From 6e36116f7681a2820e82f101d3568e9936d881af Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 8 Aug 2018 14:56:33 +0200
Subject: [PATCH] wip, mol-script
---
.../model/properties/custom/descriptor.ts | 12 ++++++--
src/mol-script/language/symbol.ts | 11 +++++++
src/mol-script/runtime/query/compiler.ts | 10 ++++++-
src/mol-script/runtime/query/table.ts | 14 +++------
src/perf-tests/mol-script.ts | 30 +++++++++++++++----
5 files changed, 58 insertions(+), 19 deletions(-)
diff --git a/src/mol-model/structure/model/properties/custom/descriptor.ts b/src/mol-model/structure/model/properties/custom/descriptor.ts
index d86dd94a6..fd60c265d 100644
--- a/src/mol-model/structure/model/properties/custom/descriptor.ts
+++ b/src/mol-model/structure/model/properties/custom/descriptor.ts
@@ -6,14 +6,22 @@
import { CifWriter } from 'mol-io/writer/cif'
import { CifExportContext } from '../../../export/mmcif';
+import { QuerySymbolRuntime } from 'mol-script/runtime/query/compiler';
-interface ModelPropertyDescriptor {
+interface ModelPropertyDescriptor<Symbols extends { [name: string]: QuerySymbolRuntime } = { }> {
readonly isStatic: boolean,
readonly name: string,
cifExport: {
categories: CifWriter.Category<CifExportContext>[]
- }
+ },
+
+ // TODO: add aliases when lisp-like mol-script is done
+ symbols?: Symbols
+}
+
+function ModelPropertyDescriptor<Desc extends ModelPropertyDescriptor>(desc: Desc) {
+ return desc;
}
export { ModelPropertyDescriptor }
\ No newline at end of file
diff --git a/src/mol-script/language/symbol.ts b/src/mol-script/language/symbol.ts
index de9b53665..bb935ee6f 100644
--- a/src/mol-script/language/symbol.ts
+++ b/src/mol-script/language/symbol.ts
@@ -74,6 +74,17 @@ export function MSymbol<A extends Arguments, T extends Type>(name: string, args:
return symbol;
}
+export function CustomPropSymbol<T extends Type>(namespace: string, name: string, type: T, description?: string) {
+ const symbol: MSymbol<Arguments<{}>, T> = function(args: ExpressionArguments<Arguments<{}>['@type']>) {
+ return Expression.Apply(Expression.Symbol(symbol.id), args as any);
+ } as any;
+ symbol.info = { namespace, name, description };
+ symbol.id = `${namespace}.${name}`;
+ symbol.args = Arguments.None;
+ symbol.type = type;
+ return symbol;
+}
+
export function isSymbol(x: any): x is MSymbol {
const s = x as MSymbol;
return typeof s === 'function' && !!s.info && !!s.args && typeof s.info.namespace === 'string' && !!s.type;
diff --git a/src/mol-script/runtime/query/compiler.ts b/src/mol-script/runtime/query/compiler.ts
index 63598bb4c..aa3c6b652 100644
--- a/src/mol-script/runtime/query/compiler.ts
+++ b/src/mol-script/runtime/query/compiler.ts
@@ -5,7 +5,7 @@
*/
import Expression from '../../language/expression';
-import { QueryContext, QueryFn, Structure } from 'mol-model/structure';
+import { QueryContext, QueryFn, Structure, ModelPropertyDescriptor } from 'mol-model/structure';
import { MSymbol } from '../../language/symbol';
export class QueryRuntimeTable {
@@ -15,6 +15,14 @@ export class QueryRuntimeTable {
this.map.set(runtime.symbol.id, runtime);
}
+ addCustomProp(desc: ModelPropertyDescriptor) {
+ if (!desc.symbols) return;
+
+ for (const k of Object.keys(desc.symbols)) {
+ this.addSymbol((desc.symbols as any)[k]);
+ }
+ }
+
getRuntime(id: string) {
return this.map.get(id);
}
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index d5c4217d7..e0d555655 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -30,6 +30,10 @@ const symbols = [
C(MolScript.core.rel.lte, (ctx, v) => v[0](ctx) <= v[1](ctx)),
C(MolScript.core.rel.gr, (ctx, v) => v[0](ctx) > v[1](ctx)),
C(MolScript.core.rel.gre, (ctx, v) => v[0](ctx) >= v[1](ctx)),
+ C(MolScript.core.rel.inRange, (ctx, v) => {
+ const x = v[0](ctx);
+ return x >= v[1](ctx) && x <= v[2](ctx);
+ }),
// ============= TYPES ================
C(MolScript.structureQuery.type.elementSymbol, (ctx, v) => ElementSymbol(v[0](ctx))),
@@ -46,16 +50,6 @@ const symbols = [
// ============= ATOM PROPERTIES ================
D(MolScript.structureQuery.atomProperty.macromolecular.label_comp_id, (ctx, _) => StructureProperties.residue.label_comp_id(ctx.element)),
D(MolScript.structureQuery.atomProperty.core.elementSymbol, (ctx, _) => StructureProperties.atom.type_symbol(ctx.element))
-
- // Symbol(MolQL.core.rel.neq, staticAttr)((env, v) => v[0](env) !== v[1](env)),
- // Symbol(MolQL.core.rel.lt, staticAttr)((env, v) => v[0](env) < v[1](env)),
- // Symbol(MolQL.core.rel.lte, staticAttr)((env, v) => v[0](env) <= v[1](env)),
- // Symbol(MolQL.core.rel.gr, staticAttr)((env, v) => v[0](env) > v[1](env)),
- // Symbol(MolQL.core.rel.gre, staticAttr)((env, v) => v[0](env) >= v[1](env)),
- // Symbol(MolQL.core.rel.inRange, staticAttr)((env, v) => {
- // const x = v[0](env);
- // return x >= v[1](env) && x <= v[2](env)
- // }),
];
(function () {
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 104c6c194..5f6cfcc9e 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -1,7 +1,9 @@
import { MolScriptBuilder } from 'mol-script/language/builder';
-import { compile } from 'mol-script/runtime/query/compiler';
-import { QueryContext, Structure, StructureQuery } from 'mol-model/structure';
+import { compile, QuerySymbolRuntime, DefaultQueryRuntimeTable } from 'mol-script/runtime/query/compiler';
+import { QueryContext, Structure, StructureQuery, ModelPropertyDescriptor } from 'mol-model/structure';
import { readCifFile, getModelsAndStructure } from '../apps/structure-info/model';
+import { CustomPropSymbol } from 'mol-script/language/symbol';
+import Type from 'mol-script/language/type';
// import Examples from 'mol-script/script/mol-script/examples'
// import { parseMolScript } from 'mol-script/script/mol-script/parser'
@@ -27,6 +29,21 @@ const compiled = compile<number>(expr);
const result = compiled(new QueryContext(Structure.Empty));
console.log(result);
+const CustomProp = ModelPropertyDescriptor({
+ name: 'test_prop',
+ isStatic: true,
+ cifExport: { categories: [ ]},
+ symbols: {
+ residueIndex: QuerySymbolRuntime.Dynamic(CustomPropSymbol('custom.test-prop', 'residue-index', Type.Num), ctx => {
+ const e = ctx.element;
+ //console.log(e.element, e.unit.model.atomicHierarchy.residueAtomSegments.index[e.element])
+ return e.unit.model.atomicHierarchy.residueAtomSegments.index[e.element];
+ })
+ }
+});
+
+DefaultQueryRuntimeTable.addCustomProp(CustomProp);
+
async function testQ() {
const frame = await readCifFile('e:/test/quick/1cbs_updated.cif');
const { structure } = await getModelsAndStructure(frame);
@@ -36,10 +53,11 @@ async function testQ() {
MolScriptBuilder.struct.atomProperty.core.elementSymbol(),
MolScriptBuilder.es('C')
]),
- 'residue-test': MolScriptBuilder.core.rel.eq([
- MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(),
- 'REA'
- ])
+ // 'residue-test': MolScriptBuilder.core.rel.eq([
+ // MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(),
+ // 'REA'
+ // ])
+ 'residue-test': MolScriptBuilder.core.rel.inRange([CustomProp.symbols.residueIndex.symbol(), 1, 5])
});
const compiled = compile<StructureQuery>(expr);
--
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