Skip to content
Snippets Groups Projects
Commit dfb7f781 authored by Alexander Rose's avatar Alexander Rose
Browse files

support coarse elements in atomGroups generator

parent cc344257
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
src/mol-model/structure/query/queries/generators.ts
+ 88
− 46
View file @ dfb7f781
/**
* 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);
}
}
}
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment