molstar 3.26.0 → 3.28.0

package/lib/mol-model-formats/volume/segmentation.js

@@ -0,0 +1,135 @@
+/**
+ * Copyright (c) 2018-2022 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>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Volume } from '../../mol-model/volume';
+import { Task } from '../../mol-task';
+import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
+import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
+import { CustomProperties } from '../../mol-model/custom-property';
+import { objectForEach } from '../../mol-util/object';
+export function volumeFromSegmentationData(source, params) {
+    var _this = this;
+    return Task.create('Create Segmentation Volume', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var info, values, cell, axis_order_fast_to_slow, normalizeOrder, sample_count, tensorSpace, t, origin, dimensions, v, segments, sets, _a, segment_id, set_id, i, il, segment, set, c, getCoords, d, _b, xn, yn, zn, xn1, yn1, zn1, setBounds, i, il, v_1, b, bounds;
+        var _c;
+        return __generator(this, function (_d) {
+            info = source.volume_data_3d_info, values = source.segmentation_data_3d;
+            cell = SpacegroupCell.create(info.spacegroup_number.value(0), Vec3.ofArray(info.spacegroup_cell_size.value(0)), Vec3.scale(Vec3(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
+            axis_order_fast_to_slow = info.axis_order.value(0);
+            normalizeOrder = Tensor.convertToCanonicalAxisIndicesFastToSlow(axis_order_fast_to_slow);
+            sample_count = normalizeOrder(info.sample_count.value(0));
+            tensorSpace = Tensor.Space(sample_count, Tensor.invertAxisOrder(axis_order_fast_to_slow), Float32Array);
+            t = Tensor.create(tensorSpace, Tensor.Data1(values.values.toArray({ array: Float32Array })));
+            origin = Vec3.ofArray(normalizeOrder(info.origin.value(0)));
+            dimensions = Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
+            v = {
+                label: params === null || params === void 0 ? void 0 : params.label,
+                entryId: undefined,
+                grid: {
+                    transform: {
+                        kind: 'spacegroup',
+                        cell: cell,
+                        fractionalBox: Box3D.create(origin, Vec3.add(Vec3(), origin, dimensions))
+                    },
+                    cells: t,
+                    stats: {
+                        min: 0, max: 1, mean: 0, sigma: 1
+                    },
+                },
+                sourceData: SegcifFormat.create(source),
+                customProperties: new CustomProperties(),
+                _propertyData: { ownerId: params === null || params === void 0 ? void 0 : params.ownerId },
+            };
+            Volume.PickingGranularity.set(v, 'object');
+            segments = new Map();
+            sets = new Map();
+            _a = source.segmentation_data_table, segment_id = _a.segment_id, set_id = _a.set_id;
+            for (i = 0, il = segment_id.rowCount; i < il; ++i) {
+                segment = segment_id.value(i);
+                set = set_id.value(i);
+                if (set === 0 || segment === 0)
+                    continue;
+                if (!sets.has(set))
+                    sets.set(set, new Set());
+                sets.get(set).add(segment);
+            }
+            sets.forEach(function (segs, set) {
+                segs.forEach(function (seg) {
+                    if (!segments.has(seg))
+                        segments.set(seg, new Set());
+                    segments.get(seg).add(set);
+                });
+            });
+            c = [0, 0, 0];
+            getCoords = t.space.getCoords;
+            d = t.data;
+            _b = v.grid.cells.space.dimensions, xn = _b[0], yn = _b[1], zn = _b[2];
+            xn1 = xn - 1;
+            yn1 = yn - 1;
+            zn1 = zn - 1;
+            setBounds = {};
+            sets.forEach(function (v, k) {
+                setBounds[k] = [xn1, yn1, zn1, -1, -1, -1];
+            });
+            for (i = 0, il = d.length; i < il; ++i) {
+                v_1 = d[i];
+                if (v_1 === 0)
+                    continue;
+                getCoords(i, c);
+                b = setBounds[v_1];
+                if (c[0] < b[0])
+                    b[0] = c[0];
+                if (c[1] < b[1])
+                    b[1] = c[1];
+                if (c[2] < b[2])
+                    b[2] = c[2];
+                if (c[0] > b[3])
+                    b[3] = c[0];
+                if (c[1] > b[4])
+                    b[4] = c[1];
+                if (c[2] > b[5])
+                    b[5] = c[2];
+            }
+            bounds = {};
+            segments.forEach(function (v, k) {
+                bounds[k] = Box3D.create(Vec3.create(xn1, yn1, zn1), Vec3.create(-1, -1, -1));
+            });
+            objectForEach(setBounds, function (b, s) {
+                sets.get(parseInt(s)).forEach(function (seg) {
+                    var sb = bounds[seg];
+                    if (b[0] < sb.min[0])
+                        sb.min[0] = b[0];
+                    if (b[1] < sb.min[1])
+                        sb.min[1] = b[1];
+                    if (b[2] < sb.min[2])
+                        sb.min[2] = b[2];
+                    if (b[3] > sb.max[0])
+                        sb.max[0] = b[3];
+                    if (b[4] > sb.max[1])
+                        sb.max[1] = b[4];
+                    if (b[5] > sb.max[2])
+                        sb.max[2] = b[5];
+                });
+            });
+            Volume.Segmentation.set(v, { segments: segments, sets: sets, bounds: bounds, labels: (_c = params === null || params === void 0 ? void 0 : params.segmentLabels) !== null && _c !== void 0 ? _c : {} });
+            return [2 /*return*/, v];
+        });
+    }); });
+}
+//
+export { SegcifFormat };
+var SegcifFormat;
+(function (SegcifFormat) {
+    function is(x) {
+        return (x === null || x === void 0 ? void 0 : x.kind) === 'segcif';
+    }
+    SegcifFormat.is = is;
+    function create(segcif) {
+        return { kind: 'segcif', name: segcif._name, data: segcif };
+    }
+    SegcifFormat.create = create;
+})(SegcifFormat || (SegcifFormat = {}));

package/lib/mol-plugin/behavior/dynamic/representation.d.ts

@@ -12,7 +12,7 @@ export declare const HighlightLoci: import("../../../mol-state/transformer").Sta
         hoverHighlightOnly: Binding;
         hoverHighlightOnlyExtend: Binding;
     }>;
-    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
+    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "segment-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
     preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;
@@ -25,7 +25,7 @@ export declare const SelectLoci: import("../../../mol-state/transformer").StateT
         clickDeselect: Binding;
         clickDeselectAllOnEmpty: Binding;
     }>;
-    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
+    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "segment-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
     preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -22,6 +22,7 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     components: PD.MultiSelect<"target" | "surroundings" | "interactions">;
     excludeTargetFromSurroundings: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     ignoreLight: PD.BooleanParam;
     material: PD.Group<PD.Normalize<{
         metalness: number;

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -49,6 +49,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
+        ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])),
         ignoreLight: PD.Boolean(false),
         material: Material.getParam(),
         clip: PD.Group(Clip.Params),
@@ -79,7 +80,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
         return __assign(__assign({}, reprParams), { type: {
                 name: reprParams.type.name,
-                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip })
+                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, ignoreHydrogensVariant: this.params.ignoreHydrogensVariant, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {

package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        label: string; /** Precision data the server can show. */
+        /** Precision data the server can show. */
+        label: string;
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,7 +23,6 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/mol-plugin/commands.d.ts

@@ -244,6 +244,7 @@ export declare const PluginCommands: {
                         scale: any;
                         threshold: any;
                         color: any;
+                        includeTransparent: any;
                     }>, "on">;
                     antialiasing: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         edgeThreshold: any;

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.26.0';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1670184977371);
+export var PLUGIN_VERSION = '3.28.0';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1671492998173);

package/lib/mol-plugin-state/animation/built-in/model-index.js

@@ -129,6 +129,10 @@ export var AnimateModelIndex = PluginStateAnimation.create({
                                     var durationInMs = params.duration.name === 'fixed'
                                         ? params.duration.params.durationInS * 1000
                                         : Math.ceil(1000 * traj.data.frameCount / params.duration.params.targetFps);
+                                    if (params.mode.name === 'once' && t.current >= durationInMs) {
+                                        isEnd = true;
+                                        return { modelIndex: traj.data.frameCount - 1 };
+                                    }
                                     var phase = (t.current % durationInMs) / durationInMs;
                                     if (params.mode.name === 'loop') {
                                         if (params.mode.params.direction === 'backward') {
@@ -141,7 +145,6 @@ export var AnimateModelIndex = PluginStateAnimation.create({
                                             phase = 2 - phase;
                                     }
                                     var modelIndex = Math.min(Math.floor(traj.data.frameCount * phase), traj.data.frameCount - 1);
-                                    isEnd = isEnd || modelIndex === traj.data.frameCount - 1;
                                     return { modelIndex: modelIndex };
                                 }
                             });

package/lib/mol-plugin-state/builder/structure/hierarchy-preset.d.ts

@@ -66,6 +66,7 @@ export declare const PresetTrajectoryHierarchy: {
         }>, "symmetry-assembly"> | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreHydrogensVariant: any;
             ignoreLight: any;
             quality: any;
             theme: any;
@@ -91,6 +92,7 @@ export declare const PresetTrajectoryHierarchy: {
         useDefaultIfSingleModel: boolean | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreHydrogensVariant: any;
             ignoreLight: any;
             quality: any;
             theme: any;

package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts

@@ -48,6 +48,7 @@ export declare class TrajectoryHierarchyBuilder {
         }>, "symmetry-assembly"> | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreHydrogensVariant: any;
             ignoreLight: any;
             quality: any;
             theme: any;

package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts

@@ -29,13 +29,14 @@ export declare namespace StructureRepresentationPresetProvider {
     };
     const CommonParams: {
         ignoreHydrogens: PD.Base<boolean | undefined>;
+        ignoreHydrogensVariant: PD.Base<"all" | "non-polar" | undefined>;
         ignoreLight: PD.Base<boolean | undefined>;
         quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "external-volume" | undefined;
+            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "volume-segment" | "external-volume" | undefined;
             globalColorParams: any;
             carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "external-volume" | undefined;
+            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "volume-segment" | "external-volume" | undefined;
             symmetryColorParams: any;
             focus: PD.Normalize<{
                 name: any;
@@ -47,13 +48,14 @@ export declare namespace StructureRepresentationPresetProvider {
     function reprBuilder(plugin: PluginContext, params: CommonParams, structure?: Structure): {
         update: import("../../../mol-state/state/builder").StateBuilder.Root;
         builder: import("./representation").StructureRepresentationBuilder;
-        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "external-volume" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "external-volume" | undefined;
+        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "volume-segment" | "external-volume" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "hydrophobicity" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "model-index" | "structure-index" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "trajectory-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | "volume-segment" | "external-volume" | undefined;
         symmetryColorParams: any;
         globalColorParams: any;
         typeParams: {
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;
+            ignoreHydrogensVariant: "all" | "non-polar";
             ignoreLight: boolean;
         };
         ballAndStickColor: Partial<PD.Values<{
@@ -265,6 +267,7 @@ export declare const PresetStructureRepresentations: {
     empty: StructureRepresentationPresetProvider<unknown, {}>;
     auto: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -297,6 +300,7 @@ export declare const PresetStructureRepresentations: {
     'atomic-detail': StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -321,6 +325,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-cartoon': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -344,6 +349,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-and-ligand': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -382,6 +388,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'protein-and-nucleic': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -407,6 +414,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'coarse-surface': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
@@ -433,6 +441,7 @@ export declare const PresetStructureRepresentations: {
     illustrative: StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{

package/lib/mol-plugin-state/builder/structure/representation-preset.js

@@ -22,6 +22,7 @@ export function StructureRepresentationPresetProvider(repr) { return repr; }
 (function (StructureRepresentationPresetProvider) {
     StructureRepresentationPresetProvider.CommonParams = {
         ignoreHydrogens: PD.Optional(PD.Boolean(false)),
+        ignoreHydrogensVariant: PD.Optional(PD.Select('all', PD.arrayToOptions(['all', 'non-polar']))),
         ignoreLight: PD.Optional(PD.Boolean(false)),
         quality: PD.Optional(PD.Select('auto', VisualQualityOptions)),
         theme: PD.Optional(PD.Group({
@@ -50,15 +51,19 @@ export function StructureRepresentationPresetProvider(repr) { return repr; }
         var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p;
         var update = plugin.state.data.build();
         var builder = plugin.builders.structure.representation;
+        var h = plugin.managers.structure.component.state.options.hydrogens;
         var typeParams = {
             quality: plugin.managers.structure.component.state.options.visualQuality,
-            ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
+            ignoreHydrogens: h !== 'all',
+            ignoreHydrogensVariant: (h === 'only-polar' ? 'non-polar' : 'all'),
             ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
         };
         if (params.quality && params.quality !== 'auto')
             typeParams.quality = params.quality;
         if (params.ignoreHydrogens !== void 0)
             typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
+        if (params.ignoreHydrogensVariant !== void 0)
+            typeParams.ignoreHydrogensVariant = params.ignoreHydrogensVariant;
         if (params.ignoreLight !== void 0)
             typeParams.ignoreLight = !!params.ignoreLight;
         var color = ((_a = params.theme) === null || _a === void 0 ? void 0 : _a.globalName) ? (_b = params.theme) === null || _b === void 0 ? void 0 : _b.globalName : void 0;

package/lib/mol-plugin-state/builder/structure/representation.d.ts

@@ -17,6 +17,7 @@ export declare class StructureRepresentationBuilder {
     private get dataState();
     readonly defaultProvider: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreHydrogensVariant: "all" | "non-polar" | undefined;
         ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{

package/lib/mol-plugin-state/formats/provider.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -19,6 +19,6 @@ export interface DataFormatProvider<P = any, R = any, V = any> {
     visuals?(plugin: PluginContext, data: R): Promise<V> | undefined;
 }
 export declare function DataFormatProvider<P extends DataFormatProvider>(provider: P): P;
-type cifVariants = 'dscif' | 'coreCif' | -1;
+type cifVariants = 'dscif' | 'segcif' | 'coreCif' | -1;
 export declare function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants;
 export {};

package/lib/mol-plugin-state/formats/provider.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -11,15 +11,23 @@ export function guessCifVariant(info, data) {
         try {
             // TODO: find a way to run msgpackDecode only once
             //      now it is run twice, here and during file parsing
-            if (decodeMsgPack(data).encoder.startsWith('VolumeServer'))
+            var encoder = decodeMsgPack(data).encoder;
+            if (encoder.startsWith('VolumeServer'))
                 return 'dscif';
+            // TODO: assumes volseg-volume-server only serves segments
+            if (encoder.startsWith('volseg-volume-server'))
+                return 'segcif';
+        }
+        catch (e) {
+            console.error(e);
         }
-        catch (_a) { }
     }
     else if (info.ext === 'cif') {
         var str = data;
         if (str.startsWith('data_SERVER\n#\n_density_server_result'))
             return 'dscif';
+        if (str.startsWith('data_SERVER\n#\ndata_SEGMENTATION_DATA'))
+            return 'segcif';
         if (str.includes('atom_site_fract_x') || str.includes('atom_site.fract_x'))
             return 'coreCif';
     }

package/lib/mol-plugin-state/formats/registry.js

@@ -109,15 +109,16 @@ var DataFormatRegistry = /** @class */ (function () {
         this._map.delete(name);
     };
     DataFormatRegistry.prototype.auto = function (info, dataStateObject) {
+        var _a, _b;
         for (var i = 0, il = this.list.length; i < il; ++i) {
-            var provider = this._list[i].provider;
+            var p = this._list[i].provider;
             var hasExt = false;
-            if (provider.binaryExtensions && provider.binaryExtensions.indexOf(info.ext) >= 0)
+            if ((_a = p.binaryExtensions) === null || _a === void 0 ? void 0 : _a.includes(info.ext))
                 hasExt = true;
-            else if (provider.stringExtensions && provider.stringExtensions.indexOf(info.ext) >= 0)
+            else if ((_b = p.stringExtensions) === null || _b === void 0 ? void 0 : _b.includes(info.ext))
                 hasExt = true;
-            if (hasExt && (!provider.isApplicable || provider.isApplicable(info, dataStateObject.data)))
-                return provider;
+            if (hasExt && (!p.isApplicable || p.isApplicable(info, dataStateObject.data)))
+                return p;
         }
         return;
     };

package/lib/mol-plugin-state/formats/volume.d.ts

@@ -110,6 +110,20 @@ export declare const DscifProvider: {
         volumes: StateObjectSelector<PluginStateObject.Volume.Data>[];
     }) => Promise<StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[]>;
 };
+export declare const SegcifProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    binaryExtensions: string[];
+    isApplicable: (info: import("../../mol-util/file-info").FileInfo, data: string | Uint8Array) => boolean;
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>) => Promise<{
+        volumes: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
+    }>;
+    visuals: (plugin: PluginContext, data: {
+        volumes: StateObjectSelector<PluginStateObject.Volume.Data>[];
+    }) => Promise<StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[]>;
+};
 export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     label: string;
     description: string;
@@ -196,6 +210,19 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     visuals: (plugin: PluginContext, data: {
         volumes: StateObjectSelector<PluginStateObject.Volume.Data>[];
     }) => Promise<StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[]>;
+}], readonly ["segcif", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    binaryExtensions: string[];
+    isApplicable: (info: import("../../mol-util/file-info").FileInfo, data: string | Uint8Array) => boolean;
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>) => Promise<{
+        volumes: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
+    }>;
+    visuals: (plugin: PluginContext, data: {
+        volumes: StateObjectSelector<PluginStateObject.Volume.Data>[];
+    }) => Promise<StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[]>;
 }]];
 export type BuildInVolumeFormat = (typeof BuiltInVolumeFormats)[number][0];
 export {};

package/lib/mol-plugin-state/formats/volume.js

@@ -315,10 +315,74 @@ export var DscifProvider = DataFormatProvider({
         });
     }); }
 });
+export var SegcifProvider = DataFormatProvider({
+    label: 'Segmentation CIF',
+    description: 'Segmentation CIF',
+    category: VolumeFormatCategory,
+    stringExtensions: ['cif'],
+    binaryExtensions: ['bcif'],
+    isApplicable: function (info, data) {
+        return guessCifVariant(info, data) === 'segcif' ? true : false;
+    },
+    parse: function (plugin, data) { return __awaiter(void 0, void 0, void 0, function () {
+        var cifCell, b, blocks, volumes, _i, blocks_2, block;
+        var _a;
+        return __generator(this, function (_b) {
+            switch (_b.label) {
+                case 0: return [4 /*yield*/, plugin.build().to(data).apply(StateTransforms.Data.ParseCif).commit()];
+                case 1:
+                    cifCell = _b.sent();
+                    b = plugin.build().to(cifCell);
+                    blocks = cifCell.obj.data.blocks;
+                    if (blocks.length === 0)
+                        throw new Error('no data blocks');
+                    volumes = [];
+                    for (_i = 0, blocks_2 = blocks; _i < blocks_2.length; _i++) {
+                        block = blocks_2[_i];
+                        // Skip "server" data block.
+                        if (block.header.toUpperCase() === 'SERVER')
+                            continue;
+                        if (((_a = block.categories['volume_data_3d_info']) === null || _a === void 0 ? void 0 : _a.rowCount) > 0) {
+                            volumes.push(b.apply(StateTransforms.Volume.VolumeFromSegmentationCif, { blockHeader: block.header }).selector);
+                        }
+                    }
+                    return [4 /*yield*/, b.commit()];
+                case 2:
+                    _b.sent();
+                    return [2 /*return*/, { volumes: volumes }];
+            }
+        });
+    }); },
+    visuals: function (plugin, data) { return __awaiter(void 0, void 0, void 0, function () {
+        var volumes, tree, visuals, segmentation;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    volumes = data.volumes;
+                    tree = plugin.build();
+                    visuals = [];
+                    if (volumes.length > 0) {
+                        segmentation = Volume.Segmentation.get(volumes[0].data);
+                        if (segmentation) {
+                            visuals[visuals.length] = tree
+                                .to(volumes[0])
+                                .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParams(plugin, 'segment', volumes[0].data, { alpha: 1, instanceGranularity: true }, 'volume-segment', {}))
+                                .selector;
+                        }
+                    }
+                    return [4 /*yield*/, tree.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, visuals];
+            }
+        });
+    }); }
+});
 export var BuiltInVolumeFormats = [
     ['ccp4', Ccp4Provider],
     ['dsn6', Dsn6Provider],
     ['cube', CubeProvider],
     ['dx', DxProvider],
     ['dscif', DscifProvider],
+    ['segcif', SegcifProvider],
 ];

package/lib/mol-plugin-state/manager/structure/component.d.ts

@@ -58,7 +58,7 @@ declare class StructureComponentManager extends StatefulPluginComponent<Structur
 }
 declare namespace StructureComponentManager {
     const OptionsParams: {
-        showHydrogens: PD.BooleanParam;
+        hydrogens: PD.Select<"all" | "hide-all" | "only-polar">;
         visualQuality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         ignoreLight: PD.BooleanParam;
         materialStyle: PD.Group<PD.Normalize<{