From 25965d307a838c400936d320e6ce33eac39be4c8 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 26 Jun 2018 12:10:15 +0200
Subject: [PATCH] chem_comp_bond as custom property
---
src/apps/structure-info/model.ts | 2 +-
src/mol-data/int/impl/segmentation.ts | 6 +-
src/mol-data/int/segmentation.ts | 4 +-
.../export/categories/chem_comp_bond.ts | 7 --
src/mol-model/structure/export/mmcif.ts | 6 ++
.../structure/model/formats/mmcif.ts | 6 ++
.../model/formats/mmcif/bonds/comp.ts | 67 +++++++++++++++++--
.../model/properties/custom/collection.ts | 12 ++--
.../model/properties/custom/descriptor.ts | 11 +--
.../structure/unit/links/intra-compute.ts | 2 +-
10 files changed, 94 insertions(+), 29 deletions(-)
delete mode 100644 src/mol-model/structure/export/categories/chem_comp_bond.ts
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index d1252937c..f34db7c79 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -207,7 +207,7 @@ async function run(frame: CifFrame) {
printUnits(structure);
printSymmetryInfo(models[0]);
//printRings(structure);
- //printLinks(structure, true, true);
+ printLinks(structure, true, true);
//printModRes(models[0]);
//printSecStructure(models[0]);
}
diff --git a/src/mol-data/int/impl/segmentation.ts b/src/mol-data/int/impl/segmentation.ts
index 63313431f..a5534e52a 100644
--- a/src/mol-data/int/impl/segmentation.ts
+++ b/src/mol-data/int/impl/segmentation.ts
@@ -54,7 +54,7 @@ export class SegmentIterator<T extends number = number> implements Iterator<Segs
private segmentMin = 0;
private segmentMax = 0;
private setRange = Interval.Empty;
- private value: Segs.Segment<T> = { index: 0, start: 0, end: 0 };
+ private value: Segs.Segment<T> = { index: 0, start: 0 as T, end: 0 as T };
hasNext: boolean = false;
@@ -75,8 +75,8 @@ export class SegmentIterator<T extends number = number> implements Iterator<Segs
const segmentEnd = this.segments[this.segmentMin + 1];
// TODO: add optimized version for interval and array?
const setEnd = OrderedSet.findPredecessorIndexInInterval(this.set, segmentEnd, this.setRange);
- this.value.start = Interval.start(this.setRange);
- this.value.end = setEnd;
+ this.value.start = Interval.start(this.setRange) as T;
+ this.value.end = setEnd as T;
this.setRange = Interval.ofBounds(setEnd, Interval.end(this.setRange));
return setEnd > this.value.start;
}
diff --git a/src/mol-data/int/segmentation.ts b/src/mol-data/int/segmentation.ts
index 8f7c58db6..94abaaa0f 100644
--- a/src/mol-data/int/segmentation.ts
+++ b/src/mol-data/int/segmentation.ts
@@ -9,7 +9,7 @@ import OrderedSet from './ordered-set'
import * as Impl from './impl/segmentation'
namespace Segmentation {
- export interface Segment<T extends number = number> { index: number, start: number, end: number }
+ export interface Segment<T extends number = number> { index: number, start: T, end: T }
export const create: <T extends number = number>(segs: ArrayLike<T>) => Segmentation<T> = Impl.create as any;
export const ofOffsets: <T extends number = number>(offsets: ArrayLike<T>, bounds: Interval) => Segmentation<T> = Impl.ofOffsets as any;
@@ -19,7 +19,7 @@ namespace Segmentation {
export const projectValue: <T extends number = number>(segs: Segmentation<T>, set: OrderedSet<T>, value: T) => Interval = Impl.projectValue as any;
// Segment iterator that mutates a single segment object to mark all the segments.
- export const transientSegments: <T extends number = number>(segs: Segmentation<T>, set: OrderedSet<T>, segment?: Segment<T>) => Impl.SegmentIterator = Impl.segments as any;
+ export const transientSegments: <T extends number = number>(segs: Segmentation<T>, set: OrderedSet<T>, segment?: Segment<T>) => Impl.SegmentIterator<T> = Impl.segments as any;
}
interface Segmentation<T extends number = number> {
diff --git a/src/mol-model/structure/export/categories/chem_comp_bond.ts b/src/mol-model/structure/export/categories/chem_comp_bond.ts
deleted file mode 100644
index 66298c566..000000000
--- a/src/mol-model/structure/export/categories/chem_comp_bond.ts
+++ /dev/null
@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// TODO
\ 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 4458ef154..f09ee2103 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -63,6 +63,12 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structure: S
for (const cat of Categories) {
encoder.writeCategory(cat, ctx);
}
+ for (const customProp of model.customProperties.all) {
+ const cats = customProp.cifExport.categoryProvider(ctx[0]);
+ for (const cat of cats) {
+ encoder.writeCategory(cat, ctx);
+ }
+ }
}
function to_mmCIF(name: string, structure: Structure, asBinary = false) {
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 66c2bfc28..6bd490457 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -27,6 +27,7 @@ import { Element } from '../../../structure'
import { CustomProperties } from '../properties/custom';
import mmCIF_Format = Format.mmCIF
+import { ComponentBond } from './mmcif/bonds';
type AtomSite = mmCIF_Database['atom_site']
function findModelEnd({ data }: mmCIF_Format, startIndex: number) {
@@ -201,6 +202,10 @@ function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model
};
}
+function attachProps(model: Model) {
+ ComponentBond.attachFromMmCif(model);
+}
+
function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
return Task.create('Create mmCIF Model', async ctx => {
const atomCount = format.data.atom_site._rowCount;
@@ -218,6 +223,7 @@ function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
const modelEnd = findModelEnd(format, modelStart);
const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
const model = createModel(format, atom_site, models.length > 0 ? models[models.length - 1] : void 0);
+ attachProps(model);
models.push(model);
modelStart = modelEnd;
}
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
index 4b31456ab..fe0c4ab4e 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
@@ -7,12 +7,50 @@
import Model from '../../../model'
import { LinkType } from '../../../types'
+import { ModelPropertyDescriptor } from '../../../properties/custom';
+import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
+import { Structure, Unit, StructureProperties, Element } from '../../../../structure';
+import { Segmentation } from 'mol-data/int';
+import { CifWriter } from 'mol-io/writer/cif'
export interface ComponentBond {
entries: Map<string, ComponentBond.Entry>
}
export namespace ComponentBond {
+ export const Descriptor: ModelPropertyDescriptor = {
+ isStatic: true,
+ name: 'chem_comp_bond',
+ cifExport: {
+ categoryNames: ['chem_comp_bond'],
+ categoryProvider(ctx) {
+ const comp_names = getUniqueResidueNames(ctx.structure);
+ const chem_comp_bond = getChemCompBond(ctx.model);
+
+ if (!chem_comp_bond) return [];
+
+ const { comp_id, _rowCount } = chem_comp_bond;
+ const indices: number[] = [];
+ for (let i = 0; i < _rowCount; i++) {
+ if (comp_names.has(comp_id.value(i))) indices[indices.length] = i;
+ }
+
+ return [
+ () => CifWriter.Category.ofTable('chem_comp_bond', chem_comp_bond, indices)
+ ];
+ }
+ }
+ }
+
+ export function attachFromMmCif(model: Model): boolean {
+ if (model.sourceData.kind !== 'mmCIF') return false;
+ const { chem_comp_bond } = model.sourceData.data;
+ if (chem_comp_bond._rowCount === 0) return false;
+ model.customProperties.add(Descriptor);
+ model._staticPropertyData.__ComponentBondData__ = chem_comp_bond;
+ return true;
+ }
+
export class ComponentBondImpl implements ComponentBond {
entries: Map<string, ComponentBond.Entry> = new Map();
@@ -46,13 +84,15 @@ export namespace ComponentBond {
}
}
+ function getChemCompBond(model: Model) {
+ return model._staticPropertyData.__ComponentBondData__ as mmCIF_Database['chem_comp_bond'];
+ }
+
export const PropName = '__ComponentBond__';
- export function fromModel(model: Model): ComponentBond | undefined {
+ export function get(model: Model): ComponentBond | undefined {
if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
-
- if (model.sourceData.kind !== 'mmCIF') return
- const { chem_comp_bond } = model.sourceData.data;
- if (!chem_comp_bond._rowCount) return void 0;
+ if (!model.customProperties.has(Descriptor)) return void 0;
+ const chem_comp_bond = getChemCompBond(model);
let compBond = new ComponentBondImpl();
@@ -90,4 +130,21 @@ export namespace ComponentBond {
model._staticPropertyData[PropName] = compBond;
return compBond;
}
+
+ function getUniqueResidueNames(s: Structure) {
+ const prop = StructureProperties.residue.label_comp_id;
+ const names = new Set<string>();
+ const loc = Element.Location();
+ for (const unit of s.units) {
+ if (!Unit.isAtomic(unit)) continue;
+ const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueSegments, unit.elements);
+ loc.unit = unit;
+ while (residues.hasNext) {
+ const seg = residues.move();
+ loc.element = seg.start;
+ names.add(prop(loc));
+ }
+ }
+ return names;
+ }
}
\ 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
index 75dda9b2d..371889b8f 100644
--- a/src/mol-model/structure/model/properties/custom/collection.ts
+++ b/src/mol-model/structure/model/properties/custom/collection.ts
@@ -4,22 +4,22 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { PropertyDescriptor } from './descriptor'
+import { ModelPropertyDescriptor } from './descriptor'
export class CustomProperties {
- private _list: PropertyDescriptor[] = [];
- private _set = new Set<PropertyDescriptor>();
+ private _list: ModelPropertyDescriptor[] = [];
+ private _set = new Set<ModelPropertyDescriptor>();
- get all(): ReadonlyArray<PropertyDescriptor> {
+ get all(): ReadonlyArray<ModelPropertyDescriptor> {
return this._list;
}
- add(desc: PropertyDescriptor) {
+ add(desc: ModelPropertyDescriptor) {
this._list.push(desc);
this._set.add(desc);
}
- has(desc: PropertyDescriptor): boolean {
+ has(desc: ModelPropertyDescriptor): 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
index 37af3562b..89304d197 100644
--- a/src/mol-model/structure/model/properties/custom/descriptor.ts
+++ b/src/mol-model/structure/model/properties/custom/descriptor.ts
@@ -7,12 +7,15 @@
import { CifWriter } from 'mol-io/writer/cif'
import { CifExportContext } from '../../../export/mmcif';
-interface PropertyDescriptor {
+interface ModelPropertyDescriptor {
readonly isStatic: boolean,
readonly name: string,
- /** Given a structure, returns a list of category providers used for export. */
- getCifCategories: (ctx: CifExportContext) => CifWriter.Category.Provider[]
+ cifExport: {
+ /** used category names that can be used for "filtering" by the writer */
+ readonly categoryNames: ReadonlyArray<string>,
+ categoryProvider: (ctx: CifExportContext) => CifWriter.Category.Provider[]
+ }
}
-export { PropertyDescriptor }
\ No newline at end of file
+export { ModelPropertyDescriptor }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/links/intra-compute.ts b/src/mol-model/structure/structure/unit/links/intra-compute.ts
index 3f2949ec9..c17d81539 100644
--- a/src/mol-model/structure/structure/unit/links/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/links/intra-compute.ts
@@ -36,7 +36,7 @@ function _computeBonds(unit: Unit.Atomic, params: LinkComputationParameters): In
const query3d = unit.lookup3d;
const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.fromModel(unit.model) : void 0;
- const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBond.fromModel(unit.model) : void 0;
+ const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBond.get(unit.model) : void 0;
const atomA: number[] = [];
const atomB: number[] = [];
--
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