From 0328282d527eef8b347e064fc404a8f969dfa68b Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 10 Nov 2017 19:32:43 +0100
Subject: [PATCH] Started "AtomUnits"
---
src/mol-model/structure/query/selection.ts | 9 +++++
.../structure/atom/{set => impl}/builder.ts | 0
.../atom/{set => impl}/properties.ts | 0
.../atom/{set/impl.ts => impl/set.ts} | 6 +---
src/mol-model/structure/structure/atom/set.ts | 4 +--
.../structure/structure/atom/unit.ts | 34 +++++++++++++++++++
.../structure/structure/structure.ts | 2 +-
src/mol-model/structure/structure/symmetry.ts | 3 +-
src/mol-model/structure/structure/unit.ts | 13 ++-----
9 files changed, 52 insertions(+), 19 deletions(-)
rename src/mol-model/structure/structure/atom/{set => impl}/builder.ts (100%)
rename src/mol-model/structure/structure/atom/{set => impl}/properties.ts (100%)
rename src/mol-model/structure/structure/atom/{set/impl.ts => impl/set.ts} (99%)
create mode 100644 src/mol-model/structure/structure/atom/unit.ts
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index 8aec9b363..36891fbe3 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -13,11 +13,20 @@ type Selection =
| Structure // each atom is interpreted as a singleton structure
| Structure[]
+// TODO: Do not allow to change unit set in the middle of a query, create a differnt language to control assemblies etc.
+/*
+type Selection =
+ | { kind: 'sequence', units: UnitCollection, sets: AtomSet[] }
+ | { kind: 'atom-set', units: UnitCollection, set: AtomSet }
+*/
+
namespace Selection {
export const Empty: Selection = [];
function isStructure(x: Selection): x is Structure { return !!(x as Structure).units && !!(x as Structure).atoms; }
+ export const isOfSingletons = isStructure
+
export function structureCount(sel: Selection) {
if (isStructure(sel)) return AtomSet.atomCount(sel.atoms);
return sel.length;
diff --git a/src/mol-model/structure/structure/atom/set/builder.ts b/src/mol-model/structure/structure/atom/impl/builder.ts
similarity index 100%
rename from src/mol-model/structure/structure/atom/set/builder.ts
rename to src/mol-model/structure/structure/atom/impl/builder.ts
diff --git a/src/mol-model/structure/structure/atom/set/properties.ts b/src/mol-model/structure/structure/atom/impl/properties.ts
similarity index 100%
rename from src/mol-model/structure/structure/atom/set/properties.ts
rename to src/mol-model/structure/structure/atom/impl/properties.ts
diff --git a/src/mol-model/structure/structure/atom/set/impl.ts b/src/mol-model/structure/structure/atom/impl/set.ts
similarity index 99%
rename from src/mol-model/structure/structure/atom/set/impl.ts
rename to src/mol-model/structure/structure/atom/impl/set.ts
index 99bd298d1..c63d3e459 100644
--- a/src/mol-model/structure/structure/atom/set/impl.ts
+++ b/src/mol-model/structure/structure/atom/impl/set.ts
@@ -17,14 +17,10 @@ export type AtomSetImpl = Atom | AtomSetElements
export const Empty: AtomSetImpl = { sets: IntMap.Empty, offsets: new Int32Array(1), hashCode: 0, keys: SortedArray.Empty };
export function create(data: Atom | ArrayLike<Atom>): AtomSetImpl {
- if (typeof data === 'number' || Atom.is(data)) return data;
+ if (Atom.is(data)) return data;
return ofAtoms(data);
}
-export function isSingleton(set: AtomSetImpl) {
- return typeof set === 'number';
-}
-
export function getKeys(set: AtomSetImpl): SortedArray {
if (typeof set === 'number') return SortedArray.ofSingleton(set);
return (set as AtomSetElements).keys;
diff --git a/src/mol-model/structure/structure/atom/set.ts b/src/mol-model/structure/structure/atom/set.ts
index 9df795ece..ec63e2e23 100644
--- a/src/mol-model/structure/structure/atom/set.ts
+++ b/src/mol-model/structure/structure/atom/set.ts
@@ -6,8 +6,8 @@
import { OrderedSet, SortedArray, Iterator } from 'mol-data/int'
import Atom from '../atom'
-import * as Impl from './set/impl'
-import * as Builders from './set/builder'
+import * as Impl from './impl/set'
+import * as Builders from './impl/builder'
/** A map-like representation of grouped atom set */
namespace AtomSet {
diff --git a/src/mol-model/structure/structure/atom/unit.ts b/src/mol-model/structure/structure/atom/unit.ts
new file mode 100644
index 000000000..10313f912
--- /dev/null
+++ b/src/mol-model/structure/structure/atom/unit.ts
@@ -0,0 +1,34 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// TODO : wrap OrderedSet with and include "id" to identify unique (sub)sets in AtomSet and the ability to cache data (also include "ancestor" field for effictient subsets).
+
+import { OrderedSet } from 'mol-data/int'
+
+interface AtomUnit {
+ set: OrderedSet,
+ id: number,
+ ancestor?: AtomUnit
+}
+
+namespace AtomUnit {
+ export function create(set: OrderedSet, ancestor?: AtomUnit): AtomUnit {
+ if (!ancestor) {
+ return { id: nextId(), set };
+ }
+ if (OrderedSet.areEqual(set, ancestor.set)) return ancestor;
+ return { id: nextId(), set, ancestor: ancestor.ancestor || ancestor };
+ }
+
+ let _id = 0;
+ function nextId() {
+ const ret = _id;
+ _id = (_id + 1) % 0x3fffffff;
+ return ret;
+ }
+}
+
+export default AtomUnit
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 42b97a868..feca08019 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -35,7 +35,7 @@ namespace Structure {
const builder = Builder();
for (let c = 0; c < chains.count; c++) {
- const unit = Unit.create(model, SymmetryOperator.Default);
+ const unit = Unit.create(c, model, SymmetryOperator.Default);
builder.add(unit, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
}
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index ec8de5d4d..abb2e1002 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -25,6 +25,7 @@ function buildAssemblyImpl(structure: Structure, name: string) {
const assembler = Structure.Builder();
+ let unitId = 0;
for (const g of assembly.operatorGroups) {
const selection = g.selector(structure);
if (Selection.structureCount(selection) === 0) continue;
@@ -35,7 +36,7 @@ function buildAssemblyImpl(structure: Structure, name: string) {
for (const oper of g.operators) {
for (let uI = 0, _uI = unitIds.length; uI < _uI; uI++) {
const unit = units.get(unitIds[uI]);
- assembler.add(Unit.create(unit.model, oper), AtomSet.unitGetByIndex(atoms, uI));
+ assembler.add(Unit.create(unitId++, unit.model, oper), AtomSet.unitGetByIndex(atoms, uI));
}
}
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index be83164a3..b833b664c 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -28,12 +28,12 @@ interface Unit extends SymmetryOperator.ArrayMapping {
}
namespace Unit {
- export function create(model: Model, operator: SymmetryOperator): Unit {
+ export function create(id: number, model: Model, operator: SymmetryOperator): Unit {
const h = model.hierarchy;
const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.conformation);
return {
- id: nextUnitId(),
+ id,
model,
operator,
residueIndex: h.residueSegments.segmentMap,
@@ -47,11 +47,4 @@ namespace Unit {
}
}
-export default Unit;
-
-let _id = 0;
-function nextUnitId() {
- const ret = _id;
- _id = (_id + 1) % 0x3fffffff;
- return ret;
-}
\ No newline at end of file
+export default Unit;
\ No newline at end of file
--
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