diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index f83a449f078fa8080c9a9e67d5fe4857cd7895bc..97a22d6f091628b20225e3b9fba676944cc7b248 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -8,6 +8,7 @@ import { Column, Table } from 'mol-data/db';
import { Interval, Segmentation } from 'mol-data/int';
import { Spacegroup, SpacegroupCell } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
+import { Task } from 'mol-task';
import UUID from 'mol-util/uuid';
import Format from '../format';
import Model from '../model';
@@ -18,12 +19,13 @@ import { getAtomicKeys } from '../properties/utils/atomic-keys';
import { ElementSymbol } from '../types';
import { createAssemblies } from './mmcif/assembly';
import { getIHMCoarse } from './mmcif/ihm';
+import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
import { getSequence } from './mmcif/sequence';
+import { sortAtomSite } from './mmcif/sort';
+import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import mmCIF_Format = Format.mmCIF
-import { Task } from 'mol-task';
-import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
-import { sortAtomSite } from './mmcif/sort';
+type AtomSite = mmCIF_Database['atom_site']
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -34,13 +36,13 @@ function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
return Interval.ofBounds(startIndex, endIndex);
}
-function findHierarchyOffsets({ data }: mmCIF_Format, bounds: Interval) {
- if (Interval.size(bounds) === 0) return { residues: [], chains: [] };
+function findHierarchyOffsets(atom_site: AtomSite) {
+ if (atom_site._rowCount === 0) return { residues: [], chains: [] };
- const start = Interval.start(bounds), end = Interval.end(bounds);
+ const start = 0, end = atom_site._rowCount;
const residues = [start], chains = [start];
- const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = data.atom_site;
+ const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
for (let i = start + 1; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
@@ -56,15 +58,13 @@ function findHierarchyOffsets({ data }: mmCIF_Format, bounds: Interval) {
return { residues, chains };
}
-function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
- const { atom_site } = data;
- const start = Interval.start(bounds), end = Interval.end(bounds);
+function createHierarchyData(atom_site: AtomSite, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
const atoms = Table.ofColumns(AtomsSchema, {
- type_symbol: Column.ofArray({ array: Column.mapToArray(Column.window(atom_site.type_symbol, start, end), ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
- label_atom_id: Column.window(atom_site.label_atom_id, start, end),
- auth_atom_id: Column.window(atom_site.auth_atom_id, start, end),
- label_alt_id: Column.window(atom_site.label_alt_id, start, end),
- pdbx_formal_charge: Column.window(atom_site.pdbx_formal_charge, start, end)
+ type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
+ label_atom_id: atom_site.label_atom_id,
+ auth_atom_id: atom_site.auth_atom_id,
+ label_alt_id: atom_site.label_alt_id,
+ pdbx_formal_charge: atom_site.pdbx_formal_charge
});
const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
// Optimize the numeric columns
@@ -74,17 +74,15 @@ function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets:
return { atoms, residues, chains };
}
-function getConformation({ data }: mmCIF_Format, bounds: Interval): AtomicConformation {
- const start = Interval.start(bounds), end = Interval.end(bounds);
- const { atom_site } = data;
+function getConformation(atom_site: AtomSite): AtomicConformation {
return {
id: UUID.create(),
- atomId: Column.window(atom_site.id, start, end),
- occupancy: Column.window(atom_site.occupancy, start, end),
- B_iso_or_equiv: Column.window(atom_site.B_iso_or_equiv, start, end),
- x: atom_site.Cartn_x.toArray({ array: Float32Array, start, end }),
- y: atom_site.Cartn_y.toArray({ array: Float32Array, start, end }),
- z: atom_site.Cartn_z.toArray({ array: Float32Array, start, end }),
+ atomId: atom_site.id,
+ occupancy: atom_site.occupancy,
+ B_iso_or_equiv: atom_site.B_iso_or_equiv,
+ x: atom_site.Cartn_x.toArray({ array: Float32Array }),
+ y: atom_site.Cartn_y.toArray({ array: Float32Array }),
+ z: atom_site.Cartn_z.toArray({ array: Float32Array }),
}
}
@@ -133,20 +131,20 @@ function modResMap(format: mmCIF_Format) {
return map;
}
-function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model): Model {
- const hierarchyOffsets = findHierarchyOffsets(format, bounds);
- const hierarchyData = createHierarchyData(format, bounds, hierarchyOffsets);
+function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model): Model {
+ const hierarchyOffsets = findHierarchyOffsets(atom_site);
+ const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
return {
...previous,
- atomicConformation: getConformation(format, bounds)
+ atomicConformation: getConformation(atom_site)
};
}
const hierarchySegments: AtomicSegments = {
- residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, bounds),
- chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
+ residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
+ chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
}
const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
@@ -167,11 +165,11 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
id: UUID.create(),
label,
sourceData: format,
- modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
+ modelNum: format.data.atom_site.pdbx_PDB_model_num.value(0),
entities,
atomicHierarchy,
sequence: getSequence(format.data, entities, atomicHierarchy, modifiedResidueNameMap),
- atomicConformation: getConformation(format, bounds),
+ atomicConformation: getConformation(atom_site),
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
@@ -189,7 +187,7 @@ function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
if (atomCount === 0) {
return isIHM
- ? [createModel(format, Interval.Empty, void 0)]
+ ? [createModel(format, format.data.atom_site, void 0)]
: [];
}
@@ -198,8 +196,8 @@ function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
while (modelStart < atomCount) {
const bounds = findModelBounds(format, modelStart);
- // const indices = await sortAtomSite(ctx, format.data.atom_site, 0, Interval.end(bounds));
- const model = createModel(format, bounds, models.length > 0 ? models[models.length - 1] : void 0);
+ const atom_site = await sortAtomSite(ctx, format.data.atom_site, 0, Interval.end(bounds));
+ const model = createModel(format, atom_site, models.length > 0 ? models[models.length - 1] : void 0);
models.push(model);
modelStart = Interval.end(bounds);
}
diff --git a/src/mol-model/structure/model/formats/mmcif/sort.ts b/src/mol-model/structure/model/formats/mmcif/sort.ts
index aa071aedb7dba06243f94c22460dddb4945af1a7..6809d48119a2ba88860ecc64a485e6b1e46f6902 100644
--- a/src/mol-model/structure/model/formats/mmcif/sort.ts
+++ b/src/mol-model/structure/model/formats/mmcif/sort.ts
@@ -6,9 +6,16 @@
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { createRangeArray, makeBuckets } from 'mol-data/util';
-import { Column } from 'mol-data/db';
+import { Column, Table } from 'mol-data/db';
import { RuntimeContext } from 'mol-task';
+function isIdentity(xs: ArrayLike<number>) {
+ for (let i = 0, _i = xs.length; i < _i; i++) {
+ if (xs[i] !== i) return false;
+ }
+ return true;
+}
+
export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Database['atom_site'], start: number, end: number) {
const indices = createRangeArray(start, end - 1);
@@ -28,5 +35,9 @@ export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Databas
if (ctx.shouldUpdate) await ctx.update();
}
- return indices;
+ if (isIdentity(indices) && indices.length === atom_site._rowCount) {
+ return atom_site;
+ }
+
+ return Table.view(atom_site, atom_site._schema, indices) as mmCIF_Database['atom_site'];
}
\ No newline at end of file