From dfb7f7811ffc8935f49dd1f240d7d0544a04a49e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 14 Jun 2019 18:59:37 -0700
Subject: [PATCH] support coarse elements in atomGroups generator
---
.../structure/query/queries/generators.ts | 134 ++++++++++++------
1 file changed, 88 insertions(+), 46 deletions(-)
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index f370b5c2c..e0984e91a 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { StructureQuery } from '../query'
@@ -24,7 +25,7 @@ export interface AtomsQueryParams {
entityTest: QueryPredicate,
/** Query to be executed for each chain once */
chainTest: QueryPredicate,
- /** Query to be executed for each residue once */
+ /** Query to be executed for each residue (or coarse element) once */
residueTest: QueryPredicate,
/** Query to be executed for each atom */
atomTest: QueryPredicate,
@@ -86,31 +87,51 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const builder = inputStructure.subsetBuilder(true);
for (const unit of units) {
- if (unit.kind !== Unit.Kind.Atomic) continue;
-
l.unit = unit;
- const elements = unit.elements;
-
+ const { elements, model } = unit;
builder.beginUnit(unit.id);
- const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
- const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
- while (chainsIt.hasNext) {
- const chainSegment = chainsIt.move();
- l.element = elements[chainSegment.start];
- // test entity and chain
- if (!entityTest(ctx) || !chainTest(ctx)) continue;
-
- residuesIt.setSegment(chainSegment);
- while (residuesIt.hasNext) {
- const residueSegment = residuesIt.move();
- l.element = elements[residueSegment.start];
-
- // test residue
- if (!residueTest(ctx)) continue;
-
- for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+
+ if (unit.kind === Unit.Kind.Atomic) {
+ const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+ const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.element = elements[chainSegment.start];
+ // test entity and chain
+ if (!entityTest(ctx) || !chainTest(ctx)) continue;
+
+ residuesIt.setSegment(chainSegment);
+ while (residuesIt.hasNext) {
+ const residueSegment = residuesIt.move();
+ l.element = elements[residueSegment.start];
+
+ // test residue
+ if (!residueTest(ctx)) continue;
+
+ for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+ l.element = elements[j];
+ // test atom
+ if (atomTest(ctx)) {
+ builder.addElement(l.element);
+ }
+ }
+ }
+ }
+ } else {
+ const { chainElementSegments } = Unit.Kind.Spheres ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians
+ const chainsIt = Segmentation.transientSegments(chainElementSegments, elements);
+
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.element = elements[chainSegment.start];
+ // test entity and chain
+ if (!entityTest(ctx) || !chainTest(ctx)) continue;
+
+ for (let j = chainSegment.start, _j = chainSegment.end; j < _j; j++) {
l.element = elements[j];
- if (atomTest(ctx)) {
+ // test residue/coarse element
+ if (residueTest(ctx)) {
builder.addElement(l.element);
}
}
@@ -133,30 +154,51 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
const builder = new LinearGroupingBuilder(inputStructure);
for (const unit of units) {
- if (unit.kind !== Unit.Kind.Atomic) continue;
-
l.unit = unit;
- const elements = unit.elements;
-
- const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
- const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
- while (chainsIt.hasNext) {
- const chainSegment = chainsIt.move();
- l.element = elements[chainSegment.start];
- // test entity and chain
- if (!entityTest(ctx) || !chainTest(ctx)) continue;
-
- residuesIt.setSegment(chainSegment);
- while (residuesIt.hasNext) {
- const residueSegment = residuesIt.move();
- l.element = elements[residueSegment.start];
-
- // test residue
- if (!residueTest(ctx)) continue;
-
- for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+ const { elements, model } = unit;
+
+ if (unit.kind === Unit.Kind.Atomic) {
+ const chainsIt = Segmentation.transientSegments(model.atomicHierarchy.chainAtomSegments, elements);
+ const residuesIt = Segmentation.transientSegments(model.atomicHierarchy.residueAtomSegments, elements);
+
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.element = elements[chainSegment.start];
+ // test entity and chain
+ if (!entityTest(ctx) || !chainTest(ctx)) continue;
+
+ residuesIt.setSegment(chainSegment);
+ while (residuesIt.hasNext) {
+ const residueSegment = residuesIt.move();
+ l.element = elements[residueSegment.start];
+
+ // test residue
+ if (!residueTest(ctx)) continue;
+
+ for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+ l.element = elements[j];
+ // test atom
+ if (atomTest(ctx)) {
+ builder.add(groupBy(ctx), unit.id, l.element);
+ }
+ }
+ }
+ }
+ } else {
+ const { chainElementSegments } = Unit.Kind.Spheres ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians
+ const chainsIt = Segmentation.transientSegments(chainElementSegments, elements);
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.element = elements[chainSegment.start];
+ // test entity and chain
+ if (!entityTest(ctx) || !chainTest(ctx)) continue;
+
+ for (let j = chainSegment.start, _j = chainSegment.end; j < _j; j++) {
l.element = elements[j];
- if (atomTest(ctx)) builder.add(groupBy(ctx), unit.id, l.element);
+ // test residue/coarse element
+ if (residueTest(ctx)) {
+ builder.add(groupBy(ctx), unit.id, l.element);
+ }
}
}
}
--
GitLab