diff --git a/src/mol-model-formats/structure/mmcif/bonds/comp.ts b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
index 028bc6e23d3d6280ce668d37657e6654109c0fa5..a03d1a3132472e63c3e5b25fbf65dd44604ef8c9 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/comp.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/comp.ts
@@ -8,8 +8,9 @@
import { Model } from '../../../../mol-model/structure/model/model'
import { LinkType } from '../../../../mol-model/structure/model/types'
import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
-import { mmCIF_Database } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../../mol-io/writer/cif'
+import { Table } from '../../../../mol-data/db';
export interface ComponentBond {
entries: Map<string, ComponentBond.Entry>
@@ -24,7 +25,7 @@ export namespace ComponentBond {
categories: [{
name: 'chem_comp_bond',
instance(ctx) {
- const chem_comp_bond = getChemCompBond(ctx.structures[0].model);
+ const chem_comp_bond = getChemCompBond(ctx.firstModel);
if (!chem_comp_bond) return CifWriter.Category.Empty;
const comp_names = ctx.structures[0].uniqueResidueNames;
@@ -51,14 +52,23 @@ export namespace ComponentBond {
return true;
}
- export function attachFromExternalData(model: Model, bonds: ComponentBond, force = false) {
+ export function attachFromExternalData(model: Model, table: mmCIF_Database['chem_comp_bond'], force = false) {
if (!force && model.customProperties.has(Descriptor)) return true;
if (model._staticPropertyData.__ComponentBondData__) delete model._staticPropertyData.__ComponentBondData__;
+ const chem_comp_bond = chemCompBondFromTable(model, table);
+ if (chem_comp_bond._rowCount === 0) return false;
+
model.customProperties.add(Descriptor);
- model._staticPropertyData[PropName] = bonds;
+ model._staticPropertyData.__ComponentBondData__ = chem_comp_bond;
return true;
}
+ function chemCompBondFromTable(model: Model, table: mmCIF_Database['chem_comp_bond']): mmCIF_Database['chem_comp_bond'] {
+ return Table.pick(table, mmCIF_Schema.chem_comp_bond, (i: number) => {
+ return model.properties.chemicalComponentMap.has(table.comp_id.value(i))
+ })
+ }
+
export class ComponentBondImpl implements ComponentBond {
entries: Map<string, ComponentBond.Entry> = new Map();
diff --git a/src/mol-model-props/wwpdb/chem-comp-bond.ts b/src/mol-model-props/wwpdb/chem-comp-bond.ts
deleted file mode 100644
index 2395d4832d341d32eb8aa32d44dfbbaab79aafc5..0000000000000000000000000000000000000000
--- a/src/mol-model-props/wwpdb/chem-comp-bond.ts
+++ /dev/null
@@ -1,84 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Column, Table } from '../../mol-data/db';
-import { toTable } from '../../mol-io/reader/cif/schema';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
-import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
-import { CifWriter } from '../../mol-io/writer/cif';
-
-export namespace ChemCompBond {
- export type Property = Table<Schema['chem_comp_bond']>
-
- export function getFromModel(model: Model): Property {
- if (model.sourceData.kind !== 'mmCIF') return Table.ofUndefinedColumns(Schema.chem_comp_bond, 0);
- const { chem_comp_bond } = model.sourceData.data
- return Table.ofColumns(Schema.chem_comp_bond, {
- ...chem_comp_bond,
- molstar_protonation_variant: Column.Undefined(chem_comp_bond._rowCount, Column.Schema.Str())
- });
- }
-
- export function get(model: Model): Property {
- return model._staticPropertyData.__ChemCompBond__ || getFromModel(model);
- }
- function set(model: Model, prop: Property) {
- (model._staticPropertyData.__ChemCompBond__ as Property) = prop;
- }
-
- export const Schema = { chem_comp_bond: mmCIF_chemCompBond_schema };
- export type Schema = typeof Schema
-
- export const Descriptor = CustomPropertyDescriptor({
- isStatic: true,
- name: 'chem_comp_bond',
- cifExport: {
- prefix: '',
- context(ctx): Property { return get(ctx.firstModel); },
- categories: [{
- name: 'chem_comp_bond',
- instance(ctx: Property) {
- return CifWriter.Category.ofTable(ctx);
- }
- }]
- }
- });
-
- function fromCifData(model: Model): Table<Schema['chem_comp_bond']> | undefined {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const cat = model.sourceData.frame.categories.chem_comp_bond;
- if (!cat) return void 0;
- return toTable(Schema.chem_comp_bond, cat);
- }
-
- export async function attachFromCifOrTable(model: Model, params: {
- // optional Table source
- wwPDB_apiSourceTable?: (model: Model) => Promise<Table<Schema['chem_comp_bond']>>
- }) {
- if (model.customProperties.has(Descriptor)) return true;
-
- let chemCompBond: Table<Schema['chem_comp_bond']> | undefined = fromCifData(model);
- if (chemCompBond === void 0 && params.wwPDB_apiSourceTable) {
- const data = await params.wwPDB_apiSourceTable(model);
- if (!data) return false;
- chemCompBond = chemCompBondFromTable(model, data);
- } else {
- return false;
- }
-
- if (!chemCompBond) return false;
-
- model.customProperties.add(Descriptor);
- set(model, chemCompBond);
- return true;
- }
-}
-
-function chemCompBondFromTable(model: Model, table: Table<ChemCompBond.Schema['chem_comp_bond']>): Table<ChemCompBond.Schema['chem_comp_bond']> {
- return Table.pick(table, ChemCompBond.Schema.chem_comp_bond, (i: number) => {
- return model.properties.chemicalComponentMap.has(table.comp_id.value(i))
- })
-}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/wwpdb.ts b/src/servers/model/properties/providers/wwpdb.ts
index d5ea7136e5a082ff8b7140f74fd9e7a2d21e6b62..773bbbff39ca5f6df1ba867b8680e31b8bbf4152 100644
--- a/src/servers/model/properties/providers/wwpdb.ts
+++ b/src/servers/model/properties/providers/wwpdb.ts
@@ -7,34 +7,32 @@
import * as fs from 'fs'
import * as util from 'util'
import { AttachModelProperty } from '../../property-provider';
-import { ChemCompBond } from '../../../../mol-model-props/wwpdb/chem-comp-bond';
-import { Table } from '../../../../mol-data/db';
import { CIF } from '../../../../mol-io/reader/cif';
import { getParam } from '../../../common/util';
+import { ComponentBond } from '../../../../mol-model-formats/structure/mmcif/bonds';
+import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
require('util.promisify').shim()
const readFile = util.promisify(fs.readFile)
-export const wwPDB_chemCompBond: AttachModelProperty = ({ model, params }) => {
- const wwPDB_apiSourceTable = getChemCompBondTableProvider(getTablePath(params))
- return ChemCompBond.attachFromCifOrTable(model, { wwPDB_apiSourceTable });
+export const wwPDB_chemCompBond: AttachModelProperty = async ({ model, params }) => {
+ const table = await getChemCompBondTable(getTablePath(params))
+ return ComponentBond.attachFromExternalData(model, table, true)
}
async function read(path: string) {
return path.endsWith('.bcif') ? new Uint8Array(await readFile(path)) : readFile(path, 'utf8');
}
-function getChemCompBondTableProvider(path: string): () => Promise<Table<ChemCompBond.Schema['chem_comp_bond']>> {
- let chemCompBondTable: Table<ChemCompBond.Schema['chem_comp_bond']>
- return async function() {
- if (chemCompBondTable === undefined) {
- const parsed = await CIF.parse(await read(path)).run()
- if (parsed.isError) throw new Error(parsed.toString())
- const table = CIF.toDatabase(ChemCompBond.Schema, parsed.result.blocks[0])
- chemCompBondTable = table.chem_comp_bond
- }
- return chemCompBondTable
+let chemCompBondTable: mmCIF_Database['chem_comp_bond']
+async function getChemCompBondTable(path: string): Promise<mmCIF_Database['chem_comp_bond']> {
+ if (!chemCompBondTable) {
+ const parsed = await CIF.parse(await read(path)).run()
+ if (parsed.isError) throw new Error(parsed.toString())
+ const table = CIF.toDatabase(mmCIF_Schema, parsed.result.blocks[0])
+ chemCompBondTable = table.chem_comp_bond
}
+ return chemCompBondTable
}
function getTablePath(params: any) {