diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index cc83cba84f042faceab0beb0824f2ae8ae3bf3bb..e720997deff5274fea83daf79a74e54640f176aa 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, Element, StructureProperties } from 'mol-model/structure';
+import { Unit, Element, StructureProperties, ElementIndex } 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: Element.Location) {
return traceName
}
-function setTraceElement(l: Element.Location, residueSegment: Segmentation.Segment<Element>) {
+function setTraceElement(l: Element.Location, residueSegment: Segmentation.Segment<ElementIndex>) {
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<Element>
- private residueIt: SegmentIterator<Element>
- private polymerSegment: Segmentation.Segment<Element>
+ private polymerIt: SegmentIterator<ElementIndex>
+ private residueIt: SegmentIterator<ElementIndex>
+ private polymerSegment: Segmentation.Segment<ElementIndex>
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<Element>
- private polymerSegment: Segmentation.Segment<Element>
+ private polymerIt: SegmentIterator<ElementIndex>
+ private polymerSegment: Segmentation.Segment<ElementIndex>
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<Element>
- private residueIt: SegmentIterator<Element>
+ private polymerIt: SegmentIterator<ElementIndex>
+ private residueIt: SegmentIterator<ElementIndex>
// private polymerSegment: Segmentation.Segment<Element>
// private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
// private pos: SymmetryOperator.CoordinateMapper
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index 1236e534540309826fe5b69d1ca24fb2546e3e94..2612b3324834024558e3280fca57b2e9dd6bc0fc 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -13,6 +13,7 @@ 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');
@@ -91,7 +92,7 @@ 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<Element>, move = true;
+ let current: Segmentation.Segment<ElementIndex>, move = true;
while (residues.hasNext) {
if (move) current = residues.move();
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index d9ddcd2b07c529eb5cf1cdb17665f578cfab769b..14ef548036c16fc27dd53a15fe7a41dccdb8129d 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -8,7 +8,7 @@ import { Column, Table } from 'mol-data/db';
import { Interval, Segmentation } from 'mol-data/int';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import UUID from 'mol-util/uuid';
-import { Element } from '../../../../structure';
+import { ElementIndex } from '../../../../structure';
import Format from '../../format';
import { Model } from '../../model';
import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../properties/atomic';
@@ -23,11 +23,11 @@ function findHierarchyOffsets(atom_site: AtomSite) {
if (atom_site._rowCount === 0) return { residues: [], polymers: [], chains: [] };
const start = 0, end = atom_site._rowCount;
- const residues = [start as Element], chains = [start as Element], polymers = [start as Element];
+ const residues = [start as ElementIndex], chains = [start as ElementIndex], polymers = [start as ElementIndex];
const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
- for (let i = start + 1; i < end; i++) {
+ for (let i = start + 1 as ElementIndex; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !label_seq_id.areValuesEqual(i - 1, i)
@@ -36,9 +36,9 @@ function findHierarchyOffsets(atom_site: AtomSite) {
|| !label_comp_id.areValuesEqual(i - 1, i);
const newPolymer = newResidue && label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
- if (newResidue) residues[residues.length] = i as Element;
- if (newPolymer) polymers[polymers.length] = i as Element;
- if (newChain) chains[chains.length] = i as Element;
+ if (newResidue) residues[residues.length] = i;
+ if (newPolymer) polymers[polymers.length] = i;
+ if (newChain) chains[chains.length] = i;
}
return { residues, polymers, chains };
}
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
index 2d79a18b9a7c5cbeb01388be27913613d356a49f..0d14fd75c581a37af39726f307fbec89219a1107 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
@@ -6,7 +6,7 @@
*/
import { Model } from '../../../model'
-import { Element, Structure } from '../../../../structure'
+import { Structure } from '../../../../structure'
import { LinkType } from '../../../types'
import { findEntityIdByAsymId, findAtomIndexByLabelName } from '../util'
import { Column } from 'mol-data/db'
@@ -14,6 +14,7 @@ import { ModelPropertyDescriptor } from '../../../properties/custom';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { SortedArray } from 'mol-data/int';
import { CifWriter } from 'mol-io/writer/cif'
+import { ElementIndex } from '../../../indexing';
export interface StructConn {
getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry>,
@@ -34,7 +35,7 @@ export namespace StructConn {
const strConn = get(ctx.model);
if (!strConn || strConn.entries.length === 0) return [];
- const foundAtoms = new Set<Element>();
+ const foundAtoms = new Set<ElementIndex>();
const indices: number[] = [];
for (const entry of strConn.entries) {
const { partners } = entry;
@@ -61,7 +62,7 @@ export namespace StructConn {
}
}
- function hasAtom({ units }: Structure, element: Element) {
+ function hasAtom({ units }: Structure, element: ElementIndex) {
for (let i = 0, _i = units.length; i < _i; i++) {
if (SortedArray.indexOf(units[i].elements, element) >= 0) return true;
}
@@ -132,7 +133,7 @@ export namespace StructConn {
distance: number,
order: number,
flags: number,
- partners: { residueIndex: number, atomIndex: Element, symmetry: string }[]
+ partners: { residueIndex: number, atomIndex: ElementIndex, symmetry: string }[]
}
type StructConnType =
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
index 1c93c716194329740575cde23028e263816f727e..35d307a4eb7953e4746efce1a10ef7f809b04798 100644
--- a/src/mol-model/structure/model/formats/mmcif/ihm.ts
+++ b/src/mol-model/structure/model/formats/mmcif/ihm.ts
@@ -12,7 +12,7 @@ import { getCoarseKeys } from '../../properties/utils/coarse-keys';
import { UUID } from 'mol-util';
import { Segmentation, Interval } from 'mol-data/int';
import { Mat3, Tensor } from 'mol-math/linear-algebra';
-import { Element } from '../../../structure'
+import { ElementIndex } from '../../indexing';
export interface IHMData {
model_id: number,
@@ -81,14 +81,14 @@ function getGaussianConformation(data: mmCIF['ihm_gaussian_obj_site']): CoarseGa
}
function getSegments(asym_id: Column<string>, seq_id_begin: Column<number>, seq_id_end: Column<number>) {
- const polymerOffsets = [0 as Element], chainOffsets = [0 as Element];
+ const polymerOffsets = [0 as ElementIndex], chainOffsets = [0 as ElementIndex];
for (let i = 1, _i = asym_id.rowCount; i < _i; i++) {
const newChain = !asym_id.areValuesEqual(i - 1, i);
const newPolymer = newChain
|| seq_id_end.value(i - 1) !== seq_id_begin.value(i) - 1;
- if (newPolymer) polymerOffsets[polymerOffsets.length] = i as Element;
- if (newChain) chainOffsets[chainOffsets.length] = i as Element;
+ if (newPolymer) polymerOffsets[polymerOffsets.length] = i as ElementIndex;
+ if (newChain) chainOffsets[chainOffsets.length] = i as ElementIndex;
}
return {
diff --git a/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
index 835b4c440a566eec10eb662de8df9a0b729fc1b6..b16448853b3f3705fe247da037ac9e1d6471e14f 100644
--- a/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
+++ b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
@@ -8,17 +8,18 @@ import { Model } from '../../../model'
import { Table } from 'mol-data/db'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { findAtomIndexByLabelName } from '../util';
-import { Element, Unit } from '../../../../structure';
+import { Unit } from '../../../../structure';
+import { ElementIndex } from '../../../indexing';
function findAtomIndex(model: Model, entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
if (!model.atomicHierarchy.atoms.auth_atom_id.isDefined) return -1
const residueIndex = model.atomicHierarchy.findResidueKey(entityId, compId, asymId, seqId, '')
if (residueIndex < 0) return -1
- return findAtomIndexByLabelName(model, residueIndex, atomId, '') as Element
+ return findAtomIndexByLabelName(model, residueIndex, atomId, '') as ElementIndex
}
export interface IHMCrossLinkRestraint {
- getIndicesByElement: (element: Element, kind: Unit.Kind) => number[]
+ getIndicesByElement: (element: ElementIndex, kind: Unit.Kind) => number[]
data: Table<mmCIF_Schema['ihm_cross_link_restraint']>
}
@@ -47,7 +48,7 @@ export namespace IHMCrossLinkRestraint {
atom_id: ihm_cross_link_restraint.atom_id_2,
}
- function _add(map: Map<Element, number[]>, element: Element, row: number) {
+ function _add(map: Map<ElementIndex, number[]>, element: ElementIndex, row: number) {
const indices = map.get(element)
if (indices) indices.push(row)
else map.set(element, [ row ])
@@ -60,14 +61,14 @@ export namespace IHMCrossLinkRestraint {
if (ihm_cross_link_restraint.model_granularity.value(row) === 'by-atom') {
const atomicElement = findAtomIndex(model, entityId, asymId, ps.comp_id.value(row), seqId, ps.atom_id.value(row))
- if (atomicElement >= 0) _add(atomicElementMap, atomicElement as Element, row)
+ if (atomicElement >= 0) _add(atomicElementMap, atomicElement as ElementIndex, row)
} else if (model.coarseHierarchy.isDefined) {
const sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId)
if (sphereElement >= 0) {
- _add(sphereElementMap, sphereElement as Element, row)
+ _add(sphereElementMap, sphereElement, row)
} else {
const gaussianElement = model.coarseHierarchy.gaussians.findSequenceKey(entityId, asymId, seqId)
- if (gaussianElement >= 0) _add(gaussianElementMap, gaussianElement as Element, row)
+ if (gaussianElement >= 0) _add(gaussianElementMap, gaussianElement, row)
}
}
}
@@ -81,11 +82,11 @@ export namespace IHMCrossLinkRestraint {
}
/** map from atomic element to cross link indices */
- const atomicElementMap: Map<Element, number[]> = new Map()
+ const atomicElementMap: Map<ElementIndex, number[]> = new Map()
/** map from sphere element to cross link indices */
- const sphereElementMap: Map<Element, number[]> = new Map()
+ const sphereElementMap: Map<ElementIndex, number[]> = new Map()
/** map from gaussian element to cross link indices */
- const gaussianElementMap: Map<Element, number[]> = new Map()
+ const gaussianElementMap: Map<ElementIndex, number[]> = new Map()
const emptyIndexArray: number[] = [];
@@ -95,7 +96,7 @@ export namespace IHMCrossLinkRestraint {
}
const crossLinkRestraint = {
- getIndicesByElement: (element: Element, kind: Unit.Kind) => {
+ getIndicesByElement: (element: ElementIndex, kind: Unit.Kind) => {
const map = getMapByKind(kind)
const idx = map.get(element)
return idx !== undefined ? idx : emptyIndexArray
diff --git a/src/mol-model/structure/model/formats/mmcif/util.ts b/src/mol-model/structure/model/formats/mmcif/util.ts
index 5747eb1664efbcfa782082f825939f98215aa52b..044dee3a6bc4aba02a65e9d047ec0c3e7afe2188 100644
--- a/src/mol-model/structure/model/formats/mmcif/util.ts
+++ b/src/mol-model/structure/model/formats/mmcif/util.ts
@@ -5,7 +5,7 @@
*/
import { Model } from '../../model'
-import { Element } from '../../../structure'
+import { ElementIndex } from '../../indexing';
export function findEntityIdByAsymId(model: Model, asymId: string) {
if (model.sourceData.kind !== 'mmCIF') return ''
@@ -16,11 +16,11 @@ export function findEntityIdByAsymId(model: Model, asymId: string) {
return ''
}
-export function findAtomIndexByLabelName(model: Model, residueIndex: number, atomName: string, altLoc: string | null): Element {
+export function findAtomIndexByLabelName(model: Model, residueIndex: number, atomName: string, altLoc: string | null): ElementIndex {
const { offsets } = model.atomicHierarchy.residueAtomSegments;
const { label_atom_id, label_alt_id } = model.atomicHierarchy.atoms;
for (let i = offsets[residueIndex], n = offsets[residueIndex + 1]; i < n; ++i) {
- if (label_atom_id.value(i) === atomName && (!altLoc || label_alt_id.value(i) === altLoc)) return i as Element;
+ if (label_atom_id.value(i) === atomName && (!altLoc || label_alt_id.value(i) === altLoc)) return i as ElementIndex;
}
- return -1 as Element;
+ return -1 as ElementIndex;
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 0a924c80db34f953d9303643a0e3e6a1c0f6d07e..28b33a32140281c33c7cd91291507b032dd1040c 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -8,8 +8,8 @@ import { Column, Table } from 'mol-data/db'
import { Segmentation } from 'mol-data/int'
import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol } from '../../types'
-import { Element } from '../../../structure'
-import { ChainIndex, EntityIndex, ResidueIndex } from '../../indexing';
+// import { Element } from '../../../structure'
+import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../indexing';
export const AtomsSchema = {
type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
@@ -50,7 +50,7 @@ export interface AtomicData {
export interface AtomicSegments {
/** Maps residueIndex to a range of atoms [segments[rI], segments[rI + 1]) */
- residueAtomSegments: Segmentation<Element, ResidueIndex>,
+ residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>,
/**
* Maps chainIndex to a range of atoms [segments[cI], segments[cI + 1]),
*
@@ -59,12 +59,12 @@ export interface AtomicSegments {
* const start = rI[offsets[i]], const end = rI[offsets[i + 1] - 1] + 1;
* for (let j = start; j < end; i++) { }
*/
- chainAtomSegments: Segmentation<Element, ChainIndex>,
+ chainAtomSegments: Segmentation<ElementIndex, ChainIndex>,
/**
* bonded/connected stretches of polymer chains, i.e. a chain will be
* broken into multiple polymer segments if there are missing residues
*/
- polymerAtomSegments: Segmentation<Element>
+ polymerAtomSegments: Segmentation<ElementIndex>
// TODO: include entity segments?
}
diff --git a/src/mol-model/structure/model/properties/coarse/hierarchy.ts b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
index 57d3da0acaac976009976324824438a94ae7ee2e..89e74fcba953e92e1b7517a7195a59df355f3023 100644
--- a/src/mol-model/structure/model/properties/coarse/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
@@ -7,7 +7,7 @@
import { Column } from 'mol-data/db'
import { Segmentation } from 'mol-data/int';
-import { Element } from '../../../structure'
+import { ElementIndex, ChainIndex } from '../../indexing';
export interface CoarsedElementKeys {
// assign a key to each element
@@ -16,8 +16,8 @@ export interface CoarsedElementKeys {
entityKey: ArrayLike<number>,
/** find index of the residue/feature element where seq_id is included */
- findSequenceKey(entityId: string, asym_id: string, seq_id: number): number
- findChainKey(entityId: string, asym_id: string): number
+ findSequenceKey(entityId: string, asym_id: string, seq_id: number): ElementIndex
+ findChainKey(entityId: string, asym_id: string): ChainIndex
}
export interface CoarseElementData {
@@ -27,12 +27,12 @@ export interface CoarseElementData {
seq_id_begin: Column<number>,
seq_id_end: Column<number>,
- chainSegments: Segmentation<Element>,
+ chainSegments: Segmentation<ElementIndex>,
/**
* bonded/connected stretches of polymer chains, i.e. a chain will be
* broken into multiple polymer segments if there are missing residues
*/
- polymerSegments: Segmentation<Element>
+ polymerSegments: Segmentation<ElementIndex>
}
export type CoarseElements = CoarsedElementKeys & CoarseElementData
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
index 4e4f613018db6b5495a774165d6b897f5edf27e3..ac3b75edfe7306685a3ce595531e8a5fb4b161e2 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-keys.ts
+++ b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
@@ -7,6 +7,7 @@
import { Entities } from '../common';
import { CoarseElementData, CoarsedElementKeys } from '../coarse';
+import { ChainIndex, ElementIndex } from '../../indexing';
function getElementKey(map: Map<string, number>, key: string, counter: { index: number }) {
if (map.has(key)) return map.get(key)!;
@@ -26,22 +27,22 @@ function createLookUp(entities: Entities, chain: Map<number, Map<string, number>
const getEntKey = entities.getEntityIndex;
const findChainKey: CoarsedElementKeys['findChainKey'] = (e, c) => {
const eKey = getEntKey(e);
- if (eKey < 0) return -1;
+ if (eKey < 0) return -1 as ChainIndex;
const cm = chain.get(eKey)!;
- if (!cm.has(c)) return -1;
- return cm.get(c)!;
+ if (!cm.has(c)) return -1 as ChainIndex;
+ return cm.get(c)! as ChainIndex;
}
// TODO consider implementing as binary search
const findSequenceKey: CoarsedElementKeys['findSequenceKey'] = (e, c, s) => {
const eKey = getEntKey(e);
- if (eKey < 0) return -1;
+ if (eKey < 0) return -1 as ElementIndex;
const cm = chain.get(eKey);
- if (cm === undefined) return -1
+ if (cm === undefined) return -1 as ElementIndex
const cKey = cm.get(c)
- if (cKey === undefined) return -1
+ if (cKey === undefined) return -1 as ElementIndex
const sm = seq.get(cKey)!
- if (!sm.has(s)) return -1;
- return sm.get(s)!
+ if (!sm.has(s)) return -1 as ElementIndex;
+ return sm.get(s)! as ElementIndex
}
return { findChainKey, findSequenceKey };
}
diff --git a/src/mol-model/structure/query/utils/builders.ts b/src/mol-model/structure/query/utils/builders.ts
index 0abce36d09e40a367f5a8cbb36589f6fd31d1667..78125994547aeac5b4330f38a55193a96ca5fefb 100644
--- a/src/mol-model/structure/query/utils/builders.ts
+++ b/src/mol-model/structure/query/utils/builders.ts
@@ -9,6 +9,7 @@ import Selection from '../selection';
import { HashSet } from 'mol-data/generic';
import { structureUnion } from './structure';
import { StructureSubsetBuilder } from '../../structure/util/subset-builder';
+import { ElementIndex } from '../../model';
export class UniqueStructuresBuilder {
private set = HashSet(Structure.hashCode, Structure.areEqual);
@@ -36,7 +37,7 @@ export class LinearGroupingBuilder {
private builders: StructureSubsetBuilder[] = [];
private builderMap = new Map<string, StructureSubsetBuilder>();
- add(key: any, unit: number, element: Element) {
+ add(key: any, unit: number, element: ElementIndex) {
let b = this.builderMap.get(key);
if (!b) {
b = this.source.subsetBuilder(true);
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 819d17687ebacafb5e48a0fd4abf885876b9d9a1..07fd061c31cba602ac379c0145e0f1a27cc67b48 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -6,12 +6,13 @@
import { OrderedSet, SortedArray } from 'mol-data/int'
import Unit from './unit'
+import { ElementIndex } from '../model';
/** Element index in Model */
-type Element = { readonly '@type': 'element' } & number
+// type Element = { readonly '@type': 'element' } & number
namespace Element {
- export type Set = SortedArray<Element>
+ export type Set = SortedArray<ElementIndex>
/** Index into Unit.elements */
export type Index = { readonly '@type': 'element-index' } & number
@@ -20,9 +21,9 @@ namespace Element {
export interface Location<U = Unit> {
unit: U,
/** Index into element (atomic/coarse) properties of unit.model */
- element: Element
+ element: ElementIndex
}
- export function Location(unit?: Unit, element?: Element): Location { return { unit: unit as any, element: element || (0 as Element) }; }
+ export function Location(unit?: Unit, element?: ElementIndex): Location { return { unit: unit as any, element: element || (0 as ElementIndex) }; }
export interface Property<T> { (location: Location): T }
export interface Predicate extends Property<boolean> { }
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index d5f053a437c7972c30f5ff943b0645f7f44c5d18..8e939081ffdfa8c4121dc110681ca599ea97e86d 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -7,7 +7,7 @@
import { IntMap, SortedArray, Iterator, Segmentation } from 'mol-data/int'
import { UniqueArray } from 'mol-data/generic'
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
-import { Model } from '../model'
+import { Model, ElementIndex } from '../model'
import { sort, arraySwap, hash1, sortArray } from 'mol-data/util';
import Element from './element'
import Unit from './unit'
@@ -131,7 +131,7 @@ namespace Structure {
c++;
}
- const elements = SortedArray.ofBounds(start as Element, chains.offsets[c + 1] as Element);
+ const elements = SortedArray.ofBounds(start as ElementIndex, chains.offsets[c + 1] as ElementIndex);
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
}
@@ -151,7 +151,7 @@ namespace Structure {
function addCoarseUnits(builder: StructureBuilder, model: Model, elements: CoarseElements, kind: Unit.Kind) {
const { chainSegments } = elements;
for (let cI = 0; cI < chainSegments.count; cI++) {
- const elements = SortedArray.ofBounds(chainSegments.offsets[cI] as Element, chainSegments.offsets[cI + 1] as Element);
+ const elements = SortedArray.ofBounds<ElementIndex>(chainSegments.offsets[cI], chainSegments.offsets[cI + 1]);
builder.addUnit(kind, model, SymmetryOperator.Default, elements);
}
}
diff --git a/src/mol-model/structure/structure/util/subset-builder.ts b/src/mol-model/structure/structure/util/subset-builder.ts
index 96732ebb5ec238baae6839ef54feeee3f8777826..35b2b1f17db34aad453b70c144c62d8cc571129c 100644
--- a/src/mol-model/structure/structure/util/subset-builder.ts
+++ b/src/mol-model/structure/structure/util/subset-builder.ts
@@ -10,15 +10,16 @@ import Element from '../element';
import StructureSymmetry from '../symmetry';
import Unit from '../unit';
import Structure from '../structure';
+import { ElementIndex } from '../../model';
export class StructureSubsetBuilder {
private ids: number[] = [];
- private unitMap = IntMap.Mutable<Element[]>();
+ private unitMap = IntMap.Mutable<ElementIndex[]>();
private parentId = -1;
- private currentUnit: Element[] = [];
+ private currentUnit: ElementIndex[] = [];
elementCount = 0;
- addToUnit(parentId: number, e: Element) {
+ addToUnit(parentId: number, e: ElementIndex) {
const unit = this.unitMap.get(parentId);
if (!!unit) { unit[unit.length] = e; }
else {
@@ -33,7 +34,7 @@ export class StructureSubsetBuilder {
this.currentUnit = this.currentUnit.length > 0 ? [] : this.currentUnit;
}
- addElement(e: Element) {
+ addElement(e: ElementIndex) {
this.currentUnit[this.currentUnit.length] = e;
this.elementCount++;
}
@@ -45,9 +46,9 @@ export class StructureSubsetBuilder {
this.parentId = -1;
}
- setUnit(parentId: number, elements: ArrayLike<Element>) {
+ setUnit(parentId: number, elements: ArrayLike<ElementIndex>) {
this.ids[this.ids.length] = parentId;
- this.unitMap.set(parentId, elements as Element[]);
+ this.unitMap.set(parentId, elements as ElementIndex[]);
this.elementCount += elements.length;
}