0.7.0-dev.6

- whole residues
- non-standard residues from current structures
- elements from current structures

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.4",
+  "version": "0.7.0-dev.6",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.4",
+  "version": "0.7.0-dev.6",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/extensions/rcsb/assembly-symmetry/representation.ts

@@ -225,6 +225,7 @@ function getSymbolScale(symbol: string) {
 function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.RotationAxes, size: number, structure: Structure) {
     const eye = Vec3();
     const target = Vec3();
+    const dir = Vec3();
     const up = Vec3();
     let pair: Mutable<AssemblySymmetry.RotationAxes> | undefined = undefined;
 
@@ -246,8 +247,8 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
         const a5dir = Vec3.sub(Vec3(), a5.end, a5.start);
         pair = [a5];
         for (const a of axes.filter(a => a.order === 3)) {
-            let d = radToDeg(Vec3.angle(Vec3.sub(up, a.end, a.start), a5dir));
-            if (equalEps(d, 100.81, 0.1) || equalEps(d, 79.19, 0.1)) {
+            const d = radToDeg(Vec3.angle(Vec3.sub(up, a.end, a.start), a5dir));
+            if (!pair[1] && (equalEps(d, 100.81, 0.1) || equalEps(d, 79.19, 0.1))) {
                 pair[1] = a;
                 break;
             }
@@ -263,8 +264,8 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
         Vec3.copy(target, aA.end);
         if (aB) {
             Vec3.sub(up, aB.end, aB.start);
-            const d = Vec3.dot(eye, up);
-            if (d < 0) Vec3.negate(up, up);
+            Vec3.sub(dir, eye, target);
+            if (Vec3.dot(dir, up) < 0) Vec3.negate(up, up);
             Mat4.targetTo(t, eye, target, up);
             Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
         } else {

src/extensions/rcsb/validation-report/behavior.ts

@@ -340,7 +340,7 @@ export const ValidationReportDensityFitPreset = StructureRepresentationPresetPro
         description: 'Color structure based on density fit. Data from wwPDB Validation Report, obtained via RCSB PDB.'
     },
     isApplicable(a) {
-        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.hasXrayMap(a.data.models[0]);
+        return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.isFromXray(a.data.models[0]) && Model.probablyHasDensityMap(a.data.models[0]);
     },
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -67,7 +67,7 @@ export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationRep
     factory: DensityFitColorTheme,
     getParams: () => ({}),
     defaultValues: PD.getDefaultValues({}),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.hasXrayMap(ctx.structure.models[0]),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
         detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)

src/mol-model/structure/model/properties/atomic/types.ts

@@ -14,6 +14,15 @@ export const enum Elements {
     H = 'H', D = 'D', T = 'T', HE = 'HE', LI = 'LI', BE = 'BE', B = 'B', C = 'C', N = 'N', O = 'O', F = 'F', NE = 'NE', NA = 'NA', MG = 'MG', AL = 'AL', SI = 'SI', P = 'P', S = 'S', CL = 'CL', AR = 'AR', K = 'K', CA = 'CA', SC = 'SC', TI = 'TI', V = 'V', CR = 'CR', MN = 'MN', FE = 'FE', CO = 'CO', NI = 'NI', CU = 'CU', ZN = 'ZN', GA = 'GA', GE = 'GE', AS = 'AS', SE = 'SE', BR = 'BR', KR = 'KR', RB = 'RB', SR = 'SR', Y = 'Y', ZR = 'ZR', NB = 'NB', MO = 'MO', TC = 'TC', RU = 'RU', RH = 'RH', PD = 'PD', AG = 'AG', CD = 'CD', IN = 'IN', SN = 'SN', SB = 'SB', TE = 'TE', I = 'I', XE = 'XE', CS = 'CS', BA = 'BA', LA = 'LA', CE = 'CE', PR = 'PR', ND = 'ND', PM = 'PM', SM = 'SM', EU = 'EU', GD = 'GD', TB = 'TB', DY = 'DY', HO = 'HO', ER = 'ER', TM = 'TM', YB = 'YB', LU = 'LU', HF = 'HF', TA = 'TA', W = 'W', RE = 'RE', OS = 'OS', IR = 'IR', PT = 'PT', AU = 'AU', HG = 'HG', TL = 'TL', PB = 'PB', BI = 'BI', PO = 'PO', AT = 'AT', RN = 'RN', FR = 'FR', RA = 'RA', AC = 'AC', TH = 'TH', PA = 'PA', U = 'U', NP = 'NP', PU = 'PU', AM = 'AM', CM = 'CM', BK = 'BK', CF = 'CF', ES = 'ES', FM = 'FM', MD = 'MD', NO = 'NO', LR = 'LR', RF = 'RF', DB = 'DB', SG = 'SG', BH = 'BH', HS = 'HS', MT = 'MT', DS = 'DS', RG = 'RG', CN = 'CN', NH = 'NH', FL = 'FL', MC = 'MC', LV = 'LV', TS = 'TS', OG = 'OG'
 }
 
+export const ElementNames: { [k: string]: string } = {
+    'H': 'Hydrogen',
+    'C': 'Carbon',
+    'N': 'Nitrogen',
+    'O': 'Oxygen',
+    'S': 'Sulfur',
+    'FE': 'Iron',
+};
+
 export const AlkaliMetals = new Set<ElementSymbol>(['LI', 'NA', 'K', 'RB', 'CS', 'FR'] as ElementSymbol[]);
 export function isAlkaliMetal(element: ElementSymbol) { return AlkaliMetals.has(element); }
 

src/mol-model/structure/structure/structure.ts

@@ -29,6 +29,7 @@ import { CustomProperties } from '../common/custom-property';
 import { AtomicHierarchy } from '../model/properties/atomic';
 import { StructureSelection } from '../query/selection';
 import { getBoundary } from '../../../mol-math/geometry/boundary';
+import { ElementSymbol } from '../model/types';
 
 class Structure {
     /** Maps unit.id to unit */
@@ -50,6 +51,7 @@ class Structure {
         masterModel?: Model,
         representativeModel?: Model,
         uniqueResidueNames?: Set<string>,
+        uniqueElementSymbols?: Set<ElementSymbol>,
         entityIndices?: ReadonlyArray<EntityIndex>,
         uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
         serialMapping?: SerialMapping,
@@ -265,6 +267,11 @@ class Structure {
             || (this._props.uniqueResidueNames = getUniqueResidueNames(this));
     }
 
+    get uniqueElementSymbols() {
+        return this._props.uniqueElementSymbols
+            || (this._props.uniqueElementSymbols = getUniqueElementSymbols(this));
+    }
+
     get entityIndices() {
         return this._props.entityIndices
             || (this._props.entityIndices = getEntityIndices(this));
@@ -403,7 +410,8 @@ function getUniqueResidueNames(s: Structure) {
     const prop = StructureProperties.residue.label_comp_id;
     const names = new Set<string>();
     const loc = StructureElement.Location.create(s);
-    for (const unit of s.units) {
+    for (const unitGroup of s.unitSymmetryGroups) {
+        const unit = unitGroup.units[0];
         // TODO: support coarse unit?
         if (!Unit.isAtomic(unit)) continue;
         const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
@@ -417,6 +425,21 @@ function getUniqueResidueNames(s: Structure) {
     return names;
 }
 
+function getUniqueElementSymbols(s: Structure) {
+    const prop = StructureProperties.atom.type_symbol;
+    const symbols = new Set<ElementSymbol>();
+    const loc = StructureElement.Location.create(s);
+    for (const unit of s.units) {
+        if (!Unit.isAtomic(unit)) continue;
+        loc.unit = unit;
+        for (let i = 0, il = unit.elements.length; i < il; ++i) {
+            loc.element = unit.elements[i];
+            symbols.add(prop(loc));
+        }
+    }
+    return symbols;
+}
+
 function getEntityIndices(structure: Structure): ReadonlyArray<EntityIndex> {
     const { units } = structure;
     const l = StructureElement.Location.create(structure);

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -229,14 +229,14 @@ const branchedPlusConnected = StructureSelectionQuery('Carbohydrate with Connect
     MS.struct.modifier.includeConnected({
         0: branched.expression, 'layer-count': 1, 'as-whole-residues': true
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: branchedPlusConnected.expression,
         by: branched.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
     MS.struct.combinator.merge([
@@ -290,14 +290,14 @@ const ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.
         ]),
         by: branched.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligandConnectedOnly = StructureSelectionQuery('Connected to Ligand', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: ligandPlusConnected.expression,
         by: ligand.expression
     })
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 // residues connected to ligands or branched entities
 const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydrate', MS.struct.modifier.union([
@@ -305,7 +305,7 @@ const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydra
         branchedConnectedOnly.expression,
         ligandConnectedOnly.expression
     ]),
-]), { category: StructureSelectionCategory.Internal });
+]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.modifier.union([
     MS.struct.modifier.wholeResidues([
@@ -380,6 +380,16 @@ const bonded = StructureSelectionQuery('Residues Bonded to Selection', MS.struct
     referencesCurrent: true
 });
 
+const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', MS.struct.modifier.union([
+    MS.struct.modifier.wholeResidues({
+        0: MS.internal.generator.current()
+    })
+]), {
+    description: 'Expand current selection to whole residues.',
+    category: StructureSelectionCategory.Manipulate,
+    referencesCurrent: true
+});
+
 const StandardAminoAcids = [
     [['HIS'], 'HISTIDINE'],
     [['ARG'], 'ARGININE'],
@@ -390,6 +400,7 @@ const StandardAminoAcids = [
     [['TRP'], 'TRYPTOPHAN'],
     [['ALA'], 'ALANINE'],
     [['MET'], 'METHIONINE'],
+    [['PRO'], 'PROLINE'],
     [['CYS'], 'CYSTEINE'],
     [['ASN'], 'ASPARAGINE'],
     [['VAL'], 'VALINE'],
@@ -402,6 +413,7 @@ const StandardAminoAcids = [
     [['THR'], 'THREONINE'],
     [['SEC'], 'SELENOCYSTEINE'],
     [['PYL'], 'PYRROLYSINE'],
+    [['UNK'], 'UNKNOWN'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 const StandardNucleicBases = [
@@ -411,9 +423,10 @@ const StandardNucleicBases = [
     [['G', 'DG'], 'GUANOSINE'],
     [['I', 'DI'], 'INOSINE'],
     [['U', 'DU'], 'URIDINE'],
+    [['N', 'DN'], 'UNKNOWN'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
-function ResidueQuery([names, label]: [string[], string], category: string) {
+export function ResidueQuery([names, label]: [string[], string], category: string) {
     return StructureSelectionQuery(`${stringToWords(label)} (${names.join(', ')})`, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'residue-test': MS.core.set.has([MS.set(...names), MS.ammp('auth_comp_id')])
@@ -421,6 +434,14 @@ function ResidueQuery([names, label]: [string[], string], category: string) {
     ]), { category });
 }
 
+export function ElementSymbolQuery([names, label]: [string[], string], category: string) {
+    return StructureSelectionQuery(`${stringToWords(label)} (${names.join(', ')})`, MS.struct.modifier.union([
+        MS.struct.generator.atomGroups({
+            'atom-test': MS.core.set.has([MS.set(...names), MS.acp('elementSymbol')])
+        })
+    ]), { category });
+}
+
 export const StructureSelectionQueries = {
     all,
     current,
@@ -447,6 +468,7 @@ export const StructureSelectionQueries = {
     surroundings,
     complement,
     bonded,
+    wholeResidues,
 };
 
 export function applyBuiltInSelection(to: StateBuilder.To<PluginStateObject.Molecule.Structure>, query: keyof typeof StructureSelectionQueries, customTag?: string) {

src/mol-plugin-ui/structure/selection.tsx

@@ -11,7 +11,7 @@ import Brush from '@material-ui/icons/Brush';
 import Restore from '@material-ui/icons/Restore';
 import Remove from '@material-ui/icons/Remove';
 import * as React from 'react';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { StructureSelectionQueries, StructureSelectionQuery, ResidueQuery, ElementSymbolQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
 import { InteractivityManager } from '../../mol-plugin-state/manager/interactivity';
 import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
 import { StructureRef, StructureComponentRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
@@ -25,6 +25,9 @@ import { Button, ControlGroup, IconButton, ToggleButton } from '../controls/comm
 import { ParameterControls, ParamOnChange, PureSelectControl } from '../controls/parameters';
 import { Union, Subtract, Intersect, SetSvg as SetSvg, CubeSvg } from '../controls/icons';
 import { AddComponentControls } from './components';
+import { SetUtils } from '../../mol-util/set';
+import { AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol } from '../../mol-model/structure/model/types';
+import { ElementNames } from '../../mol-model/structure/model/properties/atomic/types';
 
 const StructureSelectionParams = {
     granularity: InteractivityManager.Params.granularity,
@@ -45,6 +48,10 @@ const ActionHeader = new Map<StructureSelectionModifier, string>([
     ['set', 'Set Selection']
 ] as const);
 
+const StandardResidues = SetUtils.unionMany(
+    AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames
+);
+
 export class StructureSelectionActionsControls extends PluginUIComponent<{}, StructureSelectionActionsControlsState> {
     state = {
         action: void 0 as StructureSelectionActionsControlsState['action'],
@@ -60,6 +67,9 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
             if (this.state.isEmpty !== isEmpty) {
                 this.setState({ isEmpty });
             }
+            // trigger elementQueries and nonStandardResidueQueries recalculation
+            this.queriesVersion = -1;
+            this.forceUpdate();
         });
 
         this.subscribe(this.plugin.behaviors.state.isBusy, v => {
@@ -83,15 +93,60 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
         this.plugin.managers.structure.selection.fromSelectionQuery(modifier, selectionQuery, false);
     }
 
-    selectQuery: ActionMenu.OnSelect = item => {
+    selectQuery: ActionMenu.OnSelect = (item, e) => {
         if (!item || !this.state.action) {
             this.setState({ action: void 0 });
             return;
         }
         const q = this.state.action! as StructureSelectionModifier;
-        this.setState({ action: void 0 }, () => {
+        if (e?.shiftKey) {
             this.set(q, item.value as StructureSelectionQuery);
+        } else {
+            this.setState({ action: void 0 }, () => {
+                this.set(q, item.value as StructureSelectionQuery);
+            });
+        }
+    }
+
+    get elementQueries () {
+        const uniqueElements = new Set<ElementSymbol>();
+        for (const s of this.plugin.managers.structure.hierarchy.selection.structures) {
+            const structure = s.cell.obj?.data;
+            if (!structure) continue;
+
+            structure.uniqueElementSymbols.forEach(e => uniqueElements.add(e));
+        }
+
+        const queries: StructureSelectionQuery[] = [];
+        uniqueElements.forEach(e => {
+            const label = ElementNames[e] || e;
+            queries.push(ElementSymbolQuery([[e], label], 'Element Symbol'));
         });
+        return queries;
+    }
+
+    get nonStandardResidueQueries () {
+        const residueLabels = new Map<string, string>();
+        const uniqueResidues = new Set<string>();
+        for (const s of this.plugin.managers.structure.hierarchy.selection.structures) {
+            const structure = s.cell.obj?.data;
+            if (!structure) continue;
+
+            structure.uniqueResidueNames.forEach(r => uniqueResidues.add(r));
+            for (const m of structure.models) {
+                structure.uniqueResidueNames.forEach(r => {
+                    const comp = m.properties.chemicalComponentMap.get(r);
+                    if (comp) residueLabels.set(r, comp.name);
+                });
+            }
+        }
+
+        const queries: StructureSelectionQuery[] = [];
+        SetUtils.difference(uniqueResidues, StandardResidues).forEach(r => {
+            const label = residueLabels.get(r) || r;
+            queries.push(ResidueQuery([[r], label], 'Ligand/Non-standard Residue'));
+        });
+        return queries;
     }
 
     private queriesItems: ActionMenu.Items[] = []
@@ -99,8 +154,9 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
     get queries () {
         const { registry } = this.plugin.query.structure;
         if (registry.version !== this.queriesVersion) {
-            this.queriesItems = ActionMenu.createItems(registry.list, {
-                filter: q => q !== StructureSelectionQueries.current,
+            const queries = [...registry.list, ...this.nonStandardResidueQueries, ...this.elementQueries];
+            this.queriesItems = ActionMenu.createItems(queries, {
+                filter: q => q !== StructureSelectionQueries.current && !q.isHidden,
                 label: q => q.label,
                 category: q => q.category,
                 description: q => q.description

src/servers/volume/pack/format.ts

@@ -103,7 +103,7 @@ export function getProviderFromType(type: Type): Provider {
 export async function open(name: string, filename: string, type: Type): Promise<Context> {
     const provider = getProviderFromType(type);
     const descriptor = await File.openRead(filename);
-    const file = FileHandle.fromDescriptor(descriptor);
+    const file = FileHandle.fromDescriptor(descriptor, filename);
     const header = await provider.readHeader(name, file);
     const data = { header, file, slices: void 0 as any };
     return { data, provider };

src/servers/volume/pack/sampling.ts

@@ -32,7 +32,7 @@ export async function createContext(filename: string, channels: Format.Context[]
     }
 
     const ctx: Data.Context = {
-        file: FileHandle.fromDescriptor(await File.createFile(filename)),
+        file: FileHandle.fromDescriptor(await File.createFile(filename), filename),
         isPeriodic,
         channels,
         valueType,

src/servers/volume/server/api.ts

@@ -66,7 +66,7 @@ async function readHeader(filename: string | undefined, sourceId: string) {
     let file: FileHandle | undefined;
     try {
         if (!filename) return void 0;
-        file = FileHandle.fromDescriptor(await File.openRead(filename));
+        file = FileHandle.fromDescriptor(await File.openRead(filename), filename);
         const header = await DataFormat.readHeader(file);
         return header.header;
     } catch (e) {

src/servers/volume/server/query/execute.ts

@@ -34,7 +34,7 @@ export default async function execute(params: Data.QueryParams, outputProvider:
 
     let sourceFile: FileHandle | undefined;
     try {
-        sourceFile = FileHandle.fromDescriptor(await File.openRead(params.sourceFilename));
+        sourceFile = FileHandle.fromDescriptor(await File.openRead(params.sourceFilename), params.sourceFilename);
         await _execute(sourceFile, params, guid, outputProvider);
         return true;
     } catch (e) {