diff --git a/src/mol-base/collections/column.ts b/src/mol-base/collections/column.ts
index 39285a46b073378521f35cbd9bd87ba3afa0b370..7118f96d01a9eb1fe7d14650b420e9cd1444831d 100644
--- a/src/mol-base/collections/column.ts
+++ b/src/mol-base/collections/column.ts
@@ -81,6 +81,18 @@ namespace Column {
return arrayColumn(spec);
}
+ export function ofIntArray(array: ArrayLike<number>) {
+ return arrayColumn({ array, type: Type.int });
+ }
+
+ export function ofFloatArray(array: ArrayLike<number>) {
+ return arrayColumn({ array, type: Type.float });
+ }
+
+ export function ofStringArray(array: ArrayLike<string>) {
+ return arrayColumn({ array, type: Type.str });
+ }
+
export function window<T>(column: Column<T>, start: number, end: number) {
return windowColumn(column, start, end);
}
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index 32e3ce7c6560e3445bd6ccec2f4b3397672fa194..72d66a616d7b28579134782c12cef8a116040280 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -9,6 +9,11 @@ import HierarchyProperties from './model/properties/hierarchy'
import ConformationProperties from './model/properties/conformation'
import UUID from '../mol-base/utils/uuid'
+export interface Version {
+ hierarchy: UUID,
+ conformation: UUID
+}
+
/**
* Interface to the "source data" of the molecule.
*
@@ -25,10 +30,7 @@ interface Model extends Readonly<{
conformation: ConformationProperties,
// used for diffing.
- version: {
- data: UUID,
- conformation: UUID
- },
+ version: Version,
atomCount: number
}> { }
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index f72e96514a50235e18c57e5c96f7bffdf6e70128..64143337fd8c2a79f5ed774dd8108c670624c137 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -88,7 +88,7 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval, previous?: Mod
return {
...previous,
conformation: getConformation(data, bounds),
- version: { data: previous.version.data, conformation: newUUID() }
+ version: { hierarchy: previous.version.hierarchy, conformation: newUUID() }
};
}
@@ -104,7 +104,7 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval, previous?: Mod
model_num: data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
hierarchy: { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments },
conformation: getConformation(data, bounds),
- version: { data: newUUID(), conformation: newUUID() },
+ version: { hierarchy: newUUID(), conformation: newUUID() },
atomCount: Interval.size(bounds)
};
}
diff --git a/src/mol-data/model/properties/hierarchy.ts b/src/mol-data/model/properties/hierarchy.ts
index d77b2bfc53fee0bc5b584efd3317f18cc0fefa95..ac0c96fa37b75749c53bd367949c99e599725226 100644
--- a/src/mol-data/model/properties/hierarchy.ts
+++ b/src/mol-data/model/properties/hierarchy.ts
@@ -70,12 +70,12 @@ export interface Keys {
isMonotonous: boolean,
// assign a key to each residue index.
- residueKey: ArrayLike<number>,
+ residueKey: Column<number>,
// assign a key to each chain index
- chainKey: ArrayLike<number>,
+ chainKey: Column<number>,
// assigne a key to each chain index
// also index to the Entities table.
- entityKey: ArrayLike<number>,
+ entityKey: Column<number>,
findEntityKey(id: string): number,
findChainKey(entityId: string, label_asym_id: string): number,
diff --git a/src/mol-data/model/utils/hierarchy-keys.ts b/src/mol-data/model/utils/hierarchy-keys.ts
index 96f4306e9394e8e7170bb4b099121952d6405b1e..ae9f9a176f2101f4a5187c04e767a9a8e1bec29b 100644
--- a/src/mol-data/model/utils/hierarchy-keys.ts
+++ b/src/mol-data/model/utils/hierarchy-keys.ts
@@ -104,9 +104,9 @@ function create(data: Data, segments: Segments): Keys {
return {
isMonotonous: isMonotonous && checkMonotonous(entityKey) && checkMonotonous(chainKey) && checkMonotonous(residueKey),
- residueKey: residueKey,
- chainKey: chainKey,
- entityKey: entityKey,
+ residueKey: Column.ofIntArray(residueKey),
+ chainKey: Column.ofIntArray(chainKey),
+ entityKey: Column.ofIntArray(entityKey),
findEntityKey,
findChainKey,
findResidueKey
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
index 2a71a70378571b8a98e44cc7b287a43d2e29901f..577211510693ecdaac47380505dc95cdc011c62e 100644
--- a/src/mol-data/structure.ts
+++ b/src/mol-data/structure.ts
@@ -13,7 +13,7 @@ import * as Base from './structure/base'
// TODO: do "single model" version of the structure?
export interface Structure extends Readonly<{
- units: Readonly<{ [id: number]: Unit }>,
+ units: { readonly [id: number]: Unit },
atoms: AtomSet
}> { }
diff --git a/src/mol-data/structure/atom.ts b/src/mol-data/structure/atom.ts
index a15da5213b4fba7bd6cfc1f4e3ea234e5aa14ad3..7a6ef43aa18485e03dcee664642c34c2195f0f9c 100644
--- a/src/mol-data/structure/atom.ts
+++ b/src/mol-data/structure/atom.ts
@@ -5,9 +5,6 @@
*/
import Tuple from '../../mol-base/collections/integer/tuple'
-import Structure from '../structure'
-import Unit from './unit'
-import Model from '../model'
/** Atom pointer */
interface Atom { '@type': Tuple['@type'] }
@@ -20,19 +17,6 @@ namespace Atom {
export const index: (a: Atom) => number = Tuple.snd;
export const areEqual: (a: Atom, b: Atom) => boolean = Tuple.areEqual;
export const hashCode: (a: Atom) => number = Tuple.hashCode;
-
- /** All the information required to access atom properties */
- export interface Location {
- structure: Structure,
- unit: Unit,
- model: Model,
- atomIndex: number,
- residueIndex: number,
- chainIndex: number
- }
-
- export interface Property<T> { (location: Atom): T }
- export interface Predicate extends Property<boolean> { }
}
export default Atom
\ No newline at end of file
diff --git a/src/mol-data/structure/property.ts b/src/mol-data/structure/property.ts
new file mode 100644
index 0000000000000000000000000000000000000000..70f9a9d7fedc898960dc46b318e2edebe2b76620
--- /dev/null
+++ b/src/mol-data/structure/property.ts
@@ -0,0 +1,62 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Structure from '../structure'
+import Atom from './atom'
+import Unit from './unit'
+import Model from '../model'
+import Column from '../../mol-base/collections/column'
+
+/** Atom pointer */
+interface Property<T> { (location: Property.Location): T }
+
+namespace Property {
+ export interface Predicate extends Property<boolean> { }
+
+ /** All the information required to access atom properties */
+ export interface Location {
+ structure: Structure,
+ unit: Unit,
+ atomIndex: number,
+ residueIndex: number,
+ chainIndex: number
+ }
+
+ export function create(structure?: Structure, unit?: Unit): Location {
+ return {
+ structure: structure!,
+ unit: unit!,
+ atomIndex: 0,
+ residueIndex: 0,
+ chainIndex: 0
+ };
+ }
+
+ export function update(l: Location, structure: Structure, atom: Atom) {
+ const u = structure.units[Atom.unit(atom)];
+ const i = Atom.index(atom);
+ l.structure = structure;
+ l.unit = u;
+ l.atomIndex = i;
+ l.residueIndex = u.residueIndex[i];
+ l.chainIndex = u.chainIndex[i];
+ }
+
+ export function cachedAtomColumn<T>(col: (model: Model) => Column<T>): Property<T> {
+ let lastUnit: Unit | undefined = void 0;
+ let cached: ((row: number) => T) | undefined = void 0;
+ return function (location) {
+ if (location.unit === lastUnit && !!cached) return cached(location.atomIndex);
+ lastUnit = location.unit;
+ cached = col(lastUnit.model).value;
+ return cached(location.atomIndex);
+ };
+ }
+
+ // TODO: cached versions of other properties.
+}
+
+export default Property
\ No newline at end of file
diff --git a/src/mol-data/structure/unit.ts b/src/mol-data/structure/unit.ts
index ec81e9a7247f6e254bf01adcf6c5154a2267943d..c23c5f6b0ced2ef09f67154393f406f874b6b513 100644
--- a/src/mol-data/structure/unit.ts
+++ b/src/mol-data/structure/unit.ts
@@ -16,7 +16,11 @@ interface Unit extends Readonly<{
// Determines the operation applied to this unit.
// The transform and and inverse are baked into the "getPosition" function
- operator: Operator
+ operator: Operator,
+
+ // Cache residue and chain indices for fast access.
+ residueIndex: ArrayLike<number>,
+ chainIndex: ArrayLike<number>
}> {
// // returns the untransformed position. Used for spatial queries.
// getInvariantPosition(atom: number, slot: Vec3): Vec3
@@ -27,7 +31,8 @@ interface Unit extends Readonly<{
namespace Unit {
export function create(model: Model, operator: Operator): Unit {
- return { id: nextUnitId(), model, operator };
+ const h = model.hierarchy;
+ return { id: nextUnitId(), model, operator, residueIndex: h.residueSegments.segmentMap, chainIndex: h.chainSegments.segmentMap };
}
}