From 9c046b808c295f20614c1bfce60d103528f7a0c8 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 16 Oct 2019 13:26:05 +0200
Subject: [PATCH] mol-script: added Bundle support
---
.../structure/query/queries/internal.ts | 23 +++++++++++++-
.../structure/structure/element/bundle.ts | 19 +++++++++++-
src/mol-script/language/builder.ts | 1 +
src/mol-script/language/symbol-table.ts | 3 +-
.../language/symbol-table/internal.ts | 30 +++++++++++++++++++
src/mol-script/runtime/query/table.ts | 7 +++++
6 files changed, 80 insertions(+), 3 deletions(-)
create mode 100644 src/mol-script/language/symbol-table/internal.ts
diff --git a/src/mol-model/structure/query/queries/internal.ts b/src/mol-model/structure/query/queries/internal.ts
index 23b495f72..fecbf7d10 100644
--- a/src/mol-model/structure/query/queries/internal.ts
+++ b/src/mol-model/structure/query/queries/internal.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Segmentation } from '../../../../mol-data/int';
+import { Segmentation, SortedArray } from '../../../../mol-data/int';
import StructureElement from '../../../../mol-model/structure/structure/element';
import { StructureProperties as P, Unit } from '../../structure';
import Structure from '../../structure/structure';
@@ -12,6 +12,8 @@ import { StructureQuery } from '../query';
import { StructureSelection } from '../selection';
import { QueryContext } from '../context';
import { LinkType } from '../../model/types';
+import { BundleElement, Bundle } from '../../structure/element/bundle';
+import { UnitIndex } from '../../structure/element/element';
export function defaultLinkTest(ctx: QueryContext) {
return LinkType.isCovalent(ctx.atomicLink.type);
@@ -105,4 +107,23 @@ export function spheres(): StructureQuery {
}
return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
};
+}
+
+export function bundleElementImpl(groupedUnits: number[][], ranges: number[], set: number[]): BundleElement {
+ return {
+ groupedUnits: groupedUnits as any as SortedArray<number>[],
+ ranges: ranges as any as SortedArray<UnitIndex>,
+ set: set as any as SortedArray<UnitIndex>
+ };
+}
+
+export function bundleGenerator(elements: BundleElement[]): StructureQuery {
+ return ctx => {
+ const bundle: Bundle = {
+ hash: ctx.inputStructure.hashCode,
+ elements
+ };
+
+ return StructureSelection.Sequence(ctx.inputStructure, [Bundle.toStructure(bundle, ctx.inputStructure)]);
+ };
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/element/bundle.ts b/src/mol-model/structure/structure/element/bundle.ts
index b750308df..b22289426 100644
--- a/src/mol-model/structure/structure/element/bundle.ts
+++ b/src/mol-model/structure/structure/element/bundle.ts
@@ -12,8 +12,10 @@ import { hashFnv32a, hash2 } from '../../../../mol-data/util';
import SortedRanges from '../../../../mol-data/int/sorted-ranges';
import { UnitIndex } from './element';
import { Loci } from './loci';
+import Expression from '../../../../mol-script/language/expression';
+import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
-interface BundleElement {
+export interface BundleElement {
/**
* Array (sorted by first element in sub-array) of
* arrays of `Unit.id`s that share the same `Unit.invariantId`
@@ -192,6 +194,21 @@ export namespace Bundle {
return Structure.create(units, { parent })
}
+
+ function elementToExpression(e: BundleElement): Expression {
+ return MS.internal.generator.bundleElement({
+ groupedUnits: MS.core.type.list(e.groupedUnits.map(u => MS.core.type.list(u))),
+ ranges: MS.core.type.list(e.ranges),
+ set: MS.core.type.list(e.set),
+ })
+ }
+
+ export function toExpression(bundle: Bundle): Expression {
+ return MS.internal.generator.bundle({
+ elements: MS.core.type.list(bundle.elements.map(elementToExpression))
+ });
+ }
+
export function areEqual(a: Bundle, b: Bundle) {
if (a.elements.length !== b.elements.length) return false
for (let i = 0, il = a.elements.length; i < il; ++i) {
diff --git a/src/mol-script/language/builder.ts b/src/mol-script/language/builder.ts
index c114c0ff6..16038e383 100644
--- a/src/mol-script/language/builder.ts
+++ b/src/mol-script/language/builder.ts
@@ -11,6 +11,7 @@ import { MolScriptSymbolTable as SymbolTable } from './symbol-table'
export namespace MolScriptBuilder {
export const core = SymbolTable.core;
export const struct = SymbolTable.structureQuery;
+ export const internal = SymbolTable.internal;
/** Atom-name constructor */
export function atomName(s: string) { return struct.type.atomName([s]); }
diff --git a/src/mol-script/language/symbol-table.ts b/src/mol-script/language/symbol-table.ts
index 3dec8616f..b8fde22ab 100644
--- a/src/mol-script/language/symbol-table.ts
+++ b/src/mol-script/language/symbol-table.ts
@@ -6,10 +6,11 @@
import core from './symbol-table/core'
import structureQuery from './symbol-table/structure-query'
+import internal from './symbol-table/internal'
import { normalizeTable, symbolList } from './helpers'
import { MSymbol } from './symbol'
-const MolScriptSymbolTable = { core, structureQuery };
+const MolScriptSymbolTable = { core, structureQuery, internal };
normalizeTable(MolScriptSymbolTable);
diff --git a/src/mol-script/language/symbol-table/internal.ts b/src/mol-script/language/symbol-table/internal.ts
new file mode 100644
index 000000000..d03433484
--- /dev/null
+++ b/src/mol-script/language/symbol-table/internal.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Type from '../type'
+import * as Struct from './structure-query'
+import { Arguments, Argument } from '../symbol'
+import { symbol } from '../helpers'
+
+const generator = {
+ '@header': 'Generators',
+
+ bundleElement: symbol(Arguments.Dictionary({
+ // TODO: should we use more universal unit keys? (i.e. based on chain and "operator name")
+ groupedUnits: Argument(Type.Any), // SortedArray<number>[],
+ set: Argument(Type.Any), // SortedArray<UnitIndex>
+ ranges: Argument(Type.Any) // SortedArray<UnitIndex>
+ }), Type.Any), // returns BundleElement
+
+ bundle: symbol(Arguments.Dictionary({
+ elements: Argument(Type.Any) // BundleElement[]
+ }), Struct.Types.ElementSelectionQuery, 'A selection with single structure containing represented by the bundle.'),
+}
+
+export default {
+ '@header': 'Internal Queries',
+ generator
+}
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index bf45a8836..6c1bcf441 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -15,6 +15,7 @@ import { VdwRadius, AtomWeight, AtomNumber } from '../../../mol-model/structure/
import { cantorPairing } from '../../../mol-data/util';
import C = QuerySymbolRuntime.Const
import D = QuerySymbolRuntime.Dynamic
+import { bundleElementImpl, bundleGenerator } from '../../../mol-model/structure/query/queries/internal';
const symbols = [
// ============= TYPES =============
@@ -320,6 +321,12 @@ const symbols = [
// ============= BOND PROPERTIES ================
D(MolScript.structureQuery.linkProperty.order, (ctx, xs) => ctx.atomicLink.order),
D(MolScript.structureQuery.linkProperty.flags, (ctx, xs) => ctx.atomicLink.type),
+
+
+ ////////////////////////////////////
+ // Internal
+ D(MolScript.internal.generator.bundleElement, (ctx, xs) => bundleElementImpl(xs.groupedUnits(ctx), xs.ranges(ctx), xs.set(ctx))),
+ D(MolScript.internal.generator.bundle, (ctx, xs) => bundleGenerator(xs.elements(ctx))),
];
function atomProp(p: (e: StructureElement.Location) => any): (ctx: QueryContext, _: any) => any {
--
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