From 3e6f3c3c67b80c20fcbde025436cb82fdfff39ef Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 1 Oct 2018 15:53:39 +0200
Subject: [PATCH] Refactoring custom model props
---
src/mol-io/writer/cif/encoder.ts | 5 +
.../pdbe/structure-quality-report.ts | 24 +--
src/mol-model-props/rcsb/symmetry.ts | 3 +
.../structure/model/properties/custom.ts | 2 +-
.../model/properties/custom/chain.ts | 91 +++++++++
.../model/properties/custom/indexed.ts | 88 +++++++++
.../model/properties/custom/residue.ts | 182 +++++++++---------
src/servers/model/test.ts | 8 +
8 files changed, 299 insertions(+), 104 deletions(-)
create mode 100644 src/mol-model/structure/model/properties/custom/chain.ts
create mode 100644 src/mol-model/structure/model/properties/custom/indexed.ts
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 585a221bf..a26084fb3 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -95,6 +95,11 @@ export namespace Field {
return this;
}
+ many(fields: ArrayLike<Field<K, D>>) {
+ for (let i = 0; i < fields.length; i++) this.fields.push(fields[i]);
+ return this;
+ }
+
getFields() { return this.fields; }
}
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index d69524a6a..9974478df 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, ResidueCustomProperty, ResidueIndex, StructureProperties as P, Unit } from 'mol-model/structure';
+import { Model, ModelPropertyDescriptor, ResidueIndex, StructureProperties as P, Unit, IndexedCustomProperty } from 'mol-model/structure';
import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
import { StructureElement } from 'mol-model/structure/structure';
import { CustomPropSymbol } from 'mol-script/language/symbol';
@@ -18,7 +18,7 @@ import { PropertyWrapper } from '../common/wrapper';
import CifField = CifWriter.Field;
export namespace StructureQualityReport {
- export type IssueMap = ResidueCustomProperty<string[]>
+ export type IssueMap = IndexedCustomProperty.Residue<string[]>
export type Property = PropertyWrapper<IssueMap | undefined>
export function get(model: Model): Property | undefined {
@@ -38,7 +38,7 @@ export namespace StructureQualityReport {
instance(ctx) {
return {
fields: _structure_quality_report_issues_fields,
- source: ctx.structures.map(s => ResidueCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
+ source: ctx.structures.map(s => IndexedCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
};
}
}]
@@ -111,13 +111,13 @@ export namespace StructureQualityReport {
}
}
-type ExportCtx = ResidueCustomProperty.ExportCtx<string[]>
-const _structure_quality_report_issues_fields: CifField<number, ExportCtx>[] = [
- CifField.index('id'),
- ...residueIdFields<number, ExportCtx>((i, d) => d.elements[i]),
- CifField.int<number, ExportCtx>('pdbx_PDB_model_num', (i, d) => P.unit.model_num(d.elements[i])),
- CifField.str<number, ExportCtx>('issues', (i, d) => d.property(i).join(','))
-];
+type ExportCtx = IndexedCustomProperty.ExportCtx<string[]>
+const _structure_quality_report_issues_fields: CifField<number, ExportCtx>[] = CifWriter.fields()
+ .index('id')
+ .many(residueIdFields((i, d) => d.elements[i]))
+ .int('pdbx_PDB_model_num', (i, d) => P.unit.model_num(d.elements[i]))
+ .str('issues', (i, d) => d.property(i).join(','))
+ .getFields()
function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport.IssueMap | undefined {
const ret = new Map<ResidueIndex, string[]>();
@@ -140,7 +140,7 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
}
}
- return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
+ return IndexedCustomProperty.fromResidueMap(ret, Unit.Kind.Atomic);
}
function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>): StructureQualityReport.IssueMap | undefined {
@@ -153,5 +153,5 @@ function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQua
ret.set(idx, issues.value(i));
}
- return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
+ return IndexedCustomProperty.fromResidueMap(ret, Unit.Kind.Atomic);
}
\ No newline at end of file
diff --git a/src/mol-model-props/rcsb/symmetry.ts b/src/mol-model-props/rcsb/symmetry.ts
index 36bdd5a8e..379310bde 100644
--- a/src/mol-model-props/rcsb/symmetry.ts
+++ b/src/mol-model-props/rcsb/symmetry.ts
@@ -178,6 +178,9 @@ export namespace AssemblySymmetry {
let db: Database
+ // TODO: there should be a "meta field" that indicates the property was added (see for example PDBe structure report)
+ // the reason for this is that the feature might not be present and therefore the "default" categories would
+ // not be created. This would result in an unnecessarily failed web request.
if (model.sourceData.kind === 'mmCIF' && model.sourceData.frame.categoryNames.includes('rcsb_assembly_symmetry_feature')) {
const rcsb_assembly_symmetry_feature = toTable(Schema.rcsb_assembly_symmetry_feature, model.sourceData.frame.categories.rcsb_assembly_symmetry_feature)
diff --git a/src/mol-model/structure/model/properties/custom.ts b/src/mol-model/structure/model/properties/custom.ts
index 6c8764094..9b9ab7c3d 100644
--- a/src/mol-model/structure/model/properties/custom.ts
+++ b/src/mol-model/structure/model/properties/custom.ts
@@ -6,4 +6,4 @@
export * from './custom/descriptor'
export * from './custom/collection'
-export * from './custom/residue'
\ No newline at end of file
+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
new file mode 100644
index 000000000..4e711c32e
--- /dev/null
+++ b/src/mol-model/structure/model/properties/custom/chain.ts
@@ -0,0 +1,91 @@
+// /**
+// * 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/indexed.ts b/src/mol-model/structure/model/properties/custom/indexed.ts
new file mode 100644
index 000000000..f20bf257b
--- /dev/null
+++ b/src/mol-model/structure/model/properties/custom/indexed.ts
@@ -0,0 +1,88 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { ResidueIndex, ChainIndex, ElementIndex } 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';
+import { Model } from '../../model';
+
+export class IndexedCustomProperty<Idx extends IndexedCustomProperty.Index, T = any> {
+ readonly id: UUID = UUID.create();
+ readonly kind: Unit.Kind;
+ has(idx: Idx): boolean { return this.map.has(idx); }
+ get(idx: Idx) { return this.map.get(idx); }
+
+ private getStructureElements(structure: Structure) {
+ const models = structure.models;
+ if (models.length !== 1) throw new Error(`Only works on structures with a single model.`);
+
+ const seenIndices = new Set<Idx>();
+ const unitGroups = structure.unitSymmetryGroups;
+ const loci: StructureElement[] = [];
+
+ const segments = this.segmentGetter(models[0])
+
+ for (const unitGroup of unitGroups) {
+ const unit = unitGroup.units[0];
+ if (unit.kind !== this.kind) {
+ continue;
+ }
+
+ const chains = Segmentation.transientSegments(segments, unit.elements);
+ while (chains.hasNext) {
+ const seg = chains.move();
+ if (!this.has(seg.index) || seenIndices.has(seg.index)) continue;
+ seenIndices.add(seg.index);
+ loci[loci.length] = StructureElement.create(unit, unit.elements[seg.start]);
+ }
+ }
+
+ loci.sort((x, y) => x.element - y.element);
+ return loci;
+ }
+
+ getExportContext(structure: Structure): IndexedCustomProperty.ExportCtx<T> {
+ const index = this.segmentGetter(structure.model).index;
+ const elements = this.getStructureElements(structure);
+ return { elements, property: i => this.get(index[elements[i].element])! };
+ }
+
+ constructor(private map: Map<Idx, T>, private segmentGetter: (model: Model) => Segmentation<ElementIndex, Idx>, kind: Unit.Kind) {
+ this.kind = kind;
+ }
+}
+
+export namespace IndexedCustomProperty {
+ export type Index = ResidueIndex | ChainIndex
+
+ export interface ExportCtx<T> {
+ elements: StructureElement[],
+ property(index: number): T
+ }
+
+ export function getCifDataSource<Idx extends Index, T>(structure: Structure, prop: IndexedCustomProperty<Idx, 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 = prop.getExportContext(structure);
+ const ret = { data, rowCount: data.elements.length };
+ if (cache) cache[prop.id] = ret;
+ return ret;
+ }
+
+ export type Residue<T> = IndexedCustomProperty<ResidueIndex, T>
+ const getResidueSegments = (model: Model) => model.atomicHierarchy.residueAtomSegments;
+ export function fromResidueMap<T>(map: Map<ResidueIndex, T>, kind: Unit.Kind): Residue<T> {
+ return new IndexedCustomProperty(map, getResidueSegments, kind);
+ }
+
+ export type Chain<T> = IndexedCustomProperty<ChainIndex, T>
+ const getChainSegments = (model: Model) => model.atomicHierarchy.chainAtomSegments;
+ export function fromChainMap<T>(map: Map<ChainIndex, T>, kind: Unit.Kind): Chain<T> {
+ return new IndexedCustomProperty(map, getChainSegments, kind);
+ }
+}
\ 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
index ba79b8d7b..4dd7cb130 100644
--- a/src/mol-model/structure/model/properties/custom/residue.ts
+++ b/src/mol-model/structure/model/properties/custom/residue.ts
@@ -1,91 +1,91 @@
-/**
- * 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
+// /**
+// * 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/servers/model/test.ts b/src/servers/model/test.ts
index 3e1cc6d9e..ca718fbd4 100644
--- a/src/servers/model/test.ts
+++ b/src/servers/model/test.ts
@@ -55,6 +55,14 @@ async function run() {
// atom_site: { label_comp_id: 'ALA' }
// }
// });
+ // const request = createJob({
+ // entryId: path.join(examplesPath, testFile),
+ // queryName: 'residueInteraction',
+ // queryParams: {
+ // atom_site: { label_comp_id: 'REA' },
+ // radius: 5
+ // }
+ // });
const encoder = await resolveJob(request);
const writer = wrapFile(path.join(outPath, testFile));
encoder.writeTo(writer);
--
GitLab