From abc545a99761e32e5f204d87a3646dbd496bba34 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 8 Aug 2018 14:34:00 +0200
Subject: [PATCH] wip mol-script, 1st compiled query
---
package-lock.json | Bin 411997 -> 418525 bytes
package.json | 4 +-
src/apps/structure-info/model.ts | 11 +-
src/mol-model/structure/query/context.ts | 4 +-
src/mol-model/structure/query/query.ts | 4 +-
src/mol-script/language/builder.ts | 8 +-
src/mol-script/language/symbol-table.ts | 8 +-
src/mol-script/language/symbol-table/core.ts | 9 +
src/mol-script/language/symbol.ts | 3 +-
src/mol-script/language/type.ts | 2 +-
src/mol-script/runtime/environment.ts | 60 +-
src/mol-script/runtime/expression.ts | 38 +-
src/mol-script/runtime/macro.ts | 132 ++---
src/mol-script/runtime/query/compiler.ts | 151 +++++
src/mol-script/runtime/query/table.ts | 65 +++
src/mol-script/runtime/symbol.ts | 48 +-
src/mol-script/script/mol-script/examples.ts | 206 +++----
src/mol-script/script/mol-script/macro.ts | 68 +--
src/mol-script/script/mol-script/parser.ts | 356 ++++++------
src/mol-script/script/mol-script/symbols.ts | 546 +++++++++----------
src/perf-tests/mol-script.ts | 53 +-
tsconfig.json | 3 +-
22 files changed, 1021 insertions(+), 758 deletions(-)
create mode 100644 src/mol-script/runtime/query/compiler.ts
create mode 100644 src/mol-script/runtime/query/table.ts
diff --git a/package-lock.json b/package-lock.json
index 0b0df7edaf6edb49db5b2861d5b6c4b2f321a620..4f137e24d0fb3957776c524681a389410b1a1b40 100644
GIT binary patch
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diff --git a/package.json b/package.json
index eb8afa253..40e7655c3 100644
--- a/package.json
+++ b/package.json
@@ -83,8 +83,8 @@
"file-loader": "^1.1.11",
"glslify-import": "^3.1.0",
"glslify-loader": "^1.0.2",
- "graphql-code-generator": "^0.10.6",
- "graphql-codegen-typescript-template": "^0.10.6",
+ "graphql-code-generator": "^0.10.7",
+ "graphql-codegen-typescript-template": "^0.10.7",
"graphql-tag": "^2.9.2",
"jest": "^23.4.2",
"jest-raw-loader": "^1.0.1",
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index fbc466845..c01698f91 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -22,7 +22,7 @@ async function downloadFromPdb(pdb: string) {
return parsed.blocks[0];
}
-async function readPdbFile(path: string) {
+export async function readCifFile(path: string) {
const parsed = await openCif(path);
return parsed.blocks[0];
}
@@ -197,9 +197,14 @@ export function printModelStats(models: ReadonlyArray<Model>) {
console.log();
}
-async function run(frame: CifFrame, args: Args) {
+export async function getModelsAndStructure(frame: CifFrame) {
const models = await Model.create(Format.mmCIF(frame)).run();
const structure = Structure.ofModel(models[0]);
+ return { models, structure };
+}
+
+async function run(frame: CifFrame, args: Args) {
+ const { models, structure } = await getModelsAndStructure(frame);
if (args.models) printModelStats(models);
if (args.seq) printSequence(models[0]);
@@ -218,7 +223,7 @@ async function runDL(pdb: string, args: Args) {
}
async function runFile(filename: string, args: Args) {
- const mmcif = await readPdbFile(filename);
+ const mmcif = await readCifFile(filename);
run(mmcif, args);
}
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 7541c8ac2..188aac0e7 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -58,5 +58,5 @@ export class QueryContext implements QueryContextView {
}
}
-export interface QueryPredicate { (ctx: QueryContextView): boolean }
-export interface QueryFn<T = any> { (ctx: QueryContextView): T }
\ No newline at end of file
+export interface QueryPredicate { (ctx: QueryContext): boolean }
+export interface QueryFn<T = any> { (ctx: QueryContext): T }
\ No newline at end of file
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index 4283b6b73..f7629182e 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -6,9 +6,9 @@
import { Structure } from '../structure'
import { StructureSelection } from './selection'
-import { QueryContext } from './context';
+import { QueryContext, QueryFn } from './context';
-interface StructureQuery { (ctx: QueryContext): StructureSelection }
+interface StructureQuery extends QueryFn<StructureSelection> { }
namespace StructureQuery {
export function run(query: StructureQuery, structure: Structure, timeoutMs = 0) {
return query(new QueryContext(structure, timeoutMs));
diff --git a/src/mol-script/language/builder.ts b/src/mol-script/language/builder.ts
index 213b47a7a..8c7efa07d 100644
--- a/src/mol-script/language/builder.ts
+++ b/src/mol-script/language/builder.ts
@@ -6,9 +6,9 @@
import Expression from './expression'
import { MSymbol } from './symbol'
-import SymbolTable from './symbol-table'
+import { MolScriptSymbolTable as SymbolTable } from './symbol-table'
-namespace Builder {
+export namespace MolScriptBuilder {
export const core = SymbolTable.core;
export const struct = SymbolTable.structureQuery;
@@ -35,6 +35,4 @@ namespace Builder {
export function acpSet(p: keyof typeof _acp) { return _aps([ acp(p) ]) };
export function atpSet(p: keyof typeof _atp) { return _aps([ atp(p) ]) };
export function ammpSet(p: keyof typeof _ammp) { return _aps([ ammp(p) ]) };
-}
-
-export default Builder
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-script/language/symbol-table.ts b/src/mol-script/language/symbol-table.ts
index 6f47d15d9..3dec8616f 100644
--- a/src/mol-script/language/symbol-table.ts
+++ b/src/mol-script/language/symbol-table.ts
@@ -9,11 +9,11 @@ import structureQuery from './symbol-table/structure-query'
import { normalizeTable, symbolList } from './helpers'
import { MSymbol } from './symbol'
-const table = { core, structureQuery };
+const MolScriptSymbolTable = { core, structureQuery };
-normalizeTable(table);
+normalizeTable(MolScriptSymbolTable);
-export const SymbolList = symbolList(table);
+export const SymbolList = symbolList(MolScriptSymbolTable);
export const SymbolMap = (function() {
const map: { [id: string]: MSymbol | undefined } = Object.create(null);
@@ -21,4 +21,4 @@ export const SymbolMap = (function() {
return map;
})();
-export default table
\ No newline at end of file
+export { MolScriptSymbolTable }
\ No newline at end of file
diff --git a/src/mol-script/language/symbol-table/core.ts b/src/mol-script/language/symbol-table/core.ts
index b4164f613..fa0a801d9 100644
--- a/src/mol-script/language/symbol-table/core.ts
+++ b/src/mol-script/language/symbol-table/core.ts
@@ -41,6 +41,15 @@ function binRel<A extends Type, T extends Type>(src: A, target: T, description?:
}), target, description);
}
+export const TTargs = Arguments.Dictionary({
+ 0: Argument(Type.Num),
+ 1: Argument(Type.Num)
+})
+
+const XX = { test: Argument(Type.Str) };
+const t: Arguments.PropTypes<typeof XX> = 0 as any;
+t.test
+
const type = {
'@header': 'Types',
bool: symbol(Arguments.Dictionary({ 0: Argument(Type.AnyValue) }), Type.Bool, 'Convert a value to boolean.'),
diff --git a/src/mol-script/language/symbol.ts b/src/mol-script/language/symbol.ts
index c928809b9..de9b53665 100644
--- a/src/mol-script/language/symbol.ts
+++ b/src/mol-script/language/symbol.ts
@@ -31,7 +31,8 @@ export namespace Arguments {
map: { [P in keyof T]: Argument<T[P]> },
'@type': T
}
- export function Dictionary<Map extends { [key: string]: Argument<any> }>(map: Map): Arguments<{ [P in keyof Map]: Map[P]['type']['@type'] }> {
+ export type PropTypes<Map extends { [key: string]: Argument<any> }> = { [P in keyof Map]: Map[P]['type']['@type'] }
+ export function Dictionary<Map extends { [key: string]: Argument<any> }>(map: Map): Arguments<PropTypes<Map>> {
return { kind: 'dictionary', map, '@type': 0 as any };
}
diff --git a/src/mol-script/language/type.ts b/src/mol-script/language/type.ts
index 9a50889cb..90465ec4d 100644
--- a/src/mol-script/language/type.ts
+++ b/src/mol-script/language/type.ts
@@ -9,7 +9,7 @@ type Type<T = any> =
| Type.Container<T> | Type.Union<T> | Type.OneOf<T>
namespace Type {
- export interface Any { kind: 'any', '@type': any }
+ export interface Any { kind: 'any', '@type': any }
export interface Variable<T> { kind: 'variable', name: string, type: Type, isConstraint: boolean, '@type': any }
export interface AnyValue { kind: 'any-value', '@type': any }
export interface Value<T> { kind: 'value', namespace: string, name: string, parent?: Value<any>, '@type': T }
diff --git a/src/mol-script/runtime/environment.ts b/src/mol-script/runtime/environment.ts
index 54882d11a..7592071c8 100644
--- a/src/mol-script/runtime/environment.ts
+++ b/src/mol-script/runtime/environment.ts
@@ -1,37 +1,37 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-import { MSymbol } from '../language/symbol'
-import { SymbolRuntime } from './symbol'
-import { Macro } from './macro';
-import Expression from '../language/expression';
+// import { MSymbol } from '../language/symbol'
+// import { SymbolRuntime } from './symbol'
+// import { Macro } from './macro';
+// import Expression from '../language/expression';
-class Environment {
- readonly runtimeTable: SymbolRuntime.Table;
- readonly macroTable: Macro.Table = new Map<string, Macro>();
+// class Environment {
+// readonly runtimeTable: SymbolRuntime.Table;
+// readonly macroTable: Macro.Table = new Map<string, Macro>();
- addMacro(name: string, expression: Expression, argNames: ReadonlyArray<string>): Macro {
- const argIndex: Macro['argIndex'] = {};
- for (let i = 0; i < argNames.length; i++) argIndex[argNames[i]] = i;
- const macro: Macro = { expression, argIndex, argNames };
- this.macroTable.set(name, macro);
- return macro;
- }
+// addMacro(name: string, expression: Expression, argNames: ReadonlyArray<string>): Macro {
+// const argIndex: Macro['argIndex'] = {};
+// for (let i = 0; i < argNames.length; i++) argIndex[argNames[i]] = i;
+// const macro: Macro = { expression, argIndex, argNames };
+// this.macroTable.set(name, macro);
+// return macro;
+// }
- removeMacro(name: string) {
- this.macroTable.delete(name);
- }
+// removeMacro(name: string) {
+// this.macroTable.delete(name);
+// }
- addSymbolRuntime(symbol: MSymbol, runtime: SymbolRuntime) {
- this.runtimeTable.set(symbol.id, runtime);
- }
+// addSymbolRuntime(symbol: MSymbol, runtime: SymbolRuntime) {
+// this.runtimeTable.set(symbol.id, runtime);
+// }
- removeSymbolRuntime(symbol: MSymbol) {
- this.runtimeTable.delete(symbol.id);
- }
-}
+// removeSymbolRuntime(symbol: MSymbol) {
+// this.runtimeTable.delete(symbol.id);
+// }
+// }
-export default Environment
\ No newline at end of file
+// export default Environment
\ No newline at end of file
diff --git a/src/mol-script/runtime/expression.ts b/src/mol-script/runtime/expression.ts
index c6d38827a..f12841edf 100644
--- a/src/mol-script/runtime/expression.ts
+++ b/src/mol-script/runtime/expression.ts
@@ -1,25 +1,25 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-import Environment from './environment'
+// import Environment from './environment'
-type RuntimeExpression<T = any> = (env: Environment) => T
+// type RuntimeExpression<T = any> = (env: Environment) => T
-export interface ExpressionInfo {
- isConst?: boolean
-}
+// export interface ExpressionInfo {
+// isConst?: boolean
+// }
-namespace RuntimeExpression {
- export function constant<T>(c: T): RuntimeExpression<T> {
- return env => c;
- }
+// namespace RuntimeExpression {
+// export function constant<T>(c: T): RuntimeExpression<T> {
+// return env => c;
+// }
- export function func<T>(f: (env: Environment) => T): RuntimeExpression<T> {
- return env => f(env);
- }
-}
+// export function func<T>(f: (env: Environment) => T): RuntimeExpression<T> {
+// return env => f(env);
+// }
+// }
-export default RuntimeExpression
\ No newline at end of file
+// export default RuntimeExpression
\ No newline at end of file
diff --git a/src/mol-script/runtime/macro.ts b/src/mol-script/runtime/macro.ts
index 4d5128886..d6ef5f71d 100644
--- a/src/mol-script/runtime/macro.ts
+++ b/src/mol-script/runtime/macro.ts
@@ -1,81 +1,81 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-import Expression from '../language/expression';
+// import Expression from '../language/expression';
-interface Macro {
- readonly argNames: ReadonlyArray<string>,
- readonly argIndex: { [name: string]: number },
- readonly expression: Expression
-}
+// interface Macro {
+// readonly argNames: ReadonlyArray<string>,
+// readonly argIndex: { [name: string]: number },
+// readonly expression: Expression
+// }
-namespace Macro {
- export type Table = Map<string, Macro>
+// namespace Macro {
+// export type Table = Map<string, Macro>
- function subst(table: Table, expr: Expression, argIndex: { [name: string]: number }, args: ArrayLike<Expression>): Expression {
- if (Expression.isLiteral(expr)) return expr;
- if (Expression.isSymbol(expr)) {
- const idx = argIndex[expr.name];
- if (typeof idx !== 'undefined') return args[idx];
+// function subst(table: Table, expr: Expression, argIndex: { [name: string]: number }, args: ArrayLike<Expression>): Expression {
+// if (Expression.isLiteral(expr)) return expr;
+// if (Expression.isSymbol(expr)) {
+// const idx = argIndex[expr.name];
+// if (typeof idx !== 'undefined') return args[idx];
- if (table.has(expr.name)) {
- const macro = table.get(expr.name)!;
- if (macro.argNames.length === 0) return macro.expression;
- }
+// if (table.has(expr.name)) {
+// const macro = table.get(expr.name)!;
+// if (macro.argNames.length === 0) return macro.expression;
+// }
- return expr;
- }
+// return expr;
+// }
- const head = subst(table, expr.head, argIndex, args);
- const headChanged = head === expr.head;
- if (!expr.args) {
- return headChanged ? Expression.Apply(head) : expr;
- }
+// const head = subst(table, expr.head, argIndex, args);
+// const headChanged = head === expr.head;
+// if (!expr.args) {
+// return headChanged ? Expression.Apply(head) : expr;
+// }
- let argsChanged = false;
+// let argsChanged = false;
- if (Expression.isArgumentsArray(expr.args)) {
- let newArgs: Expression[] = [];
- for (let i = 0, _i = expr.args.length; i < _i; i++) {
- const oldArg = expr.args[i];
- const newArg = subst(table, oldArg, argIndex, args);
- if (oldArg !== newArg) argsChanged = true;
- newArgs[newArgs.length] = newArg;
- }
- if (!argsChanged) newArgs = expr.args;
+// if (Expression.isArgumentsArray(expr.args)) {
+// let newArgs: Expression[] = [];
+// for (let i = 0, _i = expr.args.length; i < _i; i++) {
+// const oldArg = expr.args[i];
+// const newArg = subst(table, oldArg, argIndex, args);
+// if (oldArg !== newArg) argsChanged = true;
+// newArgs[newArgs.length] = newArg;
+// }
+// if (!argsChanged) newArgs = expr.args;
- if (Expression.isSymbol(head) && table.has(head.name)) {
- const macro = table.get(head.name)!;
- if (macro.argNames.length === newArgs.length) {
- return subst(table, macro.expression, macro.argIndex, newArgs);
- }
- }
+// if (Expression.isSymbol(head) && table.has(head.name)) {
+// const macro = table.get(head.name)!;
+// if (macro.argNames.length === newArgs.length) {
+// return subst(table, macro.expression, macro.argIndex, newArgs);
+// }
+// }
- if (!headChanged && !argsChanged) return expr;
- return Expression.Apply(head, newArgs);
- } else {
+// if (!headChanged && !argsChanged) return expr;
+// return Expression.Apply(head, newArgs);
+// } else {
- let newArgs: any = {}
- for (const key of Object.keys(expr.args)) {
- const oldArg = expr.args[key];
- const newArg = subst(table, oldArg, argIndex, args);
- if (oldArg !== newArg) argsChanged = true;
- newArgs[key] = newArg;
- }
- if (!headChanged && !argsChanged) return expr;
- if (!argsChanged) newArgs = expr.args;
+// let newArgs: any = {}
+// for (const key of Object.keys(expr.args)) {
+// const oldArg = expr.args[key];
+// const newArg = subst(table, oldArg, argIndex, args);
+// if (oldArg !== newArg) argsChanged = true;
+// newArgs[key] = newArg;
+// }
+// if (!headChanged && !argsChanged) return expr;
+// if (!argsChanged) newArgs = expr.args;
- return Expression.Apply(head, newArgs);
- }
- }
+// return Expression.Apply(head, newArgs);
+// }
+// }
- export function substitute(table: Table, macro: Macro, args: ArrayLike<Expression>) {
- if (args.length === 0) return macro.expression;
- return subst(table, macro.expression, macro.argIndex, args);
- }
-}
+// export function substitute(table: Table, macro: Macro, args: ArrayLike<Expression>) {
+// if (args.length === 0) return macro.expression;
+// return subst(table, macro.expression, macro.argIndex, args);
+// }
+// }
-export { Macro }
\ No newline at end of file
+// export { Macro }
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/compiler.ts b/src/mol-script/runtime/query/compiler.ts
new file mode 100644
index 000000000..63598bb4c
--- /dev/null
+++ b/src/mol-script/runtime/query/compiler.ts
@@ -0,0 +1,151 @@
+/**
+ * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Expression from '../../language/expression';
+import { QueryContext, QueryFn, Structure } from 'mol-model/structure';
+import { MSymbol } from '../../language/symbol';
+
+export class QueryRuntimeTable {
+ private map = new Map<string, QuerySymbolRuntime>();
+
+ addSymbol(runtime: QuerySymbolRuntime) {
+ this.map.set(runtime.symbol.id, runtime);
+ }
+
+ getRuntime(id: string) {
+ return this.map.get(id);
+ }
+}
+
+export const DefaultQueryRuntimeTable = new QueryRuntimeTable();
+
+export class QueryCompilerCtx {
+ constQueryContext: QueryContext = new QueryContext(Structure.Empty);
+
+ constructor(public table: QueryRuntimeTable) {
+
+ }
+}
+
+export type ConstQuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
+export type QuerySymbolFn<S extends MSymbol = MSymbol> = (ctx: QueryContext, args: QueryRuntimeArguments<S>) => any
+
+
+export type QueryCompiledSymbolRuntime = { kind: 'const', value: any } | { kind: 'dynamic', runtime: QuerySymbolFn }
+
+export type CompiledQueryFn<T = any> = { isConst: boolean, fn: QueryFn }
+
+export namespace QueryCompiledSymbol {
+ export function Const(value: any): QueryCompiledSymbolRuntime {
+ return { kind: 'const', value }
+ }
+
+ export function Dynamic(runtime: QuerySymbolFn): QueryCompiledSymbolRuntime {
+ return { kind: 'dynamic', runtime };
+ }
+}
+
+export namespace CompiledQueryFn {
+ export function Const(value: any): CompiledQueryFn {
+ return { isConst: true, fn: ctx => value };
+ }
+
+ export function Dynamic(fn: QueryFn): CompiledQueryFn {
+ return { isConst: false, fn };
+ }
+}
+
+export interface QuerySymbolRuntime {
+ symbol: MSymbol,
+ compile(ctx: QueryCompilerCtx, args?: Expression.Arguments): CompiledQueryFn
+}
+
+export type QueryRuntimeArguments<S extends MSymbol> =
+ { length?: number } & { [P in keyof S['args']['@type']]: QueryFn<S['args']['@type'][P]> }
+
+export namespace QuerySymbolRuntime {
+ export function Const<S extends MSymbol<any>>(symbol: S, fn: ConstQuerySymbolFn<S>): QuerySymbolRuntime {
+ return new SymbolRuntimeImpl(symbol, fn, true);
+ }
+
+ export function Dynamic<S extends MSymbol<any>>(symbol: S, fn: QuerySymbolFn<S>): QuerySymbolRuntime {
+ return new SymbolRuntimeImpl(symbol, fn, false);
+ }
+}
+
+class SymbolRuntimeImpl<S extends MSymbol> implements QuerySymbolRuntime {
+ compile(ctx: QueryCompilerCtx, inputArgs?: Expression.Arguments): CompiledQueryFn {
+ let args: any, constArgs = false;
+ if (!inputArgs) {
+ args = void 0;
+ constArgs = true;
+ } else if (Expression.isArgumentsArray(inputArgs)) {
+ args = [];
+ constArgs = false;
+ for (const arg of inputArgs) {
+ const compiled = _compile(ctx, arg);
+ constArgs = constArgs && compiled.isConst;
+ args.push(compiled.fn);
+ }
+ } else {
+ args = Object.create(null);
+ constArgs = false;
+ for (const key of Object.keys(inputArgs)) {
+ const compiled = _compile(ctx, inputArgs[key]);
+ constArgs = constArgs && compiled.isConst;
+ args[key] = compiled.fn;
+ }
+ }
+
+ if (this.isConst) {
+ if (this.isConst && constArgs) {
+ return CompiledQueryFn.Const(this.fn(ctx.constQueryContext, args))
+ }
+
+ return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
+ }
+
+ return CompiledQueryFn.Dynamic(createDynamicFn(this.fn, args));
+ }
+
+ constructor(public symbol: S, private fn: QuerySymbolFn<S>, private isConst: boolean) {
+
+ }
+}
+
+function createDynamicFn<S extends MSymbol>(fn: QuerySymbolFn<S>, args: any): QueryFn {
+ return ctx => fn(ctx, args);
+}
+
+function _compile(ctx: QueryCompilerCtx, expression: Expression): CompiledQueryFn {
+ if (Expression.isLiteral(expression)) {
+ return CompiledQueryFn.Const(expression);
+ }
+
+ if (Expression.isSymbol(expression)) {
+ // TODO: is this ok in case of constants?
+ throw new Error('Cannot compile a symbol that is not applied.');
+ }
+
+ if (!Expression.isSymbol(expression.head)) {
+ throw new Error('Can only apply symbols.');
+ }
+
+ const compiler = ctx.table.getRuntime(expression.head.name);
+
+ if (!compiler) {
+ throw new Error(`Symbol '${expression.head.name}' is not implemented.`);
+ }
+
+ return compiler.compile(ctx, expression.args);
+}
+
+export function compile<T = any>(expression: Expression): QueryFn<T> {
+ const ctx = new QueryCompilerCtx(DefaultQueryRuntimeTable);
+ return _compile(ctx, expression).fn;
+}
+
+import './table'
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
new file mode 100644
index 000000000..d5c4217d7
--- /dev/null
+++ b/src/mol-script/runtime/query/table.ts
@@ -0,0 +1,65 @@
+/**
+ * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table';
+import { DefaultQueryRuntimeTable, QuerySymbolRuntime } from './compiler';
+
+import C = QuerySymbolRuntime.Const
+import D = QuerySymbolRuntime.Dynamic
+import { Queries, StructureProperties } from 'mol-model/structure';
+import { ElementSymbol } from 'mol-model/structure/model/types';
+
+const symbols = [
+ C(MolScript.core.math.add, (ctx, xs) => {
+ let ret = 0;
+ if (typeof xs.length === 'number') {
+ for (let i = 0, _i = xs.length; i < _i; i++) ret += xs[i](ctx);
+ } else {
+ for (const k of Object.keys(xs)) ret += xs[k](ctx);
+ }
+ return ret;
+ }),
+
+ // ============= RELATIONAL ================
+ C(MolScript.core.rel.eq, (ctx, v) => v[0](ctx) === v[1](ctx)),
+ C(MolScript.core.rel.neq, (ctx, v) => v[0](ctx) !== v[1](ctx)),
+ C(MolScript.core.rel.lt, (ctx, v) => v[0](ctx) < v[1](ctx)),
+ 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)),
+
+ // ============= TYPES ================
+ C(MolScript.structureQuery.type.elementSymbol, (ctx, v) => ElementSymbol(v[0](ctx))),
+
+ // ============= GENERATORS ================
+ D(MolScript.structureQuery.generator.atomGroups, (ctx, xs) => Queries.generators.atoms({
+ entityTest: xs['entity-test'],
+ chainTest: xs['chain-test'],
+ residueTest: xs['residue-test'],
+ atomTest: xs['atom-test'],
+ groupBy: xs['group-by']
+ })(ctx)),
+
+ // ============= 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 () {
+ for (const s of symbols) {
+ DefaultQueryRuntimeTable.addSymbol(s);
+ }
+})();
\ No newline at end of file
diff --git a/src/mol-script/runtime/symbol.ts b/src/mol-script/runtime/symbol.ts
index 5a53a4ba8..b70783330 100644
--- a/src/mol-script/runtime/symbol.ts
+++ b/src/mol-script/runtime/symbol.ts
@@ -1,32 +1,32 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-import Environment from './environment'
-import RuntimeExpression from './expression'
-import Expression from '../language/expression';
+// import Environment from './environment'
+// import RuntimeExpression from './expression'
+// import Expression from '../language/expression';
-type SymbolRuntime = SymbolRuntime.Dynamic | SymbolRuntime.Static
+// type SymbolRuntime = SymbolRuntime.Dynamic | SymbolRuntime.Static
-namespace SymbolRuntime {
- export interface Static {
- kind: 'static',
- readonly runtime: (env: Environment, args: Arguments) => any,
- readonly attributes: Attributes
- }
+// namespace SymbolRuntime {
+// export interface Static {
+// kind: 'static',
+// readonly runtime: (ctx: any, args: Arguments) => any,
+// readonly attributes: Attributes
+// }
- export interface Dynamic {
- kind: 'dynamic',
- readonly compile: (env: Environment, args: Expression.Arguments) => RuntimeExpression
- }
+// export interface Dynamic {
+// kind: 'dynamic',
+// readonly compile: (env: Environment, args: Expression.Arguments) => RuntimeExpression
+// }
- export interface Attributes { isStatic: boolean }
+// export interface Attributes { isStatic: boolean }
- export type Table = Map<string, SymbolRuntime>
+// export type Table = Map<string, SymbolRuntime>
- export type Arguments = ArrayLike<RuntimeExpression> | { [name: string]: RuntimeExpression | undefined }
-}
+// export type Arguments = ArrayLike<RuntimeExpression> | { [name: string]: RuntimeExpression | undefined }
+// }
-export { SymbolRuntime }
\ No newline at end of file
+// export { SymbolRuntime }
\ No newline at end of file
diff --git a/src/mol-script/script/mol-script/examples.ts b/src/mol-script/script/mol-script/examples.ts
index 7df280f8b..1f689f1d3 100644
--- a/src/mol-script/script/mol-script/examples.ts
+++ b/src/mol-script/script/mol-script/examples.ts
@@ -1,104 +1,104 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-export default [{
- name: 'Residues connected to HEM',
- value: `(sel.atom.is-connected-to
- sel.atom.res
- :target (sel.atom.res (= atom.label_comp_id HEM))
- ;; default bond test allows only covalent bonds
- :bond-test true
- :disjunct true)`
-}, {
- name: 'All C or N atoms in ALA residues',
- value: `(sel.atom.atom-groups
- :residue-test (= atom.auth_comp_id ALA)
- :atom-test (set.has (set _C _N) atom.el))`
-}, {
- name: 'Residues 130 to 180',
- value: `(sel.atom.res (in-range atom.resno 130 180))`
-}, {
- name: 'All residues within 5 ang from Fe atom',
- value: `(sel.atom.include-surroundings
- (sel.atom.atoms (= atom.el _Fe))
- :radius 5
- :as-whole-residues true)`
-}, {
- name: 'Cluster LYS residues within 5 ang',
- value: `(sel.atom.cluster
- (sel.atom.res (= atom.label_comp_id LYS))
- :max-distance 5)`
-}, {
- name: 'Residues with max b-factor < 45',
- value: `(sel.atom.pick sel.atom.res
- :test (< (atom.set.max atom.B_iso_or_equiv) 45))`
-}, {
- name: 'Atoms between 10 and 15 ang from Fe',
- value: `(sel.atom.within sel.atom.atoms
- :target (sel.atom.atoms (= atom.el _Fe))
- :min-radius 10
- :max-radius 15)`
-}, {
- name: 'HEM and 2 layers of connected residues',
- value: `(sel.atom.include-connected
- (sel.atom.res (= atom.label_comp_id HEM))
- ;; default bond test allows only covalent bonds
- ;; another option is to use :bond-test true to allow any connection
- :bond-test (bond.is metallic covalent)
- :layer-count 2
- :as-whole-residues true)`
-}, {
- name: 'All rings',
- value: `(sel.atom.rings)`
-}, {
- name: 'CCCCN and CCNCN rings',
- value: `(sel.atom.rings
- (ringfp _C _N _C _N _C)
- ;; the "rotation" of element symbols has no effect
- ;; the following is the same as (ringfp _C _C _C _C _N)
- (ringfp _C _C _C _N _C))`
-}, {
- name: 'Sheets',
- value: `(sel.atom.atom-groups
- :residue-test (atom.sec-struct.is sheet)
- :group-by (atom.key.sec-struct))`
-}, {
- name: 'Helices formed by at least 30 residues',
- value: `(sel.atom.pick
- (sel.atom.atom-groups
- :residue-test (atom.sec-struct.is helix)
- :group-by atom.key.sec-struct)
- :test (<= 30 (atom.set.count-query sel.atom.res)))`
-}, {
- name: 'Modified residues',
- value: `(sel.atom.res atom.is-modified)`
-}, {
- name: 'Atoms participating in metallic coordination',
- value: `(sel.atom.atoms
- (> (atom.bond-count :flags (bond-flags metallic)) 0))`
-}, {
- name: 'LYS and ALA residues that are between 2 and 5 ang apart',
- value: `(sel.atom.dist-cluster
- ;; upper triangular matrix are maximum distances of corresponding selections
- ;; lower triangular matrix are minumum distances of corresponding selections
- :matrix [
- [0 5]
- [2 0]
- ]
- :selections [
- (sel.atom.res (= atom.resname LYS))
- (sel.atom.res (= atom.resname ALA))
- ])`
-}, {
- name: 'Clusters of 3 LYS residues that are mutually no more than 5 ang apart',
- value: `(sel.atom.dist-cluster
- :matrix [[0 5 5] [0 0 5] [0 0 0]]
- :selections [
- (sel.atom.res (= atom.resname LYS))
- (sel.atom.res (= atom.resname LYS))
- (sel.atom.res (= atom.resname LYS))
- ])`
-}]
\ No newline at end of file
+// export default [{
+// name: 'Residues connected to HEM',
+// value: `(sel.atom.is-connected-to
+// sel.atom.res
+// :target (sel.atom.res (= atom.label_comp_id HEM))
+// ;; default bond test allows only covalent bonds
+// :bond-test true
+// :disjunct true)`
+// }, {
+// name: 'All C or N atoms in ALA residues',
+// value: `(sel.atom.atom-groups
+// :residue-test (= atom.auth_comp_id ALA)
+// :atom-test (set.has (set _C _N) atom.el))`
+// }, {
+// name: 'Residues 130 to 180',
+// value: `(sel.atom.res (in-range atom.resno 130 180))`
+// }, {
+// name: 'All residues within 5 ang from Fe atom',
+// value: `(sel.atom.include-surroundings
+// (sel.atom.atoms (= atom.el _Fe))
+// :radius 5
+// :as-whole-residues true)`
+// }, {
+// name: 'Cluster LYS residues within 5 ang',
+// value: `(sel.atom.cluster
+// (sel.atom.res (= atom.label_comp_id LYS))
+// :max-distance 5)`
+// }, {
+// name: 'Residues with max b-factor < 45',
+// value: `(sel.atom.pick sel.atom.res
+// :test (< (atom.set.max atom.B_iso_or_equiv) 45))`
+// }, {
+// name: 'Atoms between 10 and 15 ang from Fe',
+// value: `(sel.atom.within sel.atom.atoms
+// :target (sel.atom.atoms (= atom.el _Fe))
+// :min-radius 10
+// :max-radius 15)`
+// }, {
+// name: 'HEM and 2 layers of connected residues',
+// value: `(sel.atom.include-connected
+// (sel.atom.res (= atom.label_comp_id HEM))
+// ;; default bond test allows only covalent bonds
+// ;; another option is to use :bond-test true to allow any connection
+// :bond-test (bond.is metallic covalent)
+// :layer-count 2
+// :as-whole-residues true)`
+// }, {
+// name: 'All rings',
+// value: `(sel.atom.rings)`
+// }, {
+// name: 'CCCCN and CCNCN rings',
+// value: `(sel.atom.rings
+// (ringfp _C _N _C _N _C)
+// ;; the "rotation" of element symbols has no effect
+// ;; the following is the same as (ringfp _C _C _C _C _N)
+// (ringfp _C _C _C _N _C))`
+// }, {
+// name: 'Sheets',
+// value: `(sel.atom.atom-groups
+// :residue-test (atom.sec-struct.is sheet)
+// :group-by (atom.key.sec-struct))`
+// }, {
+// name: 'Helices formed by at least 30 residues',
+// value: `(sel.atom.pick
+// (sel.atom.atom-groups
+// :residue-test (atom.sec-struct.is helix)
+// :group-by atom.key.sec-struct)
+// :test (<= 30 (atom.set.count-query sel.atom.res)))`
+// }, {
+// name: 'Modified residues',
+// value: `(sel.atom.res atom.is-modified)`
+// }, {
+// name: 'Atoms participating in metallic coordination',
+// value: `(sel.atom.atoms
+// (> (atom.bond-count :flags (bond-flags metallic)) 0))`
+// }, {
+// name: 'LYS and ALA residues that are between 2 and 5 ang apart',
+// value: `(sel.atom.dist-cluster
+// ;; upper triangular matrix are maximum distances of corresponding selections
+// ;; lower triangular matrix are minumum distances of corresponding selections
+// :matrix [
+// [0 5]
+// [2 0]
+// ]
+// :selections [
+// (sel.atom.res (= atom.resname LYS))
+// (sel.atom.res (= atom.resname ALA))
+// ])`
+// }, {
+// name: 'Clusters of 3 LYS residues that are mutually no more than 5 ang apart',
+// value: `(sel.atom.dist-cluster
+// :matrix [[0 5 5] [0 0 5] [0 0 0]]
+// :selections [
+// (sel.atom.res (= atom.resname LYS))
+// (sel.atom.res (= atom.resname LYS))
+// (sel.atom.res (= atom.resname LYS))
+// ])`
+// }]
\ No newline at end of file
diff --git a/src/mol-script/script/mol-script/macro.ts b/src/mol-script/script/mol-script/macro.ts
index a2c9c5a7c..436e06bc6 100644
--- a/src/mol-script/script/mol-script/macro.ts
+++ b/src/mol-script/script/mol-script/macro.ts
@@ -1,39 +1,39 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// * @author Alexander Rose <alexander.rose@weirdbyte.de>
+// */
-import B from '../../language/builder'
+// import B from '../../language/builder'
-export function getPositionalArgs(args: any) {
- return Object.keys(args)
- .filter(k => !isNaN(k as any))
- .map(k => +k)
- .sort((a, b) => a - b)
- .map(k => args[k]);
-}
+// export function getPositionalArgs(args: any) {
+// return Object.keys(args)
+// .filter(k => !isNaN(k as any))
+// .map(k => +k)
+// .sort((a, b) => a - b)
+// .map(k => args[k]);
+// }
-export function tryGetArg(args: any, name: string | number, defaultValue?: any) {
- return (args && args[name] !== void 0) ? args[name] : defaultValue;
-}
+// export function tryGetArg(args: any, name: string | number, defaultValue?: any) {
+// return (args && args[name] !== void 0) ? args[name] : defaultValue;
+// }
-export function pickArgs(args: any, ...names: string[]) {
- const ret = Object.create(null);
- let count = 0;
- for (let k of Object.keys(args)) {
- if (names.indexOf(k) >= 0) {
- ret[k] = args[k];
- count++;
- }
- }
- return count ? ret : void 0;
-}
+// export function pickArgs(args: any, ...names: string[]) {
+// const ret = Object.create(null);
+// let count = 0;
+// for (let k of Object.keys(args)) {
+// if (names.indexOf(k) >= 0) {
+// ret[k] = args[k];
+// count++;
+// }
+// }
+// return count ? ret : void 0;
+// }
-export function aggregate(property: any, fn: any, initial?: any){
- return B.struct.atomSet.reduce({
- initial: initial !== void 0 ? initial : property,
- value: fn([ B.struct.slot.elementSetReduce(), property ])
- });
-}
\ No newline at end of file
+// export function aggregate(property: any, fn: any, initial?: any){
+// return B.struct.atomSet.reduce({
+// initial: initial !== void 0 ? initial : property,
+// value: fn([ B.struct.slot.elementSetReduce(), property ])
+// });
+// }
\ No newline at end of file
diff --git a/src/mol-script/script/mol-script/parser.ts b/src/mol-script/script/mol-script/parser.ts
index b313de302..f9452036a 100644
--- a/src/mol-script/script/mol-script/parser.ts
+++ b/src/mol-script/script/mol-script/parser.ts
@@ -1,178 +1,178 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { MonadicParser as P } from 'mol-util/monadic-parser'
-import Expression from '../../language/expression'
-import B from '../../language/builder'
-
-export function parseMolScript(input: string) {
- return Language.parse(input);
-}
-
-namespace Language {
- type AST = ASTNode.Expression[]
-
- namespace ASTNode {
- export type Expression = Str | Symb | List | Comment
-
- export interface Str {
- kind: 'string',
- value: string
- }
-
- export interface Symb {
- kind: 'symbol',
- value: string
- }
-
- export interface List {
- kind: 'list',
- bracket: '(' | '[' | '{',
- nodes: Expression[]
- }
-
- export interface Comment {
- kind: 'comment',
- value: string
- }
-
- export function str(value: string): Str { return { kind: 'string', value }; }
- export function symb(value: string): Symb { return { kind: 'symbol', value }; }
- export function list(bracket: '(' | '[' | '{', nodes: Expression[]): List { return { kind: 'list', bracket, nodes }; }
- export function comment(value: string): Comment { return { kind: 'comment', value } }
- }
-
- const ws = P.regexp(/[\n\r\s]*/);
- const Expr: P<ASTNode.Expression> = P.lazy(() => (P.alt(Str, List, Symb, Comment).trim(ws)));
- const Str = P.takeWhile(c => c !== '`').trim('`').map(ASTNode.str);
- const Symb = P.regexp(/[^()\[\]{};`,\n\r\s]+/).map(ASTNode.symb);
- const Comment = P.regexp(/\s*;+([^\n\r]*)\n/, 1).map(ASTNode.comment);
- const Args = Expr.many();
- const List1 = Args.wrap('(', ')').map(args => ASTNode.list('(', args));
- const List2 = Args.wrap('[', ']').map(args => ASTNode.list('[', args));
- const List3 = Args.wrap('{', '}').map(args => ASTNode.list('{', args));
- const List = P.alt(List1, List2, List3);
-
- const Expressions: P<AST> = Expr.many();
-
- function getAST(input: string) { return Expressions.tryParse(input); }
-
- function visitExpr(expr: ASTNode.Expression): Expression {
- switch (expr.kind) {
- case 'string': return expr.value;
- case 'symbol': {
- const value = expr.value;
- if (value.length > 1) {
- const fst = value.charAt(0);
- switch (fst) {
- case '.': return B.atomName(value.substr(1));
- case '_': return B.struct.type.elementSymbol([value.substr(1)]);
- }
- }
- if (value === 'true') return true;
- if (value === 'false') return false;
- if (isNumber(value)) return +value;
- return Expression.Symbol(value);
- }
- case 'list': {
- switch (expr.bracket) {
- case '[': return B.core.type.list(withoutComments(expr.nodes).map(visitExpr));
- case '{': return B.core.type.set(withoutComments(expr.nodes).map(visitExpr));
- case '(': {
- const head = visitExpr(expr.nodes[0]);
- return Expression.Apply(head, getArgs(expr.nodes));
- }
- }
- return 0 as any;
- }
- default: {
- throw new Error('should not happen');
- }
- }
- }
-
- function getArgs(nodes: ASTNode.Expression[]): Expression.Arguments | undefined {
- if (nodes.length <= 1) return void 0;
- if (!hasNamedArgs(nodes)) {
- const args: Expression[] = [];
- for (let i = 1, _i = nodes.length; i < _i; i++) {
- const n = nodes[i];
- if (n.kind === 'comment') continue;
- args[args.length] = visitExpr(n);
- }
- return args;
- }
- const args: { [name: string]: Expression } = {};
- let allNumeric = true;
- let pos = 0;
- for (let i = 1, _i = nodes.length; i < _i; i++) {
- const n = nodes[i];
- if (n.kind === 'comment') continue;
- if (n.kind === 'symbol' && n.value.length > 1 && n.value.charAt(0) === ':') {
- const name = n.value.substr(1);
- ++i;
- while (i < _i && nodes[i].kind === 'comment') { i++; }
- if (i >= _i) throw new Error(`There must be a value foolowed a named arg ':${name}'.`);
- args[name] = visitExpr(nodes[i]);
- if (isNaN(+name)) allNumeric = false;
- } else {
- args[pos++] = visitExpr(n);
- }
- }
- if (allNumeric) {
- const keys = Object.keys(args).map(a => +a).sort((a, b) => a - b);
- let isArray = true;
- for (let i = 0, _i = keys.length; i < _i; i++) {
- if (keys[i] !== i) {
- isArray = false;
- break;
- }
- }
- if (isArray) {
- const arrayArgs: Expression[] = [];
- for (let i = 0, _i = keys.length; i < _i; i++) {
- arrayArgs[i] = args[i];
- }
- return arrayArgs;
- }
- }
- return args;
- }
-
- function hasNamedArgs(nodes: ASTNode.Expression[]) {
- for (let i = 1, _i = nodes.length; i < _i; i++) {
- const n = nodes[i];
- if (n.kind === 'symbol' && n.value.length > 1 && n.value.charAt(0) === ':') return true;
- }
- return false;
- }
-
- function withoutComments(nodes: ASTNode.Expression[]) {
- let hasComment = false;
- for (let i = 0, _i = nodes.length; i < _i; i++) {
- if (nodes[i].kind === 'comment') {
- hasComment = true;
- break;
- }
- }
- if (!hasComment) return nodes;
- return nodes.filter(n => n.kind !== 'comment');
- }
-
- function isNumber(value: string) {
- return /-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/.test(value);
- }
-
- export function parse(input: string): Expression[] {
- const ast = getAST(input);
- const ret: Expression[] = [];
- for (const expr of ast) {
- if (expr.kind === 'comment') continue;
- ret[ret.length] = visitExpr(expr);
- }
- return ret;
- }
-}
\ No newline at end of file
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
+
+// import { MonadicParser as P } from 'mol-util/monadic-parser'
+// import Expression from '../../language/expression'
+// import B from '../../language/builder'
+
+// export function parseMolScript(input: string) {
+// return Language.parse(input);
+// }
+
+// namespace Language {
+// type AST = ASTNode.Expression[]
+
+// namespace ASTNode {
+// export type Expression = Str | Symb | List | Comment
+
+// export interface Str {
+// kind: 'string',
+// value: string
+// }
+
+// export interface Symb {
+// kind: 'symbol',
+// value: string
+// }
+
+// export interface List {
+// kind: 'list',
+// bracket: '(' | '[' | '{',
+// nodes: Expression[]
+// }
+
+// export interface Comment {
+// kind: 'comment',
+// value: string
+// }
+
+// export function str(value: string): Str { return { kind: 'string', value }; }
+// export function symb(value: string): Symb { return { kind: 'symbol', value }; }
+// export function list(bracket: '(' | '[' | '{', nodes: Expression[]): List { return { kind: 'list', bracket, nodes }; }
+// export function comment(value: string): Comment { return { kind: 'comment', value } }
+// }
+
+// const ws = P.regexp(/[\n\r\s]*/);
+// const Expr: P<ASTNode.Expression> = P.lazy(() => (P.alt(Str, List, Symb, Comment).trim(ws)));
+// const Str = P.takeWhile(c => c !== '`').trim('`').map(ASTNode.str);
+// const Symb = P.regexp(/[^()\[\]{};`,\n\r\s]+/).map(ASTNode.symb);
+// const Comment = P.regexp(/\s*;+([^\n\r]*)\n/, 1).map(ASTNode.comment);
+// const Args = Expr.many();
+// const List1 = Args.wrap('(', ')').map(args => ASTNode.list('(', args));
+// const List2 = Args.wrap('[', ']').map(args => ASTNode.list('[', args));
+// const List3 = Args.wrap('{', '}').map(args => ASTNode.list('{', args));
+// const List = P.alt(List1, List2, List3);
+
+// const Expressions: P<AST> = Expr.many();
+
+// function getAST(input: string) { return Expressions.tryParse(input); }
+
+// function visitExpr(expr: ASTNode.Expression): Expression {
+// switch (expr.kind) {
+// case 'string': return expr.value;
+// case 'symbol': {
+// const value = expr.value;
+// if (value.length > 1) {
+// const fst = value.charAt(0);
+// switch (fst) {
+// case '.': return B.atomName(value.substr(1));
+// case '_': return B.struct.type.elementSymbol([value.substr(1)]);
+// }
+// }
+// if (value === 'true') return true;
+// if (value === 'false') return false;
+// if (isNumber(value)) return +value;
+// return Expression.Symbol(value);
+// }
+// case 'list': {
+// switch (expr.bracket) {
+// case '[': return B.core.type.list(withoutComments(expr.nodes).map(visitExpr));
+// case '{': return B.core.type.set(withoutComments(expr.nodes).map(visitExpr));
+// case '(': {
+// const head = visitExpr(expr.nodes[0]);
+// return Expression.Apply(head, getArgs(expr.nodes));
+// }
+// }
+// return 0 as any;
+// }
+// default: {
+// throw new Error('should not happen');
+// }
+// }
+// }
+
+// function getArgs(nodes: ASTNode.Expression[]): Expression.Arguments | undefined {
+// if (nodes.length <= 1) return void 0;
+// if (!hasNamedArgs(nodes)) {
+// const args: Expression[] = [];
+// for (let i = 1, _i = nodes.length; i < _i; i++) {
+// const n = nodes[i];
+// if (n.kind === 'comment') continue;
+// args[args.length] = visitExpr(n);
+// }
+// return args;
+// }
+// const args: { [name: string]: Expression } = {};
+// let allNumeric = true;
+// let pos = 0;
+// for (let i = 1, _i = nodes.length; i < _i; i++) {
+// const n = nodes[i];
+// if (n.kind === 'comment') continue;
+// if (n.kind === 'symbol' && n.value.length > 1 && n.value.charAt(0) === ':') {
+// const name = n.value.substr(1);
+// ++i;
+// while (i < _i && nodes[i].kind === 'comment') { i++; }
+// if (i >= _i) throw new Error(`There must be a value foolowed a named arg ':${name}'.`);
+// args[name] = visitExpr(nodes[i]);
+// if (isNaN(+name)) allNumeric = false;
+// } else {
+// args[pos++] = visitExpr(n);
+// }
+// }
+// if (allNumeric) {
+// const keys = Object.keys(args).map(a => +a).sort((a, b) => a - b);
+// let isArray = true;
+// for (let i = 0, _i = keys.length; i < _i; i++) {
+// if (keys[i] !== i) {
+// isArray = false;
+// break;
+// }
+// }
+// if (isArray) {
+// const arrayArgs: Expression[] = [];
+// for (let i = 0, _i = keys.length; i < _i; i++) {
+// arrayArgs[i] = args[i];
+// }
+// return arrayArgs;
+// }
+// }
+// return args;
+// }
+
+// function hasNamedArgs(nodes: ASTNode.Expression[]) {
+// for (let i = 1, _i = nodes.length; i < _i; i++) {
+// const n = nodes[i];
+// if (n.kind === 'symbol' && n.value.length > 1 && n.value.charAt(0) === ':') return true;
+// }
+// return false;
+// }
+
+// function withoutComments(nodes: ASTNode.Expression[]) {
+// let hasComment = false;
+// for (let i = 0, _i = nodes.length; i < _i; i++) {
+// if (nodes[i].kind === 'comment') {
+// hasComment = true;
+// break;
+// }
+// }
+// if (!hasComment) return nodes;
+// return nodes.filter(n => n.kind !== 'comment');
+// }
+
+// function isNumber(value: string) {
+// return /-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/.test(value);
+// }
+
+// export function parse(input: string): Expression[] {
+// const ast = getAST(input);
+// const ret: Expression[] = [];
+// for (const expr of ast) {
+// if (expr.kind === 'comment') continue;
+// ret[ret.length] = visitExpr(expr);
+// }
+// return ret;
+// }
+// }
\ No newline at end of file
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index dbbf1c5f8..70b7028af 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -1,300 +1,300 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+// /**
+// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
-import { MSymbol, Arguments, Argument } from '../../language/symbol'
-import B from '../../language/builder'
-import * as M from './macro'
-import MolScript from '../../language/symbol-table'
-import Type from '../../language/type'
-import * as Struct from '../../language/symbol-table/structure-query'
-import Expression from '../../language/expression'
-import { UniqueArray } from 'mol-data/generic'
+// import { MSymbol, Arguments, Argument } from '../../language/symbol'
+// import B from '../../language/builder'
+// import * as M from './macro'
+// import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table'
+// import Type from '../../language/type'
+// import * as Struct from '../../language/symbol-table/structure-query'
+// import Expression from '../../language/expression'
+// import { UniqueArray } from 'mol-data/generic'
-export type MolScriptSymbol =
- | { kind: 'alias', aliases: string[], symbol: MSymbol }
- | { kind: 'macro', aliases: string[], symbol: MSymbol, translate: (args: any) => Expression }
+// export type MolScriptSymbol =
+// | { kind: 'alias', aliases: string[], symbol: MSymbol }
+// | { kind: 'macro', aliases: string[], symbol: MSymbol, translate: (args: any) => Expression }
-function Alias(symbol: MSymbol<any>, ...aliases: string[]): MolScriptSymbol { return { kind: 'alias', aliases, symbol }; }
-function Macro(symbol: MSymbol<any>, translate: (args: any) => Expression, ...aliases: string[]): MolScriptSymbol {
- symbol.info.namespace = 'molscript-macro';
- symbol.id = `molscript-macro.${symbol.info.name}`;
- return { kind: 'macro', symbol, translate, aliases: [symbol.info.name, ...aliases] };
-}
+// function Alias(symbol: MSymbol<any>, ...aliases: string[]): MolScriptSymbol { return { kind: 'alias', aliases, symbol }; }
+// function Macro(symbol: MSymbol<any>, translate: (args: any) => Expression, ...aliases: string[]): MolScriptSymbol {
+// symbol.info.namespace = 'molscript-macro';
+// symbol.id = `molscript-macro.${symbol.info.name}`;
+// return { kind: 'macro', symbol, translate, aliases: [symbol.info.name, ...aliases] };
+// }
-export function isMolScriptSymbol(x: any): x is MolScriptSymbol {
- return x.kind === 'alias' || x.kind === 'macro';
-}
+// export function isMolScriptSymbol(x: any): x is MolScriptSymbol {
+// return x.kind === 'alias' || x.kind === 'macro';
+// }
-export const SymbolTable = [
- [
- 'Core symbols',
- Alias(MolScript.core.type.bool, 'bool'),
- Alias(MolScript.core.type.num, 'num'),
- Alias(MolScript.core.type.str, 'str'),
- Alias(MolScript.core.type.regex, 'regex'),
- Alias(MolScript.core.type.list, 'list'),
- Alias(MolScript.core.type.set, 'set'),
+// export const SymbolTable = [
+// [
+// 'Core symbols',
+// Alias(MolScript.core.type.bool, 'bool'),
+// Alias(MolScript.core.type.num, 'num'),
+// Alias(MolScript.core.type.str, 'str'),
+// Alias(MolScript.core.type.regex, 'regex'),
+// Alias(MolScript.core.type.list, 'list'),
+// Alias(MolScript.core.type.set, 'set'),
- Alias(MolScript.core.type.compositeKey, 'composite-key'),
- Alias(MolScript.core.logic.not, 'not'),
- Alias(MolScript.core.logic.and, 'and'),
- Alias(MolScript.core.logic.or, 'or'),
- Alias(MolScript.core.ctrl.if, 'if'),
- Alias(MolScript.core.ctrl.fn, 'fn'),
- Alias(MolScript.core.ctrl.eval, 'eval'),
- Alias(MolScript.core.math.add, 'add', '+'),
- Alias(MolScript.core.math.sub, 'sub', '-'),
- Alias(MolScript.core.math.mult, 'mult', '*'),
- Alias(MolScript.core.math.div, 'div', '/'),
- Alias(MolScript.core.math.pow, 'pow', '**'),
- Alias(MolScript.core.math.mod, 'mod'),
- Alias(MolScript.core.math.min, 'min'),
- Alias(MolScript.core.math.max, 'max'),
- Alias(MolScript.core.math.floor, 'floor'),
- Alias(MolScript.core.math.ceil, 'ceil'),
- Alias(MolScript.core.math.roundInt, 'round'),
- Alias(MolScript.core.math.abs, 'abs'),
- Alias(MolScript.core.math.sqrt, 'sqrt'),
- Alias(MolScript.core.math.sin, 'sin'),
- Alias(MolScript.core.math.cos, 'cos'),
- Alias(MolScript.core.math.tan, 'tan'),
- Alias(MolScript.core.math.asin, 'asin'),
- Alias(MolScript.core.math.acos, 'acos'),
- Alias(MolScript.core.math.atan, 'atan'),
- Alias(MolScript.core.math.sinh, 'sinh'),
- Alias(MolScript.core.math.cosh, 'cosh'),
- Alias(MolScript.core.math.tanh, 'tanh'),
- Alias(MolScript.core.math.exp, 'exp'),
- Alias(MolScript.core.math.log, 'log'),
- Alias(MolScript.core.math.log10, 'log10'),
- Alias(MolScript.core.math.atan2, 'atan2'),
- Alias(MolScript.core.rel.eq, 'eq', '='),
- Alias(MolScript.core.rel.neq, 'neq', '!='),
- Alias(MolScript.core.rel.lt, 'lt', '<'),
- Alias(MolScript.core.rel.lte, 'lte', '<='),
- Alias(MolScript.core.rel.gr, 'gr', '>'),
- Alias(MolScript.core.rel.gre, 'gre', '>='),
- Alias(MolScript.core.rel.inRange, 'in-range'),
- Alias(MolScript.core.str.concat, 'concat'),
- Alias(MolScript.core.str.match, 'regex.match'),
- Alias(MolScript.core.list.getAt, 'list.get'),
- Alias(MolScript.core.set.has, 'set.has'),
- Alias(MolScript.core.set.isSubset, 'set.subset'),
- ],
- [
- 'Structure',
- [
- 'Types',
- Alias(MolScript.structureQuery.type.entityType, 'ent-type'),
- Alias(MolScript.structureQuery.type.authResidueId, 'auth-resid'),
- Alias(MolScript.structureQuery.type.labelResidueId, 'label-resid'),
- Alias(MolScript.structureQuery.type.ringFingerprint, 'ringfp'),
- Alias(MolScript.structureQuery.type.bondFlags, 'bond-flags'),
- ],
- [
- 'Slots',
- Alias(MolScript.structureQuery.slot.elementSetReduce, 'atom.set.reduce.value'),
- ],
- [
- 'Generators',
- Alias(MolScript.structureQuery.generator.atomGroups, 'sel.atom.atom-groups'),
- Alias(MolScript.structureQuery.generator.queryInSelection, 'sel.atom.query-in-selection'),
- Alias(MolScript.structureQuery.generator.rings, 'sel.atom.rings'),
- Alias(MolScript.structureQuery.generator.empty, 'sel.atom.empty'),
+// Alias(MolScript.core.type.compositeKey, 'composite-key'),
+// Alias(MolScript.core.logic.not, 'not'),
+// Alias(MolScript.core.logic.and, 'and'),
+// Alias(MolScript.core.logic.or, 'or'),
+// Alias(MolScript.core.ctrl.if, 'if'),
+// Alias(MolScript.core.ctrl.fn, 'fn'),
+// Alias(MolScript.core.ctrl.eval, 'eval'),
+// Alias(MolScript.core.math.add, 'add', '+'),
+// Alias(MolScript.core.math.sub, 'sub', '-'),
+// Alias(MolScript.core.math.mult, 'mult', '*'),
+// Alias(MolScript.core.math.div, 'div', '/'),
+// Alias(MolScript.core.math.pow, 'pow', '**'),
+// Alias(MolScript.core.math.mod, 'mod'),
+// Alias(MolScript.core.math.min, 'min'),
+// Alias(MolScript.core.math.max, 'max'),
+// Alias(MolScript.core.math.floor, 'floor'),
+// Alias(MolScript.core.math.ceil, 'ceil'),
+// Alias(MolScript.core.math.roundInt, 'round'),
+// Alias(MolScript.core.math.abs, 'abs'),
+// Alias(MolScript.core.math.sqrt, 'sqrt'),
+// Alias(MolScript.core.math.sin, 'sin'),
+// Alias(MolScript.core.math.cos, 'cos'),
+// Alias(MolScript.core.math.tan, 'tan'),
+// Alias(MolScript.core.math.asin, 'asin'),
+// Alias(MolScript.core.math.acos, 'acos'),
+// Alias(MolScript.core.math.atan, 'atan'),
+// Alias(MolScript.core.math.sinh, 'sinh'),
+// Alias(MolScript.core.math.cosh, 'cosh'),
+// Alias(MolScript.core.math.tanh, 'tanh'),
+// Alias(MolScript.core.math.exp, 'exp'),
+// Alias(MolScript.core.math.log, 'log'),
+// Alias(MolScript.core.math.log10, 'log10'),
+// Alias(MolScript.core.math.atan2, 'atan2'),
+// Alias(MolScript.core.rel.eq, 'eq', '='),
+// Alias(MolScript.core.rel.neq, 'neq', '!='),
+// Alias(MolScript.core.rel.lt, 'lt', '<'),
+// Alias(MolScript.core.rel.lte, 'lte', '<='),
+// Alias(MolScript.core.rel.gr, 'gr', '>'),
+// Alias(MolScript.core.rel.gre, 'gre', '>='),
+// Alias(MolScript.core.rel.inRange, 'in-range'),
+// Alias(MolScript.core.str.concat, 'concat'),
+// Alias(MolScript.core.str.match, 'regex.match'),
+// Alias(MolScript.core.list.getAt, 'list.get'),
+// Alias(MolScript.core.set.has, 'set.has'),
+// Alias(MolScript.core.set.isSubset, 'set.subset'),
+// ],
+// [
+// 'Structure',
+// [
+// 'Types',
+// Alias(MolScript.structureQuery.type.entityType, 'ent-type'),
+// Alias(MolScript.structureQuery.type.authResidueId, 'auth-resid'),
+// Alias(MolScript.structureQuery.type.labelResidueId, 'label-resid'),
+// Alias(MolScript.structureQuery.type.ringFingerprint, 'ringfp'),
+// Alias(MolScript.structureQuery.type.bondFlags, 'bond-flags'),
+// ],
+// [
+// 'Slots',
+// Alias(MolScript.structureQuery.slot.elementSetReduce, 'atom.set.reduce.value'),
+// ],
+// [
+// 'Generators',
+// Alias(MolScript.structureQuery.generator.atomGroups, 'sel.atom.atom-groups'),
+// Alias(MolScript.structureQuery.generator.queryInSelection, 'sel.atom.query-in-selection'),
+// Alias(MolScript.structureQuery.generator.rings, 'sel.atom.rings'),
+// Alias(MolScript.structureQuery.generator.empty, 'sel.atom.empty'),
- Macro(MSymbol('sel.atom.atoms', Arguments.Dictionary({
- 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to each atom.' })
- }), Struct.Types.ElementSelection, 'A selection of singleton atom sets.'),
- args => B.struct.generator.atomGroups({ 'atom-test': M.tryGetArg(args, 0, true) })),
+// Macro(MSymbol('sel.atom.atoms', Arguments.Dictionary({
+// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to each atom.' })
+// }), Struct.Types.ElementSelection, 'A selection of singleton atom sets.'),
+// args => B.struct.generator.atomGroups({ 'atom-test': M.tryGetArg(args, 0, true) })),
- Macro(MSymbol('sel.atom.res', Arguments.Dictionary({
- 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each residue.' })
- }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by residue.'),
- args => B.struct.generator.atomGroups({
- 'residue-test': M.tryGetArg(args, 0, true),
- 'group-by': B.ammp('residueKey')
- })),
+// Macro(MSymbol('sel.atom.res', Arguments.Dictionary({
+// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each residue.' })
+// }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by residue.'),
+// args => B.struct.generator.atomGroups({
+// 'residue-test': M.tryGetArg(args, 0, true),
+// 'group-by': B.ammp('residueKey')
+// })),
- Macro(MSymbol('sel.atom.chains', Arguments.Dictionary({
- 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
- }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by chain.'),
- args => B.struct.generator.atomGroups({
- 'chain-test': M.tryGetArg(args, 0, true),
- 'group-by': B.ammp('chainKey')
- })),
- ],
- [
- 'Modifiers',
- Alias(MolScript.structureQuery.modifier.queryEach, 'sel.atom.query-each'),
- Alias(MolScript.structureQuery.modifier.intersectBy, 'sel.atom.intersect-by'),
- Alias(MolScript.structureQuery.modifier.exceptBy, 'sel.atom.except-by'),
- Alias(MolScript.structureQuery.modifier.unionBy, 'sel.atom.union-by'),
- Alias(MolScript.structureQuery.modifier.union, 'sel.atom.union'),
- Alias(MolScript.structureQuery.modifier.cluster, 'sel.atom.cluster'),
- Alias(MolScript.structureQuery.modifier.includeSurroundings, 'sel.atom.include-surroundings'),
- Alias(MolScript.structureQuery.modifier.includeConnected, 'sel.atom.include-connected'),
- Alias(MolScript.structureQuery.modifier.expandProperty, 'sel.atom.expand-property'),
+// Macro(MSymbol('sel.atom.chains', Arguments.Dictionary({
+// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
+// }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by chain.'),
+// args => B.struct.generator.atomGroups({
+// 'chain-test': M.tryGetArg(args, 0, true),
+// 'group-by': B.ammp('chainKey')
+// })),
+// ],
+// [
+// 'Modifiers',
+// Alias(MolScript.structureQuery.modifier.queryEach, 'sel.atom.query-each'),
+// Alias(MolScript.structureQuery.modifier.intersectBy, 'sel.atom.intersect-by'),
+// Alias(MolScript.structureQuery.modifier.exceptBy, 'sel.atom.except-by'),
+// Alias(MolScript.structureQuery.modifier.unionBy, 'sel.atom.union-by'),
+// Alias(MolScript.structureQuery.modifier.union, 'sel.atom.union'),
+// Alias(MolScript.structureQuery.modifier.cluster, 'sel.atom.cluster'),
+// Alias(MolScript.structureQuery.modifier.includeSurroundings, 'sel.atom.include-surroundings'),
+// Alias(MolScript.structureQuery.modifier.includeConnected, 'sel.atom.include-connected'),
+// Alias(MolScript.structureQuery.modifier.expandProperty, 'sel.atom.expand-property'),
- Macro(MSymbol('sel.atom.around', Arguments.Dictionary({
- 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
- }), Struct.Types.ElementSelection, 'A selection of singleton atom sets with centers within "radius" of the center of any atom in the given selection.'),
- args => B.struct.modifier.exceptBy({
- '0': B.struct.filter.within({
- '0': B.struct.generator.atomGroups(), target: M.tryGetArg(args, 0), 'max-radius': M.tryGetArg(args, 'radius')
- }),
- by: M.tryGetArg(args, 0)
- }))
- ],
- [
- 'Filters',
- Alias(MolScript.structureQuery.filter.pick, 'sel.atom.pick'),
- Alias(MolScript.structureQuery.filter.withSameAtomProperties, 'sel.atom.with-same-atom-properties'),
- Alias(MolScript.structureQuery.filter.intersectedBy, 'sel.atom.intersected-by'),
- Alias(MolScript.structureQuery.filter.within, 'sel.atom.within'),
- Alias(MolScript.structureQuery.filter.isConnectedTo, 'sel.atom.is-connected-to'),
- ],
- [
- 'Combinators',
- Alias(MolScript.structureQuery.combinator.intersect, 'sel.atom.intersect'),
- Alias(MolScript.structureQuery.combinator.merge, 'sel.atom.merge'),
- Alias(MolScript.structureQuery.combinator.distanceCluster, 'sel.atom.dist-cluster'),
- ],
- [
- 'Atom Set Properties',
- Alias(MolScript.structureQuery.atomSet.atomCount, 'atom.set.atom-count'),
- Alias(MolScript.structureQuery.atomSet.countQuery, 'atom.set.count-query'),
- Alias(MolScript.structureQuery.atomSet.reduce, 'atom.set.reduce'),
- Alias(MolScript.structureQuery.atomSet.propertySet, 'atom.set.property'),
+// Macro(MSymbol('sel.atom.around', Arguments.Dictionary({
+// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
+// }), Struct.Types.ElementSelection, 'A selection of singleton atom sets with centers within "radius" of the center of any atom in the given selection.'),
+// args => B.struct.modifier.exceptBy({
+// '0': B.struct.filter.within({
+// '0': B.struct.generator.atomGroups(), target: M.tryGetArg(args, 0), 'max-radius': M.tryGetArg(args, 'radius')
+// }),
+// by: M.tryGetArg(args, 0)
+// }))
+// ],
+// [
+// 'Filters',
+// Alias(MolScript.structureQuery.filter.pick, 'sel.atom.pick'),
+// Alias(MolScript.structureQuery.filter.withSameAtomProperties, 'sel.atom.with-same-atom-properties'),
+// Alias(MolScript.structureQuery.filter.intersectedBy, 'sel.atom.intersected-by'),
+// Alias(MolScript.structureQuery.filter.within, 'sel.atom.within'),
+// Alias(MolScript.structureQuery.filter.isConnectedTo, 'sel.atom.is-connected-to'),
+// ],
+// [
+// 'Combinators',
+// Alias(MolScript.structureQuery.combinator.intersect, 'sel.atom.intersect'),
+// Alias(MolScript.structureQuery.combinator.merge, 'sel.atom.merge'),
+// Alias(MolScript.structureQuery.combinator.distanceCluster, 'sel.atom.dist-cluster'),
+// ],
+// [
+// 'Atom Set Properties',
+// Alias(MolScript.structureQuery.atomSet.atomCount, 'atom.set.atom-count'),
+// Alias(MolScript.structureQuery.atomSet.countQuery, 'atom.set.count-query'),
+// Alias(MolScript.structureQuery.atomSet.reduce, 'atom.set.reduce'),
+// Alias(MolScript.structureQuery.atomSet.propertySet, 'atom.set.property'),
- Macro(MSymbol('atom.set.max', Arguments.Dictionary({
- 0: Argument(Type.Num, { description: 'Numeric atom property.'})
- }), Type.Num, 'Maximum of the given property in the current atom set.'),
- args => M.aggregate(M.tryGetArg(args, 0), B.core.math.max)),
+// Macro(MSymbol('atom.set.max', Arguments.Dictionary({
+// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+// }), Type.Num, 'Maximum of the given property in the current atom set.'),
+// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.max)),
- Macro(MSymbol('atom.set.sum', Arguments.Dictionary({
- 0: Argument(Type.Num, { description: 'Numeric atom property.'})
- }), Type.Num, 'Sum of the given property in the current atom set.'),
- args => M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0)),
+// Macro(MSymbol('atom.set.sum', Arguments.Dictionary({
+// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+// }), Type.Num, 'Sum of the given property in the current atom set.'),
+// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0)),
- Macro(MSymbol('atom.set.avg', Arguments.Dictionary({
- 0: Argument(Type.Num, { description: 'Numeric atom property.'})
- }), Type.Num, 'Average of the given property in the current atom set.'),
- args => B.core.math.div([ M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0), B.struct.atomSet.atomCount() ])),
+// Macro(MSymbol('atom.set.avg', Arguments.Dictionary({
+// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+// }), Type.Num, 'Average of the given property in the current atom set.'),
+// args => B.core.math.div([ M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0), B.struct.atomSet.atomCount() ])),
- Macro(MSymbol('atom.set.min', Arguments.Dictionary({
- 0: Argument(Type.Num, { description: 'Numeric atom property.'})
- }), Type.Num, 'Minimum of the given property in the current atom set.'),
- args => M.aggregate(M.tryGetArg(args, 0), B.core.math.min))
- ],
- [
- 'Atom Properties',
- Alias(MolScript.structureQuery.atomProperty.core.elementSymbol, 'atom.el'),
- Alias(MolScript.structureQuery.atomProperty.core.vdw, 'atom.vdw'),
- Alias(MolScript.structureQuery.atomProperty.core.mass, 'atom.mass'),
- Alias(MolScript.structureQuery.atomProperty.core.atomicNumber, 'atom.atomic-number'),
- Alias(MolScript.structureQuery.atomProperty.core.x, 'atom.x'),
- Alias(MolScript.structureQuery.atomProperty.core.y, 'atom.y'),
- Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
- Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
- Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
+// Macro(MSymbol('atom.set.min', Arguments.Dictionary({
+// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+// }), Type.Num, 'Minimum of the given property in the current atom set.'),
+// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.min))
+// ],
+// [
+// 'Atom Properties',
+// Alias(MolScript.structureQuery.atomProperty.core.elementSymbol, 'atom.el'),
+// Alias(MolScript.structureQuery.atomProperty.core.vdw, 'atom.vdw'),
+// Alias(MolScript.structureQuery.atomProperty.core.mass, 'atom.mass'),
+// Alias(MolScript.structureQuery.atomProperty.core.atomicNumber, 'atom.atomic-number'),
+// Alias(MolScript.structureQuery.atomProperty.core.x, 'atom.x'),
+// Alias(MolScript.structureQuery.atomProperty.core.y, 'atom.y'),
+// Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
+// Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
+// Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
- Alias(MolScript.structureQuery.atomProperty.topology.connectedComponentKey, 'atom.key.molecule'),
+// Alias(MolScript.structureQuery.atomProperty.topology.connectedComponentKey, 'atom.key.molecule'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.authResidueId, 'atom.auth-resid'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.labelResidueId, 'atom.label-resid'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.residueKey, 'atom.key.res'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.chainKey, 'atom.key.chain'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.entityKey, 'atom.key.entity'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.isHet, 'atom.is-het'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.id, 'atom.id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_atom_id, 'atom.label_atom_id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_alt_id, 'atom.label_alt_id', 'atom.altloc'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_comp_id, 'atom.label_comp_id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_asym_id, 'atom.label_asym_id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_entity_id, 'atom.label_entity_id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.label_seq_id, 'atom.label_seq_id'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_atom_id, 'atom.auth_atom_id', 'atom.name'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_comp_id, 'atom.auth_comp_id', 'atom.resname'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_asym_id, 'atom.auth_asym_id', 'atom.chain'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_seq_id, 'atom.auth_seq_id', 'atom.resno'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_PDB_ins_code, 'atom.pdbx_PDB_ins_code', 'atom.inscode'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_formal_charge, 'atom.pdbx_formal_charge'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.occupancy, 'atom.occupancy'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.authResidueId, 'atom.auth-resid'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.labelResidueId, 'atom.label-resid'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.residueKey, 'atom.key.res'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.chainKey, 'atom.key.chain'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.entityKey, 'atom.key.entity'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.isHet, 'atom.is-het'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.id, 'atom.id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_atom_id, 'atom.label_atom_id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_alt_id, 'atom.label_alt_id', 'atom.altloc'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_comp_id, 'atom.label_comp_id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_asym_id, 'atom.label_asym_id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_entity_id, 'atom.label_entity_id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_seq_id, 'atom.label_seq_id'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_atom_id, 'atom.auth_atom_id', 'atom.name'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_comp_id, 'atom.auth_comp_id', 'atom.resname'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_asym_id, 'atom.auth_asym_id', 'atom.chain'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_seq_id, 'atom.auth_seq_id', 'atom.resno'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_PDB_ins_code, 'atom.pdbx_PDB_ins_code', 'atom.inscode'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_formal_charge, 'atom.pdbx_formal_charge'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.occupancy, 'atom.occupancy'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, 'atom.key.sec-struct'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, 'atom.key.sec-struct'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.isModified, 'atom.is-modified'),
- Alias(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, 'atom.modified-parent'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.isModified, 'atom.is-modified'),
+// Alias(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, 'atom.modified-parent'),
- Macro(MSymbol('atom.sec-struct.is', Arguments.List(Struct.Types.SecondaryStructureFlag), Type.Bool,
- `Test if the current atom is part of an secondary structure. Optionally specify allowed sec. struct. types: ${Type.oneOfValues(Struct.Types.SecondaryStructureFlag).join(', ')}`),
- args => B.core.flags.hasAny([B.struct.atomProperty.macromolecular.secondaryStructureFlags(), B.struct.type.secondaryStructureFlags(args)])),
- ],
- [
- 'Bond Properties',
- Alias(MolScript.structureQuery.bondProperty.order, 'bond.order'),
- Macro(MSymbol('bond.is', Arguments.List(Struct.Types.BondFlag), Type.Bool,
- `Test if the current bond has at least one (or all if partial = false) of the specified flags: ${Type.oneOfValues(Struct.Types.BondFlag).join(', ')}`),
- args => B.core.flags.hasAny([B.struct.bondProperty.flags(), B.struct.type.bondFlags(M.getPositionalArgs(args))])),
- ]
- ]
-];
+// Macro(MSymbol('atom.sec-struct.is', Arguments.List(Struct.Types.SecondaryStructureFlag), Type.Bool,
+// `Test if the current atom is part of an secondary structure. Optionally specify allowed sec. struct. types: ${Type.oneOfValues(Struct.Types.SecondaryStructureFlag).join(', ')}`),
+// args => B.core.flags.hasAny([B.struct.atomProperty.macromolecular.secondaryStructureFlags(), B.struct.type.secondaryStructureFlags(args)])),
+// ],
+// [
+// 'Bond Properties',
+// Alias(MolScript.structureQuery.bondProperty.order, 'bond.order'),
+// Macro(MSymbol('bond.is', Arguments.List(Struct.Types.BondFlag), Type.Bool,
+// `Test if the current bond has at least one (or all if partial = false) of the specified flags: ${Type.oneOfValues(Struct.Types.BondFlag).join(', ')}`),
+// args => B.core.flags.hasAny([B.struct.bondProperty.flags(), B.struct.type.bondFlags(M.getPositionalArgs(args))])),
+// ]
+// ]
+// ];
-const list: MolScriptSymbol[] = [];
+// const list: MolScriptSymbol[] = [];
-function makeList(xs: any[]) {
- for (const x of xs) {
- if (isMolScriptSymbol(x)) list.push(x);
- else if (x instanceof Array) makeList(x);
- }
-}
+// function makeList(xs: any[]) {
+// for (const x of xs) {
+// if (isMolScriptSymbol(x)) list.push(x);
+// else if (x instanceof Array) makeList(x);
+// }
+// }
-makeList(SymbolTable);
+// makeList(SymbolTable);
-const normalized = (function () {
- const symbolList: [string, MolScriptSymbol][] = [];
- const symbolMap: { [id: string]: MolScriptSymbol | undefined } = Object.create(null);
- const namedArgs = UniqueArray.create<string, string>();
- const constants = UniqueArray.create<string, string>();
+// const normalized = (function () {
+// const symbolList: [string, MolScriptSymbol][] = [];
+// const symbolMap: { [id: string]: MolScriptSymbol | undefined } = Object.create(null);
+// const namedArgs = UniqueArray.create<string, string>();
+// const constants = UniqueArray.create<string, string>();
- for (const s of list) {
- for (const a of s.aliases) {
- symbolList.push([a, s]);
- if (symbolMap[a]) throw new Error(`Alias '${a}' already in use.`);
- symbolMap[a] = s;
- }
- const args = s.symbol.args;
- if (args.kind !== 'dictionary') {
- if (args.type.kind === 'oneof') {
- Type.oneOfValues(args.type).forEach(v => UniqueArray.add(constants, v, v));
- }
- continue;
- }
- for (const a of Object.keys(args.map)) {
- if (isNaN(a as any)) UniqueArray.add(namedArgs, a, a);
- const arg = ((args.map as any)[a]) as Argument;
- if (arg.type.kind === 'oneof') {
- Type.oneOfValues(arg.type).forEach(v => UniqueArray.add(constants, v, v));
- }
- }
- }
+// for (const s of list) {
+// for (const a of s.aliases) {
+// symbolList.push([a, s]);
+// if (symbolMap[a]) throw new Error(`Alias '${a}' already in use.`);
+// symbolMap[a] = s;
+// }
+// const args = s.symbol.args;
+// if (args.kind !== 'dictionary') {
+// if (args.type.kind === 'oneof') {
+// Type.oneOfValues(args.type).forEach(v => UniqueArray.add(constants, v, v));
+// }
+// continue;
+// }
+// for (const a of Object.keys(args.map)) {
+// if (isNaN(a as any)) UniqueArray.add(namedArgs, a, a);
+// const arg = ((args.map as any)[a]) as Argument;
+// if (arg.type.kind === 'oneof') {
+// Type.oneOfValues(arg.type).forEach(v => UniqueArray.add(constants, v, v));
+// }
+// }
+// }
- return { symbolList, symbolMap, namedArgs: namedArgs.array, constants: constants.array }
-})();
+// return { symbolList, symbolMap, namedArgs: namedArgs.array, constants: constants.array }
+// })();
-export const MolScriptSymbols = list;
-export const Constants = normalized.constants;
-export const NamedArgs = normalized.namedArgs;
-export const SymbolMap = normalized.symbolMap;
-export const SymbolList = normalized.symbolList;
+// export const MolScriptSymbols = list;
+// export const Constants = normalized.constants;
+// export const NamedArgs = normalized.namedArgs;
+// export const SymbolMap = normalized.symbolMap;
+// export const SymbolList = normalized.symbolList;
-const sortedSymbols = SymbolList.map(s => s[0]).sort((a, b) => {
- if (a.length === b.length) return (a < b) as any;
- return a.length - b.length;
-});
-export default [...sortedSymbols, ...NamedArgs.map(a => ':' + a), ...Constants];
\ No newline at end of file
+// const sortedSymbols = SymbolList.map(s => s[0]).sort((a, b) => {
+// if (a.length === b.length) return (a < b) as any;
+// return a.length - b.length;
+// });
+// export default [...sortedSymbols, ...NamedArgs.map(a => ':' + a), ...Constants];
\ No newline at end of file
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 3b488f5f5..104c6c194 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -1,12 +1,17 @@
-import Examples from 'mol-script/script/mol-script/examples'
-import { parseMolScript } from 'mol-script/script/mol-script/parser'
-import * as util from 'util'
-//import { compileAST } from 'mol-script/script/mol-script/compile';
-
-for (const e of Examples) {
- const expr = parseMolScript(e.value)[0];
- console.log(e.name, util.inspect(expr, true, 10, true));
-}
+import { MolScriptBuilder } from 'mol-script/language/builder';
+import { compile } from 'mol-script/runtime/query/compiler';
+import { QueryContext, Structure, StructureQuery } from 'mol-model/structure';
+import { readCifFile, getModelsAndStructure } from '../apps/structure-info/model';
+
+// import Examples from 'mol-script/script/mol-script/examples'
+// import { parseMolScript } from 'mol-script/script/mol-script/parser'
+// import * as util from 'util'
+// //import { compileAST } from 'mol-script/script/mol-script/compile';
+
+// for (const e of Examples) {
+// const expr = parseMolScript(e.value)[0];
+// console.log(e.name, util.inspect(expr, true, 10, true));
+// }
// const exprs = parseMolScript(`(sel.atom.atom-groups
// :residue-test (= atom.auth_comp_id ALA)
// ;; ho ho ho
@@ -15,4 +20,32 @@ for (const e of Examples) {
// ((hi) (ho))`);
// console.log(util.inspect(exprs, true, 10, true));
-// //console.log(expr);
\ No newline at end of file
+// //console.log(expr);
+
+const expr = MolScriptBuilder.core.math.add([1, 2, 3]);
+const compiled = compile<number>(expr);
+const result = compiled(new QueryContext(Structure.Empty));
+console.log(result);
+
+async function testQ() {
+ const frame = await readCifFile('e:/test/quick/1cbs_updated.cif');
+ const { structure } = await getModelsAndStructure(frame);
+
+ const expr = MolScriptBuilder.struct.generator.atomGroups({
+ 'atom-test': MolScriptBuilder.core.rel.eq([
+ MolScriptBuilder.struct.atomProperty.core.elementSymbol(),
+ MolScriptBuilder.es('C')
+ ]),
+ 'residue-test': MolScriptBuilder.core.rel.eq([
+ MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(),
+ 'REA'
+ ])
+ });
+
+ const compiled = compile<StructureQuery>(expr);
+ const result = compiled(new QueryContext(structure));
+
+ console.log(result);
+}
+
+testQ();
\ No newline at end of file
diff --git a/tsconfig.json b/tsconfig.json
index 8da5b2ddc..48fb8c0dc 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -8,7 +8,8 @@
"noUnusedLocals": true,
"strictNullChecks": true,
"strictFunctionTypes": true,
- "keyofStringsOnly": true,
+ //"keyofStringsOnly": true,
+ // temp fix for immutable package: has(key: string): key is keyof TProps; => has(key: string | number | Symbol): key is keyof TProps;
//"downlevelIteration": true,
"jsx": "react",
"lib": [ "es6", "dom", "esnext.asynciterable", "es2016" ],
--
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