From a85a4b09d5a74d44280530dbc00bba4cb98e1553 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 9 Apr 2019 14:11:38 +0200
Subject: [PATCH] wip structure level properties
---
.../structure/mmcif/bonds/comp.ts | 4 +-
.../structure/mmcif/bonds/struct_conn.ts | 4 +-
.../structure/mmcif/parser.ts | 2 +-
.../common/custom-element-property.ts | 4 +-
.../common/custom-property-registry.ts | 4 +-
.../pdbe/preferred-assembly.ts | 4 +-
src/mol-model-props/pdbe/struct-ref-domain.ts | 4 +-
.../pdbe/structure-quality-report.ts | 4 +-
src/mol-model-props/rcsb/assembly-symmetry.ts | 4 +-
src/mol-model/structure.ts | 3 +-
.../structure/common/custom-property.ts | 60 ++++++++++++
src/mol-model/structure/export/mmcif.ts | 4 +-
src/mol-model/structure/model.ts | 2 +-
src/mol-model/structure/model/model.ts | 2 +-
.../structure/model/properties/custom.ts | 9 --
.../model/properties/custom/chain.ts | 91 -------------------
.../model/properties/custom/collection.ts | 27 ------
.../model/properties/custom/descriptor.ts | 40 --------
.../model/properties/custom/residue.ts | 91 -------------------
src/mol-script/runtime/query/compiler.ts | 4 +-
src/perf-tests/mol-script.ts | 4 +-
21 files changed, 87 insertions(+), 284 deletions(-)
create mode 100644 src/mol-model/structure/common/custom-property.ts
delete mode 100644 src/mol-model/structure/model/properties/custom.ts
delete mode 100644 src/mol-model/structure/model/properties/custom/chain.ts
delete mode 100644 src/mol-model/structure/model/properties/custom/collection.ts
delete mode 100644 src/mol-model/structure/model/properties/custom/descriptor.ts
delete mode 100644 src/mol-model/structure/model/properties/custom/residue.ts
diff --git a/src/mol-model-formats/structure/mmcif/bonds/comp.ts b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
index eceb64760..9ba0b69eb 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/comp.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
@@ -7,7 +7,7 @@
import { Model } from 'mol-model/structure/model/model'
import { LinkType } from 'mol-model/structure/model/types'
-import { ModelPropertyDescriptor } from 'mol-model/structure/model/properties/custom';
+import { CustomPropertyDescriptor } from 'mol-model/structure';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { Structure, Unit, StructureProperties, StructureElement } from 'mol-model/structure';
import { Segmentation } from 'mol-data/int';
@@ -18,7 +18,7 @@ export interface ComponentBond {
}
export namespace ComponentBond {
- export const Descriptor: ModelPropertyDescriptor = {
+ export const Descriptor: CustomPropertyDescriptor = {
isStatic: true,
name: 'chem_comp_bond',
cifExport: {
diff --git a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
index 91c819e5a..69689c51d 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
@@ -10,7 +10,7 @@ import { Structure } from 'mol-model/structure'
import { LinkType } from 'mol-model/structure/model/types'
import { findEntityIdByAsymId, findAtomIndexByLabelName } from '../util'
import { Column } from 'mol-data/db'
-import { ModelPropertyDescriptor } from 'mol-model/structure/model/properties/custom';
+import { CustomPropertyDescriptor } from 'mol-model/structure';
import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { SortedArray } from 'mol-data/int';
import { CifWriter } from 'mol-io/writer/cif'
@@ -23,7 +23,7 @@ export interface StructConn {
}
export namespace StructConn {
- export const Descriptor: ModelPropertyDescriptor = {
+ export const Descriptor: CustomPropertyDescriptor = {
isStatic: true,
name: 'struct_conn',
cifExport: {
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index d31b63d1a..71063f94d 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -13,7 +13,7 @@ import { RuntimeContext } from 'mol-task';
import UUID from 'mol-util/uuid';
import { Model } from 'mol-model/structure/model/model';
import { Entities } from 'mol-model/structure/model/properties/common';
-import { CustomProperties } from 'mol-model/structure/model/properties/custom';
+import { CustomProperties } from 'mol-model/structure';
import { ModelSymmetry } from 'mol-model/structure/model/properties/symmetry';
import { createAssemblies } from './assembly';
import { getAtomicHierarchyAndConformation } from './atomic';
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index 85f930675..f5e2a6ff7 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ElementIndex, Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { ElementIndex, Model, CustomPropertyDescriptor } from 'mol-model/structure';
import { StructureElement } from 'mol-model/structure/structure';
import { Location } from 'mol-model/location';
import { CustomPropertyRegistry } from './custom-property-registry';
@@ -36,7 +36,7 @@ namespace CustomElementProperty {
export function create<T>(params: CreateParams<T>) {
const name = params.name;
- const Descriptor = ModelPropertyDescriptor({
+ const Descriptor = CustomPropertyDescriptor({
isStatic: params.isStatic,
name: params.name,
});
diff --git a/src/mol-model-props/common/custom-property-registry.ts b/src/mol-model-props/common/custom-property-registry.ts
index b537d0df3..977cade54 100644
--- a/src/mol-model-props/common/custom-property-registry.ts
+++ b/src/mol-model-props/common/custom-property-registry.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ModelPropertyDescriptor, Model } from 'mol-model/structure';
+import { CustomPropertyDescriptor, Model } from 'mol-model/structure';
import { OrderedMap } from 'immutable';
import { ParamDefinition } from 'mol-util/param-definition';
import { Task } from 'mol-task';
@@ -58,7 +58,7 @@ namespace CustomPropertyRegistry {
export interface Provider {
option: [string, string],
defaultSelected: boolean,
- descriptor: ModelPropertyDescriptor<any, any>,
+ descriptor: CustomPropertyDescriptor<any, any>,
attachableTo: (model: Model) => boolean,
attach: (model: Model) => Task<boolean>
}
diff --git a/src/mol-model-props/pdbe/preferred-assembly.ts b/src/mol-model-props/pdbe/preferred-assembly.ts
index fb5f5dc69..a5c540566 100644
--- a/src/mol-model-props/pdbe/preferred-assembly.ts
+++ b/src/mol-model-props/pdbe/preferred-assembly.ts
@@ -7,7 +7,7 @@
import { Column, Table } from 'mol-data/db';
import { toTable } from 'mol-io/reader/cif/schema';
import { CifWriter } from 'mol-io/writer/cif';
-import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { Model, CustomPropertyDescriptor } from 'mol-model/structure';
export namespace PDBePreferredAssembly {
export type Property = string
@@ -31,7 +31,7 @@ export namespace PDBePreferredAssembly {
};
export type Schema = typeof Schema
- export const Descriptor = ModelPropertyDescriptor({
+ export const Descriptor = CustomPropertyDescriptor({
isStatic: true,
name: 'pdbe_preferred_assembly',
cifExport: {
diff --git a/src/mol-model-props/pdbe/struct-ref-domain.ts b/src/mol-model-props/pdbe/struct-ref-domain.ts
index 3872d5a4d..8c3a8a7f3 100644
--- a/src/mol-model-props/pdbe/struct-ref-domain.ts
+++ b/src/mol-model-props/pdbe/struct-ref-domain.ts
@@ -7,7 +7,7 @@
import { Column, Table } from 'mol-data/db';
import { toTable } from 'mol-io/reader/cif/schema';
import { CifWriter } from 'mol-io/writer/cif';
-import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { Model, CustomPropertyDescriptor } from 'mol-model/structure';
import { PropertyWrapper } from '../common/wrapper';
export namespace PDBeStructRefDomain {
@@ -39,7 +39,7 @@ export namespace PDBeStructRefDomain {
};
export type Schema = typeof Schema
- export const Descriptor = ModelPropertyDescriptor({
+ export const Descriptor = CustomPropertyDescriptor({
isStatic: true,
name: 'pdbe_struct_ref_domain',
cifExport: {
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index b534c465f..483b95704 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -8,7 +8,7 @@ import { Column, Table } from 'mol-data/db';
import { toTable } from 'mol-io/reader/cif/schema';
import { mmCIF_residueId_schema } from 'mol-io/reader/cif/schema/mmcif-extras';
import { CifWriter } from 'mol-io/writer/cif';
-import { Model, ModelPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from 'mol-model/structure';
+import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from 'mol-model/structure';
import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
import { StructureElement, CifExportContext } from 'mol-model/structure/structure';
import { CustomPropSymbol } from 'mol-script/language/symbol';
@@ -43,7 +43,7 @@ export namespace StructureQualityReport {
};
export type Schema = typeof Schema
- export const Descriptor = ModelPropertyDescriptor({
+ export const Descriptor = CustomPropertyDescriptor({
isStatic: false,
name: 'pdbe_structure_quality_report',
cifExport: {
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index c67ed0aca..4eab86251 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -7,7 +7,7 @@
import { AssemblySymmetry as AssemblySymmetryGraphQL } from './graphql/types';
import query from './graphql/symmetry.gql';
-import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { Model, CustomPropertyDescriptor } from 'mol-model/structure';
import { CifWriter } from 'mol-io/writer/cif';
import { Database as _Database, Column, Table } from 'mol-data/db'
import { Category } from 'mol-io/writer/cif/encoder';
@@ -140,7 +140,7 @@ function createDatabaseFromCif(model: Model): AssemblySymmetry.Database {
})
}
-const _Descriptor: ModelPropertyDescriptor = {
+const _Descriptor: CustomPropertyDescriptor = {
isStatic: true,
name: 'rcsb_assembly_symmetry',
cifExport: {
diff --git a/src/mol-model/structure.ts b/src/mol-model/structure.ts
index 38d5890d5..3dff04a46 100644
--- a/src/mol-model/structure.ts
+++ b/src/mol-model/structure.ts
@@ -6,4 +6,5 @@
export * from './structure/model'
export * from './structure/structure'
-export * from './structure/query'
\ No newline at end of file
+export * from './structure/query'
+export * from './structure/common/custom-property'
\ No newline at end of file
diff --git a/src/mol-model/structure/common/custom-property.ts b/src/mol-model/structure/common/custom-property.ts
new file mode 100644
index 000000000..12f6f557c
--- /dev/null
+++ b/src/mol-model/structure/common/custom-property.ts
@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { CifWriter } from 'mol-io/writer/cif'
+import { CifExportContext } from '../export/mmcif';
+import { QuerySymbolRuntime } from 'mol-script/runtime/query/compiler';
+import { UUID } from 'mol-util';
+
+export { CustomPropertyDescriptor, CustomProperties }
+
+interface CustomPropertyDescriptor<ExportCtx = CifExportContext, Symbols extends { [name: string]: QuerySymbolRuntime } = { }> {
+ readonly isStatic: boolean,
+ readonly name: string,
+
+ cifExport?: {
+ // Prefix enforced during export.
+ prefix: string,
+ context?: (ctx: CifExportContext) => ExportCtx | undefined,
+ categories: CifWriter.Category<ExportCtx>[]
+ },
+
+ // TODO: add aliases when lisp-like mol-script is done
+ symbols?: Symbols
+}
+
+function CustomPropertyDescriptor<Ctx, Desc extends CustomPropertyDescriptor<Ctx>>(desc: Desc) {
+ return desc;
+}
+
+namespace CustomPropertyDescriptor {
+ export function getUUID(prop: CustomPropertyDescriptor): UUID {
+ if (!(prop as any).__key) {
+ (prop as any).__key = UUID.create22();
+ }
+ return (prop as any).__key;
+ }
+}
+
+class CustomProperties {
+ private _list: CustomPropertyDescriptor[] = [];
+ private _set = new Set<CustomPropertyDescriptor>();
+
+ get all(): ReadonlyArray<CustomPropertyDescriptor> {
+ return this._list;
+ }
+
+ add(desc: CustomPropertyDescriptor<any>) {
+ if (this._set.has(desc)) return;
+
+ this._list.push(desc);
+ this._set.add(desc);
+ }
+
+ has(desc: CustomPropertyDescriptor<any>): boolean {
+ return this._set.has(desc);
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index e0c189ab4..24fcf9c71 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -16,7 +16,7 @@ import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './
import { Model } from '../model';
import { getUniqueEntityIndicesFromStructures, copy_mmCif_category } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
-import { ModelPropertyDescriptor } from '../model/properties/custom';
+import { CustomPropertyDescriptor } from '../common/custom-property';
export interface CifExportContext {
structures: Structure[],
@@ -122,7 +122,7 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures:
let propCtx = ctx;
if (customProp.cifExport.context) {
- const propId = ModelPropertyDescriptor.getUUID(customProp);
+ const propId = CustomPropertyDescriptor.getUUID(customProp);
if (ctx.cache[propId + '__ctx']) propCtx = ctx.cache[propId + '__ctx'];
else {
propCtx = customProp.cifExport.context(ctx) || ctx;
diff --git a/src/mol-model/structure/model.ts b/src/mol-model/structure/model.ts
index df9e98d18..8a1dccfde 100644
--- a/src/mol-model/structure/model.ts
+++ b/src/mol-model/structure/model.ts
@@ -9,6 +9,6 @@ import * as Types from './model/types'
import { ModelSymmetry } from './model/properties/symmetry'
import StructureSequence from './model/properties/sequence'
-export * from './model/properties/custom'
+export * from './model/properties/custom/indexed'
export * from './model/indexing'
export { Model, Types, ModelSymmetry, StructureSequence }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index c777d8d55..303048fdd 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -10,7 +10,7 @@ import { AtomicHierarchy, AtomicConformation } from './properties/atomic';
import { ModelSymmetry } from './properties/symmetry';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities } from './properties/common';
-import { CustomProperties } from './properties/custom';
+import { CustomProperties } from '../common/custom-property';
import { SecondaryStructure } from './properties/seconday-structure';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from 'mol-model-formats/structure/format';
diff --git a/src/mol-model/structure/model/properties/custom.ts b/src/mol-model/structure/model/properties/custom.ts
deleted file mode 100644
index 9b9ab7c3d..000000000
--- a/src/mol-model/structure/model/properties/custom.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-export * from './custom/descriptor'
-export * from './custom/collection'
-export * from './custom/indexed'
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/custom/chain.ts b/src/mol-model/structure/model/properties/custom/chain.ts
deleted file mode 100644
index 4e711c32e..000000000
--- a/src/mol-model/structure/model/properties/custom/chain.ts
+++ /dev/null
@@ -1,91 +0,0 @@
-// /**
-// * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-// *
-// * @author David Sehnal <david.sehnal@gmail.com>
-// */
-
-// import { ChainIndex } from '../../indexing';
-// import { Unit, Structure, StructureElement } from '../../../structure';
-// import { Segmentation } from 'mol-data/int';
-// import { UUID } from 'mol-util';
-// import { CifWriter } from 'mol-io/writer/cif';
-
-// export interface ChainCustomProperty<T = any> {
-// readonly id: UUID,
-// readonly kind: Unit.Kind,
-// has(idx: ChainIndex): boolean
-// get(idx: ChainIndex): T | undefined
-// }
-
-// export namespace ChainCustomProperty {
-// export interface ExportCtx<T> {
-// elements: StructureElement[],
-// property(index: number): T
-// };
-
-// function getExportCtx<T>(prop: ChainCustomProperty<T>, structure: Structure): ExportCtx<T> {
-// const chainIndex = structure.model.atomicHierarchy.chainAtomSegments.index;
-// const elements = getStructureElements(structure, prop);
-// return { elements, property: i => prop.get(chainIndex[elements[i].element])! };
-// }
-
-// export function getCifDataSource<T>(structure: Structure, prop: ChainCustomProperty<T> | undefined, cache: any): CifWriter.Category.Instance['source'][0] {
-// if (!prop) return { rowCount: 0 };
-// if (cache && cache[prop.id]) return cache[prop.id];
-// const data = getExportCtx(prop, structure);
-// const ret = { data, rowCount: data.elements.length };
-// if (cache) cache[prop.id] = ret;
-// return ret;
-// }
-
-// class FromMap<T> implements ChainCustomProperty<T> {
-// readonly id = UUID.create();
-
-// has(idx: ChainIndex): boolean {
-// return this.map.has(idx);
-// }
-
-// get(idx: ChainIndex) {
-// return this.map.get(idx);
-// }
-
-// constructor(private map: Map<ChainIndex, T>, public kind: Unit.Kind) {
-// }
-// }
-
-// export function fromMap<T>(map: Map<ChainIndex, T>, kind: Unit.Kind) {
-// return new FromMap(map, kind);
-// }
-
-// /**
-// * Gets all StructureElements that correspond to 1st atoms of residues that have an property assigned.
-// * Only works correctly for structures with a single model.
-// */
-// export function getStructureElements(structure: Structure, property: ChainCustomProperty) {
-// const models = structure.models;
-// if (models.length !== 1) throw new Error(`Only works on structures with a single model.`);
-
-// const seenChains = new Set<ChainIndex>();
-// const unitGroups = structure.unitSymmetryGroups;
-// const loci: StructureElement[] = [];
-
-// for (const unitGroup of unitGroups) {
-// const unit = unitGroup.units[0];
-// if (unit.kind !== property.kind) {
-// continue;
-// }
-
-// const chains = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
-// while (chains.hasNext) {
-// const seg = chains.move();
-// if (!property.has(seg.index) || seenChains.has(seg.index)) continue;
-
-// seenChains.add(seg.index);
-// loci[loci.length] = StructureElement.create(unit, unit.elements[seg.start]);
-// }
-// }
-
-// loci.sort((x, y) => x.element - y.element);
-// return loci;
-// }
-// }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/custom/collection.ts b/src/mol-model/structure/model/properties/custom/collection.ts
deleted file mode 100644
index e6602fe19..000000000
--- a/src/mol-model/structure/model/properties/custom/collection.ts
+++ /dev/null
@@ -1,27 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { ModelPropertyDescriptor } from './descriptor'
-
-export class CustomProperties {
- private _list: ModelPropertyDescriptor[] = [];
- private _set = new Set<ModelPropertyDescriptor>();
-
- get all(): ReadonlyArray<ModelPropertyDescriptor> {
- return this._list;
- }
-
- add(desc: ModelPropertyDescriptor<any>) {
- if (this._set.has(desc)) return;
-
- this._list.push(desc);
- this._set.add(desc);
- }
-
- has(desc: ModelPropertyDescriptor<any>): boolean {
- return this._set.has(desc);
- }
-}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/custom/descriptor.ts b/src/mol-model/structure/model/properties/custom/descriptor.ts
deleted file mode 100644
index 1d2abb21c..000000000
--- a/src/mol-model/structure/model/properties/custom/descriptor.ts
+++ /dev/null
@@ -1,40 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { CifWriter } from 'mol-io/writer/cif'
-import { CifExportContext } from '../../../export/mmcif';
-import { QuerySymbolRuntime } from 'mol-script/runtime/query/compiler';
-import { UUID } from 'mol-util';
-
-interface ModelPropertyDescriptor<ExportCtx = CifExportContext, Symbols extends { [name: string]: QuerySymbolRuntime } = { }> {
- readonly isStatic: boolean,
- readonly name: string,
-
- cifExport?: {
- // Prefix enforced during export.
- prefix: string,
- context?: (ctx: CifExportContext) => ExportCtx | undefined,
- categories: CifWriter.Category<ExportCtx>[]
- },
-
- // TODO: add aliases when lisp-like mol-script is done
- symbols?: Symbols
-}
-
-function ModelPropertyDescriptor<Ctx, Desc extends ModelPropertyDescriptor<Ctx>>(desc: Desc) {
- return desc;
-}
-
-namespace ModelPropertyDescriptor {
- export function getUUID(prop: ModelPropertyDescriptor): UUID {
- if (!(prop as any).__key) {
- (prop as any).__key = UUID.create22();
- }
- return (prop as any).__key;
- }
-}
-
-export { ModelPropertyDescriptor }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/custom/residue.ts b/src/mol-model/structure/model/properties/custom/residue.ts
deleted file mode 100644
index 4dd7cb130..000000000
--- a/src/mol-model/structure/model/properties/custom/residue.ts
+++ /dev/null
@@ -1,91 +0,0 @@
-// /**
-// * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-// *
-// * @author David Sehnal <david.sehnal@gmail.com>
-// */
-
-// import { ResidueIndex } from '../../indexing';
-// import { Unit, Structure, StructureElement } from '../../../structure';
-// import { Segmentation } from 'mol-data/int';
-// import { UUID } from 'mol-util';
-// import { CifWriter } from 'mol-io/writer/cif';
-
-// export interface ResidueCustomProperty<T = any> {
-// readonly id: UUID,
-// readonly kind: Unit.Kind,
-// has(idx: ResidueIndex): boolean
-// get(idx: ResidueIndex): T | undefined
-// }
-
-// export namespace ResidueCustomProperty {
-// export interface ExportCtx<T> {
-// elements: StructureElement[],
-// property(index: number): T
-// };
-
-// function getExportCtx<T>(prop: ResidueCustomProperty<T>, structure: Structure): ExportCtx<T> {
-// const residueIndex = structure.model.atomicHierarchy.residueAtomSegments.index;
-// const elements = getStructureElements(structure, prop);
-// return { elements, property: i => prop.get(residueIndex[elements[i].element])! };
-// }
-
-// export function getCifDataSource<T>(structure: Structure, prop: ResidueCustomProperty<T> | undefined, cache: any): CifWriter.Category.Instance['source'][0] {
-// if (!prop) return { rowCount: 0 };
-// if (cache && cache[prop.id]) return cache[prop.id];
-// const data = getExportCtx(prop, structure);
-// const ret = { data, rowCount: data.elements.length };
-// if (cache) cache[prop.id] = ret;
-// return ret;
-// }
-
-// class FromMap<T> implements ResidueCustomProperty<T> {
-// readonly id = UUID.create();
-
-// has(idx: ResidueIndex): boolean {
-// return this.map.has(idx);
-// }
-
-// get(idx: ResidueIndex) {
-// return this.map.get(idx);
-// }
-
-// constructor(private map: Map<ResidueIndex, T>, public kind: Unit.Kind) {
-// }
-// }
-
-// export function fromMap<T>(map: Map<ResidueIndex, T>, kind: Unit.Kind) {
-// return new FromMap(map, kind);
-// }
-
-// /**
-// * Gets all StructureElements that correspond to 1st atoms of residues that have an property assigned.
-// * Only works correctly for structures with a single model.
-// */
-// export function getStructureElements(structure: Structure, property: ResidueCustomProperty) {
-// const models = structure.models;
-// if (models.length !== 1) throw new Error(`Only works on structures with a single model.`);
-
-// const seenResidues = new Set<ResidueIndex>();
-// const unitGroups = structure.unitSymmetryGroups;
-// const loci: StructureElement[] = [];
-
-// for (const unitGroup of unitGroups) {
-// const unit = unitGroup.units[0];
-// if (unit.kind !== property.kind) {
-// continue;
-// }
-
-// const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-// while (residues.hasNext) {
-// const seg = residues.move();
-// if (!property.has(seg.index) || seenResidues.has(seg.index)) continue;
-
-// seenResidues.add(seg.index);
-// loci[loci.length] = StructureElement.create(unit, unit.elements[seg.start]);
-// }
-// }
-
-// loci.sort((x, y) => x.element - y.element);
-// return loci;
-// }
-// }
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/compiler.ts b/src/mol-script/runtime/query/compiler.ts
index ce49a29c3..28b96cb52 100644
--- a/src/mol-script/runtime/query/compiler.ts
+++ b/src/mol-script/runtime/query/compiler.ts
@@ -5,7 +5,7 @@
*/
import Expression from '../../language/expression';
-import { QueryContext, QueryFn, Structure, ModelPropertyDescriptor } from 'mol-model/structure';
+import { QueryContext, QueryFn, Structure, CustomPropertyDescriptor } from 'mol-model/structure';
import { MSymbol } from '../../language/symbol';
export class QueryRuntimeTable {
@@ -18,7 +18,7 @@ export class QueryRuntimeTable {
this.map.set(runtime.symbol.id, runtime);
}
- addCustomProp(desc: ModelPropertyDescriptor<any>) {
+ addCustomProp(desc: CustomPropertyDescriptor<any>) {
if (!desc.symbols) return;
for (const k of Object.keys(desc.symbols)) {
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 3895e0f82..f459e3a20 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -1,6 +1,6 @@
import { MolScriptBuilder } from 'mol-script/language/builder';
import { compile, QuerySymbolRuntime, DefaultQueryRuntimeTable } from 'mol-script/runtime/query/compiler';
-import { QueryContext, Structure, StructureQuery, ModelPropertyDescriptor } from 'mol-model/structure';
+import { QueryContext, Structure, StructureQuery, CustomPropertyDescriptor } from 'mol-model/structure';
import { readCifFile, getModelsAndStructure } from '../apps/structure-info/model';
import { CustomPropSymbol } from 'mol-script/language/symbol';
import Type from 'mol-script/language/type';
@@ -46,7 +46,7 @@ const compiled = compile<number>(expr);
const result = compiled(new QueryContext(Structure.Empty));
console.log(result);
-const CustomProp = ModelPropertyDescriptor({
+const CustomProp = CustomPropertyDescriptor({
name: 'test_prop',
isStatic: true,
cifExport: { prefix: '', categories: [ ]},
--
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