From b4aab810ad5d999b0a6d177acdd114b1c8748450 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 10 Nov 2017 22:24:48 +0100
Subject: [PATCH] Working on structure data model
---
src/mol-model/structure/query/selection.ts | 6 ++-
src/mol-model/structure/structure.ts | 3 +-
.../structure/structure/atom/group.ts | 46 +++++++++++++++++++
.../structure/structure/atom/unit.ts | 34 --------------
.../structure/structure/structure.ts | 4 +-
src/mol-model/structure/structure/symmetry.ts | 2 +-
src/mol-model/structure/structure/unit.ts | 7 ++-
7 files changed, 62 insertions(+), 40 deletions(-)
create mode 100644 src/mol-model/structure/structure/atom/group.ts
delete 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 36891fbe3..54eef8603 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -16,8 +16,10 @@ type Selection =
// 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 }
+ | { kind: 'sequence', structure: Structure, sets: AtomSet[] }
+ | { kind: 'atom-set', structure: Structure, set: AtomSet }
+
+ structure allows for good unions.
*/
namespace Selection {
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index 0d5c8bad6..fbd004755 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -6,8 +6,9 @@
import Atom from './structure/atom'
import AtomSet from './structure/atom/set'
+import AtomGroup from './structure/atom/group'
import Structure from './structure/structure'
import Unit from './structure/unit'
import Symmetry from './structure/symmetry'
-export { Atom, AtomSet, Structure, Unit, Symmetry }
\ No newline at end of file
+export { Atom, AtomSet, AtomGroup, Structure, Unit, Symmetry }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/atom/group.ts b/src/mol-model/structure/structure/atom/group.ts
new file mode 100644
index 000000000..be6274ba2
--- /dev/null
+++ b/src/mol-model/structure/structure/atom/group.ts
@@ -0,0 +1,46 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { OrderedSet } from 'mol-data/int'
+import Unit from '../unit'
+
+interface AtomGroup {
+ set: OrderedSet,
+ id: number
+}
+
+namespace AtomGroup {
+ export const Empty = createNew(OrderedSet.Empty)
+
+ // export function singleton(idx: number) {
+ // return create(OrderedSet.ofSingleton(idx));
+ // }
+
+ export function createNew(set: OrderedSet) {
+ return { id: nextId(), set };
+ }
+
+ export function create(unit: Unit, set: OrderedSet): AtomGroup {
+ if (OrderedSet.areEqual(set, unit.naturalGroup.set)) return unit.naturalGroup;
+ return createNew(set);
+ }
+
+ // export function size(group: AtomGroup) { return OrderedSet.size(group.set); }
+ // export function has(group: AtomGroup, atom: number) { return OrderedSet.has(group.set, atom); }
+ // export function getAt(group: AtomGroup, i: number) { return OrderedSet.getAt(group.set, i); }
+ // export function indexOf(group: AtomGroup, atom: number) { return OrderedSet.indexOf(group.set, atom); }
+ // export function hashCode(group: AtomGroup) { return OrderedSet.hashCode(group.set); }
+ // export function areEqual(a: AtomGroup, b: AtomGroup) { return OrderedSet.areEqual(a.set, b.set); }
+
+ let _id = 0;
+ function nextId() {
+ const ret = _id;
+ _id = (_id + 1) % 0x3fffffff;
+ return ret;
+ }
+}
+
+export default AtomGroup
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/atom/unit.ts b/src/mol-model/structure/structure/atom/unit.ts
deleted file mode 100644
index 10313f912..000000000
--- a/src/mol-model/structure/structure/atom/unit.ts
+++ /dev/null
@@ -1,34 +0,0 @@
-/**
- * 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 feca08019..9d25590e4 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -10,6 +10,7 @@ import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
import { Model, Format } from '../model'
import Unit from './unit'
import AtomSet from './atom/set'
+import AtomGroup from './atom/group'
import Atom from './atom'
@@ -35,7 +36,8 @@ namespace Structure {
const builder = Builder();
for (let c = 0; c < chains.count; c++) {
- const unit = Unit.create(c, model, SymmetryOperator.Default);
+ const group = AtomGroup.createNew(OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
+ const unit = Unit.create(c, model, SymmetryOperator.Default, group);
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 abb2e1002..daa45f3fb 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -36,7 +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(unitId++, unit.model, oper), AtomSet.unitGetByIndex(atoms, uI));
+ assembler.add(Unit.create(unitId++, unit.model, oper, unit.naturalGroup), AtomSet.unitGetByIndex(atoms, uI));
}
}
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index b833b664c..e8edaa4c4 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -5,6 +5,7 @@
*/
import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
+import AtomGroup from './atom/group'
import { Model } from '../model'
interface Unit extends SymmetryOperator.ArrayMapping {
@@ -18,6 +19,9 @@ interface Unit extends SymmetryOperator.ArrayMapping {
// The transform and and inverse are baked into the "getPosition" function
readonly operator: SymmetryOperator,
+ // The "full" atom group corresponding to this unit.
+ readonly naturalGroup: AtomGroup,
+
// Reference some commonly accessed things for faster access.
readonly residueIndex: ArrayLike<number>,
readonly chainIndex: ArrayLike<number>,
@@ -28,7 +32,7 @@ interface Unit extends SymmetryOperator.ArrayMapping {
}
namespace Unit {
- export function create(id: number, model: Model, operator: SymmetryOperator): Unit {
+ export function create(id: number, model: Model, operator: SymmetryOperator, naturalGroup: AtomGroup): Unit {
const h = model.hierarchy;
const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.conformation);
@@ -36,6 +40,7 @@ namespace Unit {
id,
model,
operator,
+ naturalGroup,
residueIndex: h.residueSegments.segmentMap,
chainIndex: h.chainSegments.segmentMap,
hierarchy: model.hierarchy,
--
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