diff --git a/src/mol-io/reader/cif/schema/mmcif-extras.ts b/src/mol-io/reader/cif/schema/mmcif-extras.ts
new file mode 100644
index 0000000000000000000000000000000000000000..10b5e32f74df25b17eaf76414e89f7cd9d98b74b
--- /dev/null
+++ b/src/mol-io/reader/cif/schema/mmcif-extras.ts
@@ -0,0 +1,18 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+ import { mmCIF_Schema } from './mmcif';
+
+export const mmCIF_residueId_schema = {
+ label_comp_id: mmCIF_Schema.atom_site.label_comp_id,
+ label_seq_id: mmCIF_Schema.atom_site.label_seq_id,
+ pdbx_PDB_ins_code: mmCIF_Schema.atom_site.pdbx_PDB_ins_code,
+ label_asym_id: mmCIF_Schema.atom_site.label_asym_id,
+ label_entity_id: mmCIF_Schema.atom_site.label_entity_id,
+ auth_comp_id: mmCIF_Schema.atom_site.auth_atom_id,
+ auth_seq_id: mmCIF_Schema.atom_site.auth_seq_id,
+ auth_asym_id: mmCIF_Schema.atom_site.auth_asym_id
+}
\ No newline at end of file
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 98d0f440f0f3ca976e5f16677a88d94cc08b7fe8..c2d89ba0defd71442121d774987be82aa8de168f 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -9,6 +9,9 @@ import { CifWriter } from 'mol-io/writer/cif';
import { Model, ModelPropertyDescriptor, ResidueIndex, Structure, StructureElement, Unit } from 'mol-model/structure';
import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
import CifField = CifWriter.Field;
+import { mmCIF_residueId_schema } from 'mol-io/reader/cif/schema/mmcif-extras';
+import { Column, Table } from 'mol-data/db';
+import { toTable } from 'mol-io/reader/cif/schema';
type IssueMap = Map<ResidueIndex, string[]>
@@ -19,13 +22,18 @@ const _Descriptor: ModelPropertyDescriptor = {
prefix: 'pdbe',
categories: [{
name: 'pdbe_structure_quality_report',
+ instance() {
+ return { fields: _structure_quality_report_fields, rowCount: 1 }
+ }
+ }, {
+ name: 'pdbe_structure_quality_report_issues',
instance(ctx) {
const issues = StructureQualityReport.get(ctx.model);
if (!issues) return CifWriter.Category.Empty;
const residues = getResidueLoci(ctx.structure, issues);
return {
- fields: _structure_quality_report_fields,
+ fields: _structure_quality_report_issues_fields,
data: <ExportCtx>{ model: ctx.model, residues, residueIndex: ctx.model.atomicHierarchy.residueAtomSegments.index, issues },
rowCount: residues.length
};
@@ -36,12 +44,16 @@ const _Descriptor: ModelPropertyDescriptor = {
type ExportCtx = { model: Model, residueIndex: ArrayLike<ResidueIndex>, residues: StructureElement[], issues: IssueMap };
-const _structure_quality_report_fields: CifField<ResidueIndex, ExportCtx>[] = [
+const _structure_quality_report_issues_fields: CifField<ResidueIndex, ExportCtx>[] = [
CifField.index('id'),
...residueIdFields<ResidueIndex, ExportCtx>((k, d) => d.residues[k]),
CifField.str<ResidueIndex, ExportCtx>('issues', (i, d) => d.issues.get(d.residueIndex[d.residues[i].element])!.join(','))
];
+const _structure_quality_report_fields: CifField<ResidueIndex, ExportCtx>[] = [
+ CifField.str('updated_datetime_utc', () => `${new Date().toISOString().replace(/T/, ' ').replace(/\..+/, '')}`)
+];
+
function getResidueLoci(structure: Structure, issues: IssueMap) {
const seenResidues = new Set<ResidueIndex>();
const unitGroups = structure.unitSymmetryGroups;
@@ -67,7 +79,7 @@ function getResidueLoci(structure: Structure, issues: IssueMap) {
return loci;
}
-function createIssueMap(modelData: Model, data: any): IssueMap | undefined {
+function createIssueMapFromJson(modelData: Model, data: any): IssueMap | undefined {
const ret = new Map<ResidueIndex, string[]>();
if (!data.molecules) return;
@@ -91,24 +103,52 @@ function createIssueMap(modelData: Model, data: any): IssueMap | undefined {
return ret;
}
+function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>): IssueMap | undefined {
+ const ret = new Map<ResidueIndex, string[]>();
+ const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, _rowCount } = data;
+
+ for (let i = 0; i < _rowCount; i++) {
+ const idx = modelData.atomicHierarchy.findResidueKey(label_entity_id.value(i), label_asym_id.value(i), '', auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
+ ret.set(idx, issues.value(i));
+ }
+
+ return ret;
+}
+
export namespace StructureQualityReport {
export const Descriptor = _Descriptor;
+ export const Schema = {
+ pdbe_structure_quality_report: {
+ updated_datetime_utc: Column.Schema.str
+ },
+ pdbe_structure_quality_report_issues: {
+ id: Column.Schema.int,
+ ...mmCIF_residueId_schema,
+ issues: Column.Schema.List(',', x => x)
+ }
+ }
+
export async function attachFromCifOrApi(model: Model, params: {
// provide JSON from api
- pdbEapiSourceJson?: (model: Model) => Promise<any>
+ PDBe_apiSourceJson?: (model: Model) => Promise<any>
}) {
- // TODO: check if present in mmCIF on Model
- if (!params.pdbEapiSourceJson) throw new Error('Data source not defined');
-
if (model.customProperties.has(Descriptor)) return true;
- const id = model.label.toLowerCase();
- const json = await params.pdbEapiSourceJson(model);
- const data = json[id];
- if (!data) return false;
- const issueMap = createIssueMap(model, data);
- if (!issueMap || issueMap.size === 0) return false;
+ let issueMap;
+
+ if (model.sourceData.kind === 'mmCIF' && model.sourceData.frame.categoryNames.includes('pdbe_structure_quality_report')) {
+ const data = toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report);
+ issueMap = createIssueMapFromCif(model, data);
+ } else if (!params.PDBe_apiSourceJson) {
+ throw new Error('Data source not defined');
+ } else {
+ const id = model.label.toLowerCase();
+ const json = await params.PDBe_apiSourceJson(model);
+ const data = json[id];
+ if (!data) return false;
+ issueMap = createIssueMapFromJson(model, data);
+ }
model.customProperties.add(Descriptor);
model._staticPropertyData.__StructureQualityReport__ = issueMap;
diff --git a/src/servers/model/properties/pdbe.ts b/src/servers/model/properties/pdbe.ts
index 5ae5d369f826c481ff9570562d600a5759cc008d..acda123fe369344a804c4edfb3f4a8d7abfe9200 100644
--- a/src/servers/model/properties/pdbe.ts
+++ b/src/servers/model/properties/pdbe.ts
@@ -10,7 +10,7 @@ import { fetchRetry } from '../utils/fetch-retry';
export function PDBe_structureQualityReport(model: Model) {
return StructureQualityReport.attachFromCifOrApi(model, {
- pdbEapiSourceJson: async model => {
+ PDBe_apiSourceJson: async model => {
const rawData = await fetchRetry(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`, 1500, 5);
return await rawData.json();
}