From 54fcbd27e72c37eea5ccbea7cfa57f3f8041c09c Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 10 Nov 2017 10:31:00 +0100
Subject: [PATCH] Use Structure.Builder for assemblies
---
src/mol-model/structure/structure/structure.ts | 2 ++
src/mol-model/structure/structure/symmetry.ts | 17 +++++------------
src/mol-ql/TODO | 2 ++
3 files changed, 9 insertions(+), 12 deletions(-)
create mode 100644 src/mol-ql/TODO
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 0d2620412..317ea029f 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -44,6 +44,7 @@ namespace Structure {
}
export interface Builder {
+ add(unit: Unit, atoms: OrderedSet): void,
addUnit(unit: Unit): void,
addAtoms(unitId: number, atoms: OrderedSet): void,
getStructure(): Structure,
@@ -55,6 +56,7 @@ namespace Structure {
private atoms = Object.create(null);
atomCount = 0;
+ add(unit: Unit, atoms: OrderedSet) { this.addUnit(unit); this.addAtoms(unit.id, atoms); }
addUnit(unit: Unit) { this.units[unit.id] = unit; }
addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; this.atomCount += OrderedSet.size(atoms); }
getStructure(): Structure { return this.atomCount > 0 ? Structure.create(this.units, AtomSet.create(this.atoms)) : Empty; }
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 2a4ef8c37..fa1ca3ab1 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -23,12 +23,9 @@ function buildAssemblyImpl(structure: Structure, name: string) {
const assembly = ModelSymmetry.findAssembly(models[0], name);
if (!assembly) throw new Error(`Assembly '${name}' is not defined.`);
- const { operatorGroups } = assembly;
+ const assembler = Structure.Builder();
- const assemblyUnits = Object.create(null);
- const assemblyAtoms = Object.create(null);
-
- for (const g of operatorGroups) {
+ for (const g of assembly.operatorGroups) {
const selection = g.selector(structure);
if (Selection.structureCount(selection) === 0) continue;
const { units, atoms } = Selection.union(selection);
@@ -37,15 +34,11 @@ function buildAssemblyImpl(structure: Structure, name: string) {
for (const oper of g.operators) {
for (let uI = 0, _uI = unitIds.length; uI < _uI; uI++) {
- const unitId = unitIds[uI];
- const unit = units[unitId];
-
- const newUnit = Unit.create(unit.model, oper);
- assemblyUnits[newUnit.id] = newUnit;
- assemblyAtoms[newUnit.id] = AtomSet.unitGetByIndex(atoms, uI);
+ const unit = units[unitIds[uI]];
+ assembler.add(Unit.create(unit.model, oper), AtomSet.unitGetByIndex(atoms, uI));
}
}
}
- return Structure.create(assemblyUnits, AtomSet.create(assemblyAtoms));
+ return assembler.getStructure();
}
\ No newline at end of file
diff --git a/src/mol-ql/TODO b/src/mol-ql/TODO
new file mode 100644
index 000000000..e2a008501
--- /dev/null
+++ b/src/mol-ql/TODO
@@ -0,0 +1,2 @@
+- Have the ability to define schemas for output.
+ Define properties for each pattern/whatever that could be exported as CIF/CSV/JSON.
\ No newline at end of file
--
GitLab