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Commit dfb7f781 authored by Alexander Rose's avatar Alexander Rose
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support coarse elements in atomGroups generator

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/** /**
* 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 David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
import { StructureQuery } from '../query' import { StructureQuery } from '../query'
...@@ -24,7 +25,7 @@ export interface AtomsQueryParams { ...@@ -24,7 +25,7 @@ export interface AtomsQueryParams {
entityTest: QueryPredicate, entityTest: QueryPredicate,
/** Query to be executed for each chain once */ /** Query to be executed for each chain once */
chainTest: QueryPredicate, chainTest: QueryPredicate,
/** Query to be executed for each residue once */ /** Query to be executed for each residue (or coarse element) once */
residueTest: QueryPredicate, residueTest: QueryPredicate,
/** Query to be executed for each atom */ /** Query to be executed for each atom */
atomTest: QueryPredicate, atomTest: QueryPredicate,
...@@ -86,14 +87,14 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A ...@@ -86,14 +87,14 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const builder = inputStructure.subsetBuilder(true); const builder = inputStructure.subsetBuilder(true);
for (const unit of units) { for (const unit of units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
l.unit = unit; l.unit = unit;
const elements = unit.elements; const { elements, model } = unit;
builder.beginUnit(unit.id); builder.beginUnit(unit.id);
if (unit.kind === Unit.Kind.Atomic) {
const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements); const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements); const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
while (chainsIt.hasNext) { while (chainsIt.hasNext) {
const chainSegment = chainsIt.move(); const chainSegment = chainsIt.move();
l.element = elements[chainSegment.start]; l.element = elements[chainSegment.start];
...@@ -110,12 +111,32 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A ...@@ -110,12 +111,32 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) { for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
l.element = elements[j]; l.element = elements[j];
// test atom
if (atomTest(ctx)) { if (atomTest(ctx)) {
builder.addElement(l.element); 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];
// test residue/coarse element
if (residueTest(ctx)) {
builder.addElement(l.element);
}
}
}
}
builder.commitUnit(); builder.commitUnit();
ctx.throwIfTimedOut(); ctx.throwIfTimedOut();
...@@ -133,13 +154,13 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group ...@@ -133,13 +154,13 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
const builder = new LinearGroupingBuilder(inputStructure); const builder = new LinearGroupingBuilder(inputStructure);
for (const unit of units) { for (const unit of units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
l.unit = unit; l.unit = unit;
const elements = unit.elements; 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);
const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
while (chainsIt.hasNext) { while (chainsIt.hasNext) {
const chainSegment = chainsIt.move(); const chainSegment = chainsIt.move();
l.element = elements[chainSegment.start]; l.element = elements[chainSegment.start];
...@@ -156,7 +177,28 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group ...@@ -156,7 +177,28 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) { for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
l.element = elements[j]; l.element = elements[j];
if (atomTest(ctx)) builder.add(groupBy(ctx), unit.id, l.element); // 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];
// test residue/coarse element
if (residueTest(ctx)) {
builder.add(groupBy(ctx), unit.id, l.element);
}
} }
} }
} }
......
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