From bc91f0d3ff181d2037fc2504b598ba8eb0472cd7 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 24 Jul 2019 07:35:03 +0200
Subject: [PATCH] Support multiple models in
StructureElement.Loci.toScriptExpression
---
src/mol-model/structure/structure/element.ts | 38 ++++++++++++-------
.../structure/structure/properties.ts | 2 +
.../structure/structure/structure.ts | 4 ++
.../language/symbol-table/structure-query.ts | 2 +
src/mol-script/runtime/query/table.ts | 2 +
src/mol-script/script/mol-script/symbols.ts | 2 +
6 files changed, 36 insertions(+), 14 deletions(-)
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index ab0abf5b3..6c84a030a 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -309,24 +309,24 @@ namespace StructureElement {
}
export function toScriptExpression(loci: Loci) {
- if (loci.structure.models.length > 1) {
- console.warn('toScriptExpression is only supported for Structure with single model, returning empty expression.');
- return MS.struct.generator.empty();
- }
if (loci.elements.length === 0) return MS.struct.generator.empty();
- const sourceIndexMap = new Map<string, UniqueArray<number, number>>();
+ const models = loci.structure.models;
+ const sourceIndexMap = new Map<string, { modelLabel: string, modelIndex: number, xs: UniqueArray<number, number> }>();
const el = StructureElement.create(), p = StructureProperties.atom.sourceIndex;
for (const e of loci.elements) {
const { indices } = e;
const { elements } = e.unit;
- const opName = e.unit.conformation.operator.name;
+
+ const key = models.length === 1
+ ? e.unit.conformation.operator.name
+ : `${e.unit.conformation.operator.name} ${e.unit.model.label} ${e.unit.model.modelNum}`;
let sourceIndices: UniqueArray<number, number>;
- if (sourceIndexMap.has(opName)) sourceIndices = sourceIndexMap.get(opName)!;
+ if (sourceIndexMap.has(key)) sourceIndices = sourceIndexMap.get(key)!.xs;
else {
sourceIndices = UniqueArray.create<number, number>();
- sourceIndexMap.set(opName, sourceIndices);
+ sourceIndexMap.set(key, { modelLabel: e.unit.model.label, modelIndex: e.unit.model.modelNum, xs: sourceIndices });
}
el.unit = e.unit;
@@ -342,7 +342,8 @@ namespace StructureElement {
while (true) {
const k = keys.next();
if (k.done) break;
- byOpName.push(getOpNameQuery(k.value, sourceIndexMap.get(k.value)!.array));
+ const e = sourceIndexMap.get(k.value)!;
+ byOpName.push(getOpNameQuery(k.value, e.xs.array, models.length > 1, e.modelLabel, e.modelIndex));
}
return MS.struct.modifier.union([
@@ -350,7 +351,7 @@ namespace StructureElement {
]);
}
- function getOpNameQuery(opName: string, xs: number[]) {
+ function getOpNameQuery(opName: string, xs: number[], multimodel: boolean, modelLabel: string, modelIndex: number) {
sortArray(xs);
const ranges: number[] = [];
@@ -384,10 +385,19 @@ namespace StructureElement {
tests[tests.length] = MS.core.rel.inRange([siProp, ranges[2 * rI], ranges[2 * rI + 1]]);
}
- return MS.struct.generator.atomGroups({
- 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
- 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.core.operatorName(), opName])
- });
+ return multimodel
+ ? MS.struct.generator.atomGroups({
+ 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
+ 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.core.operatorName(), opName]),
+ 'entity-test': MS.core.logic.and([
+ MS.core.rel.eq([MS.struct.atomProperty.core.modelLabel(), modelLabel]),
+ MS.core.rel.eq([MS.struct.atomProperty.core.modelIndex(), modelIndex]),
+ ])
+ })
+ : MS.struct.generator.atomGroups({
+ 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
+ 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.core.operatorName(), opName])
+ });
}
}
}
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 17aa1c75a..5c6a70a0d 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -113,6 +113,8 @@ const entity = {
const unit = {
id: StructureElement.property(l => l.unit.id),
operator_name: StructureElement.property(l => l.unit.conformation.operator.name),
+ model_index: StructureElement.property(l => l.unit.model.modelNum),
+ model_label: StructureElement.property(l => l.unit.model.label),
hkl: StructureElement.property(l => l.unit.conformation.operator.hkl),
spgrOp: StructureElement.property(l => l.unit.conformation.operator.spgrOp),
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index d91b02346..000cc0a7b 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -218,6 +218,10 @@ class Structure {
return SortedArray.has(this.unitMap.get(e.unit.id).elements, e.element);
}
+ getModelIndex(m: Model) {
+ return this.model
+ }
+
private initUnits(units: ArrayLike<Unit>) {
const map = IntMap.Mutable<Unit>();
let elementCount = 0;
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 3a6ed1846..b129ba319 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -254,6 +254,8 @@ const atomProperty = {
sourceIndex: atomProp(Type.Num, 'Index of the atom/element in the input file.'),
operatorName: atomProp(Type.Str, 'Name of the symmetry operator applied to this element.'),
+ modelIndex: atomProp(Type.Num, 'Index of the model in the input file.'),
+ modelLabel: atomProp(Type.Str, 'Label/header of the model in the input file.')
},
topology: {
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index e2d75927f..ee5e68247 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -247,6 +247,8 @@ const symbols = [
D(MolScript.structureQuery.atomProperty.core.z, atomProp(StructureProperties.atom.z)),
D(MolScript.structureQuery.atomProperty.core.sourceIndex, atomProp(StructureProperties.atom.sourceIndex)),
D(MolScript.structureQuery.atomProperty.core.operatorName, atomProp(StructureProperties.unit.operator_name)),
+ D(MolScript.structureQuery.atomProperty.core.modelIndex, atomProp(StructureProperties.unit.model_index)),
+ D(MolScript.structureQuery.atomProperty.core.modelLabel, atomProp(StructureProperties.unit.model_label)),
D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, _) => cantorPairing(ctx.element.unit.id, ctx.element.element)),
// TODO:
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 4216867f9..eaa70e133 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -199,6 +199,8 @@ export const SymbolTable = [
Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
Alias(MolScript.structureQuery.atomProperty.core.sourceIndex, 'atom.src-index'),
Alias(MolScript.structureQuery.atomProperty.core.operatorName, 'atom.op-name'),
+ Alias(MolScript.structureQuery.atomProperty.core.modelIndex, 'atom.model-index'),
+ Alias(MolScript.structureQuery.atomProperty.core.modelLabel, 'atom.model-label'),
Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
--
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