Tweaks

src/mol-data/structure/model.ts

@@ -5,7 +5,7 @@
  */
 
 import Model from './model/model'
-import * as Constants from './model/constants'
+import * as Types from './model/types'
 import Format from './model/format'
 
-export { Model, Constants, Format }
+export { Model, Types, Format }

src/mol-data/structure/model/formats/mmcif.ts

@@ -4,14 +4,15 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
+import { newUUID } from 'mol-base/utils/uuid'
+import { Column, Table } from 'mol-base/collections/database'
+import { Interval, Segmentation } from 'mol-base/collections/integer'
 import Format from '../format'
 import Model from '../model'
 import * as Hierarchy from '../properties/hierarchy'
 import Conformation from '../properties/conformation'
-import { Column, Table } from 'mol-base/collections/database'
-import { Interval, Segmentation } from 'mol-base/collections/integer'
-import { newUUID } from 'mol-base/utils/uuid'
 import findHierarchyKeys from '../utils/hierarchy-keys'
+import { ElementSymbol} from '../types'
 
 import mmCIF_Format = Format.mmCIF
 
@@ -47,7 +48,7 @@ function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets:
     const { atom_site } = data;
     const start = Interval.start(bounds), end = Interval.end(bounds);
     const atoms = Table.ofColumns(Hierarchy.AtomsSchema, {
-        type_symbol: Column.ofArray({ array: Column.mapToArray(Column.window(atom_site.type_symbol, start, end), Hierarchy.ElementSymbol), type: Column.Type.aliased<Hierarchy.ElementSymbol>(Column.Type.str) }),
+        type_symbol: Column.ofArray({ array: Column.mapToArray(Column.window(atom_site.type_symbol, start, end), ElementSymbol), type: Column.Type.aliased<ElementSymbol>(Column.Type.str) }),
         label_atom_id: Column.window(atom_site.label_atom_id, start, end),
         auth_atom_id: Column.window(atom_site.auth_atom_id, start, end),
         label_alt_id: Column.window(atom_site.label_alt_id, start, end),

src/mol-data/structure/model/properties/hierarchy.ts

@@ -7,12 +7,7 @@
 import { Column, Table } from 'mol-base/collections/database'
 import { Segmentation } from 'mol-base/collections/integer'
 import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
-
-const _esCache = Object.create(null);
-export interface ElementSymbol extends String { '@type': 'element-symbol' }
-export function ElementSymbol(s: string): ElementSymbol {
-    return _esCache[s] || (_esCache[s] = s.toUpperCase());
-}
+import { ElementSymbol} from '../types'
 
 export const AtomsSchema = {
     type_symbol: Column.Type.aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),

src/mol-data/structure/model/constants.ts → src/mol-data/structure/model/types.ts

@@ -7,6 +7,12 @@
 
 import BitFlags from 'mol-base/utils/bit-flags'
 
+const _esCache = Object.create(null);
+export interface ElementSymbol extends String { '@type': 'element-symbol' }
+export function ElementSymbol(s: string): ElementSymbol {
+    return _esCache[s] || (_esCache[s] = s.toUpperCase());
+}
+
 export const enum EntityType {
     Unknown = 'unknown',
     Polymer = 'polymer',

src/mol-data/structure/query/predicates.ts

@@ -8,7 +8,7 @@ import { Atom } from '../structure'
 import P from './properties'
 
 namespace Predicates {
-    interface SetLike<A> { has(v: A): boolean }
+    export interface SetLike<A> { has(v: A): boolean }
     function isSetLike<A>(x: any): x is SetLike<A> { return !!x && !!x.has }
 
     export function eq<A>(p: Atom.Property<A>, value: A): Atom.Predicate { return l => p(l) === value; }
@@ -21,6 +21,7 @@ namespace Predicates {
         if (isSetLike(values)) {
             return l => values.has(p(l));
         } else {
+            if (values.length === 0) return P.constant.false;
             const set = new Set<A>();
             for (let i = 0; i < values.length; i++) set.add(values[i]);
             return l => set.has(p(l));

src/mol-io/reader/cif/schema/utils.ts

@@ -7,7 +7,7 @@ export function getFieldType (type: string, values?: string[]) {
         case 'code':
         case 'ucode':
             if (values && values.length) {
-                return `str as Field.Schema<'${values.join("'|'")}'>`
+                return `str as Field.Schema<'${values.join(`'|'`)}'>`
             } else {
                 return 'str'
             }

src/perf-tests/structure.ts

@@ -259,12 +259,13 @@ export namespace PropertyAccess {
         //const set =  new Set(['A', 'B', 'C', 'D']);
         //const q = Q.generators.atomGroups({ atomTest: l => auth_seq_id(l) < 3 });
         const q = Q.generators.atoms({ atomTest: Q.pred.eq(Q.props.residue.auth_comp_id, 'ALA') });
+        const P = Q.props
         //const q0 = Q.generators.atoms({ atomTest: l => auth_comp_id(l) === 'ALA' });
         const q1 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' });
         const q2 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: Q.props.residue.key });
         const q3 = Q.generators.atoms({
-            chainTest: Q.pred.inSet(Q.props.chain.auth_asym_id, ['A', 'B', 'C', 'D']),
-            residueTest: Q.pred.eq(Q.props.residue.auth_comp_id, 'ALA')
+            chainTest: Q.pred.inSet(P.chain.auth_asym_id, ['A', 'B', 'C', 'D']),
+            residueTest: Q.pred.eq(P.residue.auth_comp_id, 'ALA')
         });
         q(structures[0]);
         console.time('q1')

tslint.json

@@ -8,7 +8,7 @@
         "no-var-keyword": true,
         "ordered-imports": [false],
         "trailing-comma": [false],
-        "class-name": true,
+        "class-name": false,
         "comment-format": [
             true,
             "check-space"