diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 9c7f0d9a9876f39c78cd5887f9696ef377c1ea4b..85f118dea62635a631fdf061429976276887b339 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -72,20 +72,45 @@ export function printSecStructure(model: Model) {
}
}
-export function printBonds(structure: Structure) {
- for (const unit of structure.units) {
- if (!Unit.isAtomic(unit)) continue;
+export function printLinks(structure: Structure, showIntra: boolean, showInter: boolean) {
+ if (showIntra) {
+ console.log('\nIntra Unit Links\n=============');
+ for (const unit of structure.units) {
+ if (!Unit.isAtomic(unit)) continue;
+
+ const elements = unit.elements;
+ const { a, b } = unit.links;
+ const { model } = unit;
+
+ if (!a.length) continue;
+
+ for (let bI = 0, _bI = a.length; bI < _bI; bI++) {
+ const x = a[bI], y = b[bI];
+ if (x >= y) continue;
+ console.log(`${atomLabel(model, elements[x])} -- ${atomLabel(model, elements[y])}`);
+ }
+ }
+ }
- const elements = unit.elements;
- const { a, b } = unit.bonds;
- const { model } = unit;
+ if (showInter) {
+ console.log('\nInter Unit Links\n=============');
+ const links = structure.links;
+ for (const unit of structure.units) {
+ if (!Unit.isAtomic(unit)) continue;
+
+ for (const pairLinks of links.getLinkedUnits(unit)) {
+ if (!pairLinks.areUnitsOrdered) continue;
- if (!a.length) continue;
+ const { unitA, unitB } = pairLinks;
- for (let bI = 0, _bI = a.length; bI < _bI; bI++) {
- const x = a[bI], y = b[bI];
- if (x >= y) continue;
- console.log(`${atomLabel(model, elements[x])} -- ${atomLabel(model, elements[y])}`);
+ console.log(`${pairLinks.unitA.id} - ${pairLinks.unitB.id}: ${pairLinks.bondCount} bond(s)`);
+
+ for (const aI of pairLinks.linkedElementIndices) {
+ for (const link of pairLinks.getBonds(aI)) {
+ console.log(`${atomLabel(unitA.model, unitA.elements[aI])} -- ${atomLabel(unitB.model, unitB.elements[link.indexB])}`);
+ }
+ }
+ }
}
}
}
@@ -160,7 +185,7 @@ async function run(mmcif: mmCIF_Database) {
//printIHMModels(models[0]);
printUnits(structure);
printRings(structure);
- //printBonds(structure);
+ printLinks(structure, false, true);
//printSecStructure(models[0]);
}
@@ -175,13 +200,13 @@ async function runFile(filename: string) {
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
- description: 'Print info about a structure, mainly to test and showcase the mol-model module'
+ addHelp: true,
+ description: 'Print info about a structure, mainly to test and showcase the mol-model module'
});
-parser.addArgument([ '--download', '-d' ], {
+parser.addArgument(['--download', '-d'], {
help: 'Pdb entry id'
});
-parser.addArgument([ '--file', '-f' ], {
+parser.addArgument(['--file', '-f'], {
help: 'filename'
});
interface Args {
diff --git a/src/mol-geo/representation/structure/bond.ts b/src/mol-geo/representation/structure/bond.ts
index afb2cf89c183e25db5c24fa9f47efa2d7784f8ad..d4a30eea3782caabe13842b41d3190757d578369 100644
--- a/src/mol-geo/representation/structure/bond.ts
+++ b/src/mol-geo/representation/structure/bond.ts
@@ -8,7 +8,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, Element, Bond } from 'mol-model/structure';
+import { Unit, Element, Link } from 'mol-model/structure';
import { UnitsRepresentation, DefaultStructureProps } from './index';
import { Task } from 'mol-task'
import { createTransforms } from './utils';
@@ -29,7 +29,7 @@ function createBondMesh(unit: Unit, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const elements = unit.elements;
- const bonds = unit.bonds
+ const bonds = unit.links
const { edgeCount, a, b } = bonds
if (!edgeCount) return Mesh.createEmpty(mesh)
@@ -96,7 +96,7 @@ export default function BondUnitsRepresentation(): UnitsRepresentation<BondProps
currentGroup = group
const unit = group.units[0]
- const elementCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0
+ const elementCount = Unit.isAtomic(unit) ? unit.links.edgeCount * 2 : 0
const instanceCount = group.units.length
mesh = await createBondMesh(unit).runAsChild(ctx, 'Computing bond mesh')
@@ -164,11 +164,11 @@ export default function BondUnitsRepresentation(): UnitsRepresentation<BondProps
const { objectId, instanceId, elementId } = pickingId
const unit = currentGroup.units[instanceId]
if (cylinders.id === objectId && Unit.isAtomic(unit)) {
- return Bond.Loci([{
+ return Link.Loci([{
aUnit: unit,
- aIndex: unit.bonds.a[elementId],
+ aIndex: unit.links.a[elementId],
bUnit: unit,
- bIndex: unit.bonds.b[elementId]
+ bIndex: unit.links.b[elementId]
}])
}
return null
@@ -179,7 +179,7 @@ export default function BondUnitsRepresentation(): UnitsRepresentation<BondProps
const unit = group.units[0]
if (!Unit.isAtomic(unit)) return
- const elementCount = unit.bonds.edgeCount * 2
+ const elementCount = unit.links.edgeCount * 2
const instanceCount = group.units.length
let changed = false
@@ -187,11 +187,11 @@ export default function BondUnitsRepresentation(): UnitsRepresentation<BondProps
if (isEveryLoci(loci)) {
applyFlagAction(array, 0, elementCount * instanceCount, action)
changed = true
- } else if (Bond.isLoci(loci)) {
- for (const b of loci.bonds) {
+ } else if (Link.isLoci(loci)) {
+ for (const b of loci.links) {
const unitIdx = Unit.findUnitById(b.aUnit.id, group.units)
if (unitIdx !== -1) {
- const _idx = unit.bonds.getEdgeIndex(b.aIndex, b.bIndex)
+ const _idx = unit.links.getEdgeIndex(b.aIndex, b.bIndex)
if (_idx !== -1) {
const idx = _idx
if (applyFlagAction(array, idx, idx + 1, action) && !changed) {
diff --git a/src/mol-math/graph.ts b/src/mol-math/graph.ts
index f152b30c290df2178546c272a5008bb6f9ce65ae..f1e24c2f39e5cbaef4ae6e7c6f8e5d1ed5dc9f05 100644
--- a/src/mol-math/graph.ts
+++ b/src/mol-math/graph.ts
@@ -4,4 +4,4 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-export * from './graph/int-graph'
\ No newline at end of file
+export * from './graph/int-adjacency-graph'
\ No newline at end of file
diff --git a/src/mol-math/graph/_spec/int-graph.spec.ts b/src/mol-math/graph/_spec/int-graph.spec.ts
index 25319d11850f360bc3420b0dfc1ff6c9ecdff965..5d0315e658ef3e3662a08149f8d10b18cfe770ba 100644
--- a/src/mol-math/graph/_spec/int-graph.spec.ts
+++ b/src/mol-math/graph/_spec/int-graph.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { IntGraph } from '../int-graph';
+import { IntAdjacencyGraph } from '../int-adjacency-graph';
describe('IntGraph', () => {
const vc = 3;
@@ -12,7 +12,7 @@ describe('IntGraph', () => {
const ys = [1, 2, 0];
const _prop = [10, 11, 12];
- const builder = new IntGraph.EdgeBuilder(vc, xs, ys);
+ const builder = new IntAdjacencyGraph.EdgeBuilder(vc, xs, ys);
const prop: number[] = new Array(builder.slotCount);
for (let i = 0; i < builder.edgeCount; i++) {
builder.addNextEdge();
@@ -35,7 +35,7 @@ describe('IntGraph', () => {
});
it('induce', () => {
- const induced = IntGraph.induceByVertices(graph, [1, 2]);
+ const induced = IntAdjacencyGraph.induceByVertices(graph, [1, 2]);
expect(induced.vertexCount).toBe(2);
expect(induced.edgeCount).toBe(1);
expect(induced.edgeProps.prop[induced.getEdgeIndex(0, 1)]).toBe(11);
diff --git a/src/mol-math/graph/int-graph.ts b/src/mol-math/graph/int-adjacency-graph.ts
similarity index 88%
rename from src/mol-math/graph/int-graph.ts
rename to src/mol-math/graph/int-adjacency-graph.ts
index 601196214baae16264b22823d262b0e33e9879b5..8b5af369dbd1e71e6e166311c67d61bb11036d77 100644
--- a/src/mol-math/graph/int-graph.ts
+++ b/src/mol-math/graph/int-adjacency-graph.ts
@@ -1,11 +1,11 @@
-import { arrayPickIndices } from 'mol-data/util';
-
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import { arrayPickIndices } from 'mol-data/util';
+
/**
* Represent a graph using vertex adjacency list.
*
@@ -14,7 +14,7 @@ import { arrayPickIndices } from 'mol-data/util';
*
* Edge properties are indexed same as in the arrays a and b.
*/
-interface IntGraph<EdgeProps extends IntGraph.EdgePropsBase = {}> {
+interface IntAdjacencyGraph<EdgeProps extends IntAdjacencyGraph.EdgePropsBase = {}> {
readonly offset: ArrayLike<number>,
readonly a: ArrayLike<number>,
readonly b: ArrayLike<number>,
@@ -33,10 +33,10 @@ interface IntGraph<EdgeProps extends IntGraph.EdgePropsBase = {}> {
getVertexEdgeCount(i: number): number
}
-namespace IntGraph {
+namespace IntAdjacencyGraph {
export type EdgePropsBase = { [name: string]: ArrayLike<any> }
- class IntGraphImpl implements IntGraph<any> {
+ class IntGraphImpl implements IntAdjacencyGraph<any> {
readonly vertexCount: number;
readonly edgeProps: object;
@@ -60,8 +60,8 @@ namespace IntGraph {
}
}
- export function create<EdgeProps extends IntGraph.EdgePropsBase = {}>(offset: ArrayLike<number>, a: ArrayLike<number>, b: ArrayLike<number>, edgeCount: number, edgeProps?: EdgeProps): IntGraph<EdgeProps> {
- return new IntGraphImpl(offset, a, b, edgeCount, edgeProps) as IntGraph<EdgeProps>;
+ export function create<EdgeProps extends IntAdjacencyGraph.EdgePropsBase = {}>(offset: ArrayLike<number>, a: ArrayLike<number>, b: ArrayLike<number>, edgeCount: number, edgeProps?: EdgeProps): IntAdjacencyGraph<EdgeProps> {
+ return new IntGraphImpl(offset, a, b, edgeCount, edgeProps) as IntAdjacencyGraph<EdgeProps>;
}
export class EdgeBuilder {
@@ -77,7 +77,7 @@ namespace IntGraph {
a: Int32Array;
b: Int32Array;
- createGraph<EdgeProps extends IntGraph.EdgePropsBase = {}>(edgeProps?: EdgeProps) {
+ createGraph<EdgeProps extends IntAdjacencyGraph.EdgePropsBase = {}>(edgeProps?: EdgeProps) {
return create(this.offsets, this.a, this.b, this.edgeCount, edgeProps);
}
@@ -135,7 +135,7 @@ namespace IntGraph {
}
}
- export function induceByVertices<P extends IntGraph.EdgePropsBase>(graph: IntGraph<P>, vertexIndices: ArrayLike<number>): IntGraph<P> {
+ export function induceByVertices<P extends IntAdjacencyGraph.EdgePropsBase>(graph: IntAdjacencyGraph<P>, vertexIndices: ArrayLike<number>): IntAdjacencyGraph<P> {
const { b, offset, vertexCount, edgeProps } = graph;
const vertexMap = new Int32Array(vertexCount);
for (let i = 0, _i = vertexIndices.length; i < _i; i++) vertexMap[vertexIndices[i]] = i + 1;
@@ -177,4 +177,4 @@ namespace IntGraph {
}
}
-export { IntGraph }
\ No newline at end of file
+export { IntAdjacencyGraph }
\ No newline at end of file
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 3d10cb93063593a236d649b6a2911b492c00d300..586ee66d308c5835340cb233bcfa78125f32487b 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -5,7 +5,7 @@
*/
import { Element } from './structure'
-import { Bond } from './structure/structure/unit/bonds'
+import { Link } from './structure/structure/unit/links'
/** A Loci that includes every loci */
export const EveryLoci = { kind: 'every-loci' as 'every-loci' }
@@ -14,4 +14,4 @@ export function isEveryLoci(x: any): x is EveryLoci {
return !!x && x.kind === 'every-loci';
}
-export type Loci = Element.Loci | Bond.Loci | EveryLoci
\ No newline at end of file
+export type Loci = Element.Loci | Link.Loci | EveryLoci
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds.ts b/src/mol-model/structure/model/formats/mmcif/bonds.ts
index 89abf70d400bf0da529f3841d875bbfbd83a968f..85dca86ac533fb4b06c00f1f4c9ce31884b77998 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds.ts
@@ -6,72 +6,82 @@
*/
import Model from '../../model'
-import { BondType } from '../../types'
+import { LinkType } from '../../types'
import { findEntityIdByAsymId, findAtomIndexByLabelName } from './util'
import { Column } from 'mol-data/db'
-import { IntraUnitBonds } from '../../../structure/unit/bonds';
-export class StructConn implements IntraUnitBonds.StructConn {
- private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
- private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
+export interface StructConn {
+ getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry>
+ getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry>
+}
+
+export interface ComponentBondInfo {
+ entries: Map<string, ComponentBondInfo.Entry>
+}
- private static _resKey(rA: number, rB: number) {
+export namespace StructConn {
+ function _resKey(rA: number, rB: number) {
if (rA < rB) return `${rA}-${rB}`;
return `${rB}-${rA}`;
}
-
- private getResiduePairIndex() {
- if (this._residuePairIndex) return this._residuePairIndex;
- this._residuePairIndex = new Map();
- for (const e of this.entries) {
- const ps = e.partners;
- const l = ps.length;
- for (let i = 0; i < l - 1; i++) {
- for (let j = i + i; j < l; j++) {
- const key = StructConn._resKey(ps[i].residueIndex, ps[j].residueIndex);
- if (this._residuePairIndex.has(key)) {
- this._residuePairIndex.get(key)!.push(e);
- } else {
- this._residuePairIndex.set(key, [e]);
+ const _emptyEntry: Entry[] = [];
+
+ class StructConnImpl implements StructConn {
+ private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
+ private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
+
+ private getResiduePairIndex() {
+ if (this._residuePairIndex) return this._residuePairIndex;
+ this._residuePairIndex = new Map();
+ for (const e of this.entries) {
+ const ps = e.partners;
+ const l = ps.length;
+ for (let i = 0; i < l - 1; i++) {
+ for (let j = i + i; j < l; j++) {
+ const key = _resKey(ps[i].residueIndex, ps[j].residueIndex);
+ if (this._residuePairIndex.has(key)) {
+ this._residuePairIndex.get(key)!.push(e);
+ } else {
+ this._residuePairIndex.set(key, [e]);
+ }
}
}
}
+ return this._residuePairIndex;
}
- return this._residuePairIndex;
- }
- private getAtomIndex() {
- if (this._atomIndex) return this._atomIndex;
- this._atomIndex = new Map();
- for (const e of this.entries) {
- for (const p of e.partners) {
- const key = p.atomIndex;
- if (this._atomIndex.has(key)) {
- this._atomIndex.get(key)!.push(e);
- } else {
- this._atomIndex.set(key, [e]);
+ private getAtomIndex() {
+ if (this._atomIndex) return this._atomIndex;
+ this._atomIndex = new Map();
+ for (const e of this.entries) {
+ for (const p of e.partners) {
+ const key = p.atomIndex;
+ if (this._atomIndex.has(key)) {
+ this._atomIndex.get(key)!.push(e);
+ } else {
+ this._atomIndex.set(key, [e]);
+ }
}
}
+ return this._atomIndex;
}
- return this._atomIndex;
- }
- private static _emptyEntry = [];
- getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry> {
- return this.getResiduePairIndex().get(StructConn._resKey(residueAIndex, residueBIndex)) || StructConn._emptyEntry;
- }
+ getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry> {
+ return this.getResiduePairIndex().get(_resKey(residueAIndex, residueBIndex)) || _emptyEntry;
+ }
- getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry> {
- return this.getAtomIndex().get(atomIndex) || StructConn._emptyEntry;
- }
+ getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry> {
+ return this.getAtomIndex().get(atomIndex) || _emptyEntry;
+ }
- constructor(public entries: StructConn.Entry[]) {
+ constructor(public entries: StructConn.Entry[]) {
+ }
}
-}
-export namespace StructConn {
- export interface Entry extends IntraUnitBonds.StructConnEntry {
+
+
+ export interface Entry {
distance: number,
order: number,
flags: number,
@@ -91,7 +101,7 @@ export namespace StructConn {
| 'saltbr'
export function create(model: Model): StructConn | undefined {
- if (model.sourceData.kind !== 'mmCIF') return
+ if (model.sourceData.kind !== 'mmCIF') return;
const { struct_conn } = model.sourceData.data;
if (!struct_conn._rowCount) return void 0;
@@ -150,7 +160,7 @@ export namespace StructConn {
const type = conn_type_id.value(i)! as StructConnType;
const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
- let flags = BondType.Flag.None;
+ let flags = LinkType.Flag.None;
let order = 1;
switch (orderType) {
@@ -166,22 +176,22 @@ export namespace StructConn {
case 'covale_phosphate':
case 'covale_sugar':
case 'modres':
- flags = BondType.Flag.Covalent;
+ flags = LinkType.Flag.Covalent;
break;
- case 'disulf': flags = BondType.Flag.Covalent | BondType.Flag.Sulfide; break;
- case 'hydrog': flags = BondType.Flag.Hydrogen; break;
- case 'metalc': flags = BondType.Flag.MetallicCoordination; break;
- case 'saltbr': flags = BondType.Flag.Ion; break;
+ case 'disulf': flags = LinkType.Flag.Covalent | LinkType.Flag.Sulfide; break;
+ case 'hydrog': flags = LinkType.Flag.Hydrogen; break;
+ case 'metalc': flags = LinkType.Flag.MetallicCoordination; break;
+ case 'saltbr': flags = LinkType.Flag.Ion; break;
}
entries.push({ flags, order, distance: pdbx_dist_value.value(i), partners });
}
- return new StructConn(entries);
+ return new StructConnImpl(entries);
}
}
-export class ComponentBondInfo implements IntraUnitBonds.ComponentBondInfo {
+export class ComponentBondInfo implements ComponentBondInfo {
entries: Map<string, ComponentBondInfo.Entry> = new Map();
newEntry(id: string) {
@@ -192,7 +202,7 @@ export class ComponentBondInfo implements IntraUnitBonds.ComponentBondInfo {
}
export namespace ComponentBondInfo {
- export class Entry implements IntraUnitBonds.ComponentBondInfoEntry {
+ export class Entry implements Entry {
map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
add(a: string, b: string, order: number, flags: number, swap = true) {
@@ -238,9 +248,9 @@ export namespace ComponentBondInfo {
entry = info.newEntry(id);
}
- let flags: number = BondType.Flag.Covalent;
+ let flags: number = LinkType.Flag.Covalent;
let ord = 1;
- if (aromatic) flags |= BondType.Flag.Aromatic;
+ if (aromatic) flags |= LinkType.Flag.Aromatic;
switch (order.toLowerCase()) {
case 'doub':
case 'delo':
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 36d0cb935f3631e5fd0057526443f753472090f6..16c748b99b1d3d38f4a88614837ae8658acaed94 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -340,9 +340,9 @@ export const VdwRadii = {
}
export const DefaultVdwRadius = 2.0
-export interface BondType extends BitFlags<BondType.Flag> { }
-export namespace BondType {
- export const is: (b: BondType, f: Flag) => boolean = BitFlags.has
+export interface LinkType extends BitFlags<LinkType.Flag> { }
+export namespace LinkType {
+ export const is: (b: LinkType, f: Flag) => boolean = BitFlags.has
export const enum Flag {
None = 0x0,
Covalent = 0x1,
@@ -354,4 +354,8 @@ export namespace BondType {
Computed = 0x40
// currently at most 16 flags are supported!!
}
+
+ export function isCovalent(flags: LinkType.Flag) {
+ return (flags & LinkType.Flag.Covalent) !== 0;
+ }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index 44a299b2e5c3a9c41148e6298e8fc5488fb8c04d..bed8ae1fd045532d92ac1922e95cfdcd5b5afc04 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -8,6 +8,6 @@ import Element from './structure/element'
import Structure from './structure/structure'
import Unit from './structure/unit'
import StructureSymmetry from './structure/symmetry'
-import { Bond } from './structure/unit/bonds'
+import { Link } from './structure/unit/links'
-export { Element, Bond, Structure, Unit, StructureSymmetry }
\ No newline at end of file
+export { Element, Link, Structure, Unit, StructureSymmetry }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index cac54e0b559c6f488ad7541915907a1e5a57f061..52239bb46877b7f53cb2361fbe7345a60d445e57 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -15,6 +15,7 @@ import { StructureLookup3D } from './util/lookup3d';
import { CoarseElements } from '../model/properties/coarse';
import { StructureSubsetBuilder } from './util/subset-builder';
import { Queries } from '../query';
+import { InterUnitBonds, computeInterUnitBonds } from './unit/links';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -60,6 +61,13 @@ class Structure {
return this._lookup3d;
}
+ private _links?: InterUnitBonds = void 0;
+ get links() {
+ if (this._links) return this._links;
+ this._links = computeInterUnitBonds(this);
+ return this._links;
+ }
+
constructor(units: ArrayLike<Unit>) {
const map = IntMap.Mutable<Unit>();
let elementCount = 0;
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index e5ef8d9080ebf11d6b2b5b6e6f2a76353aee9a61..c5488a09bc76f1393318cc1b9c5620998a8daa8f 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -9,7 +9,7 @@ import { Model } from '../model'
import { GridLookup3D, Lookup3D } from 'mol-math/geometry'
import { SortedArray } from 'mol-data/int';
import { idFactory } from 'mol-util/id-factory';
-import { IntraUnitBonds, computeIntraUnitBonds } from './unit/bonds'
+import { IntraUnitLinks, computeIntraUnitBonds } from './unit/links'
import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
import { ValueRef } from 'mol-util';
import { UnitRings } from './unit/rings';
@@ -100,10 +100,10 @@ namespace Unit {
return this.props.lookup3d.ref;
}
- get bonds() {
- if (this.props.bonds.ref) return this.props.bonds.ref;
- this.props.bonds.ref = computeIntraUnitBonds(this);
- return this.props.bonds.ref;
+ get links() {
+ if (this.props.links.ref) return this.props.links.ref;
+ this.props.links.ref = computeIntraUnitBonds(this);
+ return this.props.links.ref;
}
get rings() {
@@ -127,12 +127,12 @@ namespace Unit {
interface AtomicProperties {
lookup3d: ValueRef<Lookup3D | undefined>,
- bonds: ValueRef<IntraUnitBonds | undefined>,
+ links: ValueRef<IntraUnitLinks | undefined>,
rings: ValueRef<UnitRings | undefined>
}
- function AtomicProperties() {
- return { lookup3d: ValueRef.create(void 0), bonds: ValueRef.create(void 0), rings: ValueRef.create(void 0) };
+ function AtomicProperties(): AtomicProperties {
+ return { lookup3d: ValueRef.create(void 0), links: ValueRef.create(void 0), rings: ValueRef.create(void 0) };
}
class Coarse<K extends Kind.Gaussians | Kind.Spheres, C extends CoarseSphereConformation | CoarseGaussianConformation> implements Base {
diff --git a/src/mol-model/structure/structure/unit/bonds/data.ts b/src/mol-model/structure/structure/unit/bonds/data.ts
deleted file mode 100644
index 0ffdd02fcbce683e436c0030ffe0517135c6ceda..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/bonds/data.ts
+++ /dev/null
@@ -1 +0,0 @@
-// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
deleted file mode 100644
index 0ffdd02fcbce683e436c0030ffe0517135c6ceda..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ /dev/null
@@ -1 +0,0 @@
-// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-data.ts b/src/mol-model/structure/structure/unit/bonds/inter-data.ts
deleted file mode 100644
index 0ffdd02fcbce683e436c0030ffe0517135c6ceda..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/bonds/inter-data.ts
+++ /dev/null
@@ -1 +0,0 @@
-// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
deleted file mode 100644
index ba344073c94604ba612a5dfafe4bd100770e30bb..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ /dev/null
@@ -1,214 +0,0 @@
-/**
- * Copyright (c) 2017 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { BondType, ElementSymbol } from '../../../model/types'
-import { IntraUnitBonds } from './intra-data'
-import { StructConn, ComponentBondInfo } from '../../../model/formats/mmcif/bonds'
-import Unit from '../../unit'
-import { IntGraph } from 'mol-math/graph';
-
-export interface BondComputationParameters {
- maxHbondLength: number,
- forceCompute: boolean
-}
-
-// H,D,T are all mapped to H
-const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
-
-const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
-
-const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
-
-const __DefaultBondingRadius = 2.001;
-
-const MetalsSet = (function () {
- const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
- const set = new Set<number>();
- for (const m of metals) {
- set.add(__ElementIndex[m]!);
- }
- return set;
-})();
-
-function pair(a: number, b: number) {
- if (a < b) return (a + b) * (a + b + 1) / 2 + b;
- else return (a + b) * (a + b + 1) / 2 + a;
-}
-
-function idx(e: ElementSymbol) {
- const i = __ElementIndex[e as any as string];
- if (i === void 0) return -1;
- return i;
-}
-
-function pairThreshold(i: number, j: number) {
- if (i < 0 || j < 0) return -1;
- const r = __ElementPairThresholds[pair(i, j)];
- if (r === void 0) return -1;
- return r;
-}
-
-function threshold(i: number) {
- if (i < 0) return __DefaultBondingRadius;
- const r = __ElementBondThresholds[i];
- if (r === void 0) return __DefaultBondingRadius;
- return r;
-}
-
-const H_ID = __ElementIndex['H']!;
-function isHydrogen(i: number) {
- return i === H_ID;
-}
-
-function getGraph(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number): IntraUnitBonds {
- const builder = new IntGraph.EdgeBuilder(atomCount, atomA, atomB);
- const flags = new Uint16Array(builder.slotCount);
- const order = new Int8Array(builder.slotCount);
- for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
- builder.addNextEdge();
- builder.assignProperty(flags, _flags[i]);
- builder.assignProperty(order, _order[i]);
- }
-
- return builder.createGraph({ flags, order });
-}
-
-function _computeBonds(unit: Unit.Atomic, params: BondComputationParameters): IntraUnitBonds {
- const MAX_RADIUS = 3;
-
- const { x, y, z } = unit.model.atomicConformation;
- const atomCount = unit.elements.length;
- const { elements: atoms, residueIndex } = unit;
- const { type_symbol, label_atom_id, label_alt_id } = unit.model.atomicHierarchy.atoms;
- const { label_comp_id } = unit.model.atomicHierarchy.residues;
- const query3d = unit.lookup3d;
-
- const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.create(unit.model) : void 0
- const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(unit.model) : void 0
-
- const atomA: number[] = [];
- const atomB: number[] = [];
- const flags: number[] = [];
- const order: number[] = [];
-
- let lastResidue = -1;
- let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
-
- for (let _aI = 0; _aI < atomCount; _aI++) {
- const aI = atoms[_aI];
- const raI = residueIndex[aI];
-
- if (!params.forceCompute && raI !== lastResidue) {
- const resn = label_comp_id.value(raI)!;
- if (!!component && component.entries.has(resn)) {
- componentMap = component.entries.get(resn)!.map;
- } else {
- componentMap = void 0;
- }
- }
- lastResidue = raI;
-
- const componentPairs = componentMap ? componentMap.get(label_atom_id.value(aI)) : void 0;
-
- const aeI = idx(type_symbol.value(aI)!);
-
- const { indices, count, squaredDistances } = query3d.find(x[aI], y[aI], z[aI], MAX_RADIUS);
- const isHa = isHydrogen(aeI);
- const thresholdA = threshold(aeI);
- const altA = label_alt_id.value(aI);
- const metalA = MetalsSet.has(aeI);
- const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
-
- for (let ni = 0; ni < count; ni++) {
- const _bI = indices[ni];
- const bI = atoms[_bI];
- if (bI <= aI) continue;
-
- const altB = label_alt_id.value(bI);
- if (altA && altB && altA !== altB) continue;
-
- const beI = idx(type_symbol.value(bI)!);
- const isMetal = metalA || MetalsSet.has(beI);
-
- const rbI = residueIndex[bI];
- // handle "component dictionary" bonds.
- if (raI === rbI && componentPairs) {
- const e = componentPairs.get(label_atom_id.value(bI)!);
- if (e) {
- atomA[atomA.length] = _aI;
- atomB[atomB.length] = _bI;
- order[order.length] = e.order;
- let flag = e.flags;
- if (isMetal) {
- if (flag | BondType.Flag.Covalent) flag ^= BondType.Flag.Covalent;
- flag |= BondType.Flag.MetallicCoordination;
- }
- flags[flags.length] = flag;
- }
- continue;
- }
-
- const isHb = isHydrogen(beI);
- if (isHa && isHb) continue;
-
- const dist = Math.sqrt(squaredDistances[ni]);
- if (dist === 0) continue;
-
- // handle "struct conn" bonds.
- if (structConnEntries && structConnEntries.length) {
- let added = false;
- for (const se of structConnEntries) {
- for (const p of se.partners) {
- if (p.atomIndex === bI) {
- atomA[atomA.length] = _aI;
- atomB[atomB.length] = _bI;
- flags[flags.length] = se.flags;
- order[order.length] = se.order;
- added = true;
- break;
- }
- }
- if (added) break;
- }
- if (added) continue;
- }
-
- if (isHa || isHb) {
- if (dist < params.maxHbondLength) {
- atomA[atomA.length] = _aI;
- atomB[atomB.length] = _bI;
- order[order.length] = 1;
- flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
- }
- continue;
- }
-
- const thresholdAB = pairThreshold(aeI, beI);
- const pairingThreshold = thresholdAB > 0
- ? thresholdAB
- : beI < 0 ? thresholdA : Math.max(thresholdA, threshold(beI));
-
-
- if (dist <= pairingThreshold) {
- atomA[atomA.length] = _aI;
- atomB[atomB.length] = _bI;
- order[order.length] = 1;
- flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
- }
- }
- }
-
- return getGraph(atomA, atomB, order, flags, atomCount);
-}
-
-function computeIntraUnitBonds(unit: Unit.Atomic, params?: Partial<BondComputationParameters>) {
- return _computeBonds(unit, {
- maxHbondLength: (params && params.maxHbondLength) || 1.15,
- forceCompute: !!(params && params.forceCompute),
- });
-}
-
-export { computeIntraUnitBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-data.ts b/src/mol-model/structure/structure/unit/bonds/intra-data.ts
deleted file mode 100644
index 9914145379663e38ce3882ef4634bd57ae3da57e..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/bonds/intra-data.ts
+++ /dev/null
@@ -1,38 +0,0 @@
-/**
- * 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 { BondType } from '../../../model/types'
-import { IntGraph } from 'mol-math/graph';
-
-type IntraUnitBonds = IntGraph<{ readonly order: ArrayLike<number>, readonly flags: ArrayLike<BondType.Flag> }>
-
-namespace IntraUnitBonds {
- export function createEmpty(): IntraUnitBonds {
- return IntGraph.create([], [], [], 0, { flags: [], order: [] });
- }
- export function isCovalent(flags: number) {
- return (flags & BondType.Flag.Covalent) !== 0;
- }
- export interface StructConnEntry {
- flags: BondType.Flag,
- order: number,
- distance: number,
- partners: { residueIndex: number, atomIndex: number, symmetry: string }[]
- }
- export interface StructConn {
- getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConnEntry>
- getAtomEntries(atomIndex: number): ReadonlyArray<StructConnEntry>
- }
- export interface ComponentBondInfoEntry {
- map: Map<string, Map<string, { order: number, flags: number }>>
- }
- export interface ComponentBondInfo {
- entries: Map<string, ComponentBondInfoEntry>
- }
-}
-
-export { IntraUnitBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds.ts b/src/mol-model/structure/structure/unit/links.ts
similarity index 58%
rename from src/mol-model/structure/structure/unit/bonds.ts
rename to src/mol-model/structure/structure/unit/links.ts
index d7268742832c8d7ff04d19199e218655ff48a099..20345c1bfd56e36caa39d01afe9d72ec38bc0aec 100644
--- a/src/mol-model/structure/structure/unit/bonds.ts
+++ b/src/mol-model/structure/structure/unit/links.ts
@@ -6,10 +6,11 @@
import { Unit } from '../../structure'
-export * from './bonds/intra-data'
-export * from './bonds/intra-compute'
+export * from './links/data'
+export * from './links/intra-compute'
+export * from './links/inter-compute'
-namespace Bond {
+namespace Link {
export interface Location {
readonly aUnit: Unit,
/** Index into aUnit.elements */
@@ -20,17 +21,17 @@ namespace Bond {
}
export interface Loci {
- readonly kind: 'bond-loci',
- readonly bonds: ReadonlyArray<Location>
+ readonly kind: 'link-loci',
+ readonly links: ReadonlyArray<Location>
}
- export function Loci(bonds: ArrayLike<Location>): Loci {
- return { kind: 'bond-loci', bonds: bonds as Loci['bonds'] };
+ export function Loci(links: ArrayLike<Location>): Loci {
+ return { kind: 'link-loci', links: links as Loci['links'] };
}
export function isLoci(x: any): x is Loci {
- return !!x && x.kind === 'bond-loci';
+ return !!x && x.kind === 'link-loci';
}
}
-export { Bond }
\ No newline at end of file
+export { Link }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/links/common.ts b/src/mol-model/structure/structure/unit/links/common.ts
new file mode 100644
index 0000000000000000000000000000000000000000..6457c86b89ae8bbfd20a33894dc118f271076b6d
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/links/common.ts
@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2017-2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { ElementSymbol } from '../../../model/types';
+
+export interface LinkComputationParameters {
+ maxHbondLength: number,
+ forceCompute: boolean
+}
+
+// H,D,T are all mapped to H
+const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
+
+const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
+
+const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
+
+const __DefaultBondingRadius = 2.001;
+
+export const MetalsSet = (function () {
+ const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
+ const set = new Set<number>();
+ for (const m of metals) {
+ set.add(__ElementIndex[m]!);
+ }
+ return set;
+})();
+
+function pair(a: number, b: number) {
+ if (a < b) return (a + b) * (a + b + 1) / 2 + b;
+ else return (a + b) * (a + b + 1) / 2 + a;
+}
+
+export function getElementIdx(e: ElementSymbol) {
+ const i = __ElementIndex[e as any as string];
+ if (i === void 0) return -1;
+ return i;
+}
+
+export function getElementPairThreshold(i: number, j: number) {
+ if (i < 0 || j < 0) return -1;
+ const r = __ElementPairThresholds[pair(i, j)];
+ if (r === void 0) return -1;
+ return r;
+}
+
+export function getElementThreshold(i: number) {
+ if (i < 0) return __DefaultBondingRadius;
+ const r = __ElementBondThresholds[i];
+ if (r === void 0) return __DefaultBondingRadius;
+ return r;
+}
+
+const H_ID = __ElementIndex['H']!;
+export function isHydrogen(i: number) {
+ return i === H_ID;
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/links/data.ts b/src/mol-model/structure/structure/unit/links/data.ts
new file mode 100644
index 0000000000000000000000000000000000000000..dfd9762c5a6fdc0578f94f56011bcd8605d7cbc0
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/links/data.ts
@@ -0,0 +1,59 @@
+/**
+ * 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 { LinkType } from '../../../model/types'
+import { IntAdjacencyGraph } from 'mol-math/graph';
+import Unit from '../../unit';
+
+type IntraUnitLinks = IntAdjacencyGraph<{ readonly order: ArrayLike<number>, readonly flags: ArrayLike<LinkType.Flag> }>
+
+namespace IntraUnitLinks {
+ export const Empty: IntraUnitLinks = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
+}
+
+class InterUnitBonds {
+ getLinkedUnits(unit: Unit): ReadonlyArray<InterUnitBonds.UnitPairBonds> {
+ if (!this.map.has(unit.id)) return emptyArray;
+ return this.map.get(unit.id)!;
+ }
+
+ constructor(private map: Map<number, InterUnitBonds.UnitPairBonds[]>) {
+ }
+}
+
+namespace InterUnitBonds {
+ export class UnitPairBonds {
+ hasBonds(indexA: number) {
+ return this.linkMap.has(indexA);
+ }
+
+ getBonds(indexA: number): ReadonlyArray<InterUnitBonds.BondInfo> {
+ if (!this.linkMap.has(indexA)) return emptyArray;
+ return this.linkMap.get(indexA)!;
+ }
+
+ get areUnitsOrdered() {
+ return this.unitA.id < this.unitB.id;
+ }
+
+ constructor(public unitA: Unit.Atomic, public unitB: Unit.Atomic,
+ public bondCount: number, public linkedElementIndices: ReadonlyArray<number>,
+ private linkMap: Map<number, BondInfo[]>) {
+ }
+ }
+
+ export interface BondInfo {
+ /** indexInto */
+ readonly indexB: number,
+ readonly order: number,
+ readonly flag: LinkType.Flag
+ }
+}
+
+const emptyArray: any[] = [];
+
+export { IntraUnitLinks, InterUnitBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/links/inter-compute.ts b/src/mol-model/structure/structure/unit/links/inter-compute.ts
new file mode 100644
index 0000000000000000000000000000000000000000..abb607102bf62788d4652fd7440737c1b91b6d85
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/links/inter-compute.ts
@@ -0,0 +1,149 @@
+/**
+ * Copyright (c) 2017 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructConn } from '../../../model/formats/mmcif/bonds';
+import { LinkType } from '../../../model/types';
+import Structure from '../../structure';
+import Unit from '../../unit';
+import { getElementIdx, getElementPairThreshold, getElementThreshold, isHydrogen, LinkComputationParameters, MetalsSet } from './common';
+import { InterUnitBonds } from './data';
+import { UniqueArray } from 'mol-data/generic';
+
+const MAX_RADIUS = 4;
+
+function addMapEntry<A, B>(map: Map<A, B[]>, a: A, b: B) {
+ if (map.has(a)) map.get(a)!.push(b);
+ else map.set(a, [b]);
+}
+
+interface PairState {
+ mapAB: Map<number, InterUnitBonds.BondInfo[]>,
+ mapBA: Map<number, InterUnitBonds.BondInfo[]>,
+ bondedA: UniqueArray<number, number>,
+ bondedB: UniqueArray<number, number>
+}
+
+function addLink(indexA: number, indexB: number, order: number, flag: LinkType.Flag, state: PairState) {
+ addMapEntry(state.mapAB, indexA, { indexB, order, flag });
+ addMapEntry(state.mapBA, indexB, { indexB: indexA, order, flag });
+ UniqueArray.add(state.bondedA, indexA, indexA);
+ UniqueArray.add(state.bondedB, indexB, indexB);
+}
+
+function findPairLinks(unitA: Unit.Atomic, unitB: Unit.Atomic, params: LinkComputationParameters, map: Map<number, InterUnitBonds.UnitPairBonds[]>) {
+ const state: PairState = { mapAB: new Map(), mapBA: new Map(), bondedA: UniqueArray.create(), bondedB: UniqueArray.create() };
+ let bondCount = 0;
+
+ const { elements: atomsA, conformation: { x, y, z } } = unitA;
+ const { elements: atomsB } = unitB;
+ const atomCount = unitA.elements.length;
+
+ const { type_symbol: type_symbolA, label_alt_id: label_alt_idA } = unitA.model.atomicHierarchy.atoms;
+ const { type_symbol: type_symbolB, label_alt_id: label_alt_idB } = unitB.model.atomicHierarchy.atoms;
+ const { lookup3d } = unitB;
+ const structConn = unitA.model === unitB.model && unitA.model.sourceData.kind === 'mmCIF' ? StructConn.create(unitA.model) : void 0;
+
+ for (let _aI = 0; _aI < atomCount; _aI++) {
+ const aI = atomsA[_aI];
+
+ const aeI = getElementIdx(type_symbolA.value(aI));
+ const { indices, count, squaredDistances } = lookup3d.find(x(aI), y(aI), z(aI), MAX_RADIUS);
+ const isHa = isHydrogen(aeI);
+ const thresholdA = getElementThreshold(aeI);
+ const altA = label_alt_idA.value(aI);
+ const metalA = MetalsSet.has(aeI);
+ const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
+
+ for (let ni = 0; ni < count; ni++) {
+ const _bI = indices[ni];
+ const bI = atomsB[_bI];
+
+ const altB = label_alt_idB.value(bI);
+ // TODO: check if they have the same model?
+ if (altA && altB && altA !== altB) continue;
+
+ const beI = getElementIdx(type_symbolB.value(bI)!);
+ const isMetal = metalA || MetalsSet.has(beI);
+
+ const isHb = isHydrogen(beI);
+ if (isHa && isHb) continue;
+
+ const dist = Math.sqrt(squaredDistances[ni]);
+ if (dist === 0) continue;
+
+ // handle "struct conn" bonds.
+ if (structConnEntries && structConnEntries.length) {
+ let added = false;
+ for (const se of structConnEntries) {
+ for (const p of se.partners) {
+ if (p.atomIndex === bI) {
+ addLink(_aI, _bI, se.order, se.flags, state);
+ bondCount++;
+ added = true;
+ break;
+ }
+ }
+ if (added) break;
+ }
+ if (added) continue;
+ }
+
+ if (isHa || isHb) {
+ if (dist < params.maxHbondLength) {
+ addLink(_aI, _bI, 1, LinkType.Flag.Covalent | LinkType.Flag.Computed, state); // TODO: check if correct
+ bondCount++;
+ }
+ continue;
+ }
+
+ const thresholdAB = getElementPairThreshold(aeI, beI);
+ const pairingThreshold = thresholdAB > 0
+ ? thresholdAB
+ : beI < 0 ? thresholdA : Math.max(thresholdA, getElementThreshold(beI));
+
+ if (dist <= pairingThreshold) {
+ addLink(_aI, _bI, 1, (isMetal ? LinkType.Flag.MetallicCoordination : LinkType.Flag.Covalent) | LinkType.Flag.Computed, state);
+ bondCount++;
+ }
+ }
+ }
+
+ addMapEntry(map, unitA.id, new InterUnitBonds.UnitPairBonds(unitA, unitB, bondCount, state.bondedA.array, state.mapAB));
+ addMapEntry(map, unitB.id, new InterUnitBonds.UnitPairBonds(unitB, unitA, bondCount, state.bondedB.array, state.mapBA));
+
+ return bondCount;
+}
+
+function findLinks(structure: Structure, params: LinkComputationParameters) {
+ const map = new Map<number, InterUnitBonds.UnitPairBonds[]>();
+ if (!structure.units.some(u => Unit.isAtomic(u))) return new InterUnitBonds(map);
+
+ const lookup = structure.lookup3d;
+ for (const unit of structure.units) {
+ if (!Unit.isAtomic(unit)) continue;
+
+ const bs = unit.lookup3d.boundary.sphere;
+ const closeUnits = lookup.findUnitIndices(bs.center[0], bs.center[1], bs.center[2], bs.radius + MAX_RADIUS);
+ for (let i = 0; i < closeUnits.count; i++) {
+ const other = structure.units[closeUnits.indices[i]];
+ if (!Unit.isAtomic(other) || unit.id >= other.id) continue;
+
+ if (other.elements.length >= unit.elements.length) findPairLinks(unit, other, params, map);
+ else findPairLinks(other, unit, params, map);
+ }
+ }
+
+ return new InterUnitBonds(map);
+}
+
+function computeInterUnitBonds(structure: Structure, params?: Partial<LinkComputationParameters>): InterUnitBonds {
+ return findLinks(structure, {
+ maxHbondLength: (params && params.maxHbondLength) || 1.15,
+ forceCompute: !!(params && params.forceCompute),
+ });
+}
+
+export { computeInterUnitBonds };
diff --git a/src/mol-model/structure/structure/unit/links/intra-compute.ts b/src/mol-model/structure/structure/unit/links/intra-compute.ts
new file mode 100644
index 0000000000000000000000000000000000000000..43a67a8ac5d9282a5c978658f845e47f04320e48
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/links/intra-compute.ts
@@ -0,0 +1,161 @@
+/**
+ * Copyright (c) 2017 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { LinkType } from '../../../model/types'
+import { IntraUnitLinks } from './data'
+import { StructConn, ComponentBondInfo } from '../../../model/formats/mmcif/bonds'
+import Unit from '../../unit'
+import { IntAdjacencyGraph } from 'mol-math/graph';
+import { LinkComputationParameters, getElementIdx, MetalsSet, getElementThreshold, isHydrogen, getElementPairThreshold } from './common';
+
+function getGraph(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number): IntraUnitLinks {
+ const builder = new IntAdjacencyGraph.EdgeBuilder(atomCount, atomA, atomB);
+ const flags = new Uint16Array(builder.slotCount);
+ const order = new Int8Array(builder.slotCount);
+ for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
+ builder.addNextEdge();
+ builder.assignProperty(flags, _flags[i]);
+ builder.assignProperty(order, _order[i]);
+ }
+
+ return builder.createGraph({ flags, order });
+}
+
+function _computeBonds(unit: Unit.Atomic, params: LinkComputationParameters): IntraUnitLinks {
+ const MAX_RADIUS = 4;
+
+ const { x, y, z } = unit.model.atomicConformation;
+ const atomCount = unit.elements.length;
+ const { elements: atoms, residueIndex } = unit;
+ const { type_symbol, label_atom_id, label_alt_id } = unit.model.atomicHierarchy.atoms;
+ const { label_comp_id } = unit.model.atomicHierarchy.residues;
+ const query3d = unit.lookup3d;
+
+ const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.create(unit.model) : void 0;
+ const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(unit.model) : void 0;
+
+ const atomA: number[] = [];
+ const atomB: number[] = [];
+ const flags: number[] = [];
+ const order: number[] = [];
+
+ let lastResidue = -1;
+ let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+
+ for (let _aI = 0; _aI < atomCount; _aI++) {
+ const aI = atoms[_aI];
+ const raI = residueIndex[aI];
+
+ if (!params.forceCompute && raI !== lastResidue) {
+ const resn = label_comp_id.value(raI)!;
+ if (!!component && component.entries.has(resn)) {
+ componentMap = component.entries.get(resn)!.map;
+ } else {
+ componentMap = void 0;
+ }
+ }
+ lastResidue = raI;
+
+ const componentPairs = componentMap ? componentMap.get(label_atom_id.value(aI)) : void 0;
+
+ const aeI = getElementIdx(type_symbol.value(aI)!);
+
+ const { indices, count, squaredDistances } = query3d.find(x[aI], y[aI], z[aI], MAX_RADIUS);
+ const isHa = isHydrogen(aeI);
+ const thresholdA = getElementThreshold(aeI);
+ const altA = label_alt_id.value(aI);
+ const metalA = MetalsSet.has(aeI);
+ const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
+
+ for (let ni = 0; ni < count; ni++) {
+ const _bI = indices[ni];
+ const bI = atoms[_bI];
+ if (bI <= aI) continue;
+
+ const altB = label_alt_id.value(bI);
+ if (altA && altB && altA !== altB) continue;
+
+ const beI = getElementIdx(type_symbol.value(bI)!);
+ const isMetal = metalA || MetalsSet.has(beI);
+
+ const rbI = residueIndex[bI];
+ // handle "component dictionary" bonds.
+ if (raI === rbI && componentPairs) {
+ const e = componentPairs.get(label_atom_id.value(bI)!);
+ if (e) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = e.order;
+ let flag = e.flags;
+ if (isMetal) {
+ if (flag | LinkType.Flag.Covalent) flag ^= LinkType.Flag.Covalent;
+ flag |= LinkType.Flag.MetallicCoordination;
+ }
+ flags[flags.length] = flag;
+ }
+ continue;
+ }
+
+ const isHb = isHydrogen(beI);
+ if (isHa && isHb) continue;
+
+ const dist = Math.sqrt(squaredDistances[ni]);
+ if (dist === 0) continue;
+
+ // handle "struct conn" bonds.
+ if (structConnEntries && structConnEntries.length) {
+ let added = false;
+ for (const se of structConnEntries) {
+ for (const p of se.partners) {
+ if (p.atomIndex === bI) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ flags[flags.length] = se.flags;
+ order[order.length] = se.order;
+ added = true;
+ break;
+ }
+ }
+ if (added) break;
+ }
+ if (added) continue;
+ }
+
+ if (isHa || isHb) {
+ if (dist < params.maxHbondLength) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = 1;
+ flags[flags.length] = LinkType.Flag.Covalent | LinkType.Flag.Computed; // TODO: check if correct
+ }
+ continue;
+ }
+
+ const thresholdAB = getElementPairThreshold(aeI, beI);
+ const pairingThreshold = thresholdAB > 0
+ ? thresholdAB
+ : beI < 0 ? thresholdA : Math.max(thresholdA, getElementThreshold(beI));
+
+ if (dist <= pairingThreshold) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = 1;
+ flags[flags.length] = (isMetal ? LinkType.Flag.MetallicCoordination : LinkType.Flag.Covalent) | LinkType.Flag.Computed;
+ }
+ }
+ }
+
+ return getGraph(atomA, atomB, order, flags, atomCount);
+}
+
+function computeIntraUnitBonds(unit: Unit.Atomic, params?: Partial<LinkComputationParameters>) {
+ return _computeBonds(unit, {
+ maxHbondLength: (params && params.maxHbondLength) || 1.15,
+ forceCompute: !!(params && params.forceCompute),
+ });
+}
+
+export { computeIntraUnitBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/rings/compute.ts b/src/mol-model/structure/structure/unit/rings/compute.ts
index 3a83594121a8150912f1a6daabba7278767008e2..c0bafe3e3abe380d3557ef14edfdd3225299902b 100644
--- a/src/mol-model/structure/structure/unit/rings/compute.ts
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -5,8 +5,9 @@
*/
import Unit from '../../unit';
-import { IntraUnitBonds } from '../bonds/intra-data';
+import { IntraUnitLinks } from '../links/data';
import { Segmentation } from 'mol-data/int';
+import { LinkType } from '../../../model/types';
export default function computeRings(unit: Unit.Atomic) {
const size = largestResidue(unit);
@@ -40,7 +41,7 @@ interface State {
currentColor: number,
rings: number[][],
- bonds: IntraUnitBonds,
+ bonds: IntraUnitLinks,
unit: Unit.Atomic
}
@@ -58,7 +59,7 @@ function State(unit: Unit.Atomic, capacity: number): State {
currentColor: 0,
rings: [],
unit,
- bonds: unit.bonds
+ bonds: unit.links
};
}
@@ -160,7 +161,7 @@ function findRings(state: State, from: number) {
for (let i = start; i < end; i++) {
const b = neighbor[i];
- if (b < startVertex || b >= endVertex || !IntraUnitBonds.isCovalent(bondFlags[i])) continue;
+ if (b < startVertex || b >= endVertex || !LinkType.isCovalent(bondFlags[i])) continue;
const other = b - startVertex;
diff --git a/src/mol-model/structure/structure/util/lookup3d.ts b/src/mol-model/structure/structure/util/lookup3d.ts
index 2ea308e3ec11624d1528fa28d8d9f38e49f96fd0..3c7b8b6ac24690292f4eacc144fde5fbf27368e8 100644
--- a/src/mol-model/structure/structure/util/lookup3d.ts
+++ b/src/mol-model/structure/structure/util/lookup3d.ts
@@ -17,6 +17,10 @@ export class StructureLookup3D implements Lookup3D<Element> {
private result = Result.create<Element>();
private pivot = Vec3.zero();
+ findUnitIndices(x: number, y: number, z: number, radius: number): Result<number> {
+ return this.unitLookup.find(x, y, z, radius);
+ }
+
find(x: number, y: number, z: number, radius: number): Result<Element> {
Result.reset(this.result);
const { units } = this.structure;
diff --git a/src/mol-view/label.ts b/src/mol-view/label.ts
index 578a4a7a53260c5c682edc6a7d648edf692a0031..0ea82df1ba0a07c339d76453580f942cf19a85cd 100644
--- a/src/mol-view/label.ts
+++ b/src/mol-view/label.ts
@@ -6,7 +6,7 @@
*/
import { Unit, Element, Queries } from 'mol-model/structure';
-import { Bond } from 'mol-model/structure/structure/unit/bonds';
+import { Link } from 'mol-model/structure/structure/unit/links';
import { Loci } from 'mol-model/loci';
const elementLocA = Element.Location()
@@ -23,8 +23,8 @@ export function labelFirst(loci: Loci) {
if (e && e.indices[0] !== undefined) {
return elementLabel(Element.Location(e.unit, e.indices[0]))
}
- } else if (Bond.isLoci(loci)) {
- const bond = loci.bonds[0]
+ } else if (Link.isLoci(loci)) {
+ const bond = loci.links[0]
if (bond) {
setElementLocation(elementLocA, bond.aUnit, bond.aIndex)
setElementLocation(elementLocB, bond.bUnit, bond.bIndex)