diff --git a/src/mol-model/structure/structure/element/query.ts b/src/mol-model/structure/structure/element/bundle.ts
similarity index 88%
rename from src/mol-model/structure/structure/element/query.ts
rename to src/mol-model/structure/structure/element/bundle.ts
index 7093ff9f0d1e8c51d4b693d50a7e08ef75d27f82..81d42342a14bf1d23a48c8ec20b280db1438c729 100644
--- a/src/mol-model/structure/structure/element/query.ts
+++ b/src/mol-model/structure/structure/element/bundle.ts
@@ -13,7 +13,7 @@ import SortedRanges from '../../../../mol-data/int/sorted-ranges';
import { UnitIndex } from './element';
import { Loci } from './loci';
-interface QueryElement {
+interface BundleElement {
/**
* Array (sorted by first element in sub-array) of
* arrays of `Unit.id`s that share the same `Unit.invariantId`
@@ -23,17 +23,17 @@ interface QueryElement {
ranges: SortedRanges<UnitIndex>
}
-export interface Query {
- /** Hash of the structure to which the query can be applied */
+export interface Bundle {
+ /** Hash of the structure with which the bundle is compatible */
readonly hash: number
- /** Query elements */
- readonly elements: ReadonlyArray<Readonly<QueryElement>>
+ /** Bundle elements */
+ readonly elements: ReadonlyArray<Readonly<BundleElement>>
}
-export namespace Query {
- export const Empty: Query = { hash: -1, elements: [] }
+export namespace Bundle {
+ export const Empty: Bundle = { hash: -1, elements: [] }
- export function fromLoci(loci: Loci): Query {
+ export function fromLoci(loci: Loci): Bundle {
const _elements: {
unit: Unit
set: SortedArray<UnitIndex>
@@ -98,7 +98,7 @@ export namespace Query {
}
}
- const elements: QueryElement[] = []
+ const elements: BundleElement[] = []
elementGroups.forEach(e => {
const groupedUnits: SortedArray<number>[] = []
e.groupedUnits.forEach(g => groupedUnits.push(SortedArray.ofUnsortedArray(g)))
@@ -118,12 +118,12 @@ export namespace Query {
return units
}
- export function toLoci(query: Query, parent: Structure): Loci {
- if (query.hash !== -1 && query.hash !== parent.root.hashCode) {
- new Error('Query not compatible with given structure')
+ export function toLoci(bundle: Bundle, parent: Structure): Loci {
+ if (bundle.hash !== -1 && bundle.hash !== parent.root.hashCode) {
+ new Error('Bundle not compatible with given structure')
}
const elements: Loci['elements'][0][] = []
- for (const e of query.elements) {
+ for (const e of bundle.elements) {
for (const g of e.groupedUnits) {
const units = getUnitsFromIds(g, parent)
if (units.length === 0) continue
@@ -155,12 +155,12 @@ export namespace Query {
return Loci(parent, elements)
}
- export function toStructure(query: Query, parent: Structure): Structure {
- if (query.hash !== -1 && query.hash !== parent.root.hashCode) {
- new Error('Query not compatible with given structure')
+ export function toStructure(bundle: Bundle, parent: Structure): Structure {
+ if (bundle.hash !== -1 && bundle.hash !== parent.root.hashCode) {
+ new Error('Bundle not compatible with given structure')
}
const units: Unit[] = []
- for (const e of query.elements) {
+ for (const e of bundle.elements) {
for (const g of e.groupedUnits) {
const _units = getUnitsFromIds(g, parent)
if (_units.length === 0) continue
@@ -192,7 +192,7 @@ export namespace Query {
return Structure.create(units, { parent })
}
- export function areEqual(a: Query, b: Query) {
+ export function areEqual(a: Bundle, b: Bundle) {
if (a.elements.length !== b.elements.length) return false
for (let i = 0, il = a.elements.length; i < il; ++i) {
const elementA = a.elements[i], elementB = b.elements[i]
diff --git a/src/mol-model/structure/structure/element/index.ts b/src/mol-model/structure/structure/element/index.ts
index d59dfce564dff194e4843e7b1c24c44d8d3188f0..722e195332a2a8d105a1ac57fca5ffb887d5c75e 100644
--- a/src/mol-model/structure/structure/element/index.ts
+++ b/src/mol-model/structure/structure/element/index.ts
@@ -7,6 +7,6 @@
export * from './location'
export * from './loci'
-export * from './query'
+export * from './bundle'
export * from './stats'
export * from './element'
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 3ac616e7251f07fd39165cbdf67a731239d931a3..bb7e497b72c439d7999ccbe0124aac4a1fe3cc64 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -41,7 +41,7 @@ export { TransformStructureConformation };
export { TransformStructureConformationByMatrix };
export { StructureSelection };
export { UserStructureSelection };
-export { LociStructureSelection };
+export { BundleStructureSelection as LociStructureSelection };
export { StructureComplexElement };
export { CustomModelProperties };
export { CustomStructureProperties };
@@ -435,39 +435,39 @@ function updateStructureFromQuery(query: QueryFn<Sel>, src: Structure, obj: SO.M
return true;
}
-type LociStructureSelection = typeof LociStructureSelection
-const LociStructureSelection = PluginStateTransform.BuiltIn({
- name: 'loci-structure-selection',
- display: { name: 'Structure Selection', description: 'Create a molecular structure from the specified structure-element query.' },
+type BundleStructureSelection = typeof BundleStructureSelection
+const BundleStructureSelection = PluginStateTransform.BuiltIn({
+ name: 'bundle-structure-selection',
+ display: { name: 'Structure Selection', description: 'Create a molecular structure from the specified structure-element bundle.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
params: {
- query: PD.Value<StructureElement.Query>(StructureElement.Query.Empty, { isHidden: true }),
+ bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty, { isHidden: true }),
label: PD.Optional(PD.Text('', { isHidden: true }))
}
})({
apply({ a, params, cache }) {
- if (params.query.hash !== a.data.hashCode) {
- // Query not compatible with given structure, set to empty query
- params.query = StructureElement.Query.Empty
+ if (params.bundle.hash !== a.data.hashCode) {
+ // Bundle not compatible with given structure, set to empty bundle
+ params.bundle = StructureElement.Bundle.Empty
}
(cache as { source: Structure }).source = a.data;
- const s = StructureElement.Query.toStructure(params.query, a.data);
+ const s = StructureElement.Bundle.toStructure(params.bundle, a.data);
if (s.elementCount === 0) return StateObject.Null;
const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
return new SO.Molecule.Structure(s, props);
},
update: ({ a, b, oldParams, newParams, cache }) => {
- if (!StructureElement.Query.areEqual(oldParams.query, newParams.query)) {
+ if (!StructureElement.Bundle.areEqual(oldParams.bundle, newParams.bundle)) {
return StateTransformer.UpdateResult.Recreate;
}
- if (newParams.query.hash !== a.data.hashCode) {
- // Query not compatible with given structure, set to empty query
- newParams.query = StructureElement.Query.Empty
+ if (newParams.bundle.hash !== a.data.hashCode) {
+ // Bundle not compatible with given structure, set to empty bundle
+ newParams.bundle = StructureElement.Bundle.Empty
}
if ((cache as { source: Structure }).source === a.data) {
@@ -475,7 +475,7 @@ const LociStructureSelection = PluginStateTransform.BuiltIn({
}
(cache as { source: Structure }).source = a.data;
- const s = StructureElement.Query.toStructure(newParams.query, a.data);
+ const s = StructureElement.Bundle.toStructure(newParams.bundle, a.data);
if (s.elementCount === 0) return StateTransformer.UpdateResult.Null;
b.label = `${newParams.label || 'Selection'}`;
diff --git a/src/mol-plugin/util/structure-representation-helper.ts b/src/mol-plugin/util/structure-representation-helper.ts
index 3f73b7d75b3d7b64859c1e439c77cff58f7eaf6b..9ede0cd4237d2da6695240270abd4cc3b3ce5bf8 100644
--- a/src/mol-plugin/util/structure-representation-helper.ts
+++ b/src/mol-plugin/util/structure-representation-helper.ts
@@ -57,12 +57,12 @@ export class StructureRepresentationHelper {
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
if (reprStructure) {
- const currentLoci = StructureElement.Query.toLoci(reprStructure.params!.values.query, s)
+ const currentLoci = StructureElement.Bundle.toLoci(reprStructure.params!.values.bundle, s)
const combinedLoci = getCombinedLoci(modifier, loci, currentLoci)
update.to(reprStructure).update({
...reprStructure.params!.values,
- query: StructureElement.Query.fromLoci(combinedLoci)
+ bundle: StructureElement.Bundle.fromLoci(combinedLoci)
})
} else {
const combinedLoci = getCombinedLoci(modifier, loci, StructureElement.Loci(s, []))
@@ -76,7 +76,7 @@ export class StructureRepresentationHelper {
update.to(structure.transform.ref)
.apply(
StateTransforms.Model.LociStructureSelection,
- { query: StructureElement.Query.fromLoci(combinedLoci), label: type },
+ { bundle: StructureElement.Bundle.fromLoci(combinedLoci), label: type },
{ tags: [ RepresentationManagerTag, getRepresentationManagerTag(type) ] }
)
.apply( StateTransforms.Representation.StructureRepresentation3D, params)
@@ -109,14 +109,14 @@ export class StructureRepresentationHelper {
const state = this.plugin.state.dataState;
const update = state.build()
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
- const query = StructureElement.Query.Empty
+ const bundle = StructureElement.Bundle.Empty
for (const structure of structures) {
for (let i = 0, il = registry.types.length; i < il; ++i) {
const type = registry.types[i][0]
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
if (reprStructure) {
- update.to(reprStructure).update({ ...reprStructure.params!.values, query })
+ update.to(reprStructure).update({ ...reprStructure.params!.values, bundle })
}
}
}
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 42218fb8da9e702daa01e02923b944c441d7e32c..173e7b2df43c587f298215b12b05abc05440e603 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -232,6 +232,7 @@ export const SymbolTable = [
Alias(MolScript.structureQuery.atomProperty.macromolecular.occupancy, 'atom.occupancy'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.entitySubtype, 'atom.entity-subtype'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, 'atom.object-primitive'),
Alias(MolScript.structureQuery.atomProperty.macromolecular.chemCompType, 'atom.chem-comp-type'),