From ed28bf3d3670ce4a08846c974b077cbddaed0a9e Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 2 Nov 2017 00:30:17 +0100
Subject: [PATCH] refactoring
---
.../collections/integer/impl/ordered-set.ts | 2 +-
.../collections/integer/impl/sorted-array.ts | 2 +-
.../collections/integer/sorted-array.ts | 3 +-
src/mol-base/collections/iterator.ts | 6 +-
src/mol-base/utils/bit-flags.ts | 4 ++
src/mol-data/model/properties/conformation.ts | 4 +-
src/mol-data/structure.ts | 4 +-
src/mol-data/structure/atom-set.ts | 2 +-
src/mol-data/structure/atom-set/properties.ts | 4 ++
src/mol-data/structure/atom.ts | 13 ++++
src/mol-data/structure/base.ts | 4 +-
src/mol-data/structure/property.ts | 69 -------------------
src/perf-tests/structure.ts | 63 +++++++++--------
13 files changed, 65 insertions(+), 115 deletions(-)
delete mode 100644 src/mol-data/structure/property.ts
diff --git a/src/mol-base/collections/integer/impl/ordered-set.ts b/src/mol-base/collections/integer/impl/ordered-set.ts
index dab3f4db5..255c7772f 100644
--- a/src/mol-base/collections/integer/impl/ordered-set.ts
+++ b/src/mol-base/collections/integer/impl/ordered-set.ts
@@ -248,7 +248,7 @@ function subtractIS(a: I, b: S) {
let offset = 0;
for (let i = min; i < fst; i++) ret[offset++] = i;
for (let i = fst; i <= last; i++) {
- if (S.indexOfInterval(b, i, interval) < 0) ret[offset++] = i;
+ if (S.indexOfInInterval(b, i, interval) < 0) ret[offset++] = i;
}
for (let i = last + 1; i <= max; i++) ret[offset++] = i;
return ofSortedArray(ret);
diff --git a/src/mol-base/collections/integer/impl/sorted-array.ts b/src/mol-base/collections/integer/impl/sorted-array.ts
index 27debf6fc..8056ad029 100644
--- a/src/mol-base/collections/integer/impl/sorted-array.ts
+++ b/src/mol-base/collections/integer/impl/sorted-array.ts
@@ -35,7 +35,7 @@ export function indexOf(xs: Nums, v: number) {
const l = xs.length;
return l === 0 ? -1 : xs[0] <= v && v <= xs[l - 1] ? binarySearchRange(xs, v, 0, l) : -1;
}
-export function indexOfInterval(xs: Nums, v: number, bounds: Interval) {
+export function indexOfInInterval(xs: Nums, v: number, bounds: Interval) {
const l = xs.length;
const s = Interval.start(bounds), e = Interval.end(bounds);
return l === 0 || e <= s ? -1 : xs[s] <= v && v <= xs[e - 1] ? binarySearchRange(xs, v, s, e) : -1;
diff --git a/src/mol-base/collections/integer/sorted-array.ts b/src/mol-base/collections/integer/sorted-array.ts
index 4f38bf9a6..701ea8ea3 100644
--- a/src/mol-base/collections/integer/sorted-array.ts
+++ b/src/mol-base/collections/integer/sorted-array.ts
@@ -16,8 +16,7 @@ namespace SortedArray {
export const has: (array: SortedArray, x: number) => boolean = Impl.has as any;
export const indexOf: (array: SortedArray, x: number) => number = Impl.indexOf as any;
- export const indexOfInterval: (array: SortedArray, x: number, bounds: Interval) => number = Impl.indexOfInterval as any;
- //export const getAt: (array: SortedArray, i: number) => number = Impl.getAt as any;
+ export const indexOfInInterval: (array: SortedArray, x: number, bounds: Interval) => number = Impl.indexOfInInterval as any;
export const start: (array: SortedArray) => number = Impl.start as any;
export const end: (array: SortedArray) => number = Impl.end as any;
diff --git a/src/mol-base/collections/iterator.ts b/src/mol-base/collections/iterator.ts
index 9d4ff64d6..6b5906801 100644
--- a/src/mol-base/collections/iterator.ts
+++ b/src/mol-base/collections/iterator.ts
@@ -5,12 +5,10 @@
*/
/**
- * ES6 compatible iterator.
- *
- * "Idiomatic" usage is to use the move function, because it does not make any allocations.
+ * "Idiomatic" usage:
*
* const it = ...;
- * while (it.hasNext) { const v = it.move(); ... }
+ * while (it.hasNext) { const v = it.move(); ... }
*/
interface Iterator<T> {
readonly hasNext: boolean,
diff --git a/src/mol-base/utils/bit-flags.ts b/src/mol-base/utils/bit-flags.ts
index e5cd20290..acf1fc2f5 100644
--- a/src/mol-base/utils/bit-flags.ts
+++ b/src/mol-base/utils/bit-flags.ts
@@ -7,7 +7,11 @@
interface BitFlags<Flags> { '@type': Flags }
namespace BitFlags {
+ export function create<F>(flags: F): BitFlags<F> { return flags as any; }
+
export function has<F>(flags: BitFlags<F>, flag: F) { return ((flags as any) & (flag as any)) !== 0; }
+ // toCheck must be non-zero
+ export function hasAll<F>(flags: BitFlags<F>, toCheck: BitFlags<F>) { return !!toCheck && ((flags as any) & (toCheck as any)) === (toCheck as any); }
}
export default BitFlags
\ No newline at end of file
diff --git a/src/mol-data/model/properties/conformation.ts b/src/mol-data/model/properties/conformation.ts
index f023ba707..7ea3c5243 100644
--- a/src/mol-data/model/properties/conformation.ts
+++ b/src/mol-data/model/properties/conformation.ts
@@ -11,13 +11,15 @@ interface Conformation {
id: UUID,
// ID is part of conformation because mmCIF is a leaky abstraction
- // thats assigns different atom ids to corresponding atoms in different models
+ // that assigns different atom ids to corresponding atoms in different models
// ... go figure.
atomId: Column<number>,
occupancy: Column<number>,
B_iso_or_equiv: Column<number>
+ // Coordinates. Generally, not to be accessed directly because the coordinate might be
+ // transformed by an operator. Use Unit.getPosition instead.
__x: ArrayLike<number>,
__y: ArrayLike<number>,
__z: ArrayLike<number>
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
index 577211510..4f7f15083 100644
--- a/src/mol-data/structure.ts
+++ b/src/mol-data/structure.ts
@@ -12,12 +12,12 @@ import * as Base from './structure/base'
//import Operator from './structure/operator'
// TODO: do "single model" version of the structure?
-export interface Structure extends Readonly<{
+interface Structure extends Readonly<{
units: { readonly [id: number]: Unit },
atoms: AtomSet
}> { }
-export namespace Structure {
+namespace Structure {
export const Empty = Base.Empty;
export const ofModel = Base.ofModel;
diff --git a/src/mol-data/structure/atom-set.ts b/src/mol-data/structure/atom-set.ts
index d2788a29a..a0524ecdf 100644
--- a/src/mol-data/structure/atom-set.ts
+++ b/src/mol-data/structure/atom-set.ts
@@ -46,7 +46,7 @@ namespace AtomSet {
// TODO: bounding sphere
// TODO: distance, areWithIn?
// TODO: check connected
- // TODO: add "parent" property? how to avoid using too much memory? Transitive parents?
+ // TODO: add "parent" property? how to avoid using too much memory? Transitive parents? Parent unlinking?
}
interface AtomSet { '@type': 'atom-set' }
diff --git a/src/mol-data/structure/atom-set/properties.ts b/src/mol-data/structure/atom-set/properties.ts
index d13a9ee15..6e5dfe593 100644
--- a/src/mol-data/structure/atom-set/properties.ts
+++ b/src/mol-data/structure/atom-set/properties.ts
@@ -4,3 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+// TODO: bounding sphere
+// TODO: distance, areWithIn?
+// TODO: check connected
+// TODO: add "parent" property? how to avoid using too much memory? Transitive parents? Parent unlinking?
\ No newline at end of file
diff --git a/src/mol-data/structure/atom.ts b/src/mol-data/structure/atom.ts
index 7a6ef43aa..5dfb6d5da 100644
--- a/src/mol-data/structure/atom.ts
+++ b/src/mol-data/structure/atom.ts
@@ -5,6 +5,8 @@
*/
import Tuple from '../../mol-base/collections/integer/tuple'
+import Unit from './unit'
+import Structure from '../structure'
/** Atom pointer */
interface Atom { '@type': Tuple['@type'] }
@@ -17,6 +19,17 @@ 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 { unit: Unit, atom: number }
+ export function Location(): Location { return { unit: {} as any, atom: 0 }; }
+ export interface Property<T> { (location: Location): T }
+ export interface Predicate extends Property<boolean> { }
+
+ export function setLocation(structure: Structure, l: Location, atom: Atom) {
+ l.unit = structure.units[unit(atom)];
+ l.atom = index(atom);
+ }
}
export default Atom
\ No newline at end of file
diff --git a/src/mol-data/structure/base.ts b/src/mol-data/structure/base.ts
index 1ef19f3db..9732c6a75 100644
--- a/src/mol-data/structure/base.ts
+++ b/src/mol-data/structure/base.ts
@@ -11,7 +11,7 @@ import Operator from './operator'
import AtomSet from './atom-set'
import OrderedSet from '../../mol-base/collections/integer/ordered-set'
-class Builder {
+export class StructureBuilder {
private units = Object.create(null);
private atoms = Object.create(null);
@@ -25,7 +25,7 @@ export const Empty: Structure = { units: {}, atoms: AtomSet.Empty };
export function ofModel(model: Model): Structure {
const chains = model.hierarchy.chainSegments;
- const builder = new Builder();
+ const builder = new StructureBuilder();
for (let c = 0; c < chains.count; c++) {
const unit = Unit.create(model, Operator.Identity);
diff --git a/src/mol-data/structure/property.ts b/src/mol-data/structure/property.ts
deleted file mode 100644
index 42b85e0b6..000000000
--- a/src/mol-data/structure/property.ts
+++ /dev/null
@@ -1,69 +0,0 @@
-/**
- * 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,
- // hierarchy: Model['hierarchy'],
- // conformation: Model['conformation'],
- atomIndex: number,
- // residueIndex: number,
- // chainIndex: number
- }
-
- export function createLocation(): Location {
- return {
- //structure: structure!,
- unit: {} as any,
- //hierarchy: (!unit ? void 0 : unit.model.hierarchy)!,
- //conformation: (!unit ? void 0 : unit.model.conformation)!,
- 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];
- throw 'not implemented'
- }
-
- export function naive<T>(p: Property<T>) { return p; }
-
- 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/perf-tests/structure.ts b/src/perf-tests/structure.ts
index ec9a406c2..88727ac30 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -12,7 +12,6 @@ import CIF from '../mol-io/reader/cif'
import buildModels from '../mol-data/model/builders/mmcif'
import { ofModel } from '../mol-data/structure/base'
-import Property from '../mol-data/structure/property'
import Model from '../mol-data/Model'
import Structure from '../mol-data/structure'
import OrdSet from '../mol-base/collections/integer/ordered-set'
@@ -80,10 +79,10 @@ export namespace PropertyAccess {
return s;
}
- function sumProperty(structure: Structure, p: Property<number>) {
+ function sumProperty(structure: Structure, p: Atom.Property<number>) {
const { atoms, units } = structure;
const unitIds = AtomSet.unitIds(atoms);
- const l = Property.createLocation();
+ const l = Atom.Location();
let s = 0;
@@ -92,7 +91,7 @@ export namespace PropertyAccess {
const set = AtomSet.unitGetByIndex(atoms, i);
for (let j = 0, _j = OrdSet.size(set); j < _j; j++) {
- l.atomIndex = OrdSet.getAt(set, j);
+ l.atom = OrdSet.getAt(set, j);
s += p(l);
}
}
@@ -100,10 +99,10 @@ export namespace PropertyAccess {
return s;
}
- function sumPropertySegmented(structure: Structure, p: Property<number>) {
+ function sumPropertySegmented(structure: Structure, p: Atom.Property<number>) {
const { atoms, units } = structure;
const unitIds = AtomSet.unitIds(atoms);
- const l = Property.createLocation();
+ const l = Atom.Location();
let s = 0;
@@ -120,7 +119,7 @@ export namespace PropertyAccess {
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- l.atomIndex = OrdSet.getAt(set, j);
+ l.atom = OrdSet.getAt(set, j);
s += p(l);
}
}
@@ -130,10 +129,10 @@ export namespace PropertyAccess {
return s;
}
- function sumPropertyResidue(structure: Structure, p: Property<number>) {
+ function sumPropertyResidue(structure: Structure, p: Atom.Property<number>) {
const { atoms, units } = structure;
const unitIds = AtomSet.unitIds(atoms);
- const l = Property.createLocation();
+ const l = Atom.Location();
let s = 0;
@@ -143,7 +142,7 @@ export namespace PropertyAccess {
const set = AtomSet.unitGetByIndex(atoms, i);
const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set);
while (residuesIt.hasNext) {
- l.atomIndex = OrdSet.getAt(set, residuesIt.move().start);
+ l.atom = OrdSet.getAt(set, residuesIt.move().start);
s += p(l);
}
}
@@ -151,16 +150,16 @@ export namespace PropertyAccess {
return s;
}
- function sumPropertyAtomSetIt(structure: Structure, p: Property<number>) {
+ function sumPropertyAtomSetIt(structure: Structure, p: Atom.Property<number>) {
const { atoms, units } = structure;
let s = 0;
const atomsIt = AtomSet.atoms(atoms);
- const l = Property.createLocation();
+ const l = Atom.Location();
while (atomsIt.hasNext) {
const a = atomsIt.move();
l.unit = units[Atom.unit(a)];
- l.atomIndex = Atom.index(a);
+ l.atom = Atom.index(a);
s += p(l);
}
return s;
@@ -186,7 +185,7 @@ export namespace PropertyAccess {
// while (residuesIt.hasNext) {
// const residueSegment = residuesIt.move();
// for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- // l.atomIndex = OrdSet.getAt(set, j);
+ // l.atom = OrdSet.getAt(set, j);
// s += p(l);
// }
// }
@@ -232,7 +231,7 @@ export namespace PropertyAccess {
// for (let j = 0, _j = OrdSet.size(set); j < _j; j++) {
// const aI = OrdSet.getAt(set, j);
- // l.atomIndex = aI;
+ // l.atom = aI;
// l.residueIndex = residueIndex[aI];
// l.chainIndex = chainIndex[aI];
// s[s.length] = p(l);
@@ -251,33 +250,33 @@ export namespace PropertyAccess {
console.log(baseline(models[0]));
console.log(baselineRaw(models[0]));
- console.log(sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atomIndex)));
- console.log(sumPropertySegmented(structures[0], l => l.unit.model.conformation.atomId.value(l.atomIndex)));
- //console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.atomIndex)));
- console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.conformation.atomId.value(l.atomIndex)));
- console.log(sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)));
+ console.log(sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
+ console.log(sumPropertySegmented(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
+ //console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
+ console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
+ //console.log(sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)));
console.log(sumDirect(structures[0]));
- console.log('r', sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atomIndex])));
+ console.log('r', sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])));
//const col = models[0].conformation.atomId.value;
const suite = new B.Suite();
suite
- //.add('test int', () => sumProperty(structures[0], l => col(l.atomIndex)))
+ //.add('test int', () => sumProperty(structures[0], l => col(l.atom)))
// .add('baseline raw', () => baselineRaw(models[0]))
- .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atomIndex])))
+ .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
.add('baseline', () => baseline(models[0]))
.add('direct', () => sumDirect(structures[0]))
- //.add('normal int', () => sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atomIndex)))
- //.add('atom set it int', () => sumPropertyAtomSetIt(structures[0], l => l.unit.conformation.atomId.value(l.atomIndex)))
- // .add('segmented faster int', () => sumPropertySegmented(structures[0], l => l.unit.conformation.atomId.value(l.atomIndex)))
- // .add('faster int', () => sumProperty(structures[0], l => l.unit.conformation.atomId.value(l.atomIndex)))
- .add('segmented faster _x', () => sumPropertySegmented(structures[0], l => l.unit.conformation.__x[l.atomIndex]))
- .add('faster _x', () => sumProperty(structures[0], l => l.unit.conformation.__x[l.atomIndex] + l.unit.conformation.__y[l.atomIndex] + l.unit.conformation.__z[l.atomIndex]))
- //.add('segmented mut faster int', () => sumPropertySegmentedMutable(structures[0], l => l.unit.conformation.atomId.value(l.atomIndex)))
- //.add('normal shortcut int', () => sumProperty(structures[0], l => l.conformation.atomId.value(l.atomIndex)))
+ //.add('normal int', () => sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)))
+ //.add('atom set it int', () => sumPropertyAtomSetIt(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
+ // .add('segmented faster int', () => sumPropertySegmented(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
+ // .add('faster int', () => sumProperty(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
+ .add('segmented faster _x', () => sumPropertySegmented(structures[0], l => l.unit.conformation.__x[l.atom]))
+ .add('faster _x', () => sumProperty(structures[0], l => l.unit.conformation.__x[l.atom] + l.unit.conformation.__y[l.atom] + l.unit.conformation.__z[l.atom]))
+ //.add('segmented mut faster int', () => sumPropertySegmentedMutable(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
+ //.add('normal shortcut int', () => sumProperty(structures[0], l => l.conformation.atomId.value(l.atom)))
//.add('cached int', () => sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)))
- //.add('concat str', () => concatProperty(structures[0], l => l.unit.model.hierarchy.atoms.auth_atom_id.value(l.atomIndex)))
+ //.add('concat str', () => concatProperty(structures[0], l => l.unit.model.hierarchy.atoms.auth_atom_id.value(l.atom)))
//.add('cached concat str', () => concatProperty(structures[0], Property.cachedAtomColumn(m => m.hierarchy.atoms.auth_atom_id)))
.on('cycle', (e: any) => console.log(String(e.target)))
.run();
--
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