diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 2d6b11e3f7726ef9302f5c081db4e57820154f4b..8eed13c6f251255351d7570612a7233f88ccad6f 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -5,7 +5,7 @@
*/
import { CifWriter } from 'mol-io/writer/cif';
-import { Model, ModelPropertyDescriptor, ResidueIndex, Unit, ResidueCustomProperty } from 'mol-model/structure';
+import { Model, ModelPropertyDescriptor, ResidueIndex, Unit, ResidueCustomProperty, StructureProperties as P } 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';
@@ -50,6 +50,7 @@ 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(','))
];
@@ -83,9 +84,10 @@ function createIssueMapFromJson(modelData: Model, data: any): IssueMap | undefin
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;
+ const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, pdbx_PDB_model_num, _rowCount } = data;
for (let i = 0; i < _rowCount; i++) {
+ if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue;
const idx = modelData.atomicHierarchy.index.findResidue(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));
}
@@ -103,6 +105,7 @@ export namespace StructureQualityReport {
pdbe_structure_quality_report_issues: {
id: Column.Schema.int,
...mmCIF_residueId_schema,
+ pdbx_PDB_model_num: Column.Schema.int,
issues: Column.Schema.List(',', x => x)
}
}
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 2bfa34c5609985e4f10e006109f0baffbeb80905..3f793d3d2a0634ba3a43e695d3a4b8ce51025408 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -21,8 +21,9 @@ export interface CifExportContext {
}
export namespace CifExportContext {
- export function create(structure: Structure, model: Model): CifExportContext {
- return { structure, model, cache: Object.create(null) };
+ export function create(structures: Structure | Structure[]): CifExportContext[] {
+ if (Array.isArray(structures)) return structures.map(structure => ({ structure, model: structure.models[0], cache: Object.create(null) }));
+ return [{ structure: structures, model: structures.models[0], cache: Object.create(null) }];
}
}
@@ -99,20 +100,20 @@ export const mmCIF_Export_Filters = {
}
/** Doesn't start a data block */
-export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structure: Structure, params?: { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext }) {
- const models = structure.models;
+export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext[] }) {
+ const first = Array.isArray(structures) ? structures[0] : (structures as Structure);
+ const models = first.models;
if (models.length !== 1) throw 'Can\'t export stucture composed from multiple models.';
- const model = models[0];
const _params = params || { };
-
- const ctx: CifExportContext[] = [_params.exportCtx ? _params.exportCtx : CifExportContext.create(structure, model)];
+ const ctx: CifExportContext[] = params && params.exportCtx ? params.exportCtx : CifExportContext.create(structures);
for (const cat of Categories) {
if (_params.skipCategoryNames && _params.skipCategoryNames.has(cat.name)) continue;
encoder.writeCategory(cat, ctx);
}
- for (const customProp of model.customProperties.all) {
+
+ for (const customProp of models[0].customProperties.all) {
if (!customProp.cifExport || customProp.cifExport.categories.length === 0) continue;
const prefix = customProp.cifExport.prefix;
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index f54468091666e97985aedc7a1d56855bb305e496..5047d6635cde9ec48e175cdd614d76c20d1f6136 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -25,12 +25,12 @@ export async function preprocessFile(filename: string, outputCif?: string, outpu
//ConsoleLogger.log(`${linearId}`, `Reading '${filename}'...`);
// TODO: support the custom prop provider list here.
const input = await readStructureWrapper('entry', '_local_', filename, void 0);
+ const categories = await classifyCif(input.cifFrame);
const inputStructure = (await resolveStructure(input))!;
//ConsoleLogger.log(`${linearId}`, `Classifying CIF categories...`);
- const categories = await classifyCif(input.cifFrame);
//clearLine();
- const exportCtx = CifExportContext.create(inputStructure, inputStructure.models[0]);
+ const exportCtx = CifExportContext.create(inputStructure);
if (outputCif) {
//ConsoleLogger.log(`${linearId}`, `Encoding CIF...`);
@@ -52,7 +52,7 @@ export async function preprocessFile(filename: string, outputCif?: string, outpu
// ConsoleLogger.log(`${linearId}`, `Finished '${filename}' in ${Math.round(now() - started)}ms`);
}
-function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext, writer: Writer) {
+function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext[], writer: Writer) {
return Task.create('Encode', async ctx => {
const skipCategoryNames = new Set<string>(categories.map(c => c.name));
encoder.startDataBlock(header);
diff --git a/src/servers/model/provider.ts b/src/servers/model/property-provider.ts
similarity index 100%
rename from src/servers/model/provider.ts
rename to src/servers/model/property-provider.ts
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 50c04e0c9a19ffe485c26dc956a4222d7e449eaf..35159b5dc3f4754618aca8e7933b8fdc5a53d373 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -16,7 +16,7 @@ import Version from '../version';
import { Job } from './jobs';
import { createStructureWrapperFromJob, StructureWrapper, resolveStructure } from './structure-wrapper';
import CifField = CifWriter.Field
-import { createModelPropertiesProviderFromConfig } from '../provider';
+import { createModelPropertiesProviderFromConfig } from '../property-provider';
export interface Stats {
structure: StructureWrapper,
@@ -54,7 +54,7 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
ConsoleLogger.logId(job.id, 'Query', 'Query finished.');
perf.start('encode');
- encoder.startDataBlock(structure.units[0].model.label.toUpperCase());
+ encoder.startDataBlock(structure.models[0].label.toUpperCase());
encoder.writeCategory(_model_server_result, [job]);
encoder.writeCategory(_model_server_params, [job]);
@@ -132,7 +132,7 @@ const _model_server_error_fields: CifField<number, string>[] = [
const _model_server_stats_fields: CifField<number, Stats>[] = [
int32<Stats>('io_time_ms', ctx => ctx.structure.info.readTime | 0),
int32<Stats>('parse_time_ms', ctx => ctx.structure.info.parseTime | 0),
- int32<Stats>('attach_props_time_ms', ctx => ctx.structure.info.attachPropsTime | 0),
+ // int32<Stats>('attach_props_time_ms', ctx => ctx.structure.info.attachPropsTime | 0),
int32<Stats>('create_model_time_ms', ctx => ctx.structure.info.createModelTime | 0),
int32<Stats>('query_time_ms', ctx => ctx.queryTimeMs | 0),
int32<Stats>('encode_time_ms', ctx => ctx.encodeTimeMs | 0)
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index d7ffc7f2d2da722aeaff4a45a299b4a797be05c0..60275ddc5f2a514cefd9243f536c0e752bc811cf 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -14,7 +14,7 @@ import * as fs from 'fs'
import * as zlib from 'zlib'
import { Job } from './jobs';
import { ConsoleLogger } from 'mol-util/console-logger';
-import { ModelPropertiesProvider } from '../provider';
+import { ModelPropertiesProvider } from '../property-provider';
require('util.promisify').shim();