Merge branch 'master' into seq

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.2.2",
+  "version": "0.2.3",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.2.2",
+  "version": "0.2.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/examples/proteopedia-wrapper/changelog.md

@@ -1,3 +1,8 @@
+== v3.2 ==
+
+* Fixed assembly loading.
+* Better HET group focus.
+
 == v3.0 ==
 
 * Fixed initial camera zoom.

src/examples/proteopedia-wrapper/helpers.ts

@@ -115,5 +115,6 @@ export enum StateElements {
     Water = 'water',
     WaterVisual = 'water-visual',
 
-    HetGroupFocus = 'het-group-focus'
+    HetGroupFocus = 'het-group-focus',
+    HetGroupFocusGroup = 'het-group-focus-group'
 }

src/examples/proteopedia-wrapper/index.ts

@@ -36,7 +36,7 @@ require('../../mol-plugin/skin/light.scss')
 
 class MolStarProteopediaWrapper {
     static VERSION_MAJOR = 3;
-    static VERSION_MINOR = 1;
+    static VERSION_MINOR = 2;
 
     private _ev = RxEventHelper.create();
 
@@ -81,7 +81,7 @@ class MolStarProteopediaWrapper {
         return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
     }
 
-    private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
+    private model(b: StateBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats) {
         const parsed = format === 'cif'
             ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
             : b.apply(StateTransforms.Model.TrajectoryFromPDB);
@@ -190,7 +190,7 @@ class MolStarProteopediaWrapper {
     }
 
     private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
-    async load({ url, format = 'cif', assemblyId = '', representationStyle }: LoadParams) {
+    async load({ url, format = 'cif', assemblyId = 'deposited', representationStyle }: LoadParams) {
         let loadType: 'full' | 'update' = 'full';
 
         const state = this.plugin.state.dataState;
@@ -203,14 +203,17 @@ class MolStarProteopediaWrapper {
 
         if (loadType === 'full') {
             await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
-            const modelTree = this.model(this.download(state.build().toRoot(), url), format, assemblyId);
+            const modelTree = this.model(this.download(state.build().toRoot(), url), format);
             await this.applyState(modelTree);
             const info = await this.doInfo(true);
-            const structureTree = this.structure((assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId);
+            const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
+            const structureTree = this.structure(asmId);
             await this.applyState(structureTree);
         } else {
             const tree = state.build();
-            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
+            const info = await this.doInfo(true);
+            const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
+            tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: asmId }));
             await this.applyState(tree);
         }
 
@@ -295,30 +298,30 @@ class MolStarProteopediaWrapper {
             PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
             PluginCommands.Camera.Reset.dispatch(this.plugin, { });
         },
-        focusFirst: async (resn: string) => {
+        focusFirst: async (compId: string) => {
             if (!this.state.transforms.has(StateElements.Assembly)) return;
+            await PluginCommands.Camera.Reset.dispatch(this.plugin, { });
 
             // const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
 
             const update = this.state.build();
 
-            update.delete(StateElements.HetGroupFocus);
+            update.delete(StateElements.HetGroupFocusGroup);
 
-            const surroundings = MS.struct.modifier.includeSurroundings({
-                0: MS.struct.filter.first([
-                    MS.struct.generator.atomGroups({
-                        'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), resn]),
-                        'group-by': MS.struct.atomProperty.macromolecular.residueKey()
-                    })
-                ]),
-                radius: 5,
-                'as-whole-residues': true
-            });
+            const core = MS.struct.filter.first([
+                MS.struct.generator.atomGroups({
+                    'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), compId]),
+                    'group-by': MS.core.str.concat([MS.struct.atomProperty.core.operatorName(), MS.struct.atomProperty.macromolecular.residueKey()])
+                })
+            ]);
+            const surroundings = MS.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
 
-            const sel = update.to(StateElements.Assembly)
-                .apply(StateTransforms.Model.StructureSelection, { label: resn, query: surroundings }, { ref: StateElements.HetGroupFocus });
+            const group = update.to(StateElements.Assembly).group(StateTransforms.Misc.CreateGroup, { label: compId }, { ref: StateElements.HetGroupFocusGroup });
 
-            sel.apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
+            group.apply(StateTransforms.Model.StructureSelection, { label: 'Core', query: core }, { ref: StateElements.HetGroupFocus })
+                .apply(StateTransforms.Representation.StructureRepresentation3D, this.createCoreVisualParams());
+            group.apply(StateTransforms.Model.StructureSelection, { label: 'Surroundings', query: surroundings })
+                .apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
             // sel.apply(StateTransforms.Representation.StructureLabels3D, {
             //     target: { name: 'residues', params: { } },
             //     options: {
@@ -338,7 +341,7 @@ class MolStarProteopediaWrapper {
             // const position = Vec3.sub(Vec3.zero(), sphere.center, asmCenter);
             // Vec3.normalize(position, position);
             // Vec3.scaleAndAdd(position, sphere.center, position, sphere.radius);
-            const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, 0.75 * sphere.radius);
+            const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, Math.max(sphere.radius, 5));
             PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
         }
     }
@@ -352,6 +355,15 @@ class MolStarProteopediaWrapper {
         });
     }
 
+    private createCoreVisualParams() {
+        const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
+        return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
+            repr: BuiltInStructureRepresentations['ball-and-stick'],
+            // color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
+            // size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
+        });
+    }
+
     snapshot = {
         get: () => {
             return this.plugin.state.getSnapshot();

src/mol-io/writer/_spec/cif.spec.ts

@@ -0,0 +1,183 @@
+import * as Data from '../../reader/cif/data-model'
+import { CifWriter } from '../cif';
+import decodeMsgPack from '../../common/msgpack/decode'
+import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
+import Field from '../../reader/cif/binary/field';
+import * as C from '../cif/encoder';
+
+const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
+const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
+const cartn_z = Data.CifField.ofNumbers([1, 2, 3, 4, 5, 6, 7, 8, 9].map(i => Math.sqrt(i)));
+const label_seq_id = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
+const atom_site = Data.CifCategory.ofFields('atom_site', { 'Cartn_x': cartn_x, 'Cartn_y': cartn_y, 'Cartn_z': cartn_z, 'label_seq_id': label_seq_id });
+const field1 = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
+const field2 = Data.CifField.ofNumbers([-1, -2, -3, -6, -11, -23, -47, -106, -235]);
+const other_fields = Data.CifCategory.ofFields('other_fields', { 'field1': field1, 'field2': field2 });
+
+const encoding_aware_encoder = CifWriter.createEncoder({
+    binary: true,
+    binaryAutoClassifyEncoding: true,
+    binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
+        {
+            'categoryName': 'atom_site',
+            'columnName': 'Cartn_y',
+            'encoding': 'rle',
+            'precision': 0
+        },
+        {
+            'categoryName': 'atom_site',
+            'columnName': 'Cartn_z',
+            'encoding': 'delta',
+            'precision': 1
+        },
+        {
+            'categoryName': 'atom_site',
+            'columnName': 'label_seq_id',
+            'encoding': 'delta-rle'
+        }
+    ])
+});
+
+describe('encoding-config', () => {
+    const decoded = process(encoding_aware_encoder);
+
+    const decoded_atom_site = decoded.blocks[0].categories['atom_site'];
+    const decoded_cartn_x = decoded_atom_site.getField('Cartn_x')!;
+    const decoded_cartn_y = decoded_atom_site.getField('Cartn_y')!;
+    const decoded_cartn_z = decoded_atom_site.getField('Cartn_z')!;
+    const decoded_label_seq_id = decoded_atom_site.getField('label_seq_id')!;
+
+    const delta = 0.001;
+    function assert(e: ArrayLike<number>, a: ArrayLike<number>) {
+        expect(e.length).toBe(a.length);
+        for (let i = 0; i < e.length; i++) {
+            expect(Math.abs(e[i] - a[i])).toBeLessThan(delta);
+        }
+    }
+
+    function join(field: Data.CifField) {
+        return field.binaryEncoding!.map(e => e.kind).join();
+    }
+
+    it('strategy', () => {
+        expect(join(decoded_cartn_x)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+        expect(join(decoded_cartn_y)).toBe('FixedPoint,RunLength,IntegerPacking,ByteArray');
+        expect(join(decoded_cartn_z)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+        expect(join(decoded_label_seq_id)).toBe('Delta,RunLength,IntegerPacking,ByteArray');
+    });
+
+    it('precision', () => {
+        assert(decoded_cartn_x.toFloatArray(), cartn_x.toFloatArray());
+        assert(decoded_cartn_y.toFloatArray(), cartn_y.toFloatArray().map(d => Math.round(d)));
+        assert(decoded_cartn_z.toFloatArray(), cartn_z.toFloatArray().map(d => Math.round(d * 10) / 10));
+        assert(decoded_label_seq_id.toIntArray(), label_seq_id.toIntArray());
+    });
+});
+
+const filter_aware_encoder1 = CifWriter.createEncoder({
+    binary: true,
+    binaryAutoClassifyEncoding: true
+});
+filter_aware_encoder1.setFilter(C.Category.filterOf('atom_site\n' +
+'\n' +
+'atom_site.Cartn_x\n' +
+'atom_site.Cartn_y\n'));
+
+const filter_aware_encoder2 = CifWriter.createEncoder({
+    binary: true
+});
+filter_aware_encoder2.setFilter(C.Category.filterOf('!atom_site\n' +
+'\n' +
+'!other_fields.field2\n'));
+
+describe('filtering-config', () => {
+    const decoded1 = process(filter_aware_encoder1);
+
+    const atom_site1 = decoded1.blocks[0].categories['atom_site'];
+    const cartn_x1 = atom_site1.getField('Cartn_x');
+    const cartn_y1 = atom_site1.getField('Cartn_y');
+    const cartn_z1 = atom_site1.getField('Cartn_z');
+    const label_seq_id1 = atom_site1.getField('label_seq_id');
+    const fields1 = decoded1.blocks[0].categories['other_fields'];
+
+    it('whitelist-filtering', () => {
+        expect(atom_site1).toBeDefined();
+        expect(cartn_x1).toBeDefined();
+        expect(cartn_y1).toBeDefined();
+        expect(cartn_z1).toBeUndefined();
+        expect(label_seq_id1).toBeUndefined();
+        expect(fields1).toBeUndefined();
+    });
+
+    const decoded2 = process(filter_aware_encoder2);
+
+    const atom_site2 = decoded2.blocks[0].categories['atom_site'];
+    const fields2 = decoded2.blocks[0].categories['other_fields'];
+    const field12 = fields2.getField('field1');
+    const field22 = fields2.getField('field2');
+
+    it('blacklist-filtering', () => {
+        expect(atom_site2).toBeUndefined();
+        expect(fields2).toBeDefined();
+        expect(field12).toBeDefined();
+        expect(field22).toBeUndefined();
+    });
+});
+
+function process(encoder: C.Encoder) {
+    encoder.startDataBlock('test');
+
+    for (const cat of [atom_site, other_fields]) {
+        const fields: CifWriter.Field[] = [];
+        for (const f of cat.fieldNames) {
+            fields.push(wrap(f, cat.getField(f)!))
+        }
+        encoder.writeCategory(getCategoryInstanceProvider(cat, fields));
+    }
+
+    const encoded = encoder.getData() as Uint8Array;
+
+    const unpacked = decodeMsgPack(encoded) as EncodedFile;
+    return Data.CifFile(unpacked.dataBlocks.map(block => {
+        const cats = Object.create(null);
+        for (const cat of block.categories) cats[cat.name.substr(1)] = Category(cat);
+        return Data.CifBlock(block.categories.map(c => c.name.substr(1)), cats, block.header);
+    }));
+}
+
+
+function getCategoryInstanceProvider(cat: Data.CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
+    return {
+        name: cat.name,
+        instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
+    };
+}
+
+function wrap(name: string, field: Data.CifField): CifWriter.Field {
+    const type = Data.getCifFieldType(field);
+    if (type['@type'] === 'str') {
+        return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+    } else if (type['@type'] === 'float') {
+        return { name, type: CifWriter.Field.Type.Float, value: field.float, valueKind: field.valueKind };
+    } else {
+        return { name, type: CifWriter.Field.Type.Int, value: field.int, valueKind: field.valueKind };
+    }
+}
+
+function Category(data: EncodedCategory): Data.CifCategory {
+    const map = Object.create(null);
+    const cache = Object.create(null);
+    for (const col of data.columns) map[col.name] = col;
+    return {
+        rowCount: data.rowCount,
+        name: data.name.substr(1),
+        fieldNames: data.columns.map(c => c.name),
+        getField(name) {
+            const col = map[name];
+            if (!col) return void 0;
+            if (!!cache[name]) return cache[name];
+            cache[name] = Field(col);
+            return cache[name];
+        }
+    }
+}

src/mol-io/writer/cif.ts

@@ -53,5 +53,64 @@ export namespace CifWriter {
                 return ff && ff.binaryEncoding ? ArrayEncoder.fromEncoding(ff.binaryEncoding) : void 0;
             }
         }
+    };
+
+    export function createEncodingProviderFromJsonConfig(hints: EncodingStrategyHint[]): EncodingProvider {
+        return {
+            get(c, f) {
+                for (let i = 0; i < hints.length; i++) {
+                    const hint = hints[i];
+                    if (hint.categoryName === c && hint.columnName === f) {
+                        return resolveEncoding(hint);
+                    }
+                }
+            }
+        }
+    }
+
+    function resolveEncoding(hint: EncodingStrategyHint): ArrayEncoder {
+        const precision: number | undefined = hint.precision;
+        if (precision !== void 0) {
+            const multiplier = Math.pow(10, precision);
+            const fixedPoint = E.by(E.fixedPoint(multiplier));
+            switch (hint.encoding) {
+                case 'pack':
+                    return fixedPoint.and(E.integerPacking);
+                case 'rle':
+                    return fixedPoint.and(E.runLength).and(E.integerPacking);
+                case 'delta':
+                    return fixedPoint.and(E.delta).and(E.integerPacking);
+                case 'delta-rle':
+                    return fixedPoint.and(E.delta).and(E.runLength).and(E.integerPacking);
+            };
+        } else {
+            switch (hint.encoding) {
+                case 'pack':
+                    return E.by(E.integerPacking);
+                case 'rle':
+                    return E.by(E.runLength).and(E.integerPacking);
+                case 'delta':
+                    return E.by(E.delta).and(E.integerPacking);
+                case 'delta-rle':
+                    return E.by(E.delta).and(E.runLength).and(E.integerPacking);
+            }
+        }
+        throw new Error('cannot be reached');
     }
-}
+}
+
+/**
+ * Defines the information needed to encode certain fields: category and column name as well as encoding tag, precision is optional and identifies float columns.
+ */
+export interface EncodingStrategyHint {
+    categoryName: string,
+    columnName: string,
+    // TODO would be nice to infer strategy and precision if needed
+    encoding: EncodingType,
+    /**
+     * number of decimal places to keep - must be specified to float columns
+     */
+    precision?: number
+}
+
+type EncodingType = 'pack' | 'rle' | 'delta' | 'delta-rle'

src/mol-io/writer/cif/encoder.ts

@@ -132,6 +132,60 @@ export namespace Category {
         includeField(categoryName: string, fieldName: string): boolean,
     }
 
+    export function filterOf(directives: string): Filter {
+        const cat_whitelist: string[] = [];
+        const cat_blacklist: string[] = [];
+        const field_whitelist: string[] = [];
+        const field_blacklist: string[] = [];
+
+        for (let d of directives.split(/[\r\n]+/)) {
+            d = d.trim();
+            // allow for empty lines in config
+            if (d.length === 0) continue;
+            // let ! denote blacklisted entries
+            const blacklist = /^!/.test(d);
+            if (blacklist) d = d.substr(1);
+            const split = d.split(/\./);
+            const field = split[1];
+            const list = blacklist ? (field ? field_blacklist : cat_blacklist) : (field ? field_whitelist : cat_whitelist);
+
+            list[list.length] = d;
+
+            // ensure categories are aware about whitelisted columns
+            if (field && !cat_whitelist.includes(split[0])) {
+                cat_whitelist[cat_whitelist.length] = split[0];
+            }
+        }
+
+        const wlcatcol = field_whitelist.map(it => it.split('.')[0]);
+        // blacklist has higher priority
+        return {
+            includeCategory(cat) {
+                // block if category in black
+                if (cat_blacklist.includes(cat)) {
+                    return false;
+                } else {
+                    // if there is a whitelist, the category has to be explicitly allowed
+                    return cat_whitelist.length <= 0 ||
+                            // otherwise include if whitelist contains category
+                            cat_whitelist.indexOf(cat) !== -1;
+                }
+            },
+            includeField(cat, field) {
+                // column names are assumed to follow the pattern 'category_name.column_name'
+                const full = cat + '.' + field;
+                if (field_blacklist.includes(full)) {
+                    return false;
+                } else {
+                    // if for this category no whitelist entries exist
+                    return !wlcatcol.includes(cat) ||
+                            // otherwise must be specifically allowed
+                            field_whitelist.includes(full);
+                }
+            }
+        }
+    }
+
     export const DefaultFilter: Filter = {
         includeCategory(cat) { return true; },
         includeField(cat, field) { return true; }