diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 3015361fd854614a7c237099d7999e92253bbbb7..e1621e676fe4c99082cc59ca5dd7b7af87ad131d 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -7,7 +7,6 @@
import { Structure, StructureElement, Unit } from '../structure';
import { now } from '../../../mol-util/now';
import { ElementIndex } from '../model';
-import { Link } from '../structure/unit/links';
import { LinkType } from '../model/types';
import { StructureSelection } from './selection';
@@ -32,7 +31,7 @@ export class QueryContext implements QueryContextView {
currentStructure: Structure = void 0 as any;
/** Current link between atoms */
- readonly atomicLink = QueryContextLinkInfo.empty<Unit.Atomic>();
+ readonly atomicLink = new QueryContextLinkInfo<Unit.Atomic>();
/** Supply this from the outside. Used by the internal.generator.current symbol */
currentSelection: StructureSelection | undefined = void 0;
@@ -54,7 +53,7 @@ export class QueryContext implements QueryContextView {
pushCurrentLink() {
if (this.atomicLink) this.currentAtomicLinkStack.push(this.atomicLink);
- (this.atomicLink as QueryContextLinkInfo<Unit.Atomic>) = QueryContextLinkInfo.empty();
+ (this.atomicLink as QueryContextLinkInfo<Unit.Atomic>) = new QueryContextLinkInfo();
return this.atomicLink;
}
@@ -112,14 +111,15 @@ export interface QueryContextOptions {
export interface QueryPredicate { (ctx: QueryContext): boolean }
export interface QueryFn<T = any> { (ctx: QueryContext): T }
-export interface QueryContextLinkInfo<U extends Unit = Unit> {
- link: Link.Location<U>,
- type: LinkType,
- order: number
-}
+export class QueryContextLinkInfo<U extends Unit = Unit> {
+ a: StructureElement.Location<U> = StructureElement.Location.create();
+ aIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
+ b: StructureElement.Location<U> = StructureElement.Location.create();
+ bIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
+ type: LinkType = LinkType.Flag.None;
+ order: number = 0;
-export namespace QueryContextLinkInfo {
- export function empty<U extends Unit = Unit>(): QueryContextLinkInfo<U> {
- return { link: Link.Location() as Link.Location<U>, type: LinkType.Flag.None, order: 0 };
+ get length() {
+ return StructureElement.Location.distance(this.a, this. b);
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index e65da32b899a1b7342d2a24a380f79317bd6a050..2e9880aae1cee5518ee9dd6cfd0b8d8a5fe21698 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -250,7 +250,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
const linkedUnits = interLinks.getLinkedUnits(unit);
const luCount = linkedUnits.length;
- atomicLink.link.aUnit = inputUnit;
+ atomicLink.a.unit = inputUnit;
const srcElements = unit.elements;
const inputElements = inputUnit.elements;
@@ -258,14 +258,16 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
for (let i = 0 as StructureElement.UnitIndex, _i = srcElements.length; i < _i; i++) {
const inputIndex = SortedArray.indexOf(inputElements, srcElements[i]) as StructureElement.UnitIndex;
- atomicLink.link.aIndex = inputIndex;
- atomicLink.link.bUnit = inputUnit;
+ atomicLink.aIndex = inputIndex;
+ atomicLink.a.element = srcElements[i];
+ atomicLink.b.unit = inputUnit;
tElement.unit = unit;
for (let l = offset[inputIndex], _l = offset[inputIndex + 1]; l < _l; l++) {
tElement.element = inputElements[b[l]];
if (!target.hasElement(tElement)) continue;
- atomicLink.link.bIndex = b[l] as StructureElement.UnitIndex;
+ atomicLink.bIndex = b[l] as StructureElement.UnitIndex;
+ atomicLink.b.element = inputUnit.elements[b[l]];
atomicLink.type = flags[l];
atomicLink.order = order[l];
if (linkTest(queryCtx)) return true;
@@ -274,14 +276,15 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
for (let li = 0; li < luCount; li++) {
const lu = linkedUnits[li];
tElement.unit = lu.unitB;
- atomicLink.link.bUnit = lu.unitB;
+ atomicLink.b.unit = lu.unitB;
const bElements = lu.unitB.elements;
const bonds = lu.getBonds(inputIndex);
for (let bi = 0, _bi = bonds.length; bi < _bi; bi++) {
const bond = bonds[bi];
tElement.element = bElements[bond.indexB];
if (!target.hasElement(tElement)) continue;
- atomicLink.link.bIndex = bond.indexB;
+ atomicLink.bIndex = bond.indexB;
+ atomicLink.b.element = tElement.element;
atomicLink.type = bond.flag;
atomicLink.order = bond.order;
if (linkTest(queryCtx)) return true;
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index ea02b303dac7e9154416e41b1044824778914d8a..4aa6b169b7af3a4ffd59bd32719b3c11c7884b1e 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -356,18 +356,20 @@ function expandConnected(ctx: QueryContext, structure: Structure, linkTest: Quer
const { offset: intraLinkOffset, b: intraLinkB, edgeProps: { flags, order } } = inputUnit.links;
// Process intra unit links
- atomicLink.link.aUnit = inputUnit;
- atomicLink.link.bUnit = inputUnit;
+ atomicLink.a.unit = inputUnit;
+ atomicLink.b.unit = inputUnit;
for (let i = 0, _i = unit.elements.length; i < _i; i++) {
// add the current element
builder.addToUnit(unit.id, unit.elements[i]);
const srcIndex = SortedArray.indexOf(inputUnit.elements, unit.elements[i]);
- atomicLink.link.aIndex = srcIndex as StructureElement.UnitIndex;
+ atomicLink.aIndex = srcIndex as StructureElement.UnitIndex;
+ atomicLink.a.element = unit.elements[i];
// check intra unit links
for (let lI = intraLinkOffset[srcIndex], _lI = intraLinkOffset[srcIndex + 1]; lI < _lI; lI++) {
- atomicLink.link.bIndex = intraLinkB[lI] as StructureElement.UnitIndex;
+ atomicLink.bIndex = intraLinkB[lI] as StructureElement.UnitIndex;
+ atomicLink.b.element = inputUnit.elements[intraLinkB[lI]];
atomicLink.type = flags[lI];
atomicLink.order = order[lI];
if (linkTest(ctx)) {
@@ -380,14 +382,17 @@ function expandConnected(ctx: QueryContext, structure: Structure, linkTest: Quer
for (const linkedUnit of interLinks.getLinkedUnits(inputUnit)) {
if (processedUnits.has(linkedUnit.unitA.id)) continue;
- atomicLink.link.bUnit = linkedUnit.unitB;
+ atomicLink.b.unit = linkedUnit.unitB;
for (const aI of linkedUnit.linkedElementIndices) {
// check if the element is in the expanded structure
if (!SortedArray.has(unit.elements, inputUnit.elements[aI])) continue;
- atomicLink.link.aIndex = aI;
+ atomicLink.aIndex = aI;
+ atomicLink.a.element = inputUnit.elements[aI];
for (const bond of linkedUnit.getBonds(aI)) {
- atomicLink.link.bIndex = bond.indexB;
+ atomicLink.bIndex = bond.indexB;
+ // TODO: optimize the lookup?
+ atomicLink.b.element = linkedUnit.unitB.elements[bond.indexB];
atomicLink.type = bond.flag;
atomicLink.order = bond.order;
if (linkTest(ctx)) {
diff --git a/src/mol-model/structure/structure/element/location.ts b/src/mol-model/structure/structure/element/location.ts
index f60d677475624a61977050e479004bd766831f49..92c027e3e82858c5be4dca95c1adca238bf91b9b 100644
--- a/src/mol-model/structure/structure/element/location.ts
+++ b/src/mol-model/structure/structure/element/location.ts
@@ -7,6 +7,7 @@
import { ElementIndex } from '../../model';
import Unit from '../unit';
+import { Vec3 } from '../../../../mol-math/linear-algebra';
export { Location }
@@ -18,7 +19,7 @@ interface Location<U = Unit> {
}
namespace Location {
- export function create(unit?: Unit, element?: ElementIndex): Location {
+ export function create<U extends Unit>(unit?: U, element?: ElementIndex): Location<U> {
return { kind: 'element-location', unit: unit!, element: element || (0 as ElementIndex) };
}
@@ -37,4 +38,11 @@ namespace Location {
export function is(x: any): x is Location {
return !!x && x.kind === 'element-location';
}
+
+ const pA = Vec3.zero(), pB = Vec3.zero();
+ export function distance(a: Location, b: Location) {
+ a.unit.conformation.position(a.element, pA);
+ b.unit.conformation.position(b.element, pB);
+ return Vec3.distance(pA, pB);
+ }
}
\ No newline at end of file
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index fbe722d3b76245794b99bedb63d76c1d9cc1bdf4..03e9080f4767ff32eb59102a3c34777c447328a4 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -314,7 +314,10 @@ const linkProperty = {
'@header': 'Link Properties',
flags: linkProp(Types.LinkFlags),
- order: linkProp(Type.Num)
+ order: linkProp(Type.Num),
+ length: linkProp(Type.Num),
+ atomA: linkProp(Types.ElementReference),
+ atomB: linkProp(Types.ElementReference)
}
function atomProp(type: Type, description?: string) {
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index e793f8613375edd9e673fd4fce8582ebc8b3418e..77aba6db120279eae960cd8985e4ccddfae43717 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -194,8 +194,8 @@ const symbols = [
// ============= SLOTS ================
// TODO: slots might not be needed after all: reducer simply pushes/pops current element
- C(MolScript.structureQuery.slot.element, (ctx, _) => ctx.element),
- // C(MolScript.structureQuery.slot.elementSetReduce, (ctx, _) => ctx.element),
+ // C(MolScript.structureQuery.slot.element, (ctx, _) => ctx_.element),
+ // C(MolScript.structureQuery.slot.elementSetReduce, (ctx, _) => ctx_.element),
// ============= FILTERS ================
D(MolScript.structureQuery.filter.pick, (ctx, xs) => Queries.filters.pick(xs[0] as any, xs['test'])(ctx)),
@@ -256,9 +256,9 @@ const symbols = [
// ~~~ CORE ~~~
D(MolScript.structureQuery.atomProperty.core.elementSymbol, atomProp(StructureProperties.atom.type_symbol)),
- D(MolScript.structureQuery.atomProperty.core.vdw, (ctx, _) => VdwRadius(StructureProperties.atom.type_symbol(ctx.element))),
- D(MolScript.structureQuery.atomProperty.core.mass, (ctx, _) => AtomWeight(StructureProperties.atom.type_symbol(ctx.element))),
- D(MolScript.structureQuery.atomProperty.core.atomicNumber, (ctx, _) => AtomNumber(StructureProperties.atom.type_symbol(ctx.element))),
+ D(MolScript.structureQuery.atomProperty.core.vdw, (ctx, xs) => VdwRadius(StructureProperties.atom.type_symbol((xs && xs[0] && xs[0](ctx) as any) || ctx.element))),
+ D(MolScript.structureQuery.atomProperty.core.mass, (ctx, xs) => AtomWeight(StructureProperties.atom.type_symbol((xs && xs[0] && xs[0](ctx) as any) || ctx.element))),
+ D(MolScript.structureQuery.atomProperty.core.atomicNumber, (ctx, xs) => AtomNumber(StructureProperties.atom.type_symbol((xs && xs[0] && xs[0](ctx) as any) || ctx.element))),
D(MolScript.structureQuery.atomProperty.core.x, atomProp(StructureProperties.atom.x)),
D(MolScript.structureQuery.atomProperty.core.y, atomProp(StructureProperties.atom.y)),
D(MolScript.structureQuery.atomProperty.core.z, atomProp(StructureProperties.atom.z)),
@@ -266,7 +266,10 @@ const symbols = [
D(MolScript.structureQuery.atomProperty.core.operatorName, atomProp(StructureProperties.unit.operator_name)),
D(MolScript.structureQuery.atomProperty.core.modelIndex, atomProp(StructureProperties.unit.model_index)),
D(MolScript.structureQuery.atomProperty.core.modelLabel, atomProp(StructureProperties.unit.model_label)),
- D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, _) => cantorPairing(ctx.element.unit.id, ctx.element.element)),
+ D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, xs) => {
+ const e = (xs && xs[0] && xs[0](ctx) as any) || ctx.element;
+ return cantorPairing(e.unit.id, e.element)
+ }),
// TODO:
// D(MolScript.structureQuery.atomProperty.core.bondCount, (ctx, _) => ),
@@ -283,13 +286,13 @@ const symbols = [
// authResidueId: prop((env, v) => ResidueIdentifier.authOfResidueIndex(env.context.model, getAddress(env, v).residue)),
// keys
- D(MolScript.structureQuery.atomProperty.macromolecular.residueKey, (ctx, _) => StructureElement.residueIndex(ctx.element)),
- D(MolScript.structureQuery.atomProperty.macromolecular.chainKey, (ctx, _) => StructureElement.chainIndex(ctx.element)),
- D(MolScript.structureQuery.atomProperty.macromolecular.entityKey, (ctx, _) => StructureElement.entityIndex(ctx.element)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.residueKey, (ctx, xs) => StructureElement.residueIndex((xs && xs[0] && xs[0](ctx) as any) || ctx.element)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.chainKey, (ctx, xs) => StructureElement.chainIndex((xs && xs[0] && xs[0](ctx) as any) || ctx.element)),
+ D(MolScript.structureQuery.atomProperty.macromolecular.entityKey, (ctx, xs) => StructureElement.entityIndex((xs && xs[0] && xs[0](ctx) as any) || ctx.element)),
// mmCIF
D(MolScript.structureQuery.atomProperty.macromolecular.id, atomProp(StructureProperties.atom.id)),
- D(MolScript.structureQuery.atomProperty.macromolecular.isHet, (ctx, _) => StructureProperties.residue.group_PDB(ctx.element) !== 'ATOM'),
+ D(MolScript.structureQuery.atomProperty.macromolecular.isHet, (ctx, xs) => StructureProperties.residue.group_PDB((xs && xs[0] && xs[0](ctx) as any) || ctx.element) !== 'ATOM'),
D(MolScript.structureQuery.atomProperty.macromolecular.label_atom_id, atomProp(StructureProperties.atom.label_atom_id)),
D(MolScript.structureQuery.atomProperty.macromolecular.label_alt_id, atomProp(StructureProperties.atom.label_alt_id)),
@@ -322,6 +325,9 @@ const symbols = [
// ============= BOND PROPERTIES ================
D(MolScript.structureQuery.linkProperty.order, (ctx, xs) => ctx.atomicLink.order),
D(MolScript.structureQuery.linkProperty.flags, (ctx, xs) => ctx.atomicLink.type),
+ D(MolScript.structureQuery.linkProperty.atomA, (ctx, xs) => ctx.atomicLink.a),
+ D(MolScript.structureQuery.linkProperty.atomB, (ctx, xs) => ctx.atomicLink.b),
+ D(MolScript.structureQuery.linkProperty.length, (ctx, xs) => ctx.atomicLink.length),
////////////////////////////////////
@@ -331,8 +337,8 @@ const symbols = [
D(MolScript.internal.generator.current, function internal_generator_current(ctx, xs) { return ctx.tryGetCurrentSelection() }),
];
-function atomProp(p: (e: StructureElement.Location) => any): (ctx: QueryContext, _: any) => any {
- return (ctx, _) => p(ctx.element);
+function atomProp(p: (e: StructureElement.Location) => any): (ctx: QueryContext, xs: any) => any {
+ return (ctx, xs) => p((xs && xs[0] && xs[0](ctx) as any) || ctx.element);
}
function linkFlag(current: LinkType, f: string): LinkType {
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 173e7b2df43c587f298215b12b05abc05440e603..68a9e6685a453ee2587366a38e2e60519408c628 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -248,6 +248,9 @@ export const SymbolTable = [
[
'Link Properties',
Alias(MolScript.structureQuery.linkProperty.order, 'link.order'),
+ Alias(MolScript.structureQuery.linkProperty.length, 'link.length'),
+ Alias(MolScript.structureQuery.linkProperty.atomA, 'link.atom-a'),
+ Alias(MolScript.structureQuery.linkProperty.atomB, 'link.atom-b'),
Macro(MSymbol('link.is', Arguments.List(StructureQueryTypes.LinkFlag), Type.Bool,
`Test if the current link has at least one (or all if partial = false) of the specified flags: ${Type.oneOfValues(StructureQueryTypes.LinkFlag).join(', ')}`),
args => B.core.flags.hasAny([B.struct.linkProperty.flags(), B.struct.type.linkFlags(getPositionalArgs(args))])),