diff --git a/src/mol-model/structure/export/categories/misc.ts b/src/mol-model/structure/export/categories/misc.ts
index a73be87bc3b8105b3797c32fd0ded28315eeffc5..39d3d40f2b1f0202235618e09c81e6634972b8ca 100644
--- a/src/mol-model/structure/export/categories/misc.ts
+++ b/src/mol-model/structure/export/categories/misc.ts
@@ -5,21 +5,18 @@
*/
import { Column } from 'mol-data/db';
-import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { CifWriter } from 'mol-io/writer/cif';
-import { unionMany } from 'mol-util/set';
-import { Model } from '../../model';
import { CifExportContext } from '../mmcif';
+import { getModelMmCifCategory, getUniqueResidueNamesFromStructures } from './utils';
import CifCategory = CifWriter.Category
-import { Structure } from '../../structure';
export const _chem_comp: CifCategory<CifExportContext> = {
name: 'chem_comp',
- instance({ structures, cache }) {
- const chem_comp = getCifCategory(structures[0].model, 'chem_comp');
+ instance({ firstModel, structures, cache }) {
+ const chem_comp = getModelMmCifCategory(structures[0].model, 'chem_comp');
if (!chem_comp) return CifCategory.Empty;
const { id } = chem_comp;
- const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNames(structures));
+ const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNamesFromStructures(structures));
const indices = Column.indicesOf(id, id => names.has(id));
return CifCategory.ofTable(chem_comp, indices);
}
@@ -27,21 +24,12 @@ export const _chem_comp: CifCategory<CifExportContext> = {
export const _pdbx_chem_comp_identifier: CifCategory<CifExportContext> = {
name: 'pdbx_chem_comp_identifier',
- instance({ structures, cache }) {
- const pdbx_chem_comp_identifier = getCifCategory(structures[0].model, 'pdbx_chem_comp_identifier');
+ instance({ firstModel, structures, cache }) {
+ const pdbx_chem_comp_identifier = getModelMmCifCategory(firstModel, 'pdbx_chem_comp_identifier');
if (!pdbx_chem_comp_identifier) return CifCategory.Empty;
const { comp_id } = pdbx_chem_comp_identifier;
- const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNames(structures));
+ const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNamesFromStructures(structures));
const indices = Column.indicesOf(comp_id, id => names.has(id));
return CifCategory.ofTable(pdbx_chem_comp_identifier, indices);
}
-}
-
-function getCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
- if (model.sourceData.kind !== 'mmCIF') return;
- return model.sourceData.data[name];
-}
-
-function getUniqueResidueNames(structures: Structure[]) {
- return unionMany(structures.map(s => s.uniqueResidueNames));
}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/categories/sequence.ts b/src/mol-model/structure/export/categories/sequence.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cca5c83da2bb3be7355f8d57dc8ad7aca0a29e94
--- /dev/null
+++ b/src/mol-model/structure/export/categories/sequence.ts
@@ -0,0 +1,36 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column } from 'mol-data/db';
+import { CifWriter } from 'mol-io/writer/cif';
+import { Structure } from '../../structure';
+import { CifExportContext } from '../mmcif';
+import { getModelMmCifCategory, getUniqueEntityIdsFromStructures } from './utils';
+import CifCategory = CifWriter.Category
+
+export const _struct_asym: CifCategory<CifExportContext> = createCategory('struct_asym');
+export const _entity_poly: CifCategory<CifExportContext> = createCategory('entity_poly');
+export const _entity_poly_seq: CifCategory<CifExportContext> = createCategory('entity_poly_seq');
+
+function createCategory(categoryName: 'struct_asym' | 'entity_poly' | 'entity_poly_seq'): CifCategory<CifExportContext> {
+ return {
+ name: categoryName,
+ instance({ structures, cache }) {
+ return getCategoryInstance(structures, categoryName, cache);
+ }
+ };
+}
+
+function getCategoryInstance(structures: Structure[], categoryName: 'struct_asym' | 'entity_poly' | 'entity_poly_seq', cache: any) {
+ const category = getModelMmCifCategory(structures[0].model, categoryName);
+ if (!category) return CifCategory.Empty;
+ const { entity_id } = category;
+ const names = cache.uniqueEntityIds || (cache.uniqueEntityIds = getUniqueEntityIdsFromStructures(structures));
+ const indices = Column.indicesOf(entity_id, id => names.has(id));
+ return CifCategory.ofTable(category, indices);
+
+}
+
diff --git a/src/mol-model/structure/export/categories/utils.ts b/src/mol-model/structure/export/categories/utils.ts
new file mode 100644
index 0000000000000000000000000000000000000000..be0276c94ae628f647ececf34c75e5acf2ac505b
--- /dev/null
+++ b/src/mol-model/structure/export/categories/utils.ts
@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { unionMany } from 'mol-util/set';
+import { Model } from '../../model';
+import { Structure } from '../../structure';
+import { EntityIndex } from '../../model/indexing';
+import { UniqueArray } from 'mol-data/generic';
+import { sortArray } from 'mol-data/util';
+
+export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
+ if (model.sourceData.kind !== 'mmCIF') return;
+ return model.sourceData.data[name];
+}
+
+export function getUniqueResidueNamesFromStructures(structures: Structure[]) {
+ return unionMany(structures.map(s => s.uniqueResidueNames));
+}
+
+export function getUniqueEntityIdsFromStructures(structures: Structure[]): Set<string> {
+ if (structures.length === 0) return new Set();
+
+ const names = structures[0].model.entities.data.id;
+ return new Set(getUniqueEntityIndicesFromStructures(structures).map(i => names.value(i)));
+}
+
+export function getUniqueEntityIndicesFromStructures(structures: Structure[]): ReadonlyArray<EntityIndex> {
+ if (structures.length === 0) return [];
+ if (structures.length === 1) return structures[0].entityIndices;
+ const ret = UniqueArray.create<EntityIndex, EntityIndex>();
+ for (const s of structures) {
+ for (const e of s.entityIndices) {
+ UniqueArray.add(ret, e, e);
+ }
+ }
+ sortArray(ret.array);
+ return ret.array;
+}
\ 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 e512768be0926f545428740e3d2b6c9845464b59..7ce1fcf7bfb2cca5fef1e5c59eeadc52cdc6a5af 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -14,6 +14,8 @@ import { _struct_conf, _struct_sheet_range } from './categories/secondary-struct
import { _pdbx_struct_mod_residue } from './categories/modified-residues';
import { _chem_comp, _pdbx_chem_comp_identifier } from './categories/misc';
import { Model } from '../model';
+import { getUniqueEntityIndicesFromStructures } from './categories/utils';
+import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
export interface CifExportContext {
structures: Structure[],
@@ -48,7 +50,7 @@ function copy_mmCif_category(name: keyof mmCIF_Schema): CifCategory<CifExportCon
const _entity: CifCategory<CifExportContext> = {
name: 'entity',
instance({ structures }) {
- const indices = structures[0].entityIndices;
+ const indices = getUniqueEntityIndicesFromStructures(structures);
return CifCategory.ofTable(structures[0].model.entities.data, indices);
}
}
@@ -73,9 +75,9 @@ const Categories = [
_struct_sheet_range,
// Sequence
- copy_mmCif_category('struct_asym'), // TODO: filter only present entities?
- copy_mmCif_category('entity_poly'), // TODO: filter only present entities?
- copy_mmCif_category('entity_poly_seq'), // TODO: filter only present entities?
+ _struct_asym,
+ _entity_poly,
+ _entity_poly_seq,
// Branch
copy_mmCif_category('pdbx_entity_branch'),
diff --git a/src/mol-util/set.ts b/src/mol-util/set.ts
index edc7e05e9a93651a702e0e957b9b49a6c5949372..7bc7e10d46c2d4b3937b2c41669680a30cac7bed 100644
--- a/src/mol-util/set.ts
+++ b/src/mol-util/set.ts
@@ -31,6 +31,15 @@ export function unionMany<T>(sets: Set<T>[]) {
return union;
}
+export function unionManyArrays<T>(arrays: T[][]) {
+ if (arrays.length === 0) return new Set<T>();
+ const union = new Set(arrays[0]);
+ for (let i = 1; i < arrays.length; i++) {
+ for (const elem of arrays[i]) union.add(elem);
+ }
+ return union;
+}
+
/** Create set containing elements of set a that are also in set b. */
export function intersection<T>(setA: Set<T>, setB: Set<T>): Set<T> {
const intersection = new Set();