From 0ed4d82a5b616f3cb1815945e69f248cd7182202 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 23 Aug 2018 17:41:30 +0200
Subject: [PATCH] mol-model/query added link support to QueryContext
---
src/mol-model/structure/model/types.ts | 4 +++
src/mol-model/structure/query/context.ts | 19 +++++++++++
.../structure/structure/unit/links.ts | 34 +++++++++++++++++--
.../structure/structure/unit/links/data.ts | 9 +++--
4 files changed, 61 insertions(+), 5 deletions(-)
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 159f2fe0b..58a8989b5 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -491,6 +491,10 @@ export namespace LinkType {
// currently at most 16 flags are supported!!
}
+ export function create(flags: Flag): LinkType {
+ return BitFlags.create(flags);
+ }
+
export function isCovalent(flags: LinkType.Flag) {
return (flags & LinkType.Flag.Covalent) !== 0;
}
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 245cd5b37..7404cb05f 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -7,6 +7,7 @@
import { Structure, StructureElement, Unit } from '../structure';
import { now } from 'mol-task';
import { ElementIndex } from '../model';
+import { Link } from '../structure/unit/links';
export interface QueryContextView {
readonly element: StructureElement;
@@ -15,6 +16,7 @@ export interface QueryContextView {
export class QueryContext implements QueryContextView {
private currentElementStack: StructureElement[] = [];
+ private currentAtomicLinkStack: Link.Location<Unit.Atomic>[] = [];
private currentStructureStack: Structure[] = [];
private inputStructureStack: Structure[] = [];
@@ -27,6 +29,9 @@ export class QueryContext implements QueryContextView {
readonly element: StructureElement = StructureElement.create();
currentStructure: Structure = void 0 as any;
+ /** Current link between atoms */
+ readonly atomicLink: Link.Location<Unit.Atomic> = void 0 as any;
+
setElement(unit: Unit, e: ElementIndex) {
this.element.unit = unit;
this.element.element = e;
@@ -42,6 +47,20 @@ export class QueryContext implements QueryContextView {
(this.element as StructureElement) = this.currentElementStack.pop()!;
}
+ pushCurrentLink() {
+ if (this.atomicLink) this.currentAtomicLinkStack.push(this.atomicLink);
+ (this.atomicLink as Link.Location<Unit.Atomic>) = Link.Location() as Link.Location<Unit.Atomic>;
+ return this.atomicLink;
+ }
+
+ popCurrentLink() {
+ if (this.currentAtomicLinkStack.length > 0) {
+ (this.atomicLink as Link.Location<Unit.Atomic>) = this.currentAtomicLinkStack.pop()!;
+ } else {
+ (this.atomicLink as any) = void 0;
+ }
+ }
+
pushCurrentStructure() {
if (this.currentStructure) this.currentStructureStack.push(this.currentStructure);
}
diff --git a/src/mol-model/structure/structure/unit/links.ts b/src/mol-model/structure/structure/unit/links.ts
index c7ff8e0a7..5534b62f0 100644
--- a/src/mol-model/structure/structure/unit/links.ts
+++ b/src/mol-model/structure/structure/unit/links.ts
@@ -6,18 +6,20 @@
*/
import { Unit, StructureElement } from '../../structure'
+import Structure from '../structure';
+import { LinkType } from '../../model/types';
export * from './links/data'
export * from './links/intra-compute'
export * from './links/inter-compute'
namespace Link {
- export interface Location {
+ export interface Location<U extends Unit = Unit> {
readonly kind: 'link-location',
- aUnit: Unit,
+ aUnit: U,
/** Index into aUnit.elements */
aIndex: StructureElement.UnitIndex,
- bUnit: Unit,
+ bUnit: U,
/** Index into bUnit.elements */
bIndex: StructureElement.UnitIndex,
}
@@ -42,6 +44,32 @@ namespace Link {
export function isLoci(x: any): x is Loci {
return !!x && x.kind === 'link-loci';
}
+
+ export function getType(structure: Structure, link: Location<Unit.Atomic>): LinkType {
+ if (link.aUnit === link.bUnit) {
+ const links = link.aUnit.links;
+ const idx = links.getEdgeIndex(link.aIndex, link.bIndex);
+ if (idx < 0) return LinkType.create(LinkType.Flag.None);
+ return LinkType.create(links.edgeProps.flags[idx]);
+ } else {
+ const bond = structure.links.getBondFromLocation(link);
+ if (bond) return LinkType.create(bond.flag);
+ return LinkType.create(LinkType.Flag.None);
+ }
+ }
+
+ export function getOrder(structure: Structure, link: Location<Unit.Atomic>): number {
+ if (link.aUnit === link.bUnit) {
+ const links = link.aUnit.links;
+ const idx = links.getEdgeIndex(link.aIndex, link.bIndex);
+ if (idx < 0) return 0;
+ return links.edgeProps.order[idx];
+ } else {
+ const bond = structure.links.getBondFromLocation(link);
+ if (bond) return bond.order;
+ return 0;
+ }
+ }
}
export { Link }
\ 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
index 74ff5bd2d..e2c56ae49 100644
--- a/src/mol-model/structure/structure/unit/links/data.ts
+++ b/src/mol-model/structure/structure/unit/links/data.ts
@@ -9,6 +9,7 @@ import { LinkType } from '../../../model/types'
import { IntAdjacencyGraph } from 'mol-math/graph';
import Unit from '../../unit';
import StructureElement from '../../element';
+import { Link } from '../links';
type IntraUnitLinks = IntAdjacencyGraph<{ readonly order: ArrayLike<number>, readonly flags: ArrayLike<LinkType.Flag> }>
@@ -27,17 +28,21 @@ class InterUnitBonds {
}
/** Index into this.bonds */
- getBondIndex(indexA: number, unitA: Unit, indexB: number, unitB: Unit): number {
+ getBondIndex(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): number {
const key = InterUnitBonds.getBondKey(indexA, unitA, indexB, unitB)
const index = this.bondKeyIndex.get(key)
return index !== undefined ? index : -1
}
- getBond(indexA: number, unitA: Unit, indexB: number, unitB: Unit): InterUnitBonds.Bond | undefined {
+ getBond(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): InterUnitBonds.Bond | undefined {
const index = this.getBondIndex(indexA, unitA, indexB, unitB)
return index !== -1 ? this.bonds[index] : undefined
}
+ getBondFromLocation(l: Link.Location) {
+ return this.getBond(l.aIndex, l.aUnit, l.bIndex, l.bUnit);
+ }
+
constructor(private map: Map<number, InterUnitBonds.UnitPairBonds[]>) {
let count = 0
const bonds: (InterUnitBonds.Bond)[] = []
--
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