diff --git a/src/mol-app/ui/visualization/sequence-view.tsx b/src/mol-app/ui/visualization/sequence-view.tsx
index 6025eea22076a5e71ed57bc3c2d5be2ded4be068..69a88950239c43d2f3584337264af20a39d8a24e 100644
--- a/src/mol-app/ui/visualization/sequence-view.tsx
+++ b/src/mol-app/ui/visualization/sequence-view.tsx
@@ -7,10 +7,9 @@
import * as React from 'react'
import { View } from '../view';
import { SequenceViewController } from '../../controller/visualization/sequence-view';
-import { Structure, StructureSequence, Queries, Selection, StructureProperties } from 'mol-model/structure';
+import { Structure, StructureSequence, Queries, StructureSelection, StructureProperties, StructureQuery } from 'mol-model/structure';
import { Context } from '../../context/context';
import { InteractivityEvents } from '../../event/basic';
-import { SyncRuntimeContext } from 'mol-task/execution/synchronous';
import { EmptyLoci } from 'mol-model/loci';
export class SequenceView extends View<SequenceViewController, {}, {}> {
@@ -27,8 +26,8 @@ export class SequenceView extends View<SequenceViewController, {}, {}> {
function createQuery(entityId: string, label_seq_id: number) {
return Queries.generators.atoms({
- entityTest: l => StructureProperties.entity.id(l) === entityId,
- residueTest: l => StructureProperties.residue.label_seq_id(l) === label_seq_id
+ entityTest: ctx => StructureProperties.entity.id(ctx.element) === entityId,
+ residueTest: ctx => StructureProperties.residue.label_seq_id(ctx.element) === label_seq_id
});
}
@@ -42,7 +41,7 @@ class EntitySequence extends React.Component<{ ctx: Context, seq: StructureSeque
}
const query = createQuery(this.props.seq.entityId, seqId);
- const loci = Selection.toLoci(await query(this.props.structure, SyncRuntimeContext));
+ const loci = StructureSelection.toLoci(await StructureQuery.run(query, this.props.structure));
if (loci.elements.length === 0) InteractivityEvents.HighlightLoci.dispatch(this.props.ctx, EmptyLoci);
else InteractivityEvents.HighlightLoci.dispatch(this.props.ctx, loci);
}
diff --git a/src/mol-model/structure/model/formats/mmcif/assembly.ts b/src/mol-model/structure/model/formats/mmcif/assembly.ts
index c86abd27cfd5b2d3a156268cc3ed5967e7639160..e89690e1723ca31eca3c7295114331e97c9c786a 100644
--- a/src/mol-model/structure/model/formats/mmcif/assembly.ts
+++ b/src/mol-model/structure/model/formats/mmcif/assembly.ts
@@ -8,7 +8,7 @@ import { Mat4, Tensor } from 'mol-math/linear-algebra'
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import Format from '../../format'
import { Assembly, OperatorGroup, OperatorGroups } from '../../properties/symmetry'
-import { Queries as Q, Query } from '../../../query'
+import { Queries as Q } from '../../../query'
import mmCIF_Format = Format.mmCIF
import { StructureProperties } from '../../../structure';
@@ -58,10 +58,10 @@ function operatorGroupsProvider(generators: Generator[], matrices: Matrices): ()
const operatorList = parseOperatorList(gen.expression);
const operatorNames = expandOperators(operatorList);
const operators = getAssemblyOperators(matrices, operatorNames, operatorOffset);
- const selector = Query(Q.generators.atoms({ chainTest: Q.pred.and(
- Q.pred.eq(StructureProperties.unit.operator_name, SymmetryOperator.DefaultName),
- Q.pred.inSet(StructureProperties.chain.label_asym_id, gen.asymIds)
- )}));
+ const selector = Q.generators.atoms({ chainTest: Q.pred.and(
+ Q.pred.eq(ctx => StructureProperties.unit.operator_name(ctx.element), SymmetryOperator.DefaultName),
+ Q.pred.inSet(ctx => StructureProperties.chain.label_asym_id(ctx.element), gen.asymIds)
+ )});
groups[groups.length] = { selector, operators };
operatorOffset += operators.length;
}
diff --git a/src/mol-model/structure/model/properties/symmetry.ts b/src/mol-model/structure/model/properties/symmetry.ts
index fab3c37987b0b2c7cb36e7810ff97b93d2a9b913..c1ffee05e76c293118f5455a847157f9b820af39 100644
--- a/src/mol-model/structure/model/properties/symmetry.ts
+++ b/src/mol-model/structure/model/properties/symmetry.ts
@@ -6,13 +6,13 @@
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { arrayFind } from 'mol-data/util'
-import { Query } from '../../query'
+import { StructureQuery } from '../../query'
import { Model } from '../../model'
import { Spacegroup } from 'mol-math/geometry';
/** Determine an atom set and a list of operators that should be applied to that set */
export interface OperatorGroup {
- readonly selector: Query,
+ readonly selector: StructureQuery,
readonly operators: ReadonlyArray<SymmetryOperator>
}
diff --git a/src/mol-model/structure/query.ts b/src/mol-model/structure/query.ts
index 428d976d85872f423b3c4756cc77340d96844c7e..e4f3190a4303e31567ba5b95d81369ef5ad1c93e 100644
--- a/src/mol-model/structure/query.ts
+++ b/src/mol-model/structure/query.ts
@@ -4,8 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Selection from './query/selection'
-import Query from './query/query'
+import { StructureSelection } from './query/selection'
+import { StructureQuery } from './query/query'
+export * from './query/context'
import * as generators from './query/generators'
import * as modifiers from './query/modifiers'
import pred from './query/predicates'
@@ -16,4 +17,4 @@ export const Queries = {
pred
}
-export { Selection, Query }
\ No newline at end of file
+export { StructureSelection, StructureQuery }
\ No newline at end of file
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index f116f6f15e1c95941f0f2fd5ca8600fcc95040b6..eedd8d3e3988679615591e243846dee69b51a287 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -8,7 +8,6 @@ import { RuntimeContext } from 'mol-task';
import { Structure, StructureElement } from '../structure';
export interface QueryContextView {
- readonly taskCtx: RuntimeContext;
readonly element: StructureElement;
}
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index 1985a40680e5c7b7a73a7f9cb9c689221470f669..a4c87dc503374201ae19c3f9fa125f714963a0fc 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { RuntimeContext } from 'mol-task'
+import { RuntimeContext, Task } from 'mol-task'
import { Structure } from '../structure'
import { StructureSelection } from './selection'
import { QueryContext } from './context';
@@ -14,6 +14,10 @@ namespace StructureQuery {
export function run(query: StructureQuery, structure: Structure, ctx?: RuntimeContext) {
return query(new QueryContext(structure, ctx || RuntimeContext.Synchronous))
}
+
+ export function asTask(query: StructureQuery, structure: Structure) {
+ return Task.create('Structure Query', ctx => query(new QueryContext(structure, ctx)));
+ }
}
export { StructureQuery }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 5c71b11142568faa9c0fbbc5a49312cd60265170..c5f8d25165114be3bdfded5d64774c03c51b3dd3 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -5,7 +5,7 @@
*/
import Structure from './structure'
-import { Selection } from '../query'
+import { StructureSelection, QueryContext } from '../query'
import { ModelSymmetry } from '../model'
import { Task, RuntimeContext } from 'mol-task';
import { SortedArray } from 'mol-data/int';
@@ -25,12 +25,14 @@ namespace StructureSymmetry {
const assembler = Structure.Builder();
+ const queryCtx = new QueryContext(structure, ctx);
+
for (const g of assembly.operatorGroups) {
- const selection = await g.selector(structure).runAsChild(ctx);
- if (Selection.structureCount(selection) === 0) {
+ const selection = await g.selector(queryCtx);
+ if (StructureSelection.structureCount(selection) === 0) {
continue;
}
- const { units } = Selection.unionStructure(selection);
+ const { units } = StructureSelection.unionStructure(selection);
for (const oper of g.operators) {
for (const unit of units) {
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 90566d25f7202a16ad1ef7c6bb458297f41b3d29..ba9543895b7f7d0102bde4c834890f58bb23f964 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,7 +11,7 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, StructureElement, Selection, StructureSymmetry, Query, Format, StructureProperties as SP } from 'mol-model/structure'
+import { Structure, Model, Queries as Q, StructureElement, StructureSelection, StructureSymmetry, StructureQuery, Format, StructureProperties as SP } from 'mol-model/structure'
//import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
@@ -325,13 +325,13 @@ export namespace PropertyAccess {
const auth_comp_id = SP.residue.auth_comp_id, op = SP.unit.operator_name;
//const q1 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'REA' });
const q1 = Q.modifiers.includeSurroundings(Q.generators.atoms({
- chainTest: l => op(l) === '1_555',
- residueTest: l => auth_comp_id(l) === 'REA'
+ chainTest: l => op(l.element) === '1_555',
+ residueTest: l => auth_comp_id(l.element) === 'REA'
}), {
radius: 5,
wholeResidues: true
});
- const surr = Selection.unionStructure(await query(Query(q1), a));
+ const surr = StructureSelection.unionStructure(await StructureQuery.run(q1, a));
console.timeEnd('symmetry')
// for (const u of surr.units) {
@@ -371,8 +371,8 @@ export namespace PropertyAccess {
// console.log('group count', uniqueGroups.groups.length);
// }
- function query(q: Query, s: Structure) {
- return q(s).run();
+ function query(q: StructureQuery, s: Structure) {
+ return StructureQuery.run(q, s);
}
export async function run() {
@@ -431,14 +431,14 @@ export namespace PropertyAccess {
//const auth_asym_id = SP.chain.auth_asym_id;
//const set = new Set(['A', 'B', 'C', 'D']);
//const q = Q.generators.atomGroups({ atomTest: l => auth_seq_id(l) < 3 });
- const q = Query(Q.generators.atoms({ atomTest: Q.pred.eq(SP.residue.auth_comp_id, 'ALA') }));
+ const q = Q.generators.atoms({ atomTest: Q.pred.eq(l => SP.residue.auth_comp_id(l.element), 'ALA') });
const P = SP
//const q0 = Q.generators.atoms({ atomTest: l => auth_comp_id(l) === 'ALA' });
- const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
- const q2 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: SP.residue.key }));
- const q3 = Query(Q.generators.atoms({
- chainTest: Q.pred.inSet(P.chain.auth_asym_id, ['A', 'B', 'C', 'D']),
- residueTest: Q.pred.eq(P.residue.auth_comp_id, 'ALA')
+ const q1 = (Q.generators.atoms({ residueTest: l => auth_comp_id(l.element) === 'ALA' }));
+ const q2 = (Q.generators.atoms({ residueTest: l => auth_comp_id(l.element) === 'ALA', groupBy: l => SP.residue.key(l.element) }));
+ const q3 = (Q.generators.atoms({
+ chainTest: Q.pred.inSet(l => P.chain.auth_asym_id(l.element), ['A', 'B', 'C', 'D']),
+ residueTest: Q.pred.eq(l => P.residue.auth_comp_id(l.element), 'ALA')
}));
await query(q, structures[0]);
//console.log(to_mmCIF('test', Selection.union(q0r)));
@@ -452,7 +452,7 @@ export namespace PropertyAccess {
console.time('q2')
const q2r = await query(q2, structures[0]);
console.timeEnd('q2')
- console.log(Selection.structureCount(q2r));
+ console.log(StructureSelection.structureCount(q2r));
//console.log(q1(structures[0]));
const col = models[0].atomicConformation.atomId.value;
diff --git a/src/servers/model/server/api.ts b/src/servers/model/server/api.ts
index 0e60d47074d27b278086f6eb3015906ae65153b9..95879cce0d577d835c825e8c12f643b6cc4878e5 100644
--- a/src/servers/model/server/api.ts
+++ b/src/servers/model/server/api.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Query, Queries, Structure, StructureElement, StructureSymmetry, StructureProperties as Props } from 'mol-model/structure';
+import { StructureQuery, Queries, Structure, StructureElement, StructureSymmetry, StructureProperties as Props, QueryPredicate } from 'mol-model/structure';
export enum QueryParamType {
String,
@@ -26,7 +26,7 @@ export interface QueryDefinition {
name: string,
niceName: string,
exampleId: string, // default is 1cbs
- query: (params: any, structure: Structure) => Query,
+ query: (params: any, structure: Structure) => StructureQuery,
description: string,
params: QueryParamInfo[],
structureTransform?: (params: any, s: Structure) => Promise<Structure>
@@ -51,25 +51,25 @@ const AtomSiteParameters = {
// return Element.property(l => p(l) === id);
// }
-function entityTest1_555(params: any): StructureElement.Predicate | undefined {
- if (typeof params.entity_id === 'undefined') return StructureElement.property(l => l.unit.conformation.operator.isIdentity);
+function entityTest1_555(params: any): QueryPredicate | undefined {
+ if (typeof params.entity_id === 'undefined') return ctx => ctx.element.unit.conformation.operator.isIdentity;
const p = Props.entity.id, id = '' + params.entityId;
- return StructureElement.property(l => l.unit.conformation.operator.isIdentity && p(l) === id);
+ return ctx => ctx.element.unit.conformation.operator.isIdentity && p(ctx.element) === id;
}
-function chainTest(params: any): StructureElement.Predicate | undefined {
+function chainTest(params: any): QueryPredicate | undefined {
if (typeof params.label_asym_id !== 'undefined') {
const p = Props.chain.label_asym_id, id = '' + params.label_asym_id;
- return StructureElement.property(l => p(l) === id);
+ return ctx => p(ctx.element) === id;
}
if (typeof params.auth_asym_id !== 'undefined') {
const p = Props.chain.auth_asym_id, id = '' + params.auth_asym_id;
- return StructureElement.property(l => p(l) === id);
+ return ctx => p(ctx.element) === id;
}
return void 0;
}
-function residueTest(params: any): StructureElement.Predicate | undefined {
+function residueTest(params: any): QueryPredicate | undefined {
const props: StructureElement.Property<any>[] = [], values: any[] = [];
if (typeof params.label_seq_id !== 'undefined') {
@@ -99,15 +99,15 @@ function residueTest(params: any): StructureElement.Predicate | undefined {
switch (props.length) {
case 0: return void 0;
- case 1: return StructureElement.property(l => props[0](l) === values[0]);
- case 2: return StructureElement.property(l => props[0](l) === values[0] && props[1](l) === values[1]);
- case 3: return StructureElement.property(l => props[0](l) === values[0] && props[1](l) === values[1] && props[2](l) === values[2]);
+ case 1: return ctx => props[0](ctx.element) === values[0];
+ case 2: return ctx => props[0](ctx.element) === values[0] && props[1](ctx.element) === values[1];
+ case 3: return ctx => props[0](ctx.element) === values[0] && props[1](ctx.element) === values[1] && props[2](ctx.element) === values[2];
default: {
const len = props.length;
- return StructureElement.property(l => {
- for (let i = 0; i < len; i++) if (!props[i](l) !== values[i]) return false;
+ return ctx => {
+ for (let i = 0; i < len; i++) if (!props[i](ctx.element) !== values[i]) return false;
return true;
- });
+ };
}
}
}
@@ -117,13 +117,13 @@ function residueTest(params: any): StructureElement.Predicate | undefined {
// }
const QueryMap: { [id: string]: Partial<QueryDefinition> } = {
- 'full': { niceName: 'Full Structure', query: () => Query(Queries.generators.all), description: 'The full structure.' },
+ 'full': { niceName: 'Full Structure', query: () => Queries.generators.all, description: 'The full structure.' },
'residueInteraction': {
niceName: 'Residues Inside a Sphere',
description: 'Identifies all residues within the given radius from the source residue.',
query(p) {
const center = Queries.generators.atoms({ entityTest: entityTest1_555(p), chainTest: chainTest(p), residueTest: residueTest(p) });
- return Query(Queries.modifiers.includeSurroundings(center, { radius: p.radius, wholeResidues: true }));
+ return Queries.modifiers.includeSurroundings(center, { radius: p.radius, wholeResidues: true });
},
structureTransform(p, s) {
return StructureSymmetry.builderSymmetryMates(s, p.radius).run();
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 2dc635c4ee79bdeaa7735533615cd7a49a7e2f5d..4a1049524fb9698e8a8d63d71e21e5700718f6c6 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -13,7 +13,7 @@ import { ConsoleLogger } from 'mol-util/console-logger';
import Writer from 'mol-io/writer/writer';
import { CifWriter } from 'mol-io/writer/cif'
import { encode_mmCIF_categories } from 'mol-model/structure/export/mmcif';
-import { Selection } from 'mol-model/structure';
+import { StructureSelection, StructureQuery } from 'mol-model/structure';
import Version from '../version'
import { Column } from 'mol-data/db';
import { PerformanceMonitor } from 'mol-util/performance-monitor';
@@ -69,7 +69,7 @@ export async function resolveRequest(req: Request, writer: Writer) {
? await req.queryDefinition.structureTransform(req.normalizedParams, wrappedStructure.structure)
: wrappedStructure.structure;
const query = req.queryDefinition.query(req.normalizedParams, structure);
- const result = Selection.unionStructure(await query(structure).run(abortingObserver, 250));
+ const result = StructureSelection.unionStructure(await StructureQuery.asTask(query, structure).run(abortingObserver, 250));
perf.end('query');
ConsoleLogger.logId(req.id, 'Query', 'Query finished.');