diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index b1873f5ca463e0954ddcca443aef752ceb8a32d0..c04627418a078014a7f89f061b8f0d5bbde55fef 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -119,7 +119,7 @@ export function printSequence(model: Model) {
export function printModRes(model: Model) {
console.log('\nModified Residues\n=============');
- const map = model.properties.modifiedResidueNameMap;
+ const map = model.properties.modifiedResidues.parentId;
const { label_comp_id, _rowCount } = model.atomicHierarchy.residues;
for (let i = 0; i < _rowCount; i++) {
const comp_id = label_comp_id.value(i);
diff --git a/src/mol-data/int/impl/segmentation.ts b/src/mol-data/int/impl/segmentation.ts
index c43d04ba368c1bbadac09414221c27bf1d733e6b..0b1e6eba5f8235b4d60cd54654d3f6ba8fb92312 100644
--- a/src/mol-data/int/impl/segmentation.ts
+++ b/src/mol-data/int/impl/segmentation.ts
@@ -50,18 +50,18 @@ export function projectValue({ offsets }: Segmentation, set: OrderedSet, value:
return OrderedSet.findRange(set, OrderedSet.getAt(offsets, idx), OrderedSet.getAt(offsets, idx + 1) - 1);
}
-export class SegmentIterator<T extends number = number> implements Iterator<Segs.Segment<T>> {
+export class SegmentIterator<I extends number = number> implements Iterator<Segs.Segment<I>> {
private segmentMin = 0;
private segmentMax = 0;
private setRange = Interval.Empty;
- private value: Segs.Segment<T> = { index: 0, start: 0 as T, end: 0 as T };
+ private value: Segs.Segment<I> = { index: 0 as I, start: 0, end: 0 };
hasNext: boolean = false;
move() {
while (this.hasNext) {
if (this.updateValue()) {
- this.value.index = this.segmentMin++;
+ this.value.index = this.segmentMin++ as I;
this.hasNext = this.segmentMax >= this.segmentMin && Interval.size(this.setRange) > 0;
break;
} else {
@@ -75,8 +75,8 @@ export class SegmentIterator<T extends number = number> implements Iterator<Segs
const segmentEnd = this.segments[this.segmentMin + 1];
// TODO: add optimized version for interval and array?
const setEnd = OrderedSet.findPredecessorIndexInInterval(this.set, segmentEnd, this.setRange);
- this.value.start = Interval.start(this.setRange) as T;
- this.value.end = setEnd as T;
+ this.value.start = Interval.start(this.setRange);
+ this.value.end = setEnd;
this.setRange = Interval.ofBounds(setEnd, Interval.end(this.setRange));
return setEnd > this.value.start;
}
@@ -94,7 +94,7 @@ export class SegmentIterator<T extends number = number> implements Iterator<Segs
this.hasNext = this.segmentMax >= this.segmentMin;
}
- setSegment(segment: Segs.Segment<T>) {
+ setSegment(segment: Segs.Segment<number>) {
this.setRange = Interval.ofBounds(segment.start, segment.end);
this.updateSegmentRange();
}
diff --git a/src/mol-data/int/segmentation.ts b/src/mol-data/int/segmentation.ts
index 2afdd6a55089cf18f2316d5559a7eff80e053654..b472ea3d79dad03cc8f403191291ebb673e865f5 100644
--- a/src/mol-data/int/segmentation.ts
+++ b/src/mol-data/int/segmentation.ts
@@ -9,7 +9,7 @@ import OrderedSet from './ordered-set'
import * as Impl from './impl/segmentation'
namespace Segmentation {
- export interface Segment<T extends number = number, I extends number = number> { index: number, start: T, end: T }
+ export interface Segment<I extends number = number> { index: I, start: number, end: number }
export const create: <T extends number = number, I extends number = number>(segs: ArrayLike<T>) => Segmentation<T, I> = Impl.create as any;
export const ofOffsets: <T extends number = number, I extends number = number>(offsets: ArrayLike<T>, bounds: Interval) => Segmentation<T, I> = Impl.ofOffsets as any;
@@ -19,7 +19,7 @@ namespace Segmentation {
export const projectValue: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, set: OrderedSet<T>, value: T) => Interval = Impl.projectValue as any;
// Segment iterator that mutates a single segment object to mark all the segments.
- export const transientSegments: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, set: OrderedSet<T>, segment?: Segment<T>) => Impl.SegmentIterator<T> = Impl.segments as any;
+ export const transientSegments: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, set: OrderedSet<T>, segment?: Segment) => Impl.SegmentIterator<I> = Impl.segments as any;
}
interface Segmentation<T extends number = number, I extends number = number> {
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 4c80e946627cb549211a8514c1d1b9e68c908b25..bfb90b50ec4839fb25c90c9b319fbc3c695691bc 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, StructureProperties, ElementIndex } from 'mol-model/structure';
+import { Unit, StructureElement, StructureProperties } from 'mol-model/structure';
import { Segmentation } from 'mol-data/int';
import { MoleculeType } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
@@ -50,7 +50,7 @@ function getTraceName(l: StructureElement) {
return traceName
}
-function setTraceElement(l: StructureElement, residueSegment: Segmentation.Segment<ElementIndex>) {
+function setTraceElement(l: StructureElement, residueSegment: Segmentation.Segment) {
const elements = l.unit.elements
l.element = elements[residueSegment.start]
const traceName = getTraceName(l)
@@ -97,9 +97,9 @@ const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextR
export class AtomicPolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
private value: PolymerBackbonePair
- private polymerIt: SegmentIterator<ElementIndex>
- private residueIt: SegmentIterator<ElementIndex>
- private polymerSegment: Segmentation.Segment<ElementIndex>
+ private polymerIt: SegmentIterator
+ private residueIt: SegmentIterator
+ private polymerSegment: Segmentation.Segment
private state: AtomicPolymerBackboneIteratorState = AtomicPolymerBackboneIteratorState.nextPolymer
private pos: SymmetryOperator.CoordinateMapper
@@ -161,8 +161,8 @@ const enum CoarsePolymerBackboneIteratorState { nextPolymer, firstElement, nextE
export class CoarsePolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
private value: PolymerBackbonePair
- private polymerIt: SegmentIterator<ElementIndex>
- private polymerSegment: Segmentation.Segment<ElementIndex>
+ private polymerIt: SegmentIterator
+ private polymerSegment: Segmentation.Segment
private state: CoarsePolymerBackboneIteratorState = CoarsePolymerBackboneIteratorState.nextPolymer
private pos: SymmetryOperator.CoordinateMapper
private elementIndex: number
@@ -268,8 +268,8 @@ function createPolymerTraceElement (unit: Unit) {
export class AtomicPolymerTraceIterator<T extends number = number> implements Iterator<PolymerTraceElement> {
private value: PolymerTraceElement
- private polymerIt: SegmentIterator<ElementIndex>
- private residueIt: SegmentIterator<ElementIndex>
+ private polymerIt: SegmentIterator
+ private residueIt: SegmentIterator
// private polymerSegment: Segmentation.Segment<Element>
// private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
// private pos: SymmetryOperator.CoordinateMapper
diff --git a/src/mol-model/structure/export/categories/modified-residues.ts b/src/mol-model/structure/export/categories/modified-residues.ts
new file mode 100644
index 0000000000000000000000000000000000000000..58cdc137fb9daf474b9089c67b3ba9cacb69f7d2
--- /dev/null
+++ b/src/mol-model/structure/export/categories/modified-residues.ts
@@ -0,0 +1,61 @@
+/**
+ * Copyright (c) 2017-2018 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 { Segmentation } from 'mol-data/int';
+import { CifWriter } from 'mol-io/writer/cif';
+import { StructureElement, StructureProperties as P, Unit } from '../../../structure';
+import { CifExportContext } from '../mmcif';
+
+import CifField = CifWriter.Field
+import CifCategory = CifWriter.Category
+
+export function _pdbx_struct_mod_residue(ctx: CifExportContext): CifCategory {
+ const residues = getModifiedResidues(ctx);
+ return {
+ data: residues,
+ name: 'pdbx_struct_mod_residue',
+ fields: pdbx_struct_mod_residue_fields,
+ rowCount: residues.length
+ };
+}
+
+const pdbx_struct_mod_residue_fields: CifField<number, StructureElement[]>[] = [
+ CifField.index('id'),
+ CifField.str(`label_comp_id`, (i, xs) => P.residue.label_comp_id(xs[i])),
+ CifField.int(`label_seq_id`, (i, xs) => P.residue.label_seq_id(xs[i])),
+ CifField.str(`pdbx_PDB_ins_code`, (i, xs) => P.residue.pdbx_PDB_ins_code(xs[i])),
+ CifField.str(`label_asym_id`, (i, xs) => P.chain.label_asym_id(xs[i])),
+ CifField.str(`label_entity_id`, (i, xs) => P.chain.label_entity_id(xs[i])),
+ CifField.str(`auth_comp_id`, (i, xs) => P.residue.auth_comp_id(xs[i])),
+ CifField.int(`auth_seq_id`, (i, xs) => P.residue.auth_seq_id(xs[i])),
+ CifField.str(`auth_asym_id`, (i, xs) => P.chain.auth_asym_id(xs[i])),
+ CifField.str<number, StructureElement[]>('parent_comp_id', (i, xs) => xs[i].unit.model.properties.modifiedResidues.parentId.get(P.residue.label_comp_id(xs[i]))!),
+ CifField.str('details', (i, xs) => xs[i].unit.model.properties.modifiedResidues.details.get(P.residue.label_comp_id(xs[i]))!)
+];
+
+function getModifiedResidues({ model, structure }: CifExportContext): StructureElement[] {
+ const map = model.properties.modifiedResidues.parentId;
+ if (!map.size) return [];
+
+ const ret = [];
+ const prop = P.residue.label_comp_id;
+ const loc = StructureElement.create();
+ for (const unit of structure.units) {
+ if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
+ const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+ loc.unit = unit;
+ while (residues.hasNext) {
+ const seg = residues.move();
+ loc.element = unit.elements[seg.start];
+ const name = prop(loc);
+ if (map.has(name)) {
+ ret[ret.length] = StructureElement.create(loc.unit, loc.element);
+ }
+ }
+ }
+ return ret;
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index dbc7b29ab534cfc3b432c93f2a2d7b7e2acab5d2..aa794fd078d7650ca5180e19076e136d24c85c56 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -9,11 +9,9 @@ import { CifWriter } from 'mol-io/writer/cif';
import { SecondaryStructure } from '../../model/properties/seconday-structure';
import { StructureElement, Unit, StructureProperties as P } from '../../structure';
import { CifExportContext } from '../mmcif';
-
import CifField = CifWriter.Field
import CifCategory = CifWriter.Category
import { Column } from 'mol-data/db';
-import { ElementIndex } from '../../model';
export function _struct_conf(ctx: CifExportContext): CifCategory {
const elements = findElements(ctx, 'helix');
@@ -42,7 +40,7 @@ function compare_ssr(x: SSElement<SecondaryStructure.Sheet>, y: SSElement<Second
const struct_conf_fields: CifField[] = [
CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data) => data[i].element.type_id),
- CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
+ CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
...residueIdFields('beg_', e => e.start),
...residueIdFields('end_', e => e.end),
CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('pdbx_PDB_helix_class', (i, data) => data[i].element.helix_class),
@@ -53,8 +51,8 @@ const struct_conf_fields: CifField[] = [
];
const struct_sheet_range_fields: CifField[] = [
- CifField.index('id'),
CifField.str<number, SSElement<SecondaryStructure.Sheet>[]>('sheet_id', (i, data) => data[i].element.sheet_id),
+ CifField.index('id'),
...residueIdFields('beg_', e => e.start),
...residueIdFields('end_', e => e.end),
CifField.str('symmetry', (i, data) => '', { valueKind: (i, d) => Column.ValueKind.Unknown })
@@ -66,7 +64,7 @@ function residueIdFields(prefix: string, loc: (e: SSElement<any>) => StructureEl
CifField.int(`${prefix}label_seq_id`, (i, d) => P.residue.label_seq_id(loc(d[i]))),
CifField.str(`pdbx_${prefix}PDB_ins_code`, (i, d) => P.residue.pdbx_PDB_ins_code(loc(d[i]))),
CifField.str(`${prefix}label_asym_id`, (i, d) => P.chain.label_asym_id(loc(d[i]))),
- CifField.str(`${prefix}_entity_id`, (i, d) => P.chain.label_entity_id(loc(d[i]))),
+ CifField.str(`${prefix}label_entity_id`, (i, d) => P.chain.label_entity_id(loc(d[i]))),
CifField.str(`${prefix}auth_comp_id`, (i, d) => P.residue.auth_comp_id(loc(d[i]))),
CifField.int(`${prefix}auth_seq_id`, (i, d) => P.residue.auth_seq_id(loc(d[i]))),
CifField.str(`${prefix}auth_asym_id`, (i, d) => P.chain.auth_asym_id(loc(d[i])))
@@ -92,7 +90,7 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
const segs = unit.model.atomicHierarchy.residueAtomSegments;
const residues = Segmentation.transientSegments(segs, unit.elements);
- let current: Segmentation.Segment<ElementIndex>, move = true;
+ let current: Segmentation.Segment, move = true;
while (residues.hasNext) {
if (move) current = residues.move();
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index c783b552e041369ec50d4466e299357d476119c1..89d18e9b1963eebf2cf0121db230eca462d4056f 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -18,6 +18,7 @@ export interface CifExportContext {
import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
+import { _pdbx_struct_mod_residue } from './categories/modified-residues';
function copy_mmCif_category(name: keyof mmCIF_Schema) {
return ({ model }: CifExportContext) => {
@@ -57,6 +58,8 @@ const Categories = [
copy_mmCif_category('chem_comp'),
copy_mmCif_category('atom_sites'),
+ _pdbx_struct_mod_residue,
+
// Atoms
_atom_site
];
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 46fd62b3ec67f34bb46e2df353eae2f71afccdd1..48faa3d3f3088fa97e0e601ea0bd5b194af08171 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -70,17 +70,20 @@ function getNcsOperators(format: mmCIF_Format) {
}
return opers;
}
-function getModifiedResidueNameMap(format: mmCIF_Format) {
+function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['modifiedResidues'] {
const data = format.data.pdbx_struct_mod_residue;
- const map = new Map<string, string>();
+ const parentId = new Map<string, string>();
+ const details = new Map<string, string>();
const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
- const parent_id = data.parent_comp_id;
+ const parent_id = data.parent_comp_id, details_data = data.details;
for (let i = 0; i < data._rowCount; i++) {
- map.set(comp_id.value(i), parent_id.value(i));
+ const id = comp_id.value(i);
+ parentId.set(id, parent_id.value(i));
+ details.set(id, details_data.value(i));
}
- return map;
+ return { parentId, details };
}
function getAsymIdSerialMap(format: mmCIF_Format) {
@@ -132,7 +135,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
? format.data.entry.id.value(0)
: format.data._name;
- const modifiedResidueNameMap = getModifiedResidueNameMap(format);
+ const modifiedResidues = getModifiedResidueNameMap(format);
const asymIdSerialMap = getAsymIdSerialMap(format)
const chemicalComponentMap = getChemicalComponentMap(format)
@@ -143,14 +146,14 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
modelNum: atom_site.pdbx_PDB_model_num.value(0),
entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, entities, atomic.hierarchy, modifiedResidueNameMap),
+ sequence: getSequence(format.data, entities, atomic.hierarchy, modifiedResidues.parentId),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- modifiedResidueNameMap,
+ modifiedResidues,
asymIdSerialMap,
chemicalComponentMap
},
@@ -163,7 +166,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
function createModelIHM(format: mmCIF_Format, data: IHMData): Model {
const atomic = getAtomicHierarchyAndConformation(format, data.atom_site, data.entities);
const coarse = getIHMCoarse(data);
- const modifiedResidueNameMap = getModifiedResidueNameMap(format);
+ const modifiedResidues = getModifiedResidueNameMap(format);
const asymIdSerialMap = getAsymIdSerialMap(format)
const chemicalComponentMap = getChemicalComponentMap(format)
@@ -174,14 +177,14 @@ function createModelIHM(format: mmCIF_Format, data: IHMData): Model {
modelNum: data.model_id,
entities: data.entities,
symmetry: getSymmetry(format),
- sequence: getSequence(format.data, data.entities, atomic.hierarchy, modifiedResidueNameMap),
+ sequence: getSequence(format.data, data.entities, atomic.hierarchy, modifiedResidues.parentId),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
- modifiedResidueNameMap,
+ modifiedResidues,
asymIdSerialMap,
chemicalComponentMap
},
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
index 21761059d9308730ab07eaf1e7b29c60a1555441..1cdbcb6be294603128c847379e1c885ae60ad6ee 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
@@ -141,7 +141,7 @@ export namespace ComponentBond {
loc.unit = unit;
while (residues.hasNext) {
const seg = residues.move();
- loc.element = seg.start;
+ loc.element = unit.elements[seg.start];
names.add(prop(loc));
}
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 4ffd21aac6f6cb8f6b3e1dfa21d6cedc49475025..03c962fde8304a20953a3d7906173f45d4d32de8 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -42,7 +42,10 @@ export interface Model extends Readonly<{
/** secondary structure provided by the input file */
readonly secondaryStructure: SecondaryStructure,
/** maps modified residue name to its parent */
- readonly modifiedResidueNameMap: Map<string, string>,
+ readonly modifiedResidues: {
+ parentId: Map<string, string>,
+ details: Map<string, string>
+ },
/** maps asym id to unique serial number */
readonly asymIdSerialMap: Map<string, number>
/** maps residue name to `ChemicalComponent` data */
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
index ecb4cea9ef649cc4c03057d010903d421627002b..9000205da2eb9c4aaa1c77141abdde5adecba0ac 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -7,7 +7,7 @@
import Query from './query'
import Selection from './selection'
import { StructureElement, Unit, StructureProperties as P } from '../structure'
-import { OrderedSet, Segmentation } from 'mol-data/int'
+import { Segmentation } from 'mol-data/int'
import { LinearGroupingBuilder } from './utils/builders';
export const all: Query.Provider = async (s, ctx) => Selection.Singletons(s, s);
@@ -87,20 +87,20 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
while (chainsIt.hasNext) {
const chainSegment = chainsIt.move();
- l.element = OrderedSet.getAt(elements, chainSegment.start);
+ l.element = elements[chainSegment.start];
// test entity and chain
if (!entityTest(l) || !chainTest(l)) continue;
residuesIt.setSegment(chainSegment);
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();
- l.element = OrderedSet.getAt(elements, residueSegment.start);
+ l.element = elements[residueSegment.start];
// test residue
if (!residueTest(l)) continue;
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- l.element = OrderedSet.getAt(elements, j);
+ l.element = elements[j];
if (atomTest(l)) {
builder.addElement(l.element);
}
@@ -134,20 +134,20 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
while (chainsIt.hasNext) {
const chainSegment = chainsIt.move();
- l.element = OrderedSet.getAt(elements, chainSegment.start);
+ l.element = elements[chainSegment.start];
// test entity and chain
if (!entityTest(l) || !chainTest(l)) continue;
residuesIt.setSegment(chainSegment);
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();
- l.element = OrderedSet.getAt(elements, residueSegment.start);
+ l.element = elements[residueSegment.start];
// test residue
if (!residueTest(l)) continue;
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- l.element = OrderedSet.getAt(elements, j);
+ l.element = elements[j];
if (atomTest(l)) builder.add(groupBy(l), unit.id, l.element);
}
}