);
+    var currentStencilBackPassDepthFail = gl.getParameter(gl.STENCIL_BACK_PASS_DEPTH_FAIL);
     var maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);
     var vertexAttribsState = [];
     var currentViewport = gl.getParameter(gl.VIEWPORT);
@@ -137,6 +151,114 @@ function createState(gl) {
                 currentBlendColor[3] = alpha;
             }
         },
+        stencilFunc: function (func, ref, mask) {
+            if (func !== currentStencilFunc || ref !== currentStencilRef || mask !== currentStencilValueMask || func !== currentStencilBackFunc || ref !== currentStencilBackRef || mask !== currentStencilBackValueMask) {
+                gl.stencilFunc(func, ref, mask);
+                currentStencilFunc = func;
+                currentStencilRef = ref;
+                currentStencilValueMask = mask;
+                currentStencilBackFunc = func;
+                currentStencilBackRef = ref;
+                currentStencilBackValueMask = mask;
+            }
+        },
+        stencilFuncSeparate: function (face, func, ref, mask) {
+            if (face === gl.FRONT) {
+                if (func !== currentStencilFunc || ref !== currentStencilRef || mask !== currentStencilValueMask) {
+                    gl.stencilFuncSeparate(face, func, ref, mask);
+                    currentStencilFunc = func;
+                    currentStencilRef = ref;
+                    currentStencilValueMask = mask;
+                }
+            }
+            else if (face === gl.BACK) {
+                if (func !== currentStencilBackFunc || ref !== currentStencilBackRef || mask !== currentStencilBackValueMask) {
+                    gl.stencilFuncSeparate(face, func, ref, mask);
+                    currentStencilBackFunc = func;
+                    currentStencilBackRef = ref;
+                    currentStencilBackValueMask = mask;
+                }
+            }
+            else if (face === gl.FRONT_AND_BACK) {
+                if (func !== currentStencilFunc || ref !== currentStencilRef || mask !== currentStencilValueMask || func !== currentStencilBackFunc || ref !== currentStencilBackRef || mask !== currentStencilBackValueMask) {
+                    gl.stencilFuncSeparate(face, func, ref, mask);
+                    currentStencilFunc = func;
+                    currentStencilRef = ref;
+                    currentStencilValueMask = mask;
+                    currentStencilBackFunc = func;
+                    currentStencilBackRef = ref;
+                    currentStencilBackValueMask = mask;
+                }
+            }
+        },
+        stencilMask: function (mask) {
+            if (mask !== currentStencilWriteMask || mask !== currentStencilBackWriteMask) {
+                gl.stencilMask(mask);
+                currentStencilWriteMask = mask;
+                currentStencilBackWriteMask = mask;
+            }
+        },
+        stencilMaskSeparate: function (face, mask) {
+            if (face === gl.FRONT) {
+                if (mask !== currentStencilWriteMask) {
+                    gl.stencilMaskSeparate(face, mask);
+                    currentStencilWriteMask = mask;
+                }
+            }
+            else if (face === gl.BACK) {
+                if (mask !== currentStencilBackWriteMask) {
+                    gl.stencilMaskSeparate(face, mask);
+                    currentStencilBackWriteMask = mask;
+                }
+            }
+            else if (face === gl.FRONT_AND_BACK) {
+                if (mask !== currentStencilWriteMask || mask !== currentStencilBackWriteMask) {
+                    gl.stencilMaskSeparate(face, mask);
+                    currentStencilWriteMask = mask;
+                    currentStencilBackWriteMask = mask;
+                }
+            }
+        },
+        stencilOp: function (fail, zfail, zpass) {
+            if (fail !== currentStencilFail || zfail !== currentStencilPassDepthFail || zpass !== currentStencilPassDepthPass || fail !== currentStencilBackFail || zfail !== currentStencilBackPassDepthFail || zpass !== currentStencilBackPassDepthPass) {
+                gl.stencilOp(fail, zfail, zpass);
+                currentStencilFail = fail;
+                currentStencilPassDepthFail = zfail;
+                currentStencilPassDepthPass = zpass;
+                currentStencilBackFail = fail;
+                currentStencilBackPassDepthFail = zfail;
+                currentStencilBackPassDepthPass = zpass;
+            }
+        },
+        stencilOpSeparate: function (face, fail, zfail, zpass) {
+            if (face === gl.FRONT) {
+                if (fail !== currentStencilFail || zfail !== currentStencilPassDepthFail || zpass !== currentStencilPassDepthPass) {
+                    gl.stencilOpSeparate(face, fail, zfail, zpass);
+                    currentStencilFail = fail;
+                    currentStencilPassDepthFail = zfail;
+                    currentStencilPassDepthPass = zpass;
+                }
+            }
+            else if (face === gl.BACK) {
+                if (fail !== currentStencilBackFail || zfail !== currentStencilBackPassDepthFail || zpass !== currentStencilBackPassDepthPass) {
+                    gl.stencilOpSeparate(face, fail, zfail, zpass);
+                    currentStencilBackFail = fail;
+                    currentStencilBackPassDepthFail = zfail;
+                    currentStencilBackPassDepthPass = zpass;
+                }
+            }
+            else if (face === gl.FRONT_AND_BACK) {
+                if (fail !== currentStencilFail || zfail !== currentStencilPassDepthFail || zpass !== currentStencilPassDepthPass || fail !== currentStencilBackFail || zfail !== currentStencilBackPassDepthFail || zpass !== currentStencilBackPassDepthPass) {
+                    gl.stencilOpSeparate(face, fail, zfail, zpass);
+                    currentStencilFail = fail;
+                    currentStencilPassDepthFail = zfail;
+                    currentStencilPassDepthPass = zpass;
+                    currentStencilBackFail = fail;
+                    currentStencilBackPassDepthFail = zfail;
+                    currentStencilBackPassDepthPass = zpass;
+                }
+            }
+        },
         enableVertexAttrib: function (index) {
             gl.enableVertexAttribArray(index);
             vertexAttribsState[index] = 1;
@@ -182,6 +304,20 @@ function createState(gl) {
             currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
             currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
             currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
+            currentStencilFunc = gl.getParameter(gl.STENCIL_FUNC);
+            currentStencilValueMask = gl.getParameter(gl.STENCIL_VALUE_MASK);
+            currentStencilRef = gl.getParameter(gl.STENCIL_REF);
+            currentStencilBackFunc = gl.getParameter(gl.STENCIL_BACK_FUNC);
+            currentStencilBackValueMask = gl.getParameter(gl.STENCIL_BACK_VALUE_MASK);
+            currentStencilBackRef = gl.getParameter(gl.STENCIL_BACK_REF);
+            currentStencilWriteMask = gl.getParameter(gl.STENCIL_WRITEMASK);
+            currentStencilBackWriteMask = gl.getParameter(gl.STENCIL_BACK_WRITEMASK);
+            currentStencilFail = gl.getParameter(gl.STENCIL_FAIL);
+            currentStencilPassDepthPass = gl.getParameter(gl.STENCIL_PASS_DEPTH_PASS);
+            currentStencilPassDepthFail = gl.getParameter(gl.STENCIL_PASS_DEPTH_FAIL);
+            currentStencilBackFail = gl.getParameter(gl.STENCIL_BACK_FAIL);
+            currentStencilBackPassDepthPass = gl.getParameter(gl.STENCIL_BACK_PASS_DEPTH_PASS);
+            currentStencilBackPassDepthFail = gl.getParameter(gl.STENCIL_BACK_PASS_DEPTH_FAIL);
             maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);
             vertexAttribsState.length = 0;
             for (var i = 0; i < maxVertexAttribs; ++i) {

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

@@ -0,0 +1,38 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Column, Database } from '../../../../mol-data/db';
+import Schema = Column.Schema;
+export declare const Segmentation_Data_Schema: {
+    volume_data_3d_info: {
+        name: Schema.Str;
+        axis_order: Schema.Tensor;
+        origin: Schema.Tensor;
+        dimensions: Schema.Tensor;
+        sample_rate: Schema.Int;
+        sample_count: Schema.Tensor;
+        spacegroup_number: Schema.Int;
+        spacegroup_cell_size: Schema.Tensor;
+        spacegroup_cell_angles: Schema.Tensor;
+        mean_source: Schema.Float;
+        mean_sampled: Schema.Float;
+        sigma_source: Schema.Float;
+        sigma_sampled: Schema.Float;
+        min_source: Schema.Float;
+        min_sampled: Schema.Float;
+        max_source: Schema.Float;
+        max_sampled: Schema.Float;
+    };
+    segmentation_data_table: {
+        set_id: Schema.Int;
+        segment_id: Schema.Int;
+    };
+    segmentation_data_3d: {
+        values: Schema.Int;
+    };
+};
+export type Segmentation_Data_Schema = typeof Segmentation_Data_Schema;
+export interface Segmentation_Data_Database extends Database<Segmentation_Data_Schema> {
+}

package/lib/commonjs/mol-io/reader/cif/schema/segmentation.js

@@ -0,0 +1,22 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Segmentation_Data_Schema = void 0;
+var db_1 = require("../../../../mol-data/db");
+var density_server_1 = require("./density-server");
+var Schema = db_1.Column.Schema;
+var int = Schema.int;
+exports.Segmentation_Data_Schema = {
+    volume_data_3d_info: density_server_1.DensityServer_Data_Schema.volume_data_3d_info,
+    segmentation_data_table: {
+        set_id: int,
+        segment_id: int,
+    },
+    segmentation_data_3d: {
+        values: int
+    }
+};

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -14,6 +14,7 @@ import { BIRD_Database } from './cif/schema/bird';
 import { dic_Database } from './cif/schema/dic';
 import { DensityServer_Data_Database } from './cif/schema/density-server';
 import { CifCore_Database } from './cif/schema/cif-core';
+import { Segmentation_Data_Database } from './cif/schema/segmentation';
 export declare const CIF: {
     parse: (data: string | Uint8Array) => import("../../mol-task/task").Task<import("./result").ReaderResult<import("./cif/data-model").CifFile>>;
     parseText: typeof parseCifText;
@@ -27,6 +28,7 @@ export declare const CIF: {
         dic: (frame: CifFrame) => dic_Database;
         cifCore: (frame: CifFrame) => CifCore_Database;
         densityServer: (frame: CifFrame) => DensityServer_Data_Database;
+        segmentation: (frame: CifFrame) => Segmentation_Data_Database;
     };
 };
 export * from './cif/data-model';

package/lib/commonjs/mol-io/reader/cif.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -17,6 +17,7 @@ var bird_1 = require("./cif/schema/bird");
 var dic_1 = require("./cif/schema/dic");
 var density_server_1 = require("./cif/schema/density-server");
 var cif_core_1 = require("./cif/schema/cif-core");
+var segmentation_1 = require("./cif/schema/segmentation");
 exports.CIF = {
     parse: function (data) { return typeof data === 'string' ? (0, parser_1.parseCifText)(data) : (0, parser_2.parseCifBinary)(data); },
     parseText: parser_1.parseCifText,
@@ -30,6 +31,7 @@ exports.CIF = {
         dic: function (frame) { return (0, schema_1.toDatabase)(dic_1.dic_Schema, frame); },
         cifCore: function (frame) { return (0, schema_1.toDatabase)(cif_core_1.CifCore_Schema, frame, cif_core_1.CifCore_Aliases); },
         densityServer: function (frame) { return (0, schema_1.toDatabase)(density_server_1.DensityServer_Data_Schema, frame); },
+        segmentation: function (frame) { return (0, schema_1.toDatabase)(segmentation_1.Segmentation_Data_Schema, frame); },
     }
 };
 tslib_1.__exportStar(require("./cif/data-model"), exports);

package/lib/commonjs/mol-model/location.d.ts

@@ -7,6 +7,7 @@ import { StructureElement } from './structure';
 import { Bond } from './structure/structure/unit/bonds';
 import { ShapeGroup } from './shape/shape';
 import { PositionLocation } from '../mol-geo/util/location-iterator';
+import { Volume } from './volume';
 /** A null value Location */
 export declare const NullLocation: {
     kind: "null-location";
@@ -22,4 +23,4 @@ export interface DataLocation<T = unknown, E = unknown> {
 }
 export declare function DataLocation<T = unknown, E = unknown>(tag: string, data: T, element: E): DataLocation<T, E>;
 export declare function isDataLocation(x: any): x is DataLocation;
-export type Location = StructureElement.Location | Bond.Location | ShapeGroup.Location | PositionLocation | DataLocation | NullLocation;
+export type Location = StructureElement.Location | Bond.Location | ShapeGroup.Location | PositionLocation | DataLocation | NullLocation | Volume.Segment.Location;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -39,7 +39,7 @@ export declare function areDataLociEqual(a: DataLoci, b: DataLoci): boolean;
 export declare function isDataLociEmpty(loci: DataLoci): boolean;
 export declare function DataLoci<T = unknown, E = unknown>(tag: string, data: T, elements: ReadonlyArray<E>, getBoundingSphere: DataLoci<T, E>['getBoundingSphere'], getLabel: DataLoci<T, E>['getLabel']): DataLoci<T, E>;
 export { Loci };
-type Loci = StructureElement.Loci | Structure.Loci | Bond.Loci | EveryLoci | EmptyLoci | DataLoci | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci;
+type Loci = StructureElement.Loci | Structure.Loci | Bond.Loci | EveryLoci | EmptyLoci | DataLoci | Shape.Loci | ShapeGroup.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci;
 declare namespace Loci {
     export interface Bundle<L extends number> {
         loci: FiniteArray<Loci, L>;
@@ -54,47 +54,47 @@ 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 | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | {
+        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci;
-        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Volume.Segment.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -104,6 +104,9 @@ var Loci;
         if (volume_1.Volume.Cell.isLoci(lociA) && volume_1.Volume.Cell.isLoci(lociB)) {
             return volume_1.Volume.Cell.areLociEqual(lociA, lociB);
         }
+        if (volume_1.Volume.Segment.isLoci(lociA) && volume_1.Volume.Segment.isLoci(lociB)) {
+            return volume_1.Volume.Segment.areLociEqual(lociA, lociB);
+        }
         return false;
     }
     Loci.areEqual = areEqual;
@@ -134,6 +137,8 @@ var Loci;
             return volume_1.Volume.Isosurface.isLociEmpty(loci);
         if (volume_1.Volume.Cell.isLoci(loci))
             return volume_1.Volume.Cell.isLociEmpty(loci);
+        if (volume_1.Volume.Segment.isLoci(loci))
+            return volume_1.Volume.Segment.isLociEmpty(loci);
         return false;
     }
     Loci.isEmpty = isEmpty;
@@ -185,6 +190,9 @@ var Loci;
         else if (loci.kind === 'cell-loci') {
             return volume_1.Volume.Cell.getBoundingSphere(loci.volume, loci.indices, boundingSphere);
         }
+        else if (loci.kind === 'segment-loci') {
+            return volume_1.Volume.Segment.getBoundingSphere(loci.volume, loci.segments, boundingSphere);
+        }
     }
     Loci.getBoundingSphere = getBoundingSphere;
     var tmpSphere3D = geometry_1.Sphere3D.zero();
@@ -230,6 +238,10 @@ var Loci;
             // TODO
             return void 0;
         }
+        else if (loci.kind === 'segment-loci') {
+            // TODO
+            return void 0;
+        }
     }
     Loci.getPrincipalAxes = getPrincipalAxes;
     //

package/lib/commonjs/mol-model/sequence/alignment/sequence.d.ts

@@ -3,7 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { StructureElement } from '../../structure/structure';
+import { StructureElement, Unit } from '../../structure/structure';
 import { AlignmentOptions } from './alignment';
 export { AlignSequences };
 declare namespace AlignSequences {
@@ -17,5 +17,8 @@ declare namespace AlignSequences {
         b: StructureElement.Loci.Element;
         score: number;
     };
+    function createSeqIdIndicesMap(element: StructureElement.Loci.Element): Map<number, StructureElement.UnitIndex[]>;
     function compute(input: Input, options?: Partial<AlignmentOptions>): Result;
 }
+export declare function entityKey(unit: Unit): import("../../structure").EntityIndex;
+export declare function getSequence(unit: Unit): import("../sequence").Sequence;

package/lib/commonjs/mol-model/sequence/alignment/sequence.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.AlignSequences = void 0;
+exports.getSequence = exports.entityKey = exports.AlignSequences = void 0;
 var structure_1 = require("../../structure/structure");
 var alignment_1 = require("./alignment");
 var int_1 = require("../../../mol-data/int");
@@ -39,6 +39,7 @@ var AlignSequences;
         }
         return seqIds;
     }
+    AlignSequences.createSeqIdIndicesMap = createSeqIdIndicesMap;
     function compute(input, options) {
         if (options === void 0) { options = {}; }
         var seqA = getSequence(input.a.unit);
@@ -91,6 +92,8 @@ function entityKey(unit) {
             return unit.model.coarseHierarchy.gaussians.entityKey[unit.elements[0]];
     }
 }
+exports.entityKey = entityKey;
 function getSequence(unit) {
     return unit.model.sequence.byEntityKey[entityKey(unit)].sequence;
 }
+exports.getSequence = getSequence;

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

@@ -147,6 +147,12 @@ export interface AtomicIndex {
      */
     findResidue(key: AtomicIndex.ResidueKey): ResidueIndex;
     findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex;
+    /**
+     * Index of the 1st occurence of this residue using "all-label" address.
+     * Doesn't work for "ligands" as they don't have a label seq id assigned.
+     * @returns index or -1 if not present.
+     */
+    findResidueLabel(key: AtomicIndex.ResidueLabelKey): ResidueIndex;
     /**
      * Index of the 1st occurence of this residue.
      * @param key.pdbx_PDB_ins_code Empty string for undefined

package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js

@@ -100,6 +100,14 @@ var Index = /** @class */ (function () {
         var id = getResidueId(key.auth_seq_id, key.pdbx_PDB_ins_code || '');
         return rm.has(id) ? rm.get(id) : -1;
     };
+    Index.prototype.findResidueLabel = function (key) {
+        var cI = this.findChainLabel(key);
+        if (cI < 0)
+            return -1;
+        var rm = this.map.chain_index_label_seq_id.get(cI);
+        var id = getResidueId(key.label_seq_id, key.pdbx_PDB_ins_code || '');
+        return rm.has(id) ? rm.get(id) : -1;
+    };
     Index.prototype.findResidueAuth = function (key) {
         var cI = this.findChainAuth(key);
         if (cI < 0)

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

@@ -110,8 +110,8 @@ function findPairBonds(unitA, unitB, props, builder) {
         var structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
         if (structConnEntries && structConnEntries.length) {
             var added = false;
-            for (var _i = 0, structConnEntries_1 = structConnEntries; _i < structConnEntries_1.length; _i++) {
-                var se = structConnEntries_1[_i];
+            for (var _g = 0, structConnEntries_1 = structConnEntries; _g < structConnEntries_1.length; _g++) {
+                var se = structConnEntries_1[_g];
                 var partnerA = se.partnerA, partnerB = se.partnerB;
                 var p = partnerA.atomIndex === aI ? partnerB : partnerA;
                 var _bI = int_1.SortedArray.indexOf(unitB.elements, p.atomIndex);
@@ -132,7 +132,7 @@ function findPairBonds(unitA, unitB, props, builder) {
             continue;
         var occA = occupancyA.value(aI);
         var lookup3d = unitB.lookup3d;
-        var _g = lookup3d.find(_imageA[0], _imageA[1], _imageA[2], maxRadius), indices = _g.indices, count = _g.count, squaredDistances = _g.squaredDistances;
+        var _h = lookup3d.find(_imageA[0], _imageA[1], _imageA[2], maxRadius), indices = _h.indices, count = _h.count, squaredDistances = _h.squaredDistances;
         if (count === 0)
             continue;
         var aeI = (0, common_1.getElementIdx)(type_symbolA.value(aI));
@@ -203,9 +203,25 @@ function computeInterUnitBonds(structure, props) {
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* MoleculeType.Water */) &&
                 (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* MoleculeType.Water */));
-            var notIon = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* MoleculeType.Ion */) &&
-                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* MoleculeType.Ion */));
+            var sameModel = a.model === b.model;
+            var notIonA = (!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* MoleculeType.Ion */) || (sameModel && hasStructConnRecord(a));
+            var notIonB = (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* MoleculeType.Ion */) || (sameModel && hasStructConnRecord(b));
+            var notIon = notIonA && notIonB;
             return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }
 exports.computeInterUnitBonds = computeInterUnitBonds;
+function hasStructConnRecord(unit) {
+    if (!unit_1.Unit.isAtomic(unit))
+        return false;
+    var elements = unit.elements;
+    var structConn = struct_conn_1.StructConn.Provider.get(unit.model);
+    if (structConn) {
+        for (var i = 0, _i = elements.length; i < _i; i++) {
+            if (structConn.byAtomIndex.get(elements[i])) {
+                return true;
+            }
+        }
+    }
+    return false;
+}

package/lib/commonjs/mol-model/structure/structure/util/superposition.d.ts

@@ -11,4 +11,5 @@ type AlignAndSuperposeResult = MinimizeRmsd.Result & {
     alignmentScore: number;
 };
 export declare function alignAndSuperpose(xs: StructureElement.Loci[]): AlignAndSuperposeResult[];
+export declare function getPositionTable(xs: StructureElement.Loci, n: number): MinimizeRmsd.Positions;
 export {};

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperpose = exports.superpose = void 0;
+exports.getPositionTable = exports.alignAndSuperpose = exports.superpose = void 0;
 var tslib_1 = require("tslib");
 var minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
 var element_1 = require("../element");
@@ -77,6 +77,7 @@ function getPositionTable(xs, n) {
     }
     return ret;
 }
+exports.getPositionTable = getPositionTable;
 function getMinSize(xs) {
     if (xs.length === 0)
         return 0;

package/lib/commonjs/mol-model/volume/volume.d.ts

@@ -4,8 +4,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Grid } from './grid';
-import { OrderedSet } from '../../mol-data/int';
-import { Sphere3D } from '../../mol-math/geometry';
+import { OrderedSet, SortedArray } from '../../mol-data/int';
+import { Box3D, Sphere3D } from '../../mol-math/geometry';
 import { ModelFormat } from '../../mol-model-formats/format';
 import { CustomProperties } from '../custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -137,9 +137,42 @@ export declare namespace Volume {
         function isLociEmpty(loci: Loci): boolean;
         function getBoundingSphere(volume: Volume, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D): Sphere3D;
     }
+    namespace Segment {
+        interface Loci {
+            readonly kind: 'segment-loci';
+            readonly volume: Volume;
+            readonly segments: SortedArray;
+        }
+        function Loci(volume: Volume, segments: ArrayLike<number>): Loci;
+        function isLoci(x: any): x is Loci;
+        function areLociEqual(a: Loci, b: Loci): boolean;
+        function isLociEmpty(loci: Loci): boolean;
+        function getBoundingSphere(volume: Volume, segments: ArrayLike<number>, boundingSphere?: Sphere3D): Sphere3D;
+        interface Location {
+            readonly kind: 'segment-location';
+            volume: Volume;
+            segment: number;
+        }
+        function Location(volume?: Volume, segment?: number): Location;
+        function isLocation(x: any): x is Location;
+    }
     type PickingGranularity = 'volume' | 'object' | 'voxel';
     const PickingGranularity: {
         set(volume: Volume, granularity: PickingGranularity): void;
         get(volume: Volume): PickingGranularity;
     };
+    type Segmentation = {
+        segments: Map<number, Set<number>>;
+        sets: Map<number, Set<number>>;
+        bounds: {
+            [k: number]: Box3D;
+        };
+        labels: {
+            [k: number]: string;
+        };
+    };
+    const Segmentation: {
+        set(volume: Volume, segmentation: Segmentation): void;
+        get(volume: Volume): Segmentation | undefined;
+    };
 }